From d210b58b5fa533631a30c897bcb97fe6e196112d Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Fri, 18 Aug 2023 17:17:52 +0200
Subject: [PATCH 01/53] parameterize discovery potential significance threshold

---
 flarestack/core/ts_distributions.py | 121 +++++++++++++++-------------
 1 file changed, 67 insertions(+), 54 deletions(-)

diff --git a/flarestack/core/ts_distributions.py b/flarestack/core/ts_distributions.py
index 68aea864..dd62cbff 100644
--- a/flarestack/core/ts_distributions.py
+++ b/flarestack/core/ts_distributions.py
@@ -1,13 +1,14 @@
+import logging
+import matplotlib.pyplot as plt
 import numpy as np
 import os
-import matplotlib.pyplot as plt
+from pathlib import Path
 import scipy.optimize, scipy.stats
 from scipy.stats import norm
-import logging
+
 
 logger = logging.getLogger(__name__)
 
-raw_five_sigma = norm.cdf(5)
 n_bins = 100
 
 
@@ -168,35 +169,34 @@ def func(p):
         self.scale = res.x[2]
 
 
-def fit_background_ts(ts_array, ts_type):
+def fit_background_ts(ts_array: np.array, ts_type):
+    """
+    Fit the background TS distribution
+    """
     mask = ts_array > 0.0
-    frac_over = float(len(ts_array[mask])) / (float(len(ts_array)))
+
+    frac_positive = float(len(ts_array[mask])) / (float(len(ts_array)))
+
     threshold_err = 0.0
 
-    res = []
-    labs = []
-    cols = []
+    ts_data, labels, colors = [], [], []
 
     if np.sum(mask) > 0.0:
-        res.append(ts_array[mask])
-        labs.append("TS > 0")
-        cols.append("black")
+        ts_data.append(ts_array[mask])
+        labels.append("TS > 0")
+        colors.append("black")
     if np.sum(~mask) > 0.0:
-        res.append(ts_array[~mask])
-        labs.append("TS <= 0")
-        cols.append("grey")
-
-    # if len(res) > 1:
-    #     res = np.array(res, dtype=object)
-    #     res.shape = (2, 1)
+        ts_data.append(ts_array[~mask])
+        labels.append("TS <= 0")
+        colors.append("grey")
 
     plt.hist(
-        res,
+        ts_data,
         bins=n_bins,
         lw=2,
         histtype="step",
-        color=cols,
-        label=labs,
+        color=colors,
+        label=labels,
         density=True,
         stacked=True,
     )
@@ -205,7 +205,7 @@ def fit_background_ts(ts_array, ts_type):
         chi2 = Chi2_LeftTruncated(ts_array)
 
         if chi2._res.success:
-            frac_over = 1.0
+            frac_positive = 1.0
 
             df = chi2._f.args[0]
             loc = chi2._f.args[1]
@@ -244,7 +244,7 @@ def fit_background_ts(ts_array, ts_type):
                 scale = 1.0
 
             else:
-                frac_over = 1.0
+                frac_positive = 1.0
 
     elif ts_type in ["standard", "negative_ns"]:
         chi2 = Chi2_one_side(ts_array[ts_array > 0.0])
@@ -255,9 +255,9 @@ def fit_background_ts(ts_array, ts_type):
         threshold_err = float(chi2.sigma)
 
     else:
-        raise Exception("ts_type " + str(ts_type) + " not recognised!")
+        raise Exception(f"ts_type {ts_type} not recognised!")
 
-    return df, loc, scale, frac_over, threshold_err
+    return df, loc, scale, frac_positive, threshold_err
 
 
 def plot_expanded_negative(ts_array, path):
@@ -276,74 +276,83 @@ def plot_expanded_negative(ts_array, path):
     med = np.median(ts_array)
 
     plt.yscale("log")
-    plt.xlabel(r"Test Statistic ($\lambda$)")
+    plt.xlabel(r"Test statistic ($\lambda$)")
     plt.legend(loc="upper right")
     plt.savefig(path[:-4] + "_expanded.pdf")
     plt.close()
 
 
 def plot_background_ts_distribution(
-    ts_array, path, ts_type="Standard", ts_val=None, mock_unblind=False
+    ts_array: list,
+    path: Path,
+    ts_type: str = "standard",
+    significance_threshold: float = 5.0,
+    ts_val=None,
+    mock_unblind: bool = False,
 ):
-    try:
-        os.makedirs(os.path.dirname(path))
-    except OSError:
-        pass
+    path.mkdir(exist_ok=True)
 
     ts_array = np.array(ts_array)
 
-    if np.sum(np.isnan(ts_array)) > 0:
-        logger.warning(
-            "TS distribution has", np.sum(np.isnan(ts_array)), "nan entries."
-        )
+    # check for NaNs and filter them out
+
+    nan_count = np.sum(np.isnan(ts_array))
+
+    if nan_count > 0:
+        logger.warning(f"TS distribution has {nan_count} nan entries.")
 
     ts_array = ts_array[~np.isnan(ts_array)]
 
+    # find max ts
     max_ts = np.max(ts_array)
 
     if np.median(ts_array) < 0.0:
+        # plot separately the positive and negative values of TS
         plot_expanded_negative(ts_array, path)
 
     if max_ts == 0:
         logger.warning(
-            f"Maximum of TS is {max_ts=}, unable to calculate discovery threshold (too few trials?)"
+            f"Maximum of TS is zero, unable to calculate the TS threshold for the required significance (too few trials?)"
         )
         return np.NaN
 
-    fig = plt.figure()
-
-    ax = plt.subplot(1, 1, 1)
+    df, loc, scale, frac_positive, t_err = fit_background_ts(ts_array, ts_type)
 
-    df, loc, scale, frac_over, t_err = fit_background_ts(ts_array, ts_type)
+    frac_nonpositive = 1.0 - frac_positive
 
-    frac_under = 1 - frac_over
+    # cumulative fraction of trials required to reach the desired significance
+    cdf_threshold = norm.cdf(significance_threshold)
+    # determine corresponding threshold for the CDF of
+    positive_cdf_threshold = (cdf_threshold - frac_nonpositive) / frac_positive
 
-    five_sigma = (raw_five_sigma - frac_under) / (1.0 - frac_under)
+    disc_potential = scipy.stats.chi2.ppf(positive_cdf_threshold, df, loc, scale)
 
-    plt.axhline(frac_over * (1 - five_sigma), color="r", linestyle="--")
+    # plotting
+    fig = plt.figure()
+    ax = plt.subplot(1, 1, 1)
 
-    disc_potential = scipy.stats.chi2.ppf(five_sigma, df, loc, scale)
+    plt.axhline(frac_positive * (1 - positive_cdf_threshold), color="r", linestyle="--")
 
     x_range = np.linspace(0.0, max(max_ts, disc_potential), 100)
 
     plt.plot(
         x_range,
-        frac_over * scipy.stats.chi2.pdf(x_range, df, loc, scale),
+        frac_positive * scipy.stats.chi2.pdf(x_range, df, loc, scale),
         color="blue",
-        label=r"$\chi^{2}$ Distribution",
+        label=r"$\chi^{2}$ distribution",
     )
 
     if t_err is not None:
         plt.fill_between(
             x_range,
-            frac_over * scipy.stats.chi2.pdf(x_range, df + t_err, loc, scale),
-            frac_over * scipy.stats.chi2.pdf(x_range, df - t_err, loc, scale),
+            frac_positive * scipy.stats.chi2.pdf(x_range, df + t_err, loc, scale),
+            frac_positive * scipy.stats.chi2.pdf(x_range, df - t_err, loc, scale),
             alpha=0.1,
             color="blue",
         )
 
     def integral(x):
-        return frac_under * np.sign(x) + frac_over * (
+        return frac_nonpositive * np.sign(x) + frac_positive * (
             scipy.stats.chi2.cdf(x, df, loc, scale)
         )
 
@@ -355,7 +364,9 @@ def integral(x):
         label=r"1 - $\int f(x)$ (p-value)",
     )
 
-    plt.axvline(disc_potential, color="r", label=r"5 $\sigma$ Threshold")
+    plt.axvline(
+        disc_potential, color="r", label=rf"{significance_threshold} $\sigma$ threshold"
+    )
 
     if ts_val is not None:
         if not isinstance(ts_val, float):
@@ -366,7 +377,9 @@ def integral(x):
         if ts_val > np.median(ts_array):
             # val = (ts_val - frac_under) / (1. - frac_under)
 
-            cdf = frac_under + frac_over * scipy.stats.chi2.cdf(ts_val, df, loc, scale)
+            cdf = frac_nonpositive + frac_positive * scipy.stats.chi2.cdf(
+                ts_val, df, loc, scale
+            )
 
             sig = norm.ppf(cdf)
 
@@ -375,7 +388,7 @@ def integral(x):
             sig = 0.0
 
         logger.info(f"Pre-trial P-value is {1-cdf:.2E}")
-        logger.info(f"Significance is {sig:.2f} Sigma")
+        logger.info(f"Significance is {sig:.2f} sigma")
 
         plt.axvline(
             ts_val,
@@ -388,7 +401,7 @@ def integral(x):
 
     else:
         plt.annotate(
-            "{:.1f}".format(100 * frac_under)
+            "{:.1f}".format(100 * frac_nonpositive)
             + "% of data in delta. \n"
             + r"$\chi^{2}$ Distribution:"
             + "\n   * d.o.f.="
@@ -408,7 +421,7 @@ def integral(x):
     )
 
     plt.yscale("log")
-    plt.xlabel(r"Test Statistic ($\lambda$)")
+    plt.xlabel(r"Test statistic ($\lambda$)")
     plt.legend(loc="upper right")
 
     if mock_unblind:

From 1818f639f1d4abc6c7cd01ec50efcc7facb7bcc7 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Fri, 18 Aug 2023 18:32:57 +0200
Subject: [PATCH 02/53] work in progress rework of results handler

---
 flarestack/core/results.py          | 228 +++++++++++++++++-----------
 flarestack/core/ts_distributions.py |  41 ++---
 2 files changed, 163 insertions(+), 106 deletions(-)

diff --git a/flarestack/core/results.py b/flarestack/core/results.py
index 09c6d0cc..9ac90d88 100644
--- a/flarestack/core/results.py
+++ b/flarestack/core/results.py
@@ -1,12 +1,19 @@
-import os
-import pickle as Pickle
+import logging
 import numpy as np
+import os
+import pickle
+from pydantic import BaseModel
 import scipy
 import scipy.stats
 import matplotlib.cm as cm
 import matplotlib.colors as colors
 import matplotlib.animation as animation
 import matplotlib.pyplot as plt
+from pathlib import Path
+import sys
+from typing import Final, Optional, Tuple
+
+
 from flarestack.shared import (
     name_pickle_output_dir,
     plot_output_dir,
@@ -16,6 +23,7 @@
     flux_to_k,
 )
 from flarestack.core.ts_distributions import (
+    calc_ts_threshold,
     plot_background_ts_distribution,
     plot_fit_results,
     get_ts_fit_type,
@@ -24,8 +32,7 @@
 from flarestack.core.minimisation import MinimisationHandler
 from flarestack.core.time_pdf import TimePDF
 from flarestack.utils.catalogue_loader import load_catalogue
-import sys
-import logging
+
 
 logger = logging.getLogger(__name__)
 
@@ -34,7 +41,33 @@ class OverfluctuationError(Exception):
     pass
 
 
+class Result(BaseModel):
+    background_median: Optional[float] = None
+    reference_ts = Optional[float] = None
+    reference_ts_overfluctuation_fraction = Optional[float] = None
+
+    sensitivity_value: Optional[float] = None
+    sensitivity_error: Optional[Tuple[float]] = None
+    sensitivity_extrapolated: Optional[bool] = False
+
+    discovery_potential_3sigma_threshold: Optional[float] = None
+    discovery_potential_3sigma_value: Optional[float] = None
+    discovery_potential_3sigma_error: Optional[Tuple[float]] = None
+
+    discovery_potential_5sigma_threshold: Optional[float] = None
+    discovery_potential_5sigma_value: Optional[float] = None
+    discovery_potential_5sigma_error: Optional[Tuple[float]] = None  # currently unused
+    discovery_potential_TS25_value: Optional[float] = None
+    discovery_potential_TS25_error: Optional[Tuple[float]] = None
+
+    discovery_potential_extrapolated: Optional[bool] = False
+
+    flux_to_ns: Optional[float] = None
+
+
 class ResultsHandler(object):
+    TS_DISTRIBUTION_SUBDIR: Final[str] = "ts_distributions"
+
     def __init__(self, rh_dict, do_sens=True, do_disc=True, bias_error="std"):
         self.sources = load_catalogue(rh_dict["catalogue"])
 
@@ -42,15 +75,28 @@ def __init__(self, rh_dict, do_sens=True, do_disc=True, bias_error="std"):
         self.mh_name = rh_dict["mh_name"]
         self.scale = rh_dict["scale"]
 
+        # Dictionary with the analysis results.
+        # Loaded by `merge_pickled_data`
         self.results = dict()
+
         self.pickle_output_dir = name_pickle_output_dir(self.name)
-        self.plot_dir = plot_output_dir(self.name)
+
+        self.plot_dir = Path(plot_output_dir(self.name))
+
+        self.ts_distribution_dir = self.plot_dir / TS_DISTRIBUTION_SUBDIR
+
         self.merged_dir = os.path.join(self.pickle_output_dir, "merged")
 
         self.allow_extrapolation = rh_dict.get("allow_extrapolated_sensitivity", True)
 
         self.valid = True
 
+        self.default_overfluctuation_msg = "(Almost) all tested signal injection values result in > 95% of trials above the chosen TS threshold.\n \
+            This makes impossible to properly interpolate the sensitivity or discovery potential value. \n \
+            Possible causes of this behaviour are:\n \
+            - all the `scale` steps are too high in value;\n \
+            - the `injection_weight_modifier` values of the catalogue are improperly set, check the actual number of injected neutrinos."
+
         # Checks if the code should search for flares. By default, this is
         # not done.
         # self.flare = self.mh_name == "flare"
@@ -82,6 +128,8 @@ def __init__(self, rh_dict, do_sens=True, do_disc=True, bias_error="std"):
         # elif self.negative_n_s:
         #     self.ts_type = "Negative n_s"
         # else:
+
+        # Inspects rh_dict for "mh_name" and determines whether to use flare fitting.
         self.ts_type = get_ts_fit_type(rh_dict)
 
         # print "negative_ns", self.negative_n_s
@@ -93,25 +141,12 @@ def __init__(self, rh_dict, do_sens=True, do_disc=True, bias_error="std"):
         self.bounds = bounds
         self.p0 = p0
 
-        # if cleanup:
-        #     self.clean_merged_data()
-
         # this will have the TS threshold values as keys and a tuple containing
         # (injection scale, relative overfluctuations, error on overfluctuations)
         # as values
         self.overfluctuations = dict()
 
-        self.sensitivity = np.nan
-        self.sensitivity_err = np.nan
-        self.bkg_median = np.nan
-        self.frac_over = np.nan
-        self.disc_potential = np.nan
-        self.disc_err = np.nan
-        self.disc_potential_25 = np.nan
-        self.disc_ts_threshold = np.nan
-        self.extrapolated_sens = False
-        self.extrapolated_disc = False
-        self.flux_to_ns = np.nan
+        self.result = Result()
 
         try:
             # if self.show_inj:
@@ -173,13 +208,20 @@ def __str__(self):
             extrapolated = (
                 "extrapolated" if self.extrapolated_sens else "not extrapolated"
             )
-            out += f"Sensitivity = {self.sensitivity:.2e} (+{self.sensitivity_err[0]:.2e}/-{self.sensitivity_err[1]:.2e}) [{extrapolated}]\n"
-            out += f"Discovery potential (5 sigma from TS distribution) = {self.disc_potential:.2e}\n"
-            out += f"Discovery potential (TS = 25) = {self.disc_potential_25:.2e}"
+            out += f"Sensitivity = {self.result.sensitivity_value:.2e} (+{self.result.sensitivity_error[0]:.2e}/-{self.result.sensitivity_error[1]:.2e}) [{extrapolated}]\n"
+            out += f"Discovery potential (5 sigma from TS distribution) = {self.result.discovery_potential_5sigma_value:.2e}\n"
+            out += f"Discovery potential (TS = 25) = {self.result.discovery_potential_TS25_value:.2e}"
         else:
             out += "Result is invalid. Check the log messages."
         return out
 
+    def get_background_trials(self):
+        try:
+            return self.results[scale_shortener(0.0)]
+        except KeyError:
+            logger.error("No key equal to '0'")
+            return
+
     @property
     def scales_float(self):
         """directly return the injected scales as floats"""
@@ -255,8 +297,10 @@ def astro_values(self, e_pdf_dict):
         discovery potential
         """
 
-        astro_sens = self.nu_astronomy(self.sensitivity, e_pdf_dict)
-        astro_disc = self.nu_astronomy(self.disc_potential, e_pdf_dict)
+        astro_sens = self.nu_astronomy(self.result.sensitivity_value, e_pdf_dict)
+        astro_disc = self.nu_astronomy(
+            self.result.discovery_potential_5sigma_value, e_pdf_dict
+        )
 
         return astro_sens, astro_disc
 
@@ -304,7 +348,7 @@ def load_injection_values(self):
             if os.path.isfile(path):
                 try:
                     with open(path, "rb") as f:
-                        inj_values[os.path.splitext(file)[0]] = Pickle.load(f)
+                        inj_values[os.path.splitext(file)[0]] = pickle.load(f)
                 except EOFError as e:
                     logger.warning(f"{path}: EOFError: {e}! Can not use this scale!")
 
@@ -335,7 +379,7 @@ def merge_pickle_data(self):
             if os.path.isfile(merged_path):
                 logger.debug(f"loading merged data from {merged_path}")
                 with open(merged_path, "rb") as mp:
-                    merged_data = Pickle.load(mp)
+                    merged_data = pickle.load(mp)
             else:
                 merged_data = {}
 
@@ -344,7 +388,7 @@ def merge_pickle_data(self):
 
                 try:
                     with open(path, "rb") as f:
-                        data = Pickle.load(f)
+                        data = pickle.load(f)
                 except (EOFError, IsADirectoryError):
                     logger.warning("Failed loading: {0}".format(path))
                     continue
@@ -367,7 +411,7 @@ def merge_pickle_data(self):
                                     raise KeyError(m)
 
             with open(merged_path, "wb") as mp:
-                Pickle.dump(merged_data, mp)
+                pickle.dump(merged_data, mp)
 
             if len(list(merged_data.keys())) > 0:
                 self.results[scale_shortener(float(sub_dir_name))] = merged_data
@@ -484,7 +528,7 @@ def find_sensitivity(self):
         """
 
         try:
-            bkg_dict = self.results[scale_shortener(0.0)]
+            bkg_dict = self.get_background_trials()
         except KeyError:
             logger.error("No key equal to '0'")
             return
@@ -492,18 +536,18 @@ def find_sensitivity(self):
         bkg_ts = bkg_dict["TS"]
 
         bkg_median = np.median(bkg_ts)
-        self.bkg_median = bkg_median
+        self.result.background_median = bkg_median
 
         savepath = os.path.join(self.plot_dir, "sensitivity.pdf")
 
         (
-            self.sensitivity,
-            self.sensitivity_err,
+            self.result.sensitivity_value,
+            self.result.sensitivity_error,
             self.extrapolated_sens,
         ) = self.find_overfluctuations(bkg_median, savepath)
 
         msg = "EXTRAPOLATED " if self.extrapolated_sens else ""
-        logger.info(f"{msg}Sensitivity is {self.sensitivity:.3g}")
+        logger.info(f"{msg}Sensitivity is {self.result.sensitivity_value:.3g}")
 
     # def set_upper_limit(self, ts_val, savepath):
     #     """Set an upper limit, based on a Test Statistic value from
@@ -561,6 +605,8 @@ def find_overfluctuations(self, ts_val, savepath=None):
 
         yerr = []
 
+        self.result.reference_ts = ts_val
+
         for scale in x:
             ts_array = np.array(self.results[scale]["TS"])
             frac = float(len(ts_array[ts_array > ts_val])) / (float(len(ts_array)))
@@ -572,7 +618,8 @@ def find_overfluctuations(self, ts_val, savepath=None):
             )
 
             if scale == scale_shortener(0.0):
-                self.frac_over = frac
+                # Note: this value depends on the chosen ts_val!
+                self.result.reference_ts_overfluctuation_fraction = frac_over
 
             if len(ts_array) > 1:
                 y.append(frac)
@@ -587,9 +634,7 @@ def find_overfluctuations(self, ts_val, savepath=None):
                         f"Fraction of overfluctuations is {frac=}, skipping plot for {scale=}"
                     )
         if len(np.where(np.array(y) < 0.95)[0]) < 2:
-            raise OverfluctuationError(
-                f"Not enough points with overfluctuations under 95%, lower injection scale!"
-            )
+            raise OverfluctuationError(self.default_overfluctuation_msg)
 
         x = np.array(x_acc)
         self.overfluctuations[ts_val] = x, y, yerr
@@ -671,58 +716,54 @@ def best_f(x, sd=0.0):
         plt.close()
 
         if len(np.where(np.array(y) < 0.95)[0]) < 2:
-            raise OverfluctuationError(
-                f"Not enough points with overfluctuations under 95%, lower injection scale!"
-            )
+            raise OverfluctuationError(self.default_overfluctuation_msg)
 
         fit_err = np.array([fit - lower, upper - fit]).T[0]
 
         return fit, fit_err, extrapolated
 
     def find_disc_potential(self):
-        ts_path = os.path.join(self.plot_dir, "ts_distributions/0.pdf")
+        ts_plot_filename: Path = self.ts_distribution_dir / "0.pdf"
 
-        try:
-            bkg_dict = self.results[scale_shortener(0.0)]
-        except KeyError:
-            logger.error("No key equal to '0'")
-            return
+        bkg_trials: dict = self.get_background_trials()
 
-        bkg_ts = bkg_dict["TS"]
+        bkg_ts = np.array(bkg_trials["TS"])
 
-        disc_threshold = plot_background_ts_distribution(
-            bkg_ts, ts_path, ts_type=self.ts_type
-        )
+        SIGNIFICANCE_VALUES: Final[tuple[float]] = (3.0, 5.0)
 
-        self.disc_ts_threshold = disc_threshold
+        ts_thresholds = {}
 
-        bkg_median = np.median(bkg_ts)
-        x = sorted(self.results.keys())
-        y = []
-        y_25 = []
+        for significance in SIGNIFICANCE_VALUES:
+            ts_thresholds[significance] = calc_ts_threshold(
+                bkg_ts, significance_value=significance, ts_type=self.ts_type
+            )
 
-        x = [scale_shortener(i) for i in sorted([float(j) for j in x])]
+        plot_background_ts_distribution(bkg_ts, ts_plot_filename, ts_type=self.ts_type)
+
+        self.result.discovery_potential_5sigma_threshold = ts_threshold_5sigma
 
-        if np.isnan(disc_threshold):
+        if np.isnan(ts_threshold_5sigma):
             logger.warning(
-                f"Invalid discovery threshold {disc_threshold=} will be ingnored. Using TS = 25.0 only."
+                f"Invalid discovery threshold {ts_threshold_5sigma=} will be ignored. Using TS = 25.0 only."
             )
 
-        for scale in x:
+        # store fraction of overfluctuations above TS threshold as a function of injection values
+        overfluctuation_fraction_5sigma, overfluctuation_fraction_25 = [], []
+
+        for scale in self.scales:
             ts_array = np.array(self.results[scale]["TS"])
 
-            if not np.isnan(disc_threshold):
-                frac = float(len(ts_array[ts_array > disc_threshold])) / (
+            if not np.isnan(ts_threshold_5sigma):
+                # calculate fraction of trials above threshold
+                frac = float(len(ts_array[ts_array > ts_threshold_5sigma])) / (
                     float(len(ts_array))
                 )
 
                 logger.info(
-                    "Fraction of overfluctuations is {0:.2f} above {1:.2f} (N_trials={2}) (Scale={3})".format(
-                        frac, disc_threshold, len(ts_array), scale
-                    )
+                    f"Fraction of overfluctuations is {frac:.2f} above {ts_threshold_5sigma:.2f} (N_trials={len(ts_array)}) (scale={scale})"
                 )
 
-                y.append(frac)
+                overfluctuation_fraction_5sigma.append(frac)
 
             frac_25 = float(len(ts_array[ts_array > 25.0])) / (float(len(ts_array)))
 
@@ -732,7 +773,7 @@ def find_disc_potential(self):
                 )
             )
 
-            y_25.append(frac_25)
+            overfluctuation_fraction_25.append(frac_25)
 
             # if frac != 0.0:
             #    logger.info(f"Making plot for {scale=}, {frac=}")
@@ -742,29 +783,28 @@ def find_disc_potential(self):
             #        f"Fraction of overfluctuations is {frac=}, skipping plot for {scale=}"
             #    )
 
-        x = np.array([float(s) for s in x])
+        x = np.array(self.scales_float)
 
         x_flux = k_to_flux(x)
 
-        threshold = 0.5
-
-        sols = []
+        # 50% of trials must be above ts threshold
+        significance = 0.5
 
         """
         Calculate the discovery potential based on the 5-sigma threshold of the TS distribution only if the distribution is non-degenerate. Otherwise, use only the TS=25 threshold.
         """
 
-        y_list = [y_25]
+        y_list = [overfluctuation_fraction_25]
         out_list = ["disc_potential_25"]
 
-        if not np.isnan(disc_threshold):
-            y_list.append(y)
+        if not np.isnan(ts_threshold_5sigma):
+            y_list.append(overfluctuation_fraction_5sigma)
             out_list.append("disc_potential")
 
         for i, y_val in enumerate(y_list):
-
+            # define a gamma function to represent the overfluctuation fraction vs injection scale value trend
             def f(x, a, b, c):
-                value = scipy.stats.gamma.cdf(x, a, b, c)
+                value = scipy.stats.gamma.cdf(x, a=a, loc=b, scale=c)
                 return value
 
             best_f = None
@@ -790,24 +830,28 @@ def best_f(x):
             except RuntimeError as e:
                 logger.warning(f"RuntimeError for discovery potential!: {e}")
 
+            # Now we plot something.
             xrange = np.linspace(0.0, 1.1 * max(x), 1000)
 
+            # Need to define a sensible output naming scheme.
             savepath = os.path.join(self.plot_dir, "disc" + ["", "_25"][i] + ".pdf")
 
             fig = plt.figure()
             ax1 = fig.add_subplot(111)
             ax1.scatter(x_flux, y_val, color="black")
 
-            if not isinstance(best_f, type(None)):
+            if best_f is not None:
                 ax1.plot(k_to_flux(xrange), best_f(xrange), color="blue")
 
-            ax1.axhline(threshold, lw=1, color="red", linestyle="--")
-            ax1.axvline(self.sensitivity, lw=2, color="black", linestyle="--")
-            ax1.axvline(self.disc_potential, lw=2, color="red")
+            ax1.axhline(significance, lw=1, color="red", linestyle="--")
+            ax1.axvline(
+                self.result.sensitivity_value, lw=2, color="black", linestyle="--"
+            )
+            ax1.axvline(self.result.discovery_potential_5sigma_value, lw=2, color="red")
             ax1.set_ylim(0.0, 1.0)
             ax1.set_xlim(0.0, k_to_flux(max(xrange)))
-            ax1.set_ylabel(r"Overfluctuations relative to 5 $\sigma$ Threshold")
-            plt.xlabel(r"Flux Normalisation @ 1GeV [ GeV$^{-1}$ cm$^{-2}$ s$^{-1}$]")
+            ax1.set_ylabel(r"Overfluctuations relative to 5 $\sigma$ threshold")
+            plt.xlabel(r"Flux normalisation @ 1GeV [ GeV$^{-1}$ cm$^{-2}$ s$^{-1}$]")
 
             if not np.isnan(self.flux_to_ns):
                 ax2 = ax1.twiny()
@@ -818,7 +862,7 @@ def best_f(x):
             fig.savefig(savepath)
             plt.close()
 
-        if self.disc_potential > max(x_flux):
+        if self.result.discovery_potential_5sigma_value > max(x_flux):
             self.extrapolated_disc = True
 
         msg = ""
@@ -827,10 +871,12 @@ def best_f(x):
             msg = "EXTRAPOLATED "
 
         logger.info(
-            "{0}Discovery Potential is {1:.3g}".format(msg, self.disc_potential)
+            "{0}Discovery potential is {1:.3g}".format(
+                msg, self.result.discovery_potential_5sigma_value
+            )
         )
         logger.info(
-            "Discovery Potential (TS=25) is {0:.3g}".format(self.disc_potential_25)
+            "Discovery potential (TS = 25) is {0:.3g}".format(self.disc_potential_25)
         )
 
     def noflare_plots(self, scale):
@@ -922,13 +968,16 @@ def ts_distribution_evolution(self):
         all_scales_floats = [float(sc) for sc in all_scales]
 
         logger.debug("all scales: " + str(all_scales_floats))
-        logger.debug("sensitivity scale: " + str(flux_to_k(self.sensitivity)))
+        logger.debug(
+            "sensitivity scale: " + str(flux_to_k(self.result.sensitivity_value))
+        )
 
         sens_scale = all_scales[
-            all_scales_floats >= np.array(flux_to_k(self.sensitivity))
+            all_scales_floats >= np.array(flux_to_k(self.result.sensitivity_value))
         ][0]
         disc_scale = all_scales[
-            all_scales_floats >= np.array(flux_to_k(self.disc_potential))
+            all_scales_floats
+            >= np.array(flux_to_k(self.result.discovery_potential_5sigma_value))
         ][0]
 
         scales = [all_scales[0], sens_scale, disc_scale]
@@ -968,7 +1017,10 @@ def ts_distribution_evolution(self):
             label="signal: {:.2} signal neutrinos".format(n_s[1]),
         )
         ax.axvline(
-            self.bkg_median, ls="--", label="sensitivity threshold", color="orange"
+            self.result.background_median,
+            ls="--",
+            label="sensitivity threshold",
+            color="orange",
         )
 
         ax.hist(
diff --git a/flarestack/core/ts_distributions.py b/flarestack/core/ts_distributions.py
index dd62cbff..a54248d0 100644
--- a/flarestack/core/ts_distributions.py
+++ b/flarestack/core/ts_distributions.py
@@ -282,8 +282,23 @@ def plot_expanded_negative(ts_array, path):
     plt.close()
 
 
+def filter_nan(values: list) -> np.array:
+    arr = np.array(values)
+
+    nan_count = np.sum(np.isnan(arr))
+
+    if nan_count > 0:
+        logger.warning(f"TS distribution has {nan_count} NaN entries.")
+
+    return arr[~np.isnan(arr)]
+
+
+def calc_ts_threshold(ts_values: list, significance: float, ts_type: str = "standard"):
+    ts_arr = filter_nan(ts_values)
+
+
 def plot_background_ts_distribution(
-    ts_array: list,
+    ts_values: list,
     path: Path,
     ts_type: str = "standard",
     significance_threshold: float = 5.0,
@@ -292,23 +307,13 @@ def plot_background_ts_distribution(
 ):
     path.mkdir(exist_ok=True)
 
-    ts_array = np.array(ts_array)
-
-    # check for NaNs and filter them out
-
-    nan_count = np.sum(np.isnan(ts_array))
-
-    if nan_count > 0:
-        logger.warning(f"TS distribution has {nan_count} nan entries.")
-
-    ts_array = ts_array[~np.isnan(ts_array)]
-
     # find max ts
-    max_ts = np.max(ts_array)
+    ts_arr = filter_nan(ts_values)
+    max_ts = np.max(ts_arr)
 
-    if np.median(ts_array) < 0.0:
+    if np.median(ts_arr) < 0.0:
         # plot separately the positive and negative values of TS
-        plot_expanded_negative(ts_array, path)
+        plot_expanded_negative(ts_arr, path)
 
     if max_ts == 0:
         logger.warning(
@@ -316,7 +321,7 @@ def plot_background_ts_distribution(
         )
         return np.NaN
 
-    df, loc, scale, frac_positive, t_err = fit_background_ts(ts_array, ts_type)
+    df, loc, scale, frac_positive, t_err = fit_background_ts(ts_arr, ts_type)
 
     frac_nonpositive = 1.0 - frac_positive
 
@@ -374,7 +379,7 @@ def integral(x):
 
         logger.info(f"Quantifying TS: {ts_val:.2f}")
 
-        if ts_val > np.median(ts_array):
+        if ts_val > np.median(ts_arr):
             # val = (ts_val - frac_under) / (1. - frac_under)
 
             cdf = frac_nonpositive + frac_positive * scipy.stats.chi2.cdf(
@@ -416,7 +421,7 @@ def integral(x):
         )
 
     yrange = min(
-        1.0 / (float(len(ts_array)) * n_bins),
+        1.0 / (float(len(ts_arr)) * n_bins),
         scipy.stats.chi2.pdf(disc_potential, df, loc, scale),
     )
 

From 327f18f9f8d590938f5561183b30b81621721ba1 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Sat, 19 Aug 2023 15:58:49 +0200
Subject: [PATCH 03/53] update dependencies

---
 poetry.lock    | 3071 +++++++++++++++++++++++++++++-------------------
 pyproject.toml |    1 +
 2 files changed, 1889 insertions(+), 1183 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 4b4c4f80..1bbdc3f9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,17 +1,54 @@
-# This file is automatically @generated by Poetry and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
-version = "0.7.12"
+version = "0.7.13"
 description = "A configurable sidebar-enabled Sphinx theme"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
+
+[[package]]
+name = "annotated-types"
+version = "0.5.0"
+description = "Reusable constraint types to use with typing.Annotated"
+category = "main"
+optional = false
+python-versions = ">=3.7"
 files = [
-    {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"},
-    {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
+    {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
+    {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
 ]
 
+[package.dependencies]
+typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""}
+
+[[package]]
+name = "anyio"
+version = "3.7.1"
+description = "High level compatibility layer for multiple asynchronous event loop implementations"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"},
+    {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"},
+]
+
+[package.dependencies]
+exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
+idna = ">=2.8"
+sniffio = ">=1.1"
+
+[package.extras]
+doc = ["Sphinx", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery"]
+test = ["anyio[trio]", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
+trio = ["trio (<0.22)"]
+
 [[package]]
 name = "appnope"
 version = "0.1.3"
@@ -26,23 +63,24 @@ files = [
 
 [[package]]
 name = "argon2-cffi"
-version = "21.3.0"
-description = "The secure Argon2 password hashing algorithm."
+version = "23.1.0"
+description = "Argon2 for Python"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "argon2-cffi-21.3.0.tar.gz", hash = "sha256:d384164d944190a7dd7ef22c6aa3ff197da12962bd04b17f64d4e93d934dba5b"},
-    {file = "argon2_cffi-21.3.0-py3-none-any.whl", hash = "sha256:8c976986f2c5c0e5000919e6de187906cfd81fb1c72bf9d88c01177e77da7f80"},
+    {file = "argon2_cffi-23.1.0-py3-none-any.whl", hash = "sha256:c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea"},
+    {file = "argon2_cffi-23.1.0.tar.gz", hash = "sha256:879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08"},
 ]
 
 [package.dependencies]
 argon2-cffi-bindings = "*"
 
 [package.extras]
-dev = ["cogapp", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "pre-commit", "pytest", "sphinx", "sphinx-notfound-page", "tomli"]
-docs = ["furo", "sphinx", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"]
+dev = ["argon2-cffi[tests,typing]", "tox (>4)"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-copybutton", "sphinx-notfound-page"]
+tests = ["hypothesis", "pytest"]
+typing = ["mypy"]
 
 [[package]]
 name = "argon2-cffi-bindings"
@@ -82,6 +120,21 @@ cffi = ">=1.0.1"
 dev = ["cogapp", "pre-commit", "pytest", "wheel"]
 tests = ["pytest"]
 
+[[package]]
+name = "arrow"
+version = "1.2.3"
+description = "Better dates & times for Python"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"},
+    {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"},
+]
+
+[package.dependencies]
+python-dateutil = ">=2.7.0"
+
 [[package]]
 name = "astropy"
 version = "5.2.2"
@@ -138,54 +191,70 @@ test-all = ["coverage[toml]", "ipython (>=4.2)", "objgraph", "pytest (>=7.0)", "
 
 [[package]]
 name = "asttokens"
-version = "2.0.8"
+version = "2.2.1"
 description = "Annotate AST trees with source code positions"
 category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "asttokens-2.0.8-py2.py3-none-any.whl", hash = "sha256:e3305297c744ae53ffa032c45dc347286165e4ffce6875dc662b205db0623d86"},
-    {file = "asttokens-2.0.8.tar.gz", hash = "sha256:c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b"},
+    {file = "asttokens-2.2.1-py2.py3-none-any.whl", hash = "sha256:6b0ac9e93fb0335014d382b8fa9b3afa7df546984258005da0b9e7095b3deb1c"},
+    {file = "asttokens-2.2.1.tar.gz", hash = "sha256:4622110b2a6f30b77e1473affaa97e711bc2f07d3f10848420ff1898edbe94f3"},
 ]
 
 [package.dependencies]
 six = "*"
 
 [package.extras]
-test = ["astroid (<=2.5.3)", "pytest"]
+test = ["astroid", "pytest"]
+
+[[package]]
+name = "async-lru"
+version = "2.0.4"
+description = "Simple LRU cache for asyncio"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "async-lru-2.0.4.tar.gz", hash = "sha256:b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627"},
+    {file = "async_lru-2.0.4-py3-none-any.whl", hash = "sha256:ff02944ce3c288c5be660c42dbcca0742b32c3b279d6dceda655190240b99224"},
+]
+
+[package.dependencies]
+typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "attrs"
-version = "22.1.0"
+version = "23.1.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.7"
 files = [
-    {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"},
-    {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"},
+    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
 ]
 
 [package.extras]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
-tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
 [[package]]
-name = "Babel"
-version = "2.10.3"
+name = "babel"
+version = "2.12.1"
 description = "Internationalization utilities"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.10.3-py3-none-any.whl", hash = "sha256:ff56f4892c1c4bf0d814575ea23471c230d544203c7748e8c68f0089478d48eb"},
-    {file = "Babel-2.10.3.tar.gz", hash = "sha256:7614553711ee97490f732126dc077f8d0ae084ebc6a96e23db1482afabdb2c51"},
+    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
+    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
 ]
 
 [package.dependencies]
-pytz = ">=2015.7"
+pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
 
 [[package]]
 name = "backcall"
@@ -201,14 +270,14 @@ files = [
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.11.1"
+version = "4.12.2"
 description = "Screen-scraping library"
 category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
-    {file = "beautifulsoup4-4.11.1-py3-none-any.whl", hash = "sha256:58d5c3d29f5a36ffeb94f02f0d786cd53014cf9b3b3951d42e0080d8a9498d30"},
-    {file = "beautifulsoup4-4.11.1.tar.gz", hash = "sha256:ad9aa55b65ef2808eb405f46cf74df7fcb7044d5cbc26487f96eb2ef2e436693"},
+    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
+    {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
 ]
 
 [package.dependencies]
@@ -220,37 +289,34 @@ lxml = ["lxml"]
 
 [[package]]
 name = "black"
-version = "23.3.0"
+version = "23.7.0"
 description = "The uncompromising code formatter."
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "black-23.3.0-cp310-cp310-macosx_10_16_arm64.whl", hash = "sha256:0945e13506be58bf7db93ee5853243eb368ace1c08a24c65ce108986eac65915"},
-    {file = "black-23.3.0-cp310-cp310-macosx_10_16_universal2.whl", hash = "sha256:67de8d0c209eb5b330cce2469503de11bca4085880d62f1628bd9972cc3366b9"},
-    {file = "black-23.3.0-cp310-cp310-macosx_10_16_x86_64.whl", hash = "sha256:7c3eb7cea23904399866c55826b31c1f55bbcd3890ce22ff70466b907b6775c2"},
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 ]
 
 [package.dependencies]
@@ -270,14 +336,14 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "bleach"
-version = "5.0.1"
+version = "6.0.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -286,18 +352,17 @@ webencodings = "*"
 
 [package.extras]
 css = ["tinycss2 (>=1.1.0,<1.2)"]
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 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
@@ -379,29 +444,99 @@ pycparser = "*"
 
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 name = "charset-normalizer"
-version = "2.1.1"
+version = "3.2.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
-python-versions = ">=3.6.0"
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-[package.extras]
-unicode-backport = ["unicodedata2"]
-
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 name = "click"
-version = "8.1.3"
+version = "8.1.7"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
@@ -409,93 +544,83 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
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+version = "0.4.6"
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+version = "0.1.4"
+description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
+category = "main"
+optional = false
+python-versions = ">=3.6"
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+
+[package.dependencies]
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+
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+test = ["pytest"]
+typing = ["mypy (>=0.990)"]
+
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 [package.dependencies]
@@ -503,69 +628,69 @@ numpy = ">=1.16"
 
 [package.extras]
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-test-minimal = ["pytest"]
-test-no-codebase = ["Pillow", "matplotlib", "pytest"]
+docs = ["furo", "sphinx-copybutton"]
+mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.2.0)", "types-Pillow"]
+test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
+test-no-images = ["pytest", "pytest-cov", "wurlitzer"]
 
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+[package.extras]
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+
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+version = "2.18.0"
 description = "Fastest Python implementation of JSON schema"
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@@ -719,18 +850,50 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
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 lxml = ["lxml (>=4.0,<5)"]
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 symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
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+unicode = ["unicodedata2 (>=15.0.0)"]
 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
+[[package]]
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+version = "1.5.1"
+description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
+category = "main"
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+[package.extras]
+docs = ["Sphinx", "docutils (<0.18)"]
+test = ["objgraph", "psutil"]
 
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+version = "1.16.5"
 description = "Healpix tools package for Python"
 category = "main"
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-python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -837,6 +1021,9 @@ matplotlib = "*"
 numpy = ">=1.13"
 scipy = "*"
 
+[package.extras]
+test = ["pytest", "pytest-cython", "pytest-doctestplus", "requests"]
+
 [[package]]
 name = "idna"
 version = "3.4"
@@ -863,81 +1050,87 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "4.12.0"
+version = "6.8.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "importlib-resources"
-version = "5.9.0"
+version = "6.0.1"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx"]
-testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [[package]]
 name = "ipykernel"
-version = "6.15.3"
+version = "6.25.1"
 description = "IPython Kernel for Jupyter"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "ipykernel-6.25.1.tar.gz", hash = "sha256:050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f"},
 ]
 
 [package.dependencies]
 appnope = {version = "*", markers = "platform_system == \"Darwin\""}
-debugpy = ">=1.0"
+comm = ">=0.1.1"
+debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
 jupyter-client = ">=6.1.12"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
 psutil = "*"
-pyzmq = ">=17"
+pyzmq = ">=20"
 tornado = ">=6.1"
-traitlets = ">=5.1.0"
+traitlets = ">=5.4.0"
 
 [package.extras]
-test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=6.0)", "pytest-cov", "pytest-timeout"]
+cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
+pyqt5 = ["pyqt5"]
+pyside6 = ["pyside6"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "ipython"
-version = "8.5.0"
+version = "8.12.2"
 description = "IPython: Productive Interactive Computing"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipython-8.5.0-py3-none-any.whl", hash = "sha256:6f090e29ab8ef8643e521763a4f1f39dc3914db643122b1e9d3328ff2e43ada2"},
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+    {file = "ipython-8.12.2-py3-none-any.whl", hash = "sha256:ea8801f15dfe4ffb76dea1b09b847430ffd70d827b41735c64a0638a04103bfc"},
+    {file = "ipython-8.12.2.tar.gz", hash = "sha256:c7b80eb7f5a855a88efc971fda506ff7a91c280b42cdae26643e0f601ea281ea"},
 ]
 
 [package.dependencies]
@@ -949,15 +1142,16 @@ jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
 pickleshare = "*"
-prompt-toolkit = ">3.0.1,<3.1.0"
+prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
 traitlets = ">=5"
+typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
 
 [package.extras]
-all = ["Sphinx (>=1.3)", "black", "curio", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "testpath", "trio"]
+all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
 black = ["black"]
-doc = ["Sphinx (>=1.3)"]
+doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
@@ -965,10 +1159,10 @@ notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
 test = ["pytest (<7.1)", "pytest-asyncio", "testpath"]
-test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
 
 [[package]]
-name = "ipython_genutils"
+name = "ipython-genutils"
 version = "0.2.0"
 description = "Vestigial utilities from IPython"
 category = "main"
@@ -981,47 +1175,63 @@ files = [
 
 [[package]]
 name = "ipywidgets"
-version = "8.0.2"
+version = "8.1.0"
 description = "Jupyter interactive widgets"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ipywidgets-8.0.2-py3-none-any.whl", hash = "sha256:1dc3dd4ee19ded045ea7c86eb273033d238d8e43f9e7872c52d092683f263891"},
-    {file = "ipywidgets-8.0.2.tar.gz", hash = "sha256:08cb75c6e0a96836147cbfdc55580ae04d13e05d26ffbc377b4e1c68baa28b1f"},
+    {file = "ipywidgets-8.1.0-py3-none-any.whl", hash = "sha256:6c8396cc7b8c95dfb4e9ab0054f48c002f045e7e5d7ae523f559d64e525a98ab"},
+    {file = "ipywidgets-8.1.0.tar.gz", hash = "sha256:ce97dd90525b3066fd00094690964e7eac14cf9b7745d35565b5eeac20cce687"},
 ]
 
 [package.dependencies]
-ipykernel = ">=4.5.1"
+comm = ">=0.1.3"
 ipython = ">=6.1.0"
-jupyterlab-widgets = ">=3.0,<4.0"
+jupyterlab-widgets = ">=3.0.7,<3.1.0"
 traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0,<5.0"
+widgetsnbextension = ">=4.0.7,<4.1.0"
 
 [package.extras]
-test = ["jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
+test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
+
+[[package]]
+name = "isoduration"
+version = "20.11.0"
+description = "Operations with ISO 8601 durations"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"},
+    {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"},
+]
+
+[package.dependencies]
+arrow = ">=0.15.0"
 
 [[package]]
 name = "jedi"
-version = "0.18.1"
+version = "0.19.0"
 description = "An autocompletion tool for Python that can be used for text editors."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "jedi-0.18.1-py2.py3-none-any.whl", hash = "sha256:637c9635fcf47945ceb91cd7f320234a7be540ded6f3e99a50cb6febdfd1ba8d"},
-    {file = "jedi-0.18.1.tar.gz", hash = "sha256:74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab"},
+    {file = "jedi-0.19.0-py2.py3-none-any.whl", hash = "sha256:cb8ce23fbccff0025e9386b5cf85e892f94c9b822378f8da49970471335ac64e"},
+    {file = "jedi-0.19.0.tar.gz", hash = "sha256:bcf9894f1753969cbac8022a8c2eaee06bfa3724e4192470aaffe7eb6272b0c4"},
 ]
 
 [package.dependencies]
-parso = ">=0.8.0,<0.9.0"
+parso = ">=0.8.3,<0.9.0"
 
 [package.extras]
-qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
+docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
+qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
+testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
-name = "Jinja2"
+name = "jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
 category = "main"
@@ -1038,28 +1248,81 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "json5"
+version = "0.9.14"
+description = "A Python implementation of the JSON5 data format."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "json5-0.9.14-py2.py3-none-any.whl", hash = "sha256:740c7f1b9e584a468dbb2939d8d458db3427f2c93ae2139d05f47e453eae964f"},
+    {file = "json5-0.9.14.tar.gz", hash = "sha256:9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02"},
+]
+
+[package.extras]
+dev = ["hypothesis"]
+
+[[package]]
+name = "jsonpointer"
+version = "2.4"
+description = "Identify specific nodes in a JSON document (RFC 6901)"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
+files = [
+    {file = "jsonpointer-2.4-py2.py3-none-any.whl", hash = "sha256:15d51bba20eea3165644553647711d150376234112651b4f1811022aecad7d7a"},
+    {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
+]
+
 [[package]]
 name = "jsonschema"
-version = "4.16.0"
+version = "4.19.0"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.16.0-py3-none-any.whl", hash = "sha256:9e74b8f9738d6a946d70705dc692b74b5429cd0960d58e79ffecfc43b2221eb9"},
-    {file = "jsonschema-4.16.0.tar.gz", hash = "sha256:165059f076eff6971bae5b742fc029a7b4ef3f9bcf04c14e4776a7605de14b23"},
+    {file = "jsonschema-4.19.0-py3-none-any.whl", hash = "sha256:043dc26a3845ff09d20e4420d6012a9c91c9aa8999fa184e7efcfeccb41e32cb"},
+    {file = "jsonschema-4.19.0.tar.gz", hash = "sha256:6e1e7569ac13be8139b2dd2c21a55d350066ee3f80df06c608b398cdc6f30e8f"},
 ]
 
 [package.dependencies]
-attrs = ">=17.4.0"
+attrs = ">=22.2.0"
+fqdn = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+idna = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""}
+jsonschema-specifications = ">=2023.03.6"
 pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
-pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+referencing = ">=0.28.4"
+rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
+rpds-py = ">=0.7.1"
+uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-nongpl\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
 format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
 
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.7.1"
+description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jsonschema_specifications-2023.7.1-py3-none-any.whl", hash = "sha256:05adf340b659828a004220a9613be00fa3f223f2b82002e273dee62fd50524b1"},
+    {file = "jsonschema_specifications-2023.7.1.tar.gz", hash = "sha256:c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb"},
+]
+
+[package.dependencies]
+importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+referencing = ">=0.28.0"
+
 [[package]]
 name = "jupyter"
 version = "1.0.0"
@@ -1083,98 +1346,235 @@ qtconsole = "*"
 
 [[package]]
 name = "jupyter-cache"
-version = "0.5.0"
+version = "0.6.1"
 description = "A defined interface for working with a cache of jupyter notebooks."
 category = "dev"
 optional = false
-python-versions = "~=3.7"
+python-versions = "~=3.8"
 files = [
-    {file = "jupyter-cache-0.5.0.tar.gz", hash = "sha256:87408030a4c8c14fe3f8fe62e6ceeb24c84e544c7ced20bfee45968053d07801"},
-    {file = "jupyter_cache-0.5.0-py3-none-any.whl", hash = "sha256:642e434b9b75c4b94dc8346eaf5a639c8926a0673b87e5e8ef6460d5cf2c9516"},
+    {file = "jupyter-cache-0.6.1.tar.gz", hash = "sha256:26f83901143edf4af2f3ff5a91e2d2ad298e46e2cee03c8071d37a23a63ccbfc"},
+    {file = "jupyter_cache-0.6.1-py3-none-any.whl", hash = "sha256:2fce7d4975805c77f75bdfc1bc2e82bc538b8e5b1af27f2f5e06d55b9f996a82"},
 ]
 
 [package.dependencies]
 attrs = "*"
 click = "*"
 importlib-metadata = "*"
-nbclient = ">=0.2,<0.6"
+nbclient = ">=0.2,<0.8"
 nbformat = "*"
 pyyaml = "*"
-sqlalchemy = ">=1.3.12,<1.5"
+sqlalchemy = ">=1.3.12,<3"
 tabulate = "*"
 
 [package.extras]
 cli = ["click-log"]
-code-style = ["pre-commit (>=2.12,<3.0)"]
-rtd = ["jupytext", "myst-nb (>=0.12.3,<0.13.0)", "nbdime", "sphinx-book-theme (>=0.1.1,<0.2.0)", "sphinx-copybutton"]
-testing = ["coverage", "ipykernel", "jupytext", "matplotlib", "nbdime", "nbformat (>=5.1)", "numpy", "pandas", "pytest (>=6,<7)", "pytest-cov", "pytest-regressions", "sympy"]
+code-style = ["pre-commit (>=2.12,<4.0)"]
+rtd = ["ipykernel", "jupytext", "myst-nb", "nbdime", "sphinx-book-theme", "sphinx-copybutton"]
+testing = ["coverage", "ipykernel", "jupytext", "matplotlib", "nbdime", "nbformat (>=5.1)", "numpy", "pandas", "pytest (>=6,<8)", "pytest-cov", "pytest-regressions", "sympy"]
 
 [[package]]
 name = "jupyter-client"
-version = "7.3.5"
+version = "8.3.0"
 description = "Jupyter protocol implementation and client libraries"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "jupyter_client-7.3.5-py3-none-any.whl", hash = "sha256:b33222bdc9dd1714228bd286af006533a0abe2bbc093e8f3d29dc0b91bdc2be4"},
-    {file = "jupyter_client-7.3.5.tar.gz", hash = "sha256:3c58466a1b8d55dba0bf3ce0834e4f5b7760baf98d1d73db0add6f19de9ecd1d"},
+    {file = "jupyter_client-8.3.0-py3-none-any.whl", hash = "sha256:7441af0c0672edc5d28035e92ba5e32fadcfa8a4e608a434c228836a89df6158"},
+    {file = "jupyter_client-8.3.0.tar.gz", hash = "sha256:3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f"},
 ]
 
 [package.dependencies]
-entrypoints = "*"
-jupyter-core = ">=4.9.2"
-nest-asyncio = ">=1.5.4"
+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 python-dateutil = ">=2.8.2"
 pyzmq = ">=23.0"
 tornado = ">=6.2"
-traitlets = "*"
+traitlets = ">=5.3"
 
 [package.extras]
-doc = ["ipykernel", "myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
-test = ["codecov", "coverage", "ipykernel (>=6.5)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"]
+docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-console"
-version = "6.4.4"
+version = "6.6.3"
 description = "Jupyter terminal console"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "jupyter_console-6.4.4-py3-none-any.whl", hash = "sha256:756df7f4f60c986e7bc0172e4493d3830a7e6e75c08750bbe59c0a5403ad6dee"},
-    {file = "jupyter_console-6.4.4.tar.gz", hash = "sha256:172f5335e31d600df61613a97b7f0352f2c8250bbd1092ef2d658f77249f89fb"},
+    {file = "jupyter_console-6.6.3-py3-none-any.whl", hash = "sha256:309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485"},
+    {file = "jupyter_console-6.6.3.tar.gz", hash = "sha256:566a4bf31c87adbfadf22cdf846e3069b59a71ed5da71d6ba4d8aaad14a53539"},
 ]
 
 [package.dependencies]
-ipykernel = "*"
+ipykernel = ">=6.14"
 ipython = "*"
 jupyter-client = ">=7.0.0"
-prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+prompt-toolkit = ">=3.0.30"
 pygments = "*"
+pyzmq = ">=17"
+traitlets = ">=5.4"
 
 [package.extras]
-test = ["pexpect"]
+test = ["flaky", "pexpect", "pytest"]
 
 [[package]]
 name = "jupyter-core"
-version = "4.11.2"
+version = "5.3.1"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "jupyter_core-4.11.2-py3-none-any.whl", hash = "sha256:3815e80ec5272c0c19aad087a0d2775df2852cfca8f5a17069e99c9350cecff8"},
-    {file = "jupyter_core-4.11.2.tar.gz", hash = "sha256:c2909b9bc7dca75560a6c5ae78c34fd305ede31cd864da3c0d0bb2ed89aa9337"},
+    {file = "jupyter_core-5.3.1-py3-none-any.whl", hash = "sha256:ae9036db959a71ec1cac33081eeb040a79e681f08ab68b0883e9a676c7a90dce"},
+    {file = "jupyter_core-5.3.1.tar.gz", hash = "sha256:5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba"},
 ]
 
 [package.dependencies]
-pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
-traitlets = "*"
+platformdirs = ">=2.5"
+pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
+traitlets = ">=5.3"
 
 [package.extras]
+docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
 test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
 
+[[package]]
+name = "jupyter-events"
+version = "0.7.0"
+description = "Jupyter Event System library"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jupyter_events-0.7.0-py3-none-any.whl", hash = "sha256:4753da434c13a37c3f3c89b500afa0c0a6241633441421f6adafe2fb2e2b924e"},
+    {file = "jupyter_events-0.7.0.tar.gz", hash = "sha256:7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615"},
+]
+
+[package.dependencies]
+jsonschema = {version = ">=4.18.0", extras = ["format-nongpl"]}
+python-json-logger = ">=2.0.4"
+pyyaml = ">=5.3"
+referencing = "*"
+rfc3339-validator = "*"
+rfc3986-validator = ">=0.1.1"
+traitlets = ">=5.3"
+
+[package.extras]
+cli = ["click", "rich"]
+docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme", "sphinxcontrib-spelling"]
+test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "pytest-console-scripts", "rich"]
+
+[[package]]
+name = "jupyter-lsp"
+version = "2.2.0"
+description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jupyter-lsp-2.2.0.tar.gz", hash = "sha256:8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1"},
+    {file = "jupyter_lsp-2.2.0-py3-none-any.whl", hash = "sha256:9e06b8b4f7dd50300b70dd1a78c0c3b0c3d8fa68e0f2d8a5d1fbab62072aca3f"},
+]
+
+[package.dependencies]
+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
+jupyter-server = ">=1.1.2"
+
+[[package]]
+name = "jupyter-server"
+version = "2.7.2"
+description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jupyter_server-2.7.2-py3-none-any.whl", hash = "sha256:98a375347b580e837e7016007c24680a4261ed8ad7cd35196ac087d229f48e5a"},
+    {file = "jupyter_server-2.7.2.tar.gz", hash = "sha256:d64fb4e593907290e5df916e3c9399c15ab2cd7bdb71cbcd1d36452dbfb30523"},
+]
+
+[package.dependencies]
+anyio = ">=3.1.0"
+argon2-cffi = "*"
+jinja2 = "*"
+jupyter-client = ">=7.4.4"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-events = ">=0.6.0"
+jupyter-server-terminals = "*"
+nbconvert = ">=6.4.4"
+nbformat = ">=5.3.0"
+overrides = "*"
+packaging = "*"
+prometheus-client = "*"
+pywinpty = {version = "*", markers = "os_name == \"nt\""}
+pyzmq = ">=24"
+send2trash = ">=1.8.2"
+terminado = ">=0.8.3"
+tornado = ">=6.2.0"
+traitlets = ">=5.6.0"
+websocket-client = "*"
+
+[package.extras]
+docs = ["ipykernel", "jinja2", "jupyter-client", "jupyter-server", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi (>=0.8.0)", "sphinxcontrib-spelling", "sphinxemoji", "tornado", "typing-extensions"]
+test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", "pytest-jupyter[server] (>=0.4)", "pytest-timeout", "requests"]
+
+[[package]]
+name = "jupyter-server-terminals"
+version = "0.4.4"
+description = "A Jupyter Server Extension Providing Terminals."
+category = "main"
+optional = false
+python-versions = ">=3.8"
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 [[package]]
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 version = "2.2.0"
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 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
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+    {file = "matplotlib-3.7.2.tar.gz", hash = "sha256:a8cdb91dddb04436bd2f098b8fdf4b81352e68cf4d2c6756fcc414791076569b"},
 ]
 
 [package.dependencies]
@@ -1498,7 +1849,7 @@ kiwisolver = ">=1.0.1"
 numpy = ">=1.20"
 packaging = ">=20.0"
 pillow = ">=6.2.0"
-pyparsing = ">=2.3.1"
+pyparsing = ">=2.3.1,<3.1"
 python-dateutil = ">=2.7"
 
 [[package]]
@@ -1550,26 +1901,26 @@ files = [
 
 [[package]]
 name = "mistune"
-version = "2.0.4"
-description = "A sane Markdown parser with useful plugins and renderers"
+version = "3.0.1"
+description = "A sane and fast Markdown parser with useful plugins and renderers"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 files = [
-    {file = "mistune-2.0.4-py2.py3-none-any.whl", hash = "sha256:182cc5ee6f8ed1b807de6b7bb50155df7b66495412836b9a74c8fbdfc75fe36d"},
-    {file = "mistune-2.0.4.tar.gz", hash = "sha256:9ee0a66053e2267aba772c71e06891fa8f1af6d4b01d5e84e267b4570d4d9808"},
+    {file = "mistune-3.0.1-py3-none-any.whl", hash = "sha256:b9b3e438efbb57c62b5beb5e134dab664800bdf1284a7ee09e8b12b13eb1aac6"},
+    {file = "mistune-3.0.1.tar.gz", hash = "sha256:e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c"},
 ]
 
 [[package]]
 name = "mypy-extensions"
-version = "0.4.3"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
+version = "1.0.0"
+description = "Type system extensions for programs checked with the mypy type checker."
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
 files = [
-    {file = "mypy_extensions-0.4.3-py2.py3-none-any.whl", hash = "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d"},
-    {file = "mypy_extensions-0.4.3.tar.gz", hash = "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"},
+    {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
+    {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
 ]
 
 [[package]]
@@ -1630,76 +1981,76 @@ testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=6,<7)", "pytest-cov",
 
 [[package]]
 name = "nbclient"
-version = "0.5.13"
+version = "0.7.4"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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-    {file = "nbclient-0.5.13.tar.gz", hash = "sha256:40c52c9b5e3c31faecaee69f202b3f53e38d7c1c563de0fadde9d7eda0fdafe8"},
+    {file = "nbclient-0.7.4-py3-none-any.whl", hash = "sha256:c817c0768c5ff0d60e468e017613e6eae27b6fa31e43f905addd2d24df60c125"},
+    {file = "nbclient-0.7.4.tar.gz", hash = "sha256:d447f0e5a4cfe79d462459aec1b3dc5c2e9152597262be8ee27f7d4c02566a0d"},
 ]
 
 [package.dependencies]
-jupyter-client = ">=6.1.5"
-nbformat = ">=5.0"
-nest-asyncio = "*"
-traitlets = ">=5.0.0"
+jupyter-client = ">=6.1.12"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+nbformat = ">=5.1"
+traitlets = ">=5.3"
 
 [package.extras]
-sphinx = ["Sphinx (>=1.7)", "mock", "moto", "myst-parser", "sphinx-book-theme"]
-test = ["black", "check-manifest", "flake8", "ipykernel", "ipython (<8.0.0)", "ipywidgets (<8.0.0)", "mypy", "pip (>=18.1)", "pytest (>=4.1)", "pytest-asyncio", "pytest-cov (>=2.6.1)", "setuptools (>=38.6.0)", "twine (>=1.11.0)", "wheel (>=0.31.0)", "xmltodict"]
+dev = ["pre-commit"]
+docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"]
+test = ["flaky", "ipykernel", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
 
 [[package]]
 name = "nbconvert"
-version = "7.0.0"
+version = "7.7.4"
 description = "Converting Jupyter Notebooks"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "nbconvert-7.7.4-py3-none-any.whl", hash = "sha256:ace26f4386d08eb5c55833596a942048c5502a95e05590cb523826a749a40a37"},
+    {file = "nbconvert-7.7.4.tar.gz", hash = "sha256:1113d039fa3fc3a846ffa5a3b0a019e85aaa94c566a09fa0c400fb7638e46087"},
 ]
 
 [package.dependencies]
 beautifulsoup4 = "*"
-bleach = "*"
+bleach = "!=5.0.0"
 defusedxml = "*"
 importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
 jinja2 = ">=3.0"
 jupyter-core = ">=4.7"
 jupyterlab-pygments = "*"
-lxml = "*"
 markupsafe = ">=2.0"
-mistune = ">=2.0.3,<3"
+mistune = ">=2.0.3,<4"
 nbclient = ">=0.5.0"
-nbformat = ">=5.1"
+nbformat = ">=5.7"
 packaging = "*"
 pandocfilters = ">=1.4.1"
 pygments = ">=2.4.1"
 tinycss2 = "*"
-traitlets = ">=5.0"
+traitlets = ">=5.1"
 
 [package.extras]
-all = ["ipykernel", "ipython", "ipywidgets (>=7)", "nbsphinx (>=0.2.12)", "pre-commit", "pyppeteer (>=1,<1.1)", "pyqtwebengine (>=5.15)", "pytest", "pytest-cov", "pytest-dependency", "sphinx (==5.0.2)", "sphinx-rtd-theme", "tornado (>=6.1)"]
-docs = ["ipython", "nbsphinx (>=0.2.12)", "sphinx (==5.0.2)", "sphinx-rtd-theme"]
-qtpdf = ["pyqtwebengine (>=5.15)"]
+all = ["nbconvert[docs,qtpdf,serve,test,webpdf]"]
+docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"]
+qtpdf = ["nbconvert[qtpng]"]
 qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
-test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pyppeteer (>=1,<1.1)", "pytest", "pytest-cov", "pytest-dependency"]
-webpdf = ["pyppeteer (>=1,<1.1)"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pre-commit", "pytest", "pytest-dependency"]
+webpdf = ["playwright"]
 
 [[package]]
 name = "nbformat"
-version = "5.6.0"
+version = "5.9.2"
 description = "The Jupyter Notebook format"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "nbformat-5.9.2-py3-none-any.whl", hash = "sha256:1c5172d786a41b82bcfd0c23f9e6b6f072e8fb49c39250219e4acfff1efe89e9"},
+    {file = "nbformat-5.9.2.tar.gz", hash = "sha256:5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192"},
 ]
 
 [package.dependencies]
@@ -1709,7 +2060,8 @@ jupyter-core = "*"
 traitlets = ">=5.1"
 
 [package.extras]
-test = ["check-manifest", "pep440", "pre-commit", "pytest", "testpath"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+test = ["pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
 name = "nbsphinx"
@@ -1733,88 +2085,97 @@ traitlets = ">=5"
 
 [[package]]
 name = "nest-asyncio"
-version = "1.5.5"
+version = "1.5.7"
 description = "Patch asyncio to allow nested event loops"
 category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
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+    {file = "nest_asyncio-1.5.7.tar.gz", hash = "sha256:6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10"},
 ]
 
 [[package]]
 name = "notebook"
-version = "6.4.12"
-description = "A web-based notebook environment for interactive computing"
+version = "7.0.2"
+description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
+[package.dependencies]
+importlib-resources = {version = ">=5.0", markers = "python_version < \"3.9\""}
+jupyter-server = ">=2.4.0,<3"
+jupyterlab = ">=4.0.2,<5"
+jupyterlab-server = ">=2.22.1,<3"
+notebook-shim = ">=0.2,<0.3"
+tornado = ">=6.2.0"
+
+[package.extras]
+dev = ["hatch", "pre-commit"]
+docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+test = ["ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.22.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
+
+[[package]]
+name = "notebook-shim"
+version = "0.2.3"
+description = "A shim layer for notebook traits and config"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
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-Send2Trash = ">=1.8.0"
-terminado = ">=0.8.3"
-tornado = ">=6.1"
-traitlets = ">=4.2.1"
+jupyter-server = ">=1.8,<3"
 
 [package.extras]
-docs = ["myst-parser", "nbsphinx", "sphinx", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
-json-logging = ["json-logging"]
-test = ["coverage", "nbval", "pytest", "pytest-cov", "requests", "requests-unixsocket", "selenium", "testpath"]
+test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"]
 
 [[package]]
 name = "numexpr"
-version = "2.8.4"
+version = "2.8.5"
 description = "Fast numerical expression evaluator for NumPy"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 python-versions = ">=3.7"
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 [[package]]
@@ -1900,14 +2273,14 @@ testing = ["docopt", "pytest (<6.0.0)"]
 
 [[package]]
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 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
 
 [[package]]
-name = "pkgutil_resolve_name"
+name = "pkgutil-resolve-name"
 version = "1.3.10"
 description = "Resolve a name to an object."
 category = "main"
@@ -2026,30 +2394,30 @@ files = [
 
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 name = "platformdirs"
-version = "2.5.2"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
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+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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-test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
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+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
 
 [[package]]
 name = "prometheus-client"
-version = "0.14.1"
+version = "0.17.1"
 description = "Python client for the Prometheus monitoring system."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [package.extras]
@@ -2057,14 +2425,14 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.31"
+version = "3.0.39"
 description = "Library for building powerful interactive command lines in Python"
 category = "main"
 optional = false
-python-versions = ">=3.6.2"
+python-versions = ">=3.7.0"
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 ]
 
 [package.dependencies]
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+version = "5.9.5"
 description = "Cross-platform lib for process and system monitoring in Python."
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 cffi = {version = "*", markers = "implementation_name == \"pypy\""}
-py = {version = "*", markers = "implementation_name == \"pypy\""}
 
 [[package]]
 name = "qtconsole"
-version = "5.3.2"
+version = "5.4.3"
 description = "Jupyter Qt console"
 category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -2494,6 +2981,7 @@ ipykernel = ">=4.1"
 ipython-genutils = "*"
 jupyter-client = ">=4.1"
 jupyter-core = "*"
+packaging = "*"
 pygments = "*"
 pyzmq = ">=17.1"
 qtpy = ">=2.0.1"
@@ -2504,15 +2992,15 @@ doc = ["Sphinx (>=1.3)"]
 test = ["flaky", "pytest", "pytest-qt"]
 
 [[package]]
-name = "QtPy"
-version = "2.2.0"
+name = "qtpy"
+version = "2.3.1"
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 category = "main"
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 python-versions = ">=3.7"
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 [package.extras]
 test = ["pytest (>=6,!=7.0.0,!=7.0.1)", "pytest-cov (>=3.0.0)", "pytest-qt"]
 
+[[package]]
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+description = "JSON Referencing + Python"
+category = "main"
+optional = false
+python-versions = ">=3.8"
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+[package.dependencies]
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+rpds-py = ">=0.7.0"
+
 [[package]]
 name = "requests"
 version = "2.31.0"
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 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
+[[package]]
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+version = "0.1.4"
+description = "A pure python RFC3339 validator"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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+
+[package.dependencies]
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+
+[[package]]
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+version = "0.1.1"
+description = "Pure python rfc3986 validator"
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+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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+
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+description = "Python bindings to Rust's persistent data structures (rpds)"
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+python-versions = ">=3.8"
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 version = "1.10.1"
@@ -2583,15 +3221,15 @@ doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (
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-name = "Send2Trash"
-version = "1.8.0"
-description = "Send file to trash natively under Mac OS X, Windows and Linux."
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+version = "1.8.2"
+description = "Send file to trash natively under Mac OS X, Windows and Linux"
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+description = "Sniff out which async library your code is running under"
+category = "main"
+optional = false
+python-versions = ">=3.7"
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 version = "2.2.0"
@@ -2625,14 +3275,14 @@ files = [
 
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 [[package]]
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 [package.extras]
@@ -2725,14 +3375,14 @@ test = ["pytest"]
 
 [[package]]
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 [package.extras]
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 test = ["pytest"]
 
 [[package]]
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+typing-extensions = ">=4.2.0"
+
+[package.extras]
+aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
-asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"]
-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"]
+asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
 mssql = ["pyodbc"]
 mssql-pymssql = ["pymssql"]
 mssql-pyodbc = ["pyodbc"]
-mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"]
-mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
+mypy = ["mypy (>=0.910)"]
+mysql = ["mysqlclient (>=1.4.0)"]
 mysql-connector = ["mysql-connector-python"]
-oracle = ["cx-oracle (>=7)", "cx-oracle (>=7,<8)"]
+oracle = ["cx-oracle (>=7)"]
+oracle-oracledb = ["oracledb (>=1.0.1)"]
 postgresql = ["psycopg2 (>=2.7)"]
 postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
-postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
+postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
+postgresql-psycopg = ["psycopg (>=3.0.7)"]
 postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
-pymysql = ["pymysql", "pymysql (<1)"]
+postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
+pymysql = ["pymysql"]
 sqlcipher = ["sqlcipher3-binary"]
 
 [[package]]
 name = "stack-data"
-version = "0.5.0"
+version = "0.6.2"
 description = "Extract data from python stack frames and tracebacks for informative displays"
 category = "main"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
-asttokens = "*"
-executing = "*"
+asttokens = ">=2.1.0"
+executing = ">=1.2.0"
 pure-eval = "*"
 
 [package.extras]
@@ -2898,14 +3552,14 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
 [[package]]
 name = "tabulate"
-version = "0.8.10"
+version = "0.9.0"
 description = "Pretty-print tabular data"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -2913,14 +3567,14 @@ widechars = ["wcwidth"]
 
 [[package]]
 name = "terminado"
-version = "0.15.0"
+version = "0.17.1"
 description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -2929,18 +3583,19 @@ pywinpty = {version = ">=1.1.0", markers = "os_name == \"nt\""}
 tornado = ">=6.1.0"
 
 [package.extras]
-test = ["pre-commit", "pytest (>=6.0)", "pytest-timeout"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
+test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"]
 
 [[package]]
 name = "tinycss2"
-version = "1.1.1"
+version = "1.2.1"
 description = "A tiny CSS parser"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -2948,7 +3603,7 @@ webencodings = ">=0.4"
 
 [package.extras]
 doc = ["sphinx", "sphinx_rtd_theme"]
-test = ["coverage[toml]", "pytest", "pytest-cov", "pytest-flake8", "pytest-isort"]
+test = ["flake8", "isort", "pytest"]
 
 [[package]]
 name = "tomli"
@@ -2964,81 +3619,114 @@ files = [
 
 [[package]]
 name = "tornado"
-version = "6.2"
+version = "6.3.3"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 category = "main"
 optional = false
-python-versions = ">= 3.7"
+python-versions = ">= 3.8"
 files = [
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 ]
 
 [[package]]
 name = "traitlets"
-version = "5.4.0"
-description = ""
+version = "5.9.0"
+description = "Traitlets Python configuration system"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
-test = ["pre-commit", "pytest"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
+test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.3.0"
+version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
+[[package]]
+name = "uri-template"
+version = "1.3.0"
+description = "RFC 6570 URI Template Processor"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.extras]
+dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake8-commas", "flake8-comprehensions", "flake8-continuation", "flake8-datetimez", "flake8-docstrings", "flake8-import-order", "flake8-literal", "flake8-modern-annotations", "flake8-noqa", "flake8-pyproject", "flake8-requirements", "flake8-typechecking-import", "flake8-use-fstring", "mypy", "pep8-naming", "types-PyYAML"]
+
 [[package]]
 name = "urllib3"
-version = "1.26.12"
+version = "2.0.4"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
+python-versions = ">=3.7"
 files = [
-    {file = "urllib3-1.26.12-py2.py3-none-any.whl", hash = "sha256:b930dd878d5a8afb066a637fbb35144fe7901e3b209d1cd4f524bd0e9deee997"},
-    {file = "urllib3-1.26.12.tar.gz", hash = "sha256:3fa96cf423e6987997fc326ae8df396db2a8b7c667747d47ddd8ecba91f4a74e"},
+    {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"},
+    {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "wcwidth"
-version = "0.2.5"
+version = "0.2.6"
 description = "Measures the displayed width of unicode strings in a terminal"
 category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},
-    {file = "wcwidth-0.2.5.tar.gz", hash = "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"},
+    {file = "wcwidth-0.2.6-py2.py3-none-any.whl", hash = "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e"},
+    {file = "wcwidth-0.2.6.tar.gz", hash = "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0"},
+]
+
+[[package]]
+name = "webcolors"
+version = "1.13"
+description = "A library for working with the color formats defined by HTML and CSS."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "webcolors-1.13-py3-none-any.whl", hash = "sha256:29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf"},
+    {file = "webcolors-1.13.tar.gz", hash = "sha256:c225b674c83fa923be93d235330ce0300373d02885cef23238813b0d5668304a"},
 ]
 
+[package.extras]
+docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"]
+tests = ["pytest", "pytest-cov"]
+
 [[package]]
 name = "webencodings"
 version = "0.5.1"
@@ -3051,35 +3739,52 @@ files = [
     {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"},
 ]
 
+[[package]]
+name = "websocket-client"
+version = "1.6.1"
+description = "WebSocket client for Python with low level API options"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "websocket-client-1.6.1.tar.gz", hash = "sha256:c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd"},
+    {file = "websocket_client-1.6.1-py3-none-any.whl", hash = "sha256:f1f9f2ad5291f0225a49efad77abf9e700b6fef553900623060dad6e26503b9d"},
+]
+
+[package.extras]
+docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"]
+optional = ["python-socks", "wsaccel"]
+test = ["websockets"]
+
 [[package]]
 name = "widgetsnbextension"
-version = "4.0.3"
+version = "4.0.8"
 description = "Jupyter interactive widgets for Jupyter Notebook"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "widgetsnbextension-4.0.3-py3-none-any.whl", hash = "sha256:7f3b0de8fda692d31ef03743b598620e31c2668b835edbd3962d080ccecf31eb"},
-    {file = "widgetsnbextension-4.0.3.tar.gz", hash = "sha256:34824864c062b0b3030ad78210db5ae6a3960dfb61d5b27562d6631774de0286"},
+    {file = "widgetsnbextension-4.0.8-py3-none-any.whl", hash = "sha256:2e37f0ce9da11651056280c7efe96f2db052fe8fc269508e3724f5cbd6c93018"},
+    {file = "widgetsnbextension-4.0.8.tar.gz", hash = "sha256:9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17"},
 ]
 
 [[package]]
 name = "zipp"
-version = "3.8.1"
+version = "3.16.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.8.1-py3-none-any.whl", hash = "sha256:47c40d7fe183a6f21403a199b3e4192cca5774656965b0a4988ad2f8feb5f009"},
-    {file = "zipp-3.8.1.tar.gz", hash = "sha256:05b45f1ee8f807d0cc928485ca40a07cb491cf092ff587c0df9cb1fd154848d2"},
+    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
+    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
 ]
 
 [package.extras]
-docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx"]
-testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8, <3.12"
-content-hash = "a784fdbab28c5cd1ccd3dad39ca1c2f0bf50247a51a2ca386fb3a56d6e29ce27"
+content-hash = "1e2dde144f1c892d61d16db1ee6857ef16e50d1d41bd6922eb79e9dd76295df5"
diff --git a/pyproject.toml b/pyproject.toml
index 547daa38..f712b699 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,6 +34,7 @@ numexpr = "^2.8.3"
 numpy = "^1.23.1"
 scipy = "^1.9.0"
 sphinx = "^5.1.1"
+pydantic = "^2.2.1"
 
 [tool.poetry.dev-dependencies]
 

From d89712fbc36e3c19f88ce7edacbcf45a68032601 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Sat, 19 Aug 2023 16:07:54 +0200
Subject: [PATCH 04/53] fix bug in pydantic model definition

---
 flarestack/core/results.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flarestack/core/results.py b/flarestack/core/results.py
index 9ac90d88..1feb5a63 100644
--- a/flarestack/core/results.py
+++ b/flarestack/core/results.py
@@ -43,7 +43,7 @@ class OverfluctuationError(Exception):
 
 class Result(BaseModel):
     background_median: Optional[float] = None
-    reference_ts = Optional[float] = None
+    reference_ts: Optional[float] = None
     reference_ts_overfluctuation_fraction = Optional[float] = None
 
     sensitivity_value: Optional[float] = None

From 5a04a4250690c5bd0a487454ac1e74beade5dad2 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Sat, 19 Aug 2023 16:09:02 +0200
Subject: [PATCH 05/53] fix bug in pydantic model definition/2

---
 flarestack/core/results.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flarestack/core/results.py b/flarestack/core/results.py
index 1feb5a63..f4c53f06 100644
--- a/flarestack/core/results.py
+++ b/flarestack/core/results.py
@@ -44,7 +44,7 @@ class OverfluctuationError(Exception):
 class Result(BaseModel):
     background_median: Optional[float] = None
     reference_ts: Optional[float] = None
-    reference_ts_overfluctuation_fraction = Optional[float] = None
+    reference_ts_overfluctuation_fraction: Optional[float] = None
 
     sensitivity_value: Optional[float] = None
     sensitivity_error: Optional[Tuple[float]] = None

From 6f7373a7d107af712f14a6ca5e21dbf6cf84b78d Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Sun, 20 Aug 2023 20:40:41 +0200
Subject: [PATCH 06/53] progress in decoupling functionality

---
 flarestack/core/results.py          |   6 +-
 flarestack/core/ts_distributions.py | 217 +++++++++++++++++++---------
 2 files changed, 150 insertions(+), 73 deletions(-)

diff --git a/flarestack/core/results.py b/flarestack/core/results.py
index f4c53f06..56650d9c 100644
--- a/flarestack/core/results.py
+++ b/flarestack/core/results.py
@@ -83,7 +83,7 @@ def __init__(self, rh_dict, do_sens=True, do_disc=True, bias_error="std"):
 
         self.plot_dir = Path(plot_output_dir(self.name))
 
-        self.ts_distribution_dir = self.plot_dir / TS_DISTRIBUTION_SUBDIR
+        self.ts_distribution_dir = self.plot_dir / self.TS_DISTRIBUTION_SUBDIR
 
         self.merged_dir = os.path.join(self.pickle_output_dir, "merged")
 
@@ -729,9 +729,11 @@ def find_disc_potential(self):
 
         bkg_ts = np.array(bkg_trials["TS"])
 
+        # significance values to be considered for the discovery potential
         SIGNIFICANCE_VALUES: Final[tuple[float]] = (3.0, 5.0)
 
-        ts_thresholds = {}
+        # each significance value will have a corresponding test statistic threshold
+        ts_thresholds: dict = {}
 
         for significance in SIGNIFICANCE_VALUES:
             ts_thresholds[significance] = calc_ts_threshold(
diff --git a/flarestack/core/ts_distributions.py b/flarestack/core/ts_distributions.py
index a54248d0..bd46548f 100644
--- a/flarestack/core/ts_distributions.py
+++ b/flarestack/core/ts_distributions.py
@@ -3,8 +3,10 @@
 import numpy as np
 import os
 from pathlib import Path
+from pydantic import BaseModel
 import scipy.optimize, scipy.stats
 from scipy.stats import norm
+from typing import Optional
 
 
 logger = logging.getLogger(__name__)
@@ -169,7 +171,19 @@ def func(p):
         self.scale = res.x[2]
 
 
-def fit_background_ts(ts_array: np.array, ts_type):
+class BackgroundFit(BaseModel):
+    df: float  # degrees of freedom
+    loc: float  # mean
+    scale: float  # variance
+    frac_positive: float  # fraction of positive TS values
+    t_err: float  # threshold error (?)
+
+    @property
+    def frac_nonpositive():
+        return 1 - self.frac_positive
+
+
+def fit_background_ts(ts_array: np.array, ts_type: str) -> BackgroundFit:
     """
     Fit the background TS distribution
     """
@@ -179,28 +193,6 @@ def fit_background_ts(ts_array: np.array, ts_type):
 
     threshold_err = 0.0
 
-    ts_data, labels, colors = [], [], []
-
-    if np.sum(mask) > 0.0:
-        ts_data.append(ts_array[mask])
-        labels.append("TS > 0")
-        colors.append("black")
-    if np.sum(~mask) > 0.0:
-        ts_data.append(ts_array[~mask])
-        labels.append("TS <= 0")
-        colors.append("grey")
-
-    plt.hist(
-        ts_data,
-        bins=n_bins,
-        lw=2,
-        histtype="step",
-        color=colors,
-        label=labels,
-        density=True,
-        stacked=True,
-    )
-
     if ts_type == "flare":
         chi2 = Chi2_LeftTruncated(ts_array)
 
@@ -257,7 +249,13 @@ def fit_background_ts(ts_array: np.array, ts_type):
     else:
         raise Exception(f"ts_type {ts_type} not recognised!")
 
-    return df, loc, scale, frac_positive, threshold_err
+    return BackgroundFit(
+        df=df,
+        loc=loc,
+        scale=scale,
+        frac_positive=frac_positive,
+        threshold_err=threshold_err,
+    )
 
 
 def plot_expanded_negative(ts_array, path):
@@ -268,7 +266,7 @@ def plot_expanded_negative(ts_array, path):
         lw=2,
         histtype="step",
         color=["black", "grey"],
-        label=["TS > 0", "TS <= 0"],
+        label=["TS > 0", "TS < 0"],
         density=True,
         stacked=True,
     )
@@ -293,18 +291,73 @@ def filter_nan(values: list) -> np.array:
     return arr[~np.isnan(arr)]
 
 
-def calc_ts_threshold(ts_values: list, significance: float, ts_type: str = "standard"):
+def fit_background(ts_values: list, ts_type: str = "standard") -> BackgroundFit:
+    """Wrapper around fit_background_ts
+
+    Args:
+        ts_values (list): list of TS values from background trials
+        ts_type (str, optional): Type of test statistic. Defaults to "standard".
+
+    Returns:
+        BackgroundFit: result of the background fit.
+    """
     ts_arr = filter_nan(ts_values)
+    max_ts = np.max(ts_arr)
+
+    if max_ts == 0:
+        logger.warning(
+            f"Maximum of TS is zero, will be unable to calculate any TS threshold (too few trials?)"
+        )
+        return np.NaN
+
+    return fit_background_ts(ts_arr, ts_type)
+
+
+class DiscoverySpec(BaseModel):
+    """For a given background TS distribution, this object holds a significance value, the corresponding CDF threshold for the distribution of positve TS values and the interpolated TS value threshold."""
+
+    significance: float
+    positive_cdf_threshold: float
+    ts_threshold: float
+
+    # @property
+    # def cdf_threshold(self):
+    #     return norm.cdf(self.significance)
+    #
+    # @property
+    # def positive_cdf_threshold(self, bg_fit: BackgroundFit):
+    #      return (self.cdf_threshold - bg_fit.frac_nonpositive) / bg_fit.frac_positive
+    #
+    # @property
+    # def ts_threshold(self, bg_fit: BackgroundFit):
+    #     return scipy.stats.chi2.ppf(self.positive_cdf_threshold, bg_fit.df, bg_fit.loc, bg_fit.scale)
+
+
+def calc_ts_threshold(bg_fit: BackgroundFit, significance: float) -> DiscoverySpec:
+    # cumulative fraction of trials required to reach the desired significance
+    cdf_threshold = norm.cdf(significance)
+    # determine corresponding threshold for the CDF of
+    positive_cdf_threshold = (
+        cdf_threshold - bg_fit.frac_nonpositive
+    ) / bg_fit.frac_positive
+    ts_threshold = scipy.stats.chi2.ppf(
+        positive_cdf_threshold, bg_fit.df, bg_fit.loc, bg_fit.scale
+    )
+    return DiscoverySpec(
+        significance=significance,
+        positive_cdf_threshold=positive_cdf_threshold,
+        ts_threshold=ts_threshold,
+    )
 
 
 def plot_background_ts_distribution(
     ts_values: list,
+    bg_fit: BackgroundFit,
+    significances: list[DiscoverySpec],
     path: Path,
-    ts_type: str = "standard",
-    significance_threshold: float = 5.0,
-    ts_val=None,
+    ts_val: Optional[float] = None,
     mock_unblind: bool = False,
-):
+) -> None:
     path.mkdir(exist_ok=True)
 
     # find max ts
@@ -315,50 +368,77 @@ def plot_background_ts_distribution(
         # plot separately the positive and negative values of TS
         plot_expanded_negative(ts_arr, path)
 
-    if max_ts == 0:
-        logger.warning(
-            f"Maximum of TS is zero, unable to calculate the TS threshold for the required significance (too few trials?)"
-        )
-        return np.NaN
-
-    df, loc, scale, frac_positive, t_err = fit_background_ts(ts_arr, ts_type)
-
-    frac_nonpositive = 1.0 - frac_positive
+    fig = plt.figure()
 
-    # cumulative fraction of trials required to reach the desired significance
-    cdf_threshold = norm.cdf(significance_threshold)
-    # determine corresponding threshold for the CDF of
-    positive_cdf_threshold = (cdf_threshold - frac_nonpositive) / frac_positive
+    ax = plt.subplot(1, 1, 1)
 
-    disc_potential = scipy.stats.chi2.ppf(positive_cdf_threshold, df, loc, scale)
+    # histogram was previously done in fit_background_ts()
+    ts_data, labels, colors = [], [], []
 
-    # plotting
-    fig = plt.figure()
-    ax = plt.subplot(1, 1, 1)
+    mask = ts_arr > 0.0
+    if np.sum(mask) > 0.0:
+        ts_data.append(ts_arr[mask])
+        labels.append("TS > 0")
+        colors.append("black")
+    if np.sum(~mask) > 0.0:
+        ts_data.append(ts_arr[~mask])
+        labels.append("TS <= 0")
+        colors.append("grey")
+    plt.hist(
+        ts_data,
+        bins=n_bins,
+        lw=2,
+        histtype="step",
+        color=colors,
+        label=labels,
+        density=True,
+        stacked=True,
+    )
 
-    plt.axhline(frac_positive * (1 - positive_cdf_threshold), color="r", linestyle="--")
+    for significance in significances:
+        plt.axhline(
+            bg_fit.frac_positive * (1 - significance.positive_cdf_threshold),
+            color="r",
+            linestyle="--",
+        )
+        plt.axvline(
+            significance.ts_threshold,
+            color="r",
+            label=rf"{significance.significance} $\sigma$ threshold",
+        )
 
-    x_range = np.linspace(0.0, max(max_ts, disc_potential), 100)
+    # determine range of x-axis (TS)
+    max_ts_threshold = max(
+        [significance.ts_threshold for significance in significances]
+    )
+    x_range = np.linspace(0.0, max(max_ts, max_ts_threshold), 100)
 
     plt.plot(
         x_range,
-        frac_positive * scipy.stats.chi2.pdf(x_range, df, loc, scale),
+        bg_fit.frac_positive
+        * scipy.stats.chi2.pdf(x_range, bg_fit.df, bg_fit.loc, bg_fit.scale),
         color="blue",
         label=r"$\chi^{2}$ distribution",
     )
 
-    if t_err is not None:
+    if bg_fit.t_err is not None:
         plt.fill_between(
             x_range,
-            frac_positive * scipy.stats.chi2.pdf(x_range, df + t_err, loc, scale),
-            frac_positive * scipy.stats.chi2.pdf(x_range, df - t_err, loc, scale),
+            bg_fit.frac_positive
+            * scipy.stats.chi2.pdf(
+                x_range, bg_fit.df + bg_fit.t_err, bg_fit.loc, bg_fit.scale
+            ),
+            bg_fit.frac_positive
+            * scipy.stats.chi2.pdf(
+                x_range, bg_fit.df - bg_fit.t_err, bg_fit.loc, bg_fit.scale
+            ),
             alpha=0.1,
             color="blue",
         )
 
     def integral(x):
-        return frac_nonpositive * np.sign(x) + frac_positive * (
-            scipy.stats.chi2.cdf(x, df, loc, scale)
+        return bg_fit.frac_nonpositive * np.sign(x) + bg_fit.frac_positive * (
+            scipy.stats.chi2.cdf(x, bg_fit.df, bg_fit.loc, bg_fit.scale)
         )
 
     plt.plot(
@@ -369,10 +449,6 @@ def integral(x):
         label=r"1 - $\int f(x)$ (p-value)",
     )
 
-    plt.axvline(
-        disc_potential, color="r", label=rf"{significance_threshold} $\sigma$ threshold"
-    )
-
     if ts_val is not None:
         if not isinstance(ts_val, float):
             ts_val = float(ts_val[0])
@@ -382,8 +458,8 @@ def integral(x):
         if ts_val > np.median(ts_arr):
             # val = (ts_val - frac_under) / (1. - frac_under)
 
-            cdf = frac_nonpositive + frac_positive * scipy.stats.chi2.cdf(
-                ts_val, df, loc, scale
+            cdf = bg_fit.frac_nonpositive + bg_fitfrac_positive * scipy.stats.chi2.cdf(
+                ts_val, bg_fit.df, bg_fit.loc, bg_fit.scale
             )
 
             sig = norm.ppf(cdf)
@@ -406,24 +482,25 @@ def integral(x):
 
     else:
         plt.annotate(
-            "{:.1f}".format(100 * frac_nonpositive)
+            "{:.1f}".format(100 * bg_fit.frac_nonpositive)
             + "% of data in delta. \n"
             + r"$\chi^{2}$ Distribution:"
             + "\n   * d.o.f.="
-            + "{:.2f} \pm {:.2f}".format(df, t_err)
+            + "{:.2f} \pm {:.2f}".format(bg_fit.df, bg_fit.t_err)
             + ",\n  * loc="
-            + "{:.2f}".format(loc)
+            + "{:.2f}".format(bg_fit.loc)
             + " \n * scale="
-            + "{:.2f}".format(scale),
+            + "{:.2f}".format(bg_fit.scale),
             xy=(0.1, 0.2),
             xycoords="axes fraction",
             fontsize=8,
         )
 
-    yrange = min(
-        1.0 / (float(len(ts_arr)) * n_bins),
-        scipy.stats.chi2.pdf(disc_potential, df, loc, scale),
-    )
+    # yrange was defined but not used, keep it commented for now
+    # yrange = min(
+    #     1.0 / (float(len(ts_arr)) * n_bins),
+    #     scipy.stats.chi2.pdf(disc_potential, bg_fit.df, bg_fit.loc, bg_fit.scale),
+    # )
 
     plt.yscale("log")
     plt.xlabel(r"Test statistic ($\lambda$)")
@@ -435,8 +512,6 @@ def integral(x):
     plt.savefig(path)
     plt.close()
 
-    return disc_potential
-
 
 def plot_fit_results(results, path, inj):
     # results = np.array(results)

From 820ab240a6181f297dbeb41ca74a5887181f5f20 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Sun, 20 Aug 2023 20:42:10 +0200
Subject: [PATCH 07/53] fix typo

---
 flarestack/core/ts_distributions.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flarestack/core/ts_distributions.py b/flarestack/core/ts_distributions.py
index bd46548f..c1cfe89c 100644
--- a/flarestack/core/ts_distributions.py
+++ b/flarestack/core/ts_distributions.py
@@ -458,7 +458,7 @@ def integral(x):
         if ts_val > np.median(ts_arr):
             # val = (ts_val - frac_under) / (1. - frac_under)
 
-            cdf = bg_fit.frac_nonpositive + bg_fitfrac_positive * scipy.stats.chi2.cdf(
+            cdf = bg_fit.frac_nonpositive + bg_fit.frac_positive * scipy.stats.chi2.cdf(
                 ts_val, bg_fit.df, bg_fit.loc, bg_fit.scale
             )
 

From ad405b2da3737af2cc9b10206c797570bccae18e Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 09:57:01 +0200
Subject: [PATCH 08/53] add mypy

---
 poetry.lock    | 287 ++++++++++++++++---------------------------------
 pyproject.toml |   4 +
 2 files changed, 94 insertions(+), 197 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 1bbdc3f9..a2a178fe 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,9 @@
-# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
 version = "0.7.13"
 description = "A configurable sidebar-enabled Sphinx theme"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -16,7 +15,6 @@ files = [
 name = "annotated-types"
 version = "0.5.0"
 description = "Reusable constraint types to use with typing.Annotated"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -31,7 +29,6 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""}
 name = "anyio"
 version = "3.7.1"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -53,7 +50,6 @@ trio = ["trio (<0.22)"]
 name = "appnope"
 version = "0.1.3"
 description = "Disable App Nap on macOS >= 10.9"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -65,7 +61,6 @@ files = [
 name = "argon2-cffi"
 version = "23.1.0"
 description = "Argon2 for Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -86,7 +81,6 @@ typing = ["mypy"]
 name = "argon2-cffi-bindings"
 version = "21.2.0"
 description = "Low-level CFFI bindings for Argon2"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -124,7 +118,6 @@ tests = ["pytest"]
 name = "arrow"
 version = "1.2.3"
 description = "Better dates & times for Python"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -139,7 +132,6 @@ python-dateutil = ">=2.7.0"
 name = "astropy"
 version = "5.2.2"
 description = "Astronomy and astrophysics core library"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -193,7 +185,6 @@ test-all = ["coverage[toml]", "ipython (>=4.2)", "objgraph", "pytest (>=7.0)", "
 name = "asttokens"
 version = "2.2.1"
 description = "Annotate AST trees with source code positions"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -211,7 +202,6 @@ test = ["astroid", "pytest"]
 name = "async-lru"
 version = "2.0.4"
 description = "Simple LRU cache for asyncio"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -226,7 +216,6 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 name = "attrs"
 version = "23.1.0"
 description = "Classes Without Boilerplate"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -245,7 +234,6 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
 name = "babel"
 version = "2.12.1"
 description = "Internationalization utilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -260,7 +248,6 @@ pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
 name = "backcall"
 version = "0.2.0"
 description = "Specifications for callback functions passed in to an API"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -272,7 +259,6 @@ files = [
 name = "beautifulsoup4"
 version = "4.12.2"
 description = "Screen-scraping library"
-category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
@@ -291,7 +277,6 @@ lxml = ["lxml"]
 name = "black"
 version = "23.7.0"
 description = "The uncompromising code formatter."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -338,7 +323,6 @@ uvloop = ["uvloop (>=0.15.2)"]
 name = "bleach"
 version = "6.0.0"
 description = "An easy safelist-based HTML-sanitizing tool."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -357,7 +341,6 @@ css = ["tinycss2 (>=1.1.0,<1.2)"]
 name = "certifi"
 version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -369,7 +352,6 @@ files = [
 name = "cffi"
 version = "1.15.1"
 description = "Foreign Function Interface for Python calling C code."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -446,7 +428,6 @@ pycparser = "*"
 name = "charset-normalizer"
 version = "3.2.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -531,7 +512,6 @@ files = [
 name = "click"
 version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -546,7 +526,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -558,7 +537,6 @@ files = [
 name = "comm"
 version = "0.1.4"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -578,7 +556,6 @@ typing = ["mypy (>=0.990)"]
 name = "contourpy"
 version = "1.1.0"
 description = "Python library for calculating contours of 2D quadrilateral grids"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -637,7 +614,6 @@ test-no-images = ["pytest", "pytest-cov", "wurlitzer"]
 name = "coverage"
 version = "6.5.0"
 description = "Code coverage measurement for Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -700,7 +676,6 @@ toml = ["tomli"]
 name = "coveralls"
 version = "3.3.1"
 description = "Show coverage stats online via coveralls.io"
-category = "main"
 optional = false
 python-versions = ">= 3.5"
 files = [
@@ -709,7 +684,7 @@ files = [
 ]
 
 [package.dependencies]
-coverage = ">=4.1,<6.0.0 || >6.1,<6.1.1 || >6.1.1,<7.0"
+coverage = ">=4.1,<6.0.dev0 || >6.1,<6.1.1 || >6.1.1,<7.0"
 docopt = ">=0.6.1"
 requests = ">=1.0.0"
 
@@ -720,7 +695,6 @@ yaml = ["PyYAML (>=3.10)"]
 name = "cycler"
 version = "0.11.0"
 description = "Composable style cycles"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -732,7 +706,6 @@ files = [
 name = "debugpy"
 version = "1.6.7.post1"
 description = "An implementation of the Debug Adapter Protocol for Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -760,7 +733,6 @@ files = [
 name = "decorator"
 version = "5.1.1"
 description = "Decorators for Humans"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -772,7 +744,6 @@ files = [
 name = "defusedxml"
 version = "0.7.1"
 description = "XML bomb protection for Python stdlib modules"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -784,7 +755,6 @@ files = [
 name = "docopt"
 version = "0.6.2"
 description = "Pythonic argument parser, that will make you smile"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -795,7 +765,6 @@ files = [
 name = "docutils"
 version = "0.18.1"
 description = "Docutils -- Python Documentation Utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -807,7 +776,6 @@ files = [
 name = "exceptiongroup"
 version = "1.1.3"
 description = "Backport of PEP 654 (exception groups)"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -822,7 +790,6 @@ test = ["pytest (>=6)"]
 name = "executing"
 version = "1.2.0"
 description = "Get the currently executing AST node of a frame, and other information"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -837,7 +804,6 @@ tests = ["asttokens", "littleutils", "pytest", "rich"]
 name = "fastjsonschema"
 version = "2.18.0"
 description = "Fastest Python implementation of JSON schema"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -850,46 +816,45 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "fonttools"
-version = "4.42.0"
+version = "4.42.1"
 description = "Tools to manipulate font files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "fonttools-4.42.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:150122ed93127a26bc3670ebab7e2add1e0983d30927733aec327ebf4255b072"},
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-    {file = "fonttools-4.42.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:58c1165f9b2662645de9b19a8c8bdd636b36294ccc07e1b0163856b74f10bafc"},
-    {file = "fonttools-4.42.0-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:2d6dc3fa91414ff4daa195c05f946e6a575bd214821e26d17ca50f74b35b0fe4"},
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 ]
 
 [package.extras]
@@ -910,7 +875,6 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 name = "fqdn"
 version = "1.5.1"
 description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
 files = [
@@ -922,7 +886,6 @@ files = [
 name = "greenlet"
 version = "2.0.2"
 description = "Lightweight in-process concurrent programming"
-category = "dev"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 files = [
@@ -996,7 +959,6 @@ test = ["objgraph", "psutil"]
 name = "healpy"
 version = "1.16.5"
 description = "Healpix tools package for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1028,7 +990,6 @@ test = ["pytest", "pytest-cython", "pytest-doctestplus", "requests"]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1040,7 +1001,6 @@ files = [
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1052,7 +1012,6 @@ files = [
 name = "importlib-metadata"
 version = "6.8.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1072,7 +1031,6 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs
 name = "importlib-resources"
 version = "6.0.1"
 description = "Read resources from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1091,7 +1049,6 @@ testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)",
 name = "ipykernel"
 version = "6.25.1"
 description = "IPython Kernel for Jupyter"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1105,7 +1062,7 @@ comm = ">=0.1.1"
 debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
@@ -1125,7 +1082,6 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio"
 name = "ipython"
 version = "8.12.2"
 description = "IPython: Productive Interactive Computing"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1165,7 +1121,6 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pa
 name = "ipython-genutils"
 version = "0.2.0"
 description = "Vestigial utilities from IPython"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1177,7 +1132,6 @@ files = [
 name = "ipywidgets"
 version = "8.1.0"
 description = "Jupyter interactive widgets"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1199,7 +1153,6 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
 name = "isoduration"
 version = "20.11.0"
 description = "Operations with ISO 8601 durations"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1214,7 +1167,6 @@ arrow = ">=0.15.0"
 name = "jedi"
 version = "0.19.0"
 description = "An autocompletion tool for Python that can be used for text editors."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1234,7 +1186,6 @@ testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 name = "jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1252,7 +1203,6 @@ i18n = ["Babel (>=2.7)"]
 name = "json5"
 version = "0.9.14"
 description = "A Python implementation of the JSON5 data format."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1267,7 +1217,6 @@ dev = ["hypothesis"]
 name = "jsonpointer"
 version = "2.4"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
@@ -1279,7 +1228,6 @@ files = [
 name = "jsonschema"
 version = "4.19.0"
 description = "An implementation of JSON Schema validation for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1311,7 +1259,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 name = "jsonschema-specifications"
 version = "2023.7.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1327,7 +1274,6 @@ referencing = ">=0.28.0"
 name = "jupyter"
 version = "1.0.0"
 description = "Jupyter metapackage. Install all the Jupyter components in one go."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1348,7 +1294,6 @@ qtconsole = "*"
 name = "jupyter-cache"
 version = "0.6.1"
 description = "A defined interface for working with a cache of jupyter notebooks."
-category = "dev"
 optional = false
 python-versions = "~=3.8"
 files = [
@@ -1376,7 +1321,6 @@ testing = ["coverage", "ipykernel", "jupytext", "matplotlib", "nbdime", "nbforma
 name = "jupyter-client"
 version = "8.3.0"
 description = "Jupyter protocol implementation and client libraries"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1386,7 +1330,7 @@ files = [
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 python-dateutil = ">=2.8.2"
 pyzmq = ">=23.0"
 tornado = ">=6.2"
@@ -1400,7 +1344,6 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 name = "jupyter-console"
 version = "6.6.3"
 description = "Jupyter terminal console"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1412,7 +1355,7 @@ files = [
 ipykernel = ">=6.14"
 ipython = "*"
 jupyter-client = ">=7.0.0"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 prompt-toolkit = ">=3.0.30"
 pygments = "*"
 pyzmq = ">=17"
@@ -1425,7 +1368,6 @@ test = ["flaky", "pexpect", "pytest"]
 name = "jupyter-core"
 version = "5.3.1"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1446,7 +1388,6 @@ test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
 name = "jupyter-events"
 version = "0.7.0"
 description = "Jupyter Event System library"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1472,7 +1413,6 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p
 name = "jupyter-lsp"
 version = "2.2.0"
 description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1488,7 +1428,6 @@ jupyter-server = ">=1.1.2"
 name = "jupyter-server"
 version = "2.7.2"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1501,7 +1440,7 @@ anyio = ">=3.1.0"
 argon2-cffi = "*"
 jinja2 = "*"
 jupyter-client = ">=7.4.4"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 jupyter-events = ">=0.6.0"
 jupyter-server-terminals = "*"
 nbconvert = ">=6.4.4"
@@ -1525,7 +1464,6 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-sc
 name = "jupyter-server-terminals"
 version = "0.4.4"
 description = "A Jupyter Server Extension Providing Terminals."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1545,7 +1483,6 @@ test = ["coverage", "jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-cov",
 name = "jupyterlab"
 version = "4.0.5"
 description = "JupyterLab computational environment"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1579,7 +1516,6 @@ test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-cons
 name = "jupyterlab-pygments"
 version = "0.2.2"
 description = "Pygments theme using JupyterLab CSS variables"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1591,7 +1527,6 @@ files = [
 name = "jupyterlab-server"
 version = "2.24.0"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1618,7 +1553,6 @@ test = ["hatch", "ipykernel", "jupyterlab-server[openapi]", "openapi-spec-valida
 name = "jupyterlab-widgets"
 version = "3.0.8"
 description = "Jupyter interactive widgets for JupyterLab"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1630,7 +1564,6 @@ files = [
 name = "kiwisolver"
 version = "1.4.4"
 description = "A fast implementation of the Cassowary constraint solver"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1708,7 +1641,6 @@ files = [
 name = "markdown-it-py"
 version = "2.2.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1733,7 +1665,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "markupsafe"
 version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1793,7 +1724,6 @@ files = [
 name = "matplotlib"
 version = "3.7.2"
 description = "Python plotting package"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1856,7 +1786,6 @@ python-dateutil = ">=2.7"
 name = "matplotlib-inline"
 version = "0.1.6"
 description = "Inline Matplotlib backend for Jupyter"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1871,7 +1800,6 @@ traitlets = "*"
 name = "mdit-py-plugins"
 version = "0.3.5"
 description = "Collection of plugins for markdown-it-py"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1891,7 +1819,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "mdurl"
 version = "0.1.2"
 description = "Markdown URL utilities"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1903,7 +1830,6 @@ files = [
 name = "mistune"
 version = "3.0.1"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1911,11 +1837,56 @@ files = [
     {file = "mistune-3.0.1.tar.gz", hash = "sha256:e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c"},
 ]
 
+[[package]]
+name = "mypy"
+version = "1.5.1"
+description = "Optional static typing for Python"
+optional = false
+python-versions = ">=3.8"
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+    {file = "mypy-1.5.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d28ddc3e3dfeab553e743e532fb95b4e6afad51d4706dd22f28e1e5e664828d2"},
+    {file = "mypy-1.5.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:57b10c56016adce71fba6bc6e9fd45d8083f74361f629390c556738565af8eeb"},
+    {file = "mypy-1.5.1-cp38-cp38-win_amd64.whl", hash = "sha256:ff0cedc84184115202475bbb46dd99f8dcb87fe24d5d0ddfc0fe6b8575c88d2f"},
+    {file = "mypy-1.5.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:8f772942d372c8cbac575be99f9cc9d9fb3bd95c8bc2de6c01411e2c84ebca8a"},
+    {file = "mypy-1.5.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:5d627124700b92b6bbaa99f27cbe615c8ea7b3402960f6372ea7d65faf376c14"},
+    {file = "mypy-1.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:361da43c4f5a96173220eb53340ace68cda81845cd88218f8862dfb0adc8cddb"},
+    {file = "mypy-1.5.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:330857f9507c24de5c5724235e66858f8364a0693894342485e543f5b07c8693"},
+    {file = "mypy-1.5.1-cp39-cp39-win_amd64.whl", hash = "sha256:c543214ffdd422623e9fedd0869166c2f16affe4ba37463975043ef7d2ea8770"},
+    {file = "mypy-1.5.1-py3-none-any.whl", hash = "sha256:f757063a83970d67c444f6e01d9550a7402322af3557ce7630d3c957386fa8f5"},
+    {file = "mypy-1.5.1.tar.gz", hash = "sha256:b031b9601f1060bf1281feab89697324726ba0c0bae9d7cd7ab4b690940f0b92"},
+]
+
+[package.dependencies]
+mypy-extensions = ">=1.0.0"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = ">=4.1.0"
+
+[package.extras]
+dmypy = ["psutil (>=4.0)"]
+install-types = ["pip"]
+reports = ["lxml"]
+
 [[package]]
 name = "mypy-extensions"
 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1927,7 +1898,6 @@ files = [
 name = "myst-nb"
 version = "0.17.2"
 description = "A Jupyter Notebook Sphinx reader built on top of the MyST markdown parser."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1956,7 +1926,6 @@ testing = ["beautifulsoup4", "coverage (>=6.4,<8.0)", "ipykernel (>=5.5,<6.0)",
 name = "myst-parser"
 version = "0.18.1"
 description = "An extended commonmark compliant parser, with bridges to docutils & sphinx."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1983,7 +1952,6 @@ testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=6,<7)", "pytest-cov",
 name = "nbclient"
 version = "0.7.4"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -1993,7 +1961,7 @@ files = [
 
 [package.dependencies]
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 nbformat = ">=5.1"
 traitlets = ">=5.3"
 
@@ -2006,7 +1974,6 @@ test = ["flaky", "ipykernel", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "p
 name = "nbconvert"
 version = "7.7.4"
 description = "Converting Jupyter Notebooks"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2045,7 +2012,6 @@ webpdf = ["playwright"]
 name = "nbformat"
 version = "5.9.2"
 description = "The Jupyter Notebook format"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2067,7 +2033,6 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 name = "nbsphinx"
 version = "0.9.2"
 description = "Jupyter Notebook Tools for Sphinx"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2087,7 +2052,6 @@ traitlets = ">=5"
 name = "nest-asyncio"
 version = "1.5.7"
 description = "Patch asyncio to allow nested event loops"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2099,7 +2063,6 @@ files = [
 name = "notebook"
 version = "7.0.2"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2124,7 +2087,6 @@ test = ["ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[tes
 name = "notebook-shim"
 version = "0.2.3"
 description = "A shim layer for notebook traits and config"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2142,7 +2104,6 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"
 name = "numexpr"
 version = "2.8.5"
 description = "Fast numerical expression evaluator for NumPy"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2185,7 +2146,6 @@ numpy = ">=1.13.3"
 name = "numpy"
 version = "1.24.4"
 description = "Fundamental package for array computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2223,7 +2183,6 @@ files = [
 name = "overrides"
 version = "7.4.0"
 description = "A decorator to automatically detect mismatch when overriding a method."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2235,7 +2194,6 @@ files = [
 name = "packaging"
 version = "23.1"
 description = "Core utilities for Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2247,7 +2205,6 @@ files = [
 name = "pandocfilters"
 version = "1.5.0"
 description = "Utilities for writing pandoc filters in python"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -2259,7 +2216,6 @@ files = [
 name = "parso"
 version = "0.8.3"
 description = "A Python Parser"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2275,7 +2231,6 @@ testing = ["docopt", "pytest (<6.0.0)"]
 name = "pathspec"
 version = "0.11.2"
 description = "Utility library for gitignore style pattern matching of file paths."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2287,7 +2242,6 @@ files = [
 name = "pexpect"
 version = "4.8.0"
 description = "Pexpect allows easy control of interactive console applications."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2302,7 +2256,6 @@ ptyprocess = ">=0.5"
 name = "pickleshare"
 version = "0.7.5"
 description = "Tiny 'shelve'-like database with concurrency support"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2314,7 +2267,6 @@ files = [
 name = "pillow"
 version = "10.0.0"
 description = "Python Imaging Library (Fork)"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2384,7 +2336,6 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 name = "pkgutil-resolve-name"
 version = "1.3.10"
 description = "Resolve a name to an object."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2396,7 +2347,6 @@ files = [
 name = "platformdirs"
 version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2412,7 +2362,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 name = "prometheus-client"
 version = "0.17.1"
 description = "Python client for the Prometheus monitoring system."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2427,7 +2376,6 @@ twisted = ["twisted"]
 name = "prompt-toolkit"
 version = "3.0.39"
 description = "Library for building powerful interactive command lines in Python"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -2442,7 +2390,6 @@ wcwidth = "*"
 name = "psutil"
 version = "5.9.5"
 description = "Cross-platform lib for process and system monitoring in Python."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -2469,7 +2416,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 name = "ptyprocess"
 version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2481,7 +2427,6 @@ files = [
 name = "pure-eval"
 version = "0.2.2"
 description = "Safely evaluate AST nodes without side effects"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2496,7 +2441,6 @@ tests = ["pytest"]
 name = "pycparser"
 version = "2.21"
 description = "C parser in Python"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -2508,7 +2452,6 @@ files = [
 name = "pydantic"
 version = "2.2.1"
 description = "Data validation using Python type hints"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2528,7 +2471,6 @@ email = ["email-validator (>=2.0.0)"]
 name = "pydantic-core"
 version = "2.6.1"
 description = ""
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2647,7 +2589,6 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 name = "pyerfa"
 version = "2.0.0.3"
 description = "Python bindings for ERFA"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2704,7 +2645,6 @@ test = ["pytest", "pytest-doctestplus (>=0.7)"]
 name = "pygments"
 version = "2.16.1"
 description = "Pygments is a syntax highlighting package written in Python."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2719,7 +2659,6 @@ plugins = ["importlib-metadata"]
 name = "pyparsing"
 version = "3.0.9"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "main"
 optional = false
 python-versions = ">=3.6.8"
 files = [
@@ -2734,7 +2673,6 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "python-dateutil"
 version = "2.8.2"
 description = "Extensions to the standard Python datetime module"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -2749,7 +2687,6 @@ six = ">=1.5"
 name = "python-json-logger"
 version = "2.0.7"
 description = "A python library adding a json log formatter"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2761,7 +2698,6 @@ files = [
 name = "pytz"
 version = "2023.3"
 description = "World timezone definitions, modern and historical"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2773,7 +2709,6 @@ files = [
 name = "pywin32"
 version = "306"
 description = "Python for Window Extensions"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2797,7 +2732,6 @@ files = [
 name = "pywinpty"
 version = "2.0.11"
 description = "Pseudo terminal support for Windows from Python."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2812,7 +2746,6 @@ files = [
 name = "pyyaml"
 version = "6.0.1"
 description = "YAML parser and emitter for Python"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2862,7 +2795,6 @@ files = [
 name = "pyzmq"
 version = "25.1.1"
 description = "Python bindings for 0MQ"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2968,7 +2900,6 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 name = "qtconsole"
 version = "5.4.3"
 description = "Jupyter Qt console"
-category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
@@ -2995,7 +2926,6 @@ test = ["flaky", "pytest", "pytest-qt"]
 name = "qtpy"
 version = "2.3.1"
 description = "Provides an abstraction layer on top of the various Qt bindings (PyQt5/6 and PySide2/6)."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3013,7 +2943,6 @@ test = ["pytest (>=6,!=7.0.0,!=7.0.1)", "pytest-cov (>=3.0.0)", "pytest-qt"]
 name = "referencing"
 version = "0.30.2"
 description = "JSON Referencing + Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3029,7 +2958,6 @@ rpds-py = ">=0.7.0"
 name = "requests"
 version = "2.31.0"
 description = "Python HTTP for Humans."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3051,7 +2979,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "rfc3339-validator"
 version = "0.1.4"
 description = "A pure python RFC3339 validator"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -3066,7 +2993,6 @@ six = "*"
 name = "rfc3986-validator"
 version = "0.1.1"
 description = "Pure python rfc3986 validator"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -3078,7 +3004,6 @@ files = [
 name = "rpds-py"
 version = "0.9.2"
 description = "Python bindings to Rust's persistent data structures (rpds)"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3185,7 +3110,6 @@ files = [
 name = "scipy"
 version = "1.10.1"
 description = "Fundamental algorithms for scientific computing in Python"
-category = "main"
 optional = false
 python-versions = "<3.12,>=3.8"
 files = [
@@ -3224,7 +3148,6 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo
 name = "send2trash"
 version = "1.8.2"
 description = "Send file to trash natively under Mac OS X, Windows and Linux"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 files = [
@@ -3241,7 +3164,6 @@ win32 = ["pywin32"]
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -3253,7 +3175,6 @@ files = [
 name = "sniffio"
 version = "1.3.0"
 description = "Sniff out which async library your code is running under"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3265,7 +3186,6 @@ files = [
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3277,7 +3197,6 @@ files = [
 name = "soupsieve"
 version = "2.4.1"
 description = "A modern CSS selector implementation for Beautiful Soup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3289,7 +3208,6 @@ files = [
 name = "sphinx"
 version = "5.3.0"
 description = "Python documentation generator"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3325,7 +3243,6 @@ test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
 name = "sphinx-rtd-theme"
 version = "1.2.2"
 description = "Read the Docs theme for Sphinx"
-category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
@@ -3345,7 +3262,6 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 name = "sphinxcontrib-applehelp"
 version = "1.0.4"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3361,7 +3277,6 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "1.0.2"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3377,7 +3292,6 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.0.1"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3393,7 +3307,6 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib-jquery"
 version = "4.1"
 description = "Extension to include jQuery on newer Sphinx releases"
-category = "dev"
 optional = false
 python-versions = ">=2.7"
 files = [
@@ -3408,7 +3321,6 @@ Sphinx = ">=1.8"
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3423,7 +3335,6 @@ test = ["flake8", "mypy", "pytest"]
 name = "sphinxcontrib-qthelp"
 version = "1.0.3"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3439,7 +3350,6 @@ test = ["pytest"]
 name = "sphinxcontrib-serializinghtml"
 version = "1.1.5"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3455,7 +3365,6 @@ test = ["pytest"]
 name = "sqlalchemy"
 version = "2.0.20"
 description = "Database Abstraction Library"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3503,7 +3412,7 @@ files = [
 ]
 
 [package.dependencies]
-greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""}
+greenlet = {version = "!=0.4.17", markers = "platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\""}
 typing-extensions = ">=4.2.0"
 
 [package.extras]
@@ -3534,7 +3443,6 @@ sqlcipher = ["sqlcipher3-binary"]
 name = "stack-data"
 version = "0.6.2"
 description = "Extract data from python stack frames and tracebacks for informative displays"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3554,7 +3462,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 name = "tabulate"
 version = "0.9.0"
 description = "Pretty-print tabular data"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3569,7 +3476,6 @@ widechars = ["wcwidth"]
 name = "terminado"
 version = "0.17.1"
 description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3590,7 +3496,6 @@ test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"]
 name = "tinycss2"
 version = "1.2.1"
 description = "A tiny CSS parser"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3609,7 +3514,6 @@ test = ["flake8", "isort", "pytest"]
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3621,7 +3525,6 @@ files = [
 name = "tornado"
 version = "6.3.3"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
-category = "main"
 optional = false
 python-versions = ">= 3.8"
 files = [
@@ -3642,7 +3545,6 @@ files = [
 name = "traitlets"
 version = "5.9.0"
 description = "Traitlets Python configuration system"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3658,7 +3560,6 @@ test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"]
 name = "typing-extensions"
 version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3670,7 +3571,6 @@ files = [
 name = "uri-template"
 version = "1.3.0"
 description = "RFC 6570 URI Template Processor"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3685,7 +3585,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 name = "urllib3"
 version = "2.0.4"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3703,7 +3602,6 @@ zstd = ["zstandard (>=0.18.0)"]
 name = "wcwidth"
 version = "0.2.6"
 description = "Measures the displayed width of unicode strings in a terminal"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3715,7 +3613,6 @@ files = [
 name = "webcolors"
 version = "1.13"
 description = "A library for working with the color formats defined by HTML and CSS."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3731,7 +3628,6 @@ tests = ["pytest", "pytest-cov"]
 name = "webencodings"
 version = "0.5.1"
 description = "Character encoding aliases for legacy web content"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3743,7 +3639,6 @@ files = [
 name = "websocket-client"
 version = "1.6.1"
 description = "WebSocket client for Python with low level API options"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3760,7 +3655,6 @@ test = ["websockets"]
 name = "widgetsnbextension"
 version = "4.0.8"
 description = "Jupyter interactive widgets for Jupyter Notebook"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3772,7 +3666,6 @@ files = [
 name = "zipp"
 version = "3.16.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3787,4 +3680,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8, <3.12"
-content-hash = "1e2dde144f1c892d61d16db1ee6857ef16e50d1d41bd6922eb79e9dd76295df5"
+content-hash = "c19444ed6e56bad7ab4d05f1c2c2a43636b989b5cd223f4cc59668bd59bf6fb5"
diff --git a/pyproject.toml b/pyproject.toml
index f712b699..b7a65094 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -48,6 +48,10 @@ myst-parser = "^0.18.0"
 nbsphinx = ">=0.8.9,<0.10.0"
 myst-nb = ">=0.16,<0.18"
 
+
+[tool.poetry.group.dev.dependencies]
+mypy = "^1.5.1"
+
 [build-system]
 requires = ["poetry-core>=1.2.0"]
 build-backend = "poetry.core.masonry.api"

From 13c9e843aa440086457e034e21caae3f0181508a Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 12:18:39 +0200
Subject: [PATCH 09/53] mypy extensions

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index b7a65094..4b945380 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,10 @@ myst-nb = ">=0.16,<0.18"
 
 [tool.poetry.group.dev.dependencies]
 mypy = "^1.5.1"
+mypy-extensions = "^1.0.0"
 
 [build-system]
 requires = ["poetry-core>=1.2.0"]
 build-backend = "poetry.core.masonry.api"
+
+

From 60eb1b1cd3fb9bed4cb0c119419ae1c26838ee3a Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 12:18:46 +0200
Subject: [PATCH 10/53] poetry lock

---
 poetry.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a2a178fe..65e1ac85 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.0 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -3412,7 +3412,7 @@ files = [
 ]
 
 [package.dependencies]
-greenlet = {version = "!=0.4.17", markers = "platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\""}
+greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""}
 typing-extensions = ">=4.2.0"
 
 [package.extras]
@@ -3680,4 +3680,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8, <3.12"
-content-hash = "c19444ed6e56bad7ab4d05f1c2c2a43636b989b5cd223f4cc59668bd59bf6fb5"
+content-hash = "c11111784294ca6a75ef59dbe53edada189b91b1ac93b97bd1a05eb1ff2484e9"

From d37cf84a335780d2da8203d2cc76930871837bf5 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 12:18:56 +0200
Subject: [PATCH 11/53] mypy first pass

---
 flarestack/core/ts_distributions.py | 33 ++++++++++++++++-------------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/flarestack/core/ts_distributions.py b/flarestack/core/ts_distributions.py
index c1cfe89c..3d6c43e5 100644
--- a/flarestack/core/ts_distributions.py
+++ b/flarestack/core/ts_distributions.py
@@ -29,10 +29,15 @@ def get_ts_fit_type(mh_dict):
     return ts_fit_type
 
 
-# Taken via Alex Stasik from Thomas Kintscher
+class Chi2Generic:
+    """Abstract class to be used as base class for custom chi2 functions."""
+
+    _res: scipy.optimize.OptimizeResult
+    _f: scipy.stats._continuous_distns.chi2_gen
 
 
-class Chi2_LeftTruncated(object):
+# Taken via Alex Stasik from Thomas Kintscher
+class Chi2_LeftTruncated(Chi2Generic):
     """A class similar to the ones from scipy.stats
     allowing to fit left-truncated chi^2 distributions.
     """
@@ -116,7 +121,7 @@ def __str__(self):
         )
 
 
-class Chi2_one_side(object):
+class Chi2_one_side(Chi2Generic):
     def __init__(self, data):
         p_start = [2.0, -1.0, 1.0]
         p_start = [1.3]
@@ -140,7 +145,7 @@ def func(p):
         self.sigma = sigma
 
 
-class Chi2_one_side_free(object):
+class Chi2_one_side_free(Chi2Generic):
     def __init__(self, data):
         # p_start = [4., -1., 1.]
         p_start = [2.0, -1.0, 1.0]
@@ -179,11 +184,11 @@ class BackgroundFit(BaseModel):
     t_err: float  # threshold error (?)
 
     @property
-    def frac_nonpositive():
+    def frac_nonpositive(self):
         return 1 - self.frac_positive
 
 
-def fit_background_ts(ts_array: np.array, ts_type: str) -> BackgroundFit:
+def fit_background_ts(ts_array: np.ndarray, ts_type: str) -> BackgroundFit:
     """
     Fit the background TS distribution
     """
@@ -194,7 +199,7 @@ def fit_background_ts(ts_array: np.array, ts_type: str) -> BackgroundFit:
     threshold_err = 0.0
 
     if ts_type == "flare":
-        chi2 = Chi2_LeftTruncated(ts_array)
+        chi2: Chi2Generic = Chi2_LeftTruncated(ts_array)
 
         if chi2._res.success:
             frac_positive = 1.0
@@ -250,11 +255,7 @@ def fit_background_ts(ts_array: np.array, ts_type: str) -> BackgroundFit:
         raise Exception(f"ts_type {ts_type} not recognised!")
 
     return BackgroundFit(
-        df=df,
-        loc=loc,
-        scale=scale,
-        frac_positive=frac_positive,
-        threshold_err=threshold_err,
+        df=df, loc=loc, scale=scale, frac_positive=frac_positive, t_err=threshold_err
     )
 
 
@@ -280,7 +281,7 @@ def plot_expanded_negative(ts_array, path):
     plt.close()
 
 
-def filter_nan(values: list) -> np.array:
+def filter_nan(values: list) -> np.ndarray:
     arr = np.array(values)
 
     nan_count = np.sum(np.isnan(arr))
@@ -291,7 +292,9 @@ def filter_nan(values: list) -> np.array:
     return arr[~np.isnan(arr)]
 
 
-def fit_background(ts_values: list, ts_type: str = "standard") -> BackgroundFit:
+def fit_background(
+    ts_values: list, ts_type: str = "standard"
+) -> Optional[BackgroundFit]:
     """Wrapper around fit_background_ts
 
     Args:
@@ -308,7 +311,7 @@ def fit_background(ts_values: list, ts_type: str = "standard") -> BackgroundFit:
         logger.warning(
             f"Maximum of TS is zero, will be unable to calculate any TS threshold (too few trials?)"
         )
-        return np.NaN
+        return None
 
     return fit_background_ts(ts_arr, ts_type)
 

From 4f7701371fbf4771301cb5e91840cda1f18f5edb Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 16:50:40 +0200
Subject: [PATCH 12/53] updates

---
 flarestack/core/results.py          | 117 +++++++++++++++-------------
 flarestack/core/ts_distributions.py |  11 +++
 2 files changed, 72 insertions(+), 56 deletions(-)

diff --git a/flarestack/core/results.py b/flarestack/core/results.py
index 56650d9c..d424d47f 100644
--- a/flarestack/core/results.py
+++ b/flarestack/core/results.py
@@ -23,6 +23,8 @@
     flux_to_k,
 )
 from flarestack.core.ts_distributions import (
+    DiscoverySpec,
+    fit_background,
     calc_ts_threshold,
     plot_background_ts_distribution,
     plot_fit_results,
@@ -95,7 +97,7 @@ def __init__(self, rh_dict, do_sens=True, do_disc=True, bias_error="std"):
             This makes impossible to properly interpolate the sensitivity or discovery potential value. \n \
             Possible causes of this behaviour are:\n \
             - all the `scale` steps are too high in value;\n \
-            - the `injection_weight_modifier` values of the catalogue are improperly set, check the actual number of injected neutrinos."
+            - the `injection_weight_modifier` values of the catalogue are improperly set: check the actual number of injected neutrinos."
 
         # Checks if the code should search for flares. By default, this is
         # not done.
@@ -728,92 +730,92 @@ def find_disc_potential(self):
         bkg_trials: dict = self.get_background_trials()
 
         bkg_ts = np.array(bkg_trials["TS"])
+        bg_fit = fit_background(bkg_ts, self.ts_type)
 
         # significance values to be considered for the discovery potential
         SIGNIFICANCE_VALUES: Final[tuple[float]] = (3.0, 5.0)
 
         # each significance value will have a corresponding test statistic threshold
-        ts_thresholds: dict = {}
+        significance_specs: list[DiscoverySpec] = list()
 
         for significance in SIGNIFICANCE_VALUES:
-            ts_thresholds[significance] = calc_ts_threshold(
-                bkg_ts, significance_value=significance, ts_type=self.ts_type
+            significance_specs.append(
+                calc_ts_threshold(bg_fit, significance_value=significance)
             )
 
-        plot_background_ts_distribution(bkg_ts, ts_plot_filename, ts_type=self.ts_type)
-
-        self.result.discovery_potential_5sigma_threshold = ts_threshold_5sigma
-
-        if np.isnan(ts_threshold_5sigma):
-            logger.warning(
-                f"Invalid discovery threshold {ts_threshold_5sigma=} will be ignored. Using TS = 25.0 only."
+        # Add a significance specification for TS = 25 from Wilks' theorem.
+        significance_specs.append(
+            DiscoverySpec(
+                significance=5.0,
+                positive_cdf_threshold=np.NaN,
+                ts_threshold=25.0,
+                wilks=True,
             )
+        )
 
-        # store fraction of overfluctuations above TS threshold as a function of injection values
-        overfluctuation_fraction_5sigma, overfluctuation_fraction_25 = [], []
+        # we should check if any of the calculated significance specs is NaN or None
+        # if np.isnan(ts_threshold_5sigma):
+        #    logger.warning(
+        #        f"Invalid discovery threshold {ts_threshold_5sigma=} will be ignored. Using TS = 25.0 only."
+        #    )
+
+        plot_background_ts_distribution(
+            bkg_ts,
+            bg_fit,
+            significances=significance_specs.values(),
+            path=ts_plot_filename,
+        )
 
-        for scale in self.scales:
-            ts_array = np.array(self.results[scale]["TS"])
+        # we should now define a dictionary, for every value of TS threshold we will store the overfluctuation fraction as a function of the injection scale.
+        overfluctuation_fraction = dict[str, np.ndarray]
 
-            if not np.isnan(ts_threshold_5sigma):
-                # calculate fraction of trials above threshold
-                frac = float(len(ts_array[ts_array > ts_threshold_5sigma])) / (
-                    float(len(ts_array))
-                )
+        n_scales = len(self.scales)
 
-                logger.info(
-                    f"Fraction of overfluctuations is {frac:.2f} above {ts_threshold_5sigma:.2f} (N_trials={len(ts_array)}) (scale={scale})"
-                )
+        for spec in significance_specs:
+            overfluctuation_fraction[spec.name] = np.zeros(shape=n_scales)
 
-                overfluctuation_fraction_5sigma.append(frac)
+        for i_s, scale in enumerate(self.scales):
+            ts_array = np.array(self.results[scale]["TS"])
 
-            frac_25 = float(len(ts_array[ts_array > 25.0])) / (float(len(ts_array)))
+            for spec in significance_specs:
+                if not np.isnan(spec.ts_threshold):
+                    # we should check this before and assume here that all significance specs are good
+                    frac = float(len(ts_array[ts_array > spec.ts_threshold])) / (
+                        float(len(ts_array))
+                    )
 
-            logger.info(
-                "Fraction of overfluctuations is {0:.2f} above 25 (N_trials={1}) (Scale={2})".format(
-                    frac_25, len(ts_array), scale
-                )
-            )
+                    logger.info(
+                        f"Fraction of overfluctuations is {frac:.2f} above {spec.ts_threshold:.2f} (N_trials={len(ts_array)}) (scale={scale})"
+                    )
 
-            overfluctuation_fraction_25.append(frac_25)
+                overfluctuation_fraction[spec.name][i_s] = frac
 
-            # if frac != 0.0:
-            #    logger.info(f"Making plot for {scale=}, {frac=}")
+            # There used to be a safeguard against frac == 0 here.
             self.make_plots(scale)
-            # else:
-            #    logger.warning(
-            #        f"Fraction of overfluctuations is {frac=}, skipping plot for {scale=}"
-            #    )
-
-        x = np.array(self.scales_float)
-
-        x_flux = k_to_flux(x)
 
         # 50% of trials must be above ts threshold
-        significance = 0.5
 
         """
-        Calculate the discovery potential based on the 5-sigma threshold of the TS distribution only if the distribution is non-degenerate. Otherwise, use only the TS=25 threshold.
+        Loop on the discovery potential specifications and calculate the corresponding flux by interpolation.
         """
+        discovery_trial_fraction: float = 0.5
 
-        y_list = [overfluctuation_fraction_25]
-        out_list = ["disc_potential_25"]
+        x = np.array(self.scales_float)
+        x_flux = k_to_flux(x)
 
-        if not np.isnan(ts_threshold_5sigma):
-            y_list.append(overfluctuation_fraction_5sigma)
-            out_list.append("disc_potential")
+        def f(x, a, b, c):
+            value = scipy.stats.gamma.cdf(x, a=a, loc=b, scale=c)
+            return value
 
-        for i, y_val in enumerate(y_list):
-            # define a gamma function to represent the overfluctuation fraction vs injection scale value trend
-            def f(x, a, b, c):
-                value = scipy.stats.gamma.cdf(x, a=a, loc=b, scale=c)
-                return value
+        for key in overfluctuation_fraction:
+            # define a gamma function to fit the overfluctuation fraction vs injection scale
+            y_vals = overfluctuation_fraction[key]
 
             best_f = None
 
             try:
                 res = scipy.optimize.curve_fit(
-                    f, x, y_val, p0=[6, -0.1 * max(x), 0.1 * max(x)]
+                    f, x, y_vals, p0=[6, -0.1 * max(x), 0.1 * max(x)]
                 )
 
                 best_a = res[0][0]
@@ -823,10 +825,13 @@ def f(x, a, b, c):
                 def best_f(x):
                     return f(x, best_a, best_b, best_c)
 
-                sol = scipy.stats.gamma.ppf(0.5, best_a, best_b, best_c)
+                sol = scipy.stats.gamma.ppf(
+                    discovery_trial_fraction, best_a, best_b, best_c
+                )
 
                 # "disc_potential" and "disc_potential_25" attributes are set here
                 # use of `setattr` makes the code a bit obscure and could be improved
+                # TODO: properly propagate to result!
                 setattr(self, out_list[i], k_to_flux(sol))
 
             except RuntimeError as e:
@@ -840,7 +845,7 @@ def best_f(x):
 
             fig = plt.figure()
             ax1 = fig.add_subplot(111)
-            ax1.scatter(x_flux, y_val, color="black")
+            ax1.scatter(x_flux, y_vals, color="black")
 
             if best_f is not None:
                 ax1.plot(k_to_flux(xrange), best_f(xrange), color="blue")
diff --git a/flarestack/core/ts_distributions.py b/flarestack/core/ts_distributions.py
index 3d6c43e5..321917ee 100644
--- a/flarestack/core/ts_distributions.py
+++ b/flarestack/core/ts_distributions.py
@@ -311,6 +311,7 @@ def fit_background(
         logger.warning(
             f"Maximum of TS is zero, will be unable to calculate any TS threshold (too few trials?)"
         )
+        # maybe a BackgroundFit with invalid values would be
         return None
 
     return fit_background_ts(ts_arr, ts_type)
@@ -322,6 +323,16 @@ class DiscoverySpec(BaseModel):
     significance: float
     positive_cdf_threshold: float
     ts_threshold: float
+    # true if ts_threshold comes from Wilks' theorem
+    # i.e. 5 sigma => TS = 25
+    wilks: Optional[bool] = False
+
+    @property
+    def name(self):
+        if self.wilks:
+            return f"{self.significance} sigma (Wilks)"
+        else:
+            return f"{self.significance}"
 
     # @property
     # def cdf_threshold(self):

From 36b48f80d60c569e72f94db5a082af319dcdb21f Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 16:50:55 +0200
Subject: [PATCH 13/53] mypy config file

---
 mypy.ini | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 mypy.ini

diff --git a/mypy.ini b/mypy.ini
new file mode 100644
index 00000000..130ec4cb
--- /dev/null
+++ b/mypy.ini
@@ -0,0 +1,21 @@
+[mypy]
+packages = flarestack
+exclude = analyses
+
+[mypy-astropy]
+ignore_missing_imports = True
+
+[mypy-astropy.coordinates]
+ignore_missing_imports = True
+
+[mypy-astropy.cosmology]
+ignore_missing_imports = True
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-matplotlib.*]
+ignore_missing_imports = True
+
+[mypy-numexpr]
+ignore_missing_imports = True
\ No newline at end of file

From 3dca19a05785719d7a087480cac2e7c33779108c Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 16:54:51 +0200
Subject: [PATCH 14/53] tentatively deprecate python 3.8

---
 .github/workflows/continous_integration.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/continous_integration.yml b/.github/workflows/continous_integration.yml
index f1638b7e..c833d513 100644
--- a/.github/workflows/continous_integration.yml
+++ b/.github/workflows/continous_integration.yml
@@ -26,7 +26,7 @@ jobs:
     # Specify the python versions to test
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

From 5fd38ecbfecded079fdceebd8fc05abf0d193663 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:08:59 +0200
Subject: [PATCH 15/53] rename plot ts distribution function

---
 flarestack/core/results.py          | 20 +++++++++-----------
 flarestack/core/ts_distributions.py |  2 +-
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/flarestack/core/results.py b/flarestack/core/results.py
index d424d47f..59ac6567 100644
--- a/flarestack/core/results.py
+++ b/flarestack/core/results.py
@@ -736,14 +736,12 @@ def find_disc_potential(self):
         SIGNIFICANCE_VALUES: Final[tuple[float]] = (3.0, 5.0)
 
         # each significance value will have a corresponding test statistic threshold
-        significance_specs: list[DiscoverySpec] = list()
-
-        for significance in SIGNIFICANCE_VALUES:
-            significance_specs.append(
-                calc_ts_threshold(bg_fit, significance_value=significance)
-            )
+        significance_specs: list[DiscoverySpec] = [
+            calc_ts_threshold(bg_fit, significance_value=significance)
+            for significance in SIGNIFICANCE_VALUES
+        ]
 
-        # Add a significance specification for TS = 25 from Wilks' theorem.
+        # add a significance specification for TS = 25 from Wilks' theorem.
         significance_specs.append(
             DiscoverySpec(
                 significance=5.0,
@@ -754,12 +752,12 @@ def find_disc_potential(self):
         )
 
         # we should check if any of the calculated significance specs is NaN or None
-        # if np.isnan(ts_threshold_5sigma):
+        # if np.isnan([...]):
         #    logger.warning(
         #        f"Invalid discovery threshold {ts_threshold_5sigma=} will be ignored. Using TS = 25.0 only."
         #    )
 
-        plot_background_ts_distribution(
+        plot_ts_distribution(
             bkg_ts,
             bg_fit,
             significances=significance_specs.values(),
@@ -890,7 +888,7 @@ def noflare_plots(self, scale):
         ts_array = np.array(self.results[scale]["TS"])
         ts_path = os.path.join(self.plot_dir, "ts_distributions/" + str(scale) + ".pdf")
 
-        plot_background_ts_distribution(ts_array, ts_path, ts_type=self.ts_type)
+        plot_ts_distribution(ts_array, ts_path, ts_type=self.ts_type)
 
         param_path = os.path.join(self.plot_dir, "params/" + str(scale) + ".pdf")
 
@@ -1067,7 +1065,7 @@ def ts_distribution_evolution(self):
     #         ts_path = self.plot_dir + source + "/ts_distributions/" + str(
     #             scale) + ".pdf"
     #
-    #         plot_background_ts_distribution(ts_array, ts_path,
+    #         plot_ts_distribution(ts_array, ts_path,
     #                                         ts_type=self.ts_type)
     #
     #         param_path = self.plot_dir + source + "/params/" + str(scale) + \
diff --git a/flarestack/core/ts_distributions.py b/flarestack/core/ts_distributions.py
index 321917ee..2612312e 100644
--- a/flarestack/core/ts_distributions.py
+++ b/flarestack/core/ts_distributions.py
@@ -364,7 +364,7 @@ def calc_ts_threshold(bg_fit: BackgroundFit, significance: float) -> DiscoverySp
     )
 
 
-def plot_background_ts_distribution(
+def plot_ts_distribution(
     ts_values: list,
     bg_fit: BackgroundFit,
     significances: list[DiscoverySpec],

From 29d7a47133e3900c70ed932e6208293f50123be4 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:14:26 +0200
Subject: [PATCH 16/53] fix errs in find_overfluctuations

---
 flarestack/core/results.py | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/flarestack/core/results.py b/flarestack/core/results.py
index 59ac6567..edbf1240 100644
--- a/flarestack/core/results.py
+++ b/flarestack/core/results.py
@@ -583,7 +583,7 @@ def find_sensitivity(self):
     #     print "Upper limit is", "{0:.3g}".format(ul)
     #     return ul, extrapolated
 
-    def find_overfluctuations(self, ts_val, savepath=None):
+    def find_overfluctuations(self, ts_val: float, savepath=None) -> tuple:
         """Uses the values of injection trials to fit an 1-exponential decay
         function to the fraction of overfluctuations above `ts_val` as a function
         of the injected flux (or n_s).
@@ -598,14 +598,9 @@ def find_overfluctuations(self, ts_val, savepath=None):
         either case, a plot of the overfluctuations as a function of the
         injected signal is produced.
         """
+        x = self.scales_float
 
-        x = sorted(self.results.keys())
-        x_acc = []
-        y = []
-
-        x = [scale_shortener(i) for i in sorted([float(j) for j in x])]
-
-        yerr = []
+        x_acc, y, yerr = [], [], []
 
         self.result.reference_ts = ts_val
 
@@ -620,8 +615,8 @@ def find_overfluctuations(self, ts_val, savepath=None):
             )
 
             if scale == scale_shortener(0.0):
-                # Note: this value depends on the chosen ts_val!
-                self.result.reference_ts_overfluctuation_fraction = frac_over
+                # Note: this value depends on the chosen ts_val in case of an unblinding.
+                self.result.reference_ts_overfluctuation_fraction = frac
 
             if len(ts_array) > 1:
                 y.append(frac)

From fadc8f8eae6aa14cff01328fc5450d3f50e1c606 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:18:25 +0200
Subject: [PATCH 17/53] add mypy

---
 mypy.ini       | 21 +++++++++++++++++
 poetry.lock    | 62 +++++++++++++++++++++++++++++++++++++++++++-------
 pyproject.toml |  4 ++++
 3 files changed, 79 insertions(+), 8 deletions(-)
 create mode 100644 mypy.ini

diff --git a/mypy.ini b/mypy.ini
new file mode 100644
index 00000000..130ec4cb
--- /dev/null
+++ b/mypy.ini
@@ -0,0 +1,21 @@
+[mypy]
+packages = flarestack
+exclude = analyses
+
+[mypy-astropy]
+ignore_missing_imports = True
+
+[mypy-astropy.coordinates]
+ignore_missing_imports = True
+
+[mypy-astropy.cosmology]
+ignore_missing_imports = True
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-matplotlib.*]
+ignore_missing_imports = True
+
+[mypy-numexpr]
+ignore_missing_imports = True
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index 55e262c2..47eea15d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.0 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -1503,15 +1503,61 @@ files = [
     {file = "mistune-2.0.4.tar.gz", hash = "sha256:9ee0a66053e2267aba772c71e06891fa8f1af6d4b01d5e84e267b4570d4d9808"},
 ]
 
+[[package]]
+name = "mypy"
+version = "1.5.1"
+description = "Optional static typing for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "mypy-1.5.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:f33592ddf9655a4894aef22d134de7393e95fcbdc2d15c1ab65828eee5c66c70"},
+    {file = "mypy-1.5.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:258b22210a4a258ccd077426c7a181d789d1121aca6db73a83f79372f5569ae0"},
+    {file = "mypy-1.5.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a9ec1f695f0c25986e6f7f8778e5ce61659063268836a38c951200c57479cc12"},
+    {file = "mypy-1.5.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:abed92d9c8f08643c7d831300b739562b0a6c9fcb028d211134fc9ab20ccad5d"},
+    {file = "mypy-1.5.1-cp310-cp310-win_amd64.whl", hash = "sha256:a156e6390944c265eb56afa67c74c0636f10283429171018446b732f1a05af25"},
+    {file = "mypy-1.5.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6ac9c21bfe7bc9f7f1b6fae441746e6a106e48fc9de530dea29e8cd37a2c0cc4"},
+    {file = "mypy-1.5.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:51cb1323064b1099e177098cb939eab2da42fea5d818d40113957ec954fc85f4"},
+    {file = "mypy-1.5.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:596fae69f2bfcb7305808c75c00f81fe2829b6236eadda536f00610ac5ec2243"},
+    {file = "mypy-1.5.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:32cb59609b0534f0bd67faebb6e022fe534bdb0e2ecab4290d683d248be1b275"},
+    {file = "mypy-1.5.1-cp311-cp311-win_amd64.whl", hash = "sha256:159aa9acb16086b79bbb0016145034a1a05360626046a929f84579ce1666b315"},
+    {file = "mypy-1.5.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:f6b0e77db9ff4fda74de7df13f30016a0a663928d669c9f2c057048ba44f09bb"},
+    {file = "mypy-1.5.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:26f71b535dfc158a71264e6dc805a9f8d2e60b67215ca0bfa26e2e1aa4d4d373"},
+    {file = "mypy-1.5.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2fc3a600f749b1008cc75e02b6fb3d4db8dbcca2d733030fe7a3b3502902f161"},
+    {file = "mypy-1.5.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:26fb32e4d4afa205b24bf645eddfbb36a1e17e995c5c99d6d00edb24b693406a"},
+    {file = "mypy-1.5.1-cp312-cp312-win_amd64.whl", hash = "sha256:82cb6193de9bbb3844bab4c7cf80e6227d5225cc7625b068a06d005d861ad5f1"},
+    {file = "mypy-1.5.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:4a465ea2ca12804d5b34bb056be3a29dc47aea5973b892d0417c6a10a40b2d65"},
+    {file = "mypy-1.5.1-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:9fece120dbb041771a63eb95e4896791386fe287fefb2837258925b8326d6160"},
+    {file = "mypy-1.5.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d28ddc3e3dfeab553e743e532fb95b4e6afad51d4706dd22f28e1e5e664828d2"},
+    {file = "mypy-1.5.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:57b10c56016adce71fba6bc6e9fd45d8083f74361f629390c556738565af8eeb"},
+    {file = "mypy-1.5.1-cp38-cp38-win_amd64.whl", hash = "sha256:ff0cedc84184115202475bbb46dd99f8dcb87fe24d5d0ddfc0fe6b8575c88d2f"},
+    {file = "mypy-1.5.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:8f772942d372c8cbac575be99f9cc9d9fb3bd95c8bc2de6c01411e2c84ebca8a"},
+    {file = "mypy-1.5.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:5d627124700b92b6bbaa99f27cbe615c8ea7b3402960f6372ea7d65faf376c14"},
+    {file = "mypy-1.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:361da43c4f5a96173220eb53340ace68cda81845cd88218f8862dfb0adc8cddb"},
+    {file = "mypy-1.5.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:330857f9507c24de5c5724235e66858f8364a0693894342485e543f5b07c8693"},
+    {file = "mypy-1.5.1-cp39-cp39-win_amd64.whl", hash = "sha256:c543214ffdd422623e9fedd0869166c2f16affe4ba37463975043ef7d2ea8770"},
+    {file = "mypy-1.5.1-py3-none-any.whl", hash = "sha256:f757063a83970d67c444f6e01d9550a7402322af3557ce7630d3c957386fa8f5"},
+    {file = "mypy-1.5.1.tar.gz", hash = "sha256:b031b9601f1060bf1281feab89697324726ba0c0bae9d7cd7ab4b690940f0b92"},
+]
+
+[package.dependencies]
+mypy-extensions = ">=1.0.0"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = ">=4.1.0"
+
+[package.extras]
+dmypy = ["psutil (>=4.0)"]
+install-types = ["pip"]
+reports = ["lxml"]
+
 [[package]]
 name = "mypy-extensions"
-version = "0.4.3"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
+version = "1.0.0"
+description = "Type system extensions for programs checked with the mypy type checker."
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
 files = [
-    {file = "mypy_extensions-0.4.3-py2.py3-none-any.whl", hash = "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d"},
-    {file = "mypy_extensions-0.4.3.tar.gz", hash = "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"},
+    {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
+    {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
 ]
 
 [[package]]
@@ -2741,7 +2787,7 @@ files = [
 ]
 
 [package.dependencies]
-greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\")"}
+greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
 
 [package.extras]
 aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
@@ -2957,4 +3003,4 @@ testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>=
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8, <3.12"
-content-hash = "a784fdbab28c5cd1ccd3dad39ca1c2f0bf50247a51a2ca386fb3a56d6e29ce27"
+content-hash = "cd3a999f9b1632f49bb00f18cfe8324ec9da2982ee21f8565942d09e970db74f"
diff --git a/pyproject.toml b/pyproject.toml
index 547daa38..bcddf15b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,6 +47,10 @@ myst-parser = "^0.18.0"
 nbsphinx = ">=0.8.9,<0.10.0"
 myst-nb = ">=0.16,<0.18"
 
+
+[tool.poetry.group.dev.dependencies]
+mypy = "^1.5.1"
+
 [build-system]
 requires = ["poetry-core>=1.2.0"]
 build-backend = "poetry.core.masonry.api"

From b9d149ff36812a2ab10e12a1d0cd701431d59a3b Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:26:25 +0200
Subject: [PATCH 18/53] type hint for subclasses

---
 flarestack/core/energy_pdf.py | 2 +-
 flarestack/core/time_pdf.py   | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/flarestack/core/energy_pdf.py b/flarestack/core/energy_pdf.py
index 9b413cf5..777069ff 100644
--- a/flarestack/core/energy_pdf.py
+++ b/flarestack/core/energy_pdf.py
@@ -63,7 +63,7 @@ class EnergyPDF(object):
     A base class for Energy PDFs.
     """
 
-    subclasses = {}
+    subclasses: dict[str, object] = {}
 
     def __init__(self, e_pdf_dict):
         """
diff --git a/flarestack/core/time_pdf.py b/flarestack/core/time_pdf.py
index 32ec3df0..30605169 100644
--- a/flarestack/core/time_pdf.py
+++ b/flarestack/core/time_pdf.py
@@ -2,6 +2,7 @@
 import numpy as np
 from scipy.interpolate import interp1d
 
+
 logger = logging.getLogger(__name__)
 
 
@@ -94,8 +95,8 @@ def read_t_pdf_dict(t_pdf_dict):
     return t_pdf_dict
 
 
-class TimePDF(object):
-    subclasses = {}
+class TimePDF:
+    subclasses: dict[str, object] = {}
 
     def __init__(self, t_pdf_dict, livetime_pdf=None):
         self.t_dict = t_pdf_dict

From 0789a92c49e315fbda68efb941a179b580332b9e Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:26:35 +0200
Subject: [PATCH 19/53] mypy compliance

---
 flarestack/shared.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/flarestack/shared.py b/flarestack/shared.py
index 67d7837d..485cc59a 100644
--- a/flarestack/shared.py
+++ b/flarestack/shared.py
@@ -6,6 +6,7 @@
 import zlib
 import logging
 from pathlib import Path
+from typing import Optional
 
 logger = logging.getLogger(__name__)
 
@@ -115,12 +116,12 @@
 
 host = socket.getfqdn()
 
+host_server: Optional[str] = None
+
 if np.logical_or("ifh.de" in host, "zeuthen.desy.de" in host):
     host_server = "DESY"
 elif "icecube.wisc.edu" in host:
     host_server = "WIPAC"
-else:
-    host_server = None
 
 # gamma_range = [1., 4.]
 # gamma_precision = .025

From 4b3d77dabf345232a4da9fe53d0e92893cdc99a3 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:27:12 +0200
Subject: [PATCH 20/53] deprecate py 3.8

---
 .github/workflows/continous_integration.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/continous_integration.yml b/.github/workflows/continous_integration.yml
index f1638b7e..c833d513 100644
--- a/.github/workflows/continous_integration.yml
+++ b/.github/workflows/continous_integration.yml
@@ -26,7 +26,7 @@ jobs:
     # Specify the python versions to test
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

From c175cffdadb0e4ff3a37bfbc71d0d0ca90e3e9b8 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:29:36 +0200
Subject: [PATCH 21/53] mypy compliance

---
 flarestack/misc/flare_llh_plots.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/flarestack/misc/flare_llh_plots.py b/flarestack/misc/flare_llh_plots.py
index 9d4578b7..986e1b28 100644
--- a/flarestack/misc/flare_llh_plots.py
+++ b/flarestack/misc/flare_llh_plots.py
@@ -102,11 +102,13 @@ def energy_ratio(e):
 n_bkg = 6
 
 
-s_t = []
+s_t_list = []
 
 for i, t in enumerate(np.random.uniform(0, 1.0, n_sig)):
-    s_t.append((t + float(i)) * 25)
-s_t = np.array(s_t)
+    s_t_list.append((t + float(i)) * 25)
+
+s_t = np.array(s_t_list)
+
 bkg_t = np.random.uniform(0, 1.0, n_bkg) * 100
 
 all_t = np.concatenate((s_t, bkg_t))

From b6f5a843aa834faeaff27b6e9515e5f30c12ad9e Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:32:03 +0200
Subject: [PATCH 22/53] ignore imports for healpy

---
 mypy.ini | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/mypy.ini b/mypy.ini
index 130ec4cb..efc46314 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -11,6 +11,9 @@ ignore_missing_imports = True
 [mypy-astropy.cosmology]
 ignore_missing_imports = True
 
+[mypy-healpy]
+ignore_missing_imports = True
+
 [mypy-scipy.*]
 ignore_missing_imports = True
 

From f7c2dbd4160bef0f682f4e3724da776a3a8184bb Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:46:42 +0200
Subject: [PATCH 23/53] subclasses typing

---
 flarestack/core/injector.py    | 4 ++--
 flarestack/core/spatial_pdf.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/flarestack/core/injector.py b/flarestack/core/injector.py
index f5bac9b9..7e17fed7 100644
--- a/flarestack/core/injector.py
+++ b/flarestack/core/injector.py
@@ -64,7 +64,7 @@ def read_injector_dict(inj_dict):
 class BaseInjector:
     """Base Injector Class"""
 
-    subclasses = {}
+    subclasses: dict[str, object] = {}
 
     def __init__(self, season, sources, **kwargs):
         kwargs = read_injector_dict(kwargs)
@@ -224,7 +224,7 @@ class MCInjector(BaseInjector):
     background. This can be either MC background, or scrambled real data.
     """
 
-    subclasses = {}
+    subclasses: dict[str, object] = {}
 
     def __init__(self, season, sources, **kwargs):
         kwargs = read_injector_dict(kwargs)
diff --git a/flarestack/core/spatial_pdf.py b/flarestack/core/spatial_pdf.py
index af774fe2..1f9d2042 100644
--- a/flarestack/core/spatial_pdf.py
+++ b/flarestack/core/spatial_pdf.py
@@ -32,7 +32,7 @@ def __init__(self, spatial_pdf_dict, season):
 class SignalSpatialPDF:
     """Base Signal Spatial PDF class."""
 
-    subclasses = {}
+    subclasses: dict[str, object] = {}
 
     def __init__(self, spatial_pdf_dict):
         pass
@@ -202,7 +202,7 @@ def signal_spatial(source, cut_data):
 
 
 class BackgroundSpatialPDF:
-    subclasses = {}
+    subclasses: dict[str, object] = {}
 
     def __init__(self, spatial_pdf_dict, season):
         pass

From 2259c150725a8d58c80fadff869a551040dabf3b Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:47:05 +0200
Subject: [PATCH 24/53] update to actually existing dataset

---
 flarestack/misc/plot_data_rate.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flarestack/misc/plot_data_rate.py b/flarestack/misc/plot_data_rate.py
index 6b598d30..7d403ceb 100644
--- a/flarestack/misc/plot_data_rate.py
+++ b/flarestack/misc/plot_data_rate.py
@@ -1,6 +1,6 @@
 import os
 import matplotlib.pyplot as plt
-from flarestack.data.icecube.northern_tracks.nt_v002_p01 import diffuse_8year
+from flarestack.data.icecube.northern_tracks.nt_v002_p05 import diffuse_8year
 from flarestack.shared import plots_dir
 from flarestack.icecube_utils.dataset_loader import data_loader, grl_loader
 

From f0e4a7939c3c86d583e2d7975168962bf32d5da9 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:48:56 +0200
Subject: [PATCH 25/53] avoid redefinitions

---
 flarestack/data/icecube/ic_season.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/flarestack/data/icecube/ic_season.py b/flarestack/data/icecube/ic_season.py
index 798c7550..3fb66ef7 100644
--- a/flarestack/data/icecube/ic_season.py
+++ b/flarestack/data/icecube/ic_season.py
@@ -11,12 +11,12 @@
 from scipy.interpolate import interp1d
 import logging
 from pathlib import Path
-from typing import Tuple
+from typing import Optional
 
 
 logger = logging.getLogger(__name__)
 
-icecube_dataset_dir = os.environ.get("FLARESTACK_DATASET_DIR")
+flarestack_dataset_dir: str = os.environ.get("FLARESTACK_DATASET_DIR")
 
 """
 Source data on the WIPAC cluster.
@@ -45,10 +45,10 @@
 """
 mirror_7yr_dirname = "mirror-7year-PS-sens"  # expected identical at all mirrors
 
-if icecube_dataset_dir is not None:
-    logger.info(f"Loading datasets from {icecube_dataset_dir} (local)")
+if flarestack_dataset_dir is not None:
+    logger.info(f"Loading datasets from {flarestack_dataset_dir} (local)")
 
-    icecube_dataset_dir = Path(icecube_dataset_dir)
+    icecube_dataset_dir = Path(flarestack_dataset_dir)
 
     ref_dir_7yr = icecube_dataset_dir / mirror_7yr_dirname
     if not ref_dir_7yr.is_dir():
@@ -68,7 +68,7 @@
 DESY_sens_path = DESY_data_path / "ref_sensitivity"
 
 # Only load from central storage if $FLARESTACK_DATASET_DIR is not set.
-if icecube_dataset_dir is None:
+if flarestack_dataset_dir is None:
     # NOTE: he following block has no failsafe against changes in the directory structure.
     if host_server == "DESY":
         icecube_dataset_dir = DESY_data_path
@@ -98,7 +98,7 @@ def get_dataset_dir() -> str:
     return dataset_dir
 
 
-def get_published_sens_ref_dir() -> Tuple[Path]:
+def get_published_sens_ref_dir() -> tuple[Path]:
     """
     Returns the paths to reference sensitivities.
     """

From 66104108255b5fc04cc5a5f30a62cdf0837579d1 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 17:49:38 +0200
Subject: [PATCH 26/53] rename function

---
 flarestack/core/results.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flarestack/core/results.py b/flarestack/core/results.py
index edbf1240..0394f2cc 100644
--- a/flarestack/core/results.py
+++ b/flarestack/core/results.py
@@ -26,7 +26,7 @@
     DiscoverySpec,
     fit_background,
     calc_ts_threshold,
-    plot_background_ts_distribution,
+    plot_ts_distribution,
     plot_fit_results,
     get_ts_fit_type,
 )

From 28104811a589939f1718a96da7b8ade9687ab113 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Mon, 21 Aug 2023 18:41:11 +0200
Subject: [PATCH 27/53] blend stuff together

---
 flarestack/core/results.py          | 73 +++++++++++++++--------------
 flarestack/core/ts_distributions.py |  8 ++--
 2 files changed, 42 insertions(+), 39 deletions(-)

diff --git a/flarestack/core/results.py b/flarestack/core/results.py
index 0394f2cc..4f5cd658 100644
--- a/flarestack/core/results.py
+++ b/flarestack/core/results.py
@@ -217,12 +217,12 @@ def __str__(self):
             out += "Result is invalid. Check the log messages."
         return out
 
-    def get_background_trials(self):
+    def get_background_trials(self) -> dict:
         try:
             return self.results[scale_shortener(0.0)]
         except KeyError:
             logger.error("No key equal to '0'")
-            return
+            return {}
 
     @property
     def scales_float(self):
@@ -719,7 +719,7 @@ def best_f(x, sd=0.0):
 
         return fit, fit_err, extrapolated
 
-    def find_disc_potential(self):
+    def find_disc_potential(self) -> None:
         ts_plot_filename: Path = self.ts_distribution_dir / "0.pdf"
 
         bkg_trials: dict = self.get_background_trials()
@@ -727,16 +727,19 @@ def find_disc_potential(self):
         bkg_ts = np.array(bkg_trials["TS"])
         bg_fit = fit_background(bkg_ts, self.ts_type)
 
-        # significance values to be considered for the discovery potential
-        SIGNIFICANCE_VALUES: Final[tuple[float]] = (3.0, 5.0)
+        if bg_fit is None:
+            # fit_background has detected that the maximum of the TS is zero, so there is not much to do.
+            return
 
-        # each significance value will have a corresponding test statistic threshold
+        # discovery potential is assessed for:
+        # - a given list of significance values (3 sigma, 5 sigma), for which the TS threshold is calculated;
+        # - a nominal 5 sigma significance corresponding to a TS threshold of 25 (from Wilks' theorem)
+        # each of these scenarios is encoded in a DiscoverySpec object
+        SIGNIFICANCE_VALUES: Final[tuple[float, ...]] = (3.0, 5.0)
         significance_specs: list[DiscoverySpec] = [
-            calc_ts_threshold(bg_fit, significance_value=significance)
+            calc_ts_threshold(bg_fit, significance=significance)
             for significance in SIGNIFICANCE_VALUES
         ]
-
-        # add a significance specification for TS = 25 from Wilks' theorem.
         significance_specs.append(
             DiscoverySpec(
                 significance=5.0,
@@ -746,21 +749,20 @@ def find_disc_potential(self):
             )
         )
 
-        # we should check if any of the calculated significance specs is NaN or None
-        # if np.isnan([...]):
-        #    logger.warning(
-        #        f"Invalid discovery threshold {ts_threshold_5sigma=} will be ignored. Using TS = 25.0 only."
-        #    )
+        # TODO: here we should check whether any DiscoverySpec has an invalid value of ts threshold?
 
+        # the plot of the background TS distribution will show thresholds according to the significances
         plot_ts_distribution(
             bkg_ts,
             bg_fit,
-            significances=significance_specs.values(),
+            significances=significance_specs,
             path=ts_plot_filename,
         )
 
-        # we should now define a dictionary, for every value of TS threshold we will store the overfluctuation fraction as a function of the injection scale.
+        # dictonary where for for every DiscoverySpec we will store the overfluctuation fraction as a function of the injection scale
         overfluctuation_fraction = dict[str, np.ndarray]
+        # dictionary where we will store the discovery potential flux
+        discovery_potential_flux = dict[str, float]
 
         n_scales = len(self.scales)
 
@@ -772,7 +774,7 @@ def find_disc_potential(self):
 
             for spec in significance_specs:
                 if not np.isnan(spec.ts_threshold):
-                    # we should check this before and assume here that all significance specs are good
+                    # TODO: just assume all specs are good and avoid (re)checking isnan
                     frac = float(len(ts_array[ts_array > spec.ts_threshold])) / (
                         float(len(ts_array))
                     )
@@ -784,10 +786,9 @@ def find_disc_potential(self):
                 overfluctuation_fraction[spec.name][i_s] = frac
 
             # There used to be a safeguard against frac == 0 here.
+            # Also this is independent from the overfluctuation fraction. Can it be decoupled?
             self.make_plots(scale)
 
-        # 50% of trials must be above ts threshold
-
         """
         Loop on the discovery potential specifications and calculate the corresponding flux by interpolation.
         """
@@ -802,7 +803,7 @@ def f(x, a, b, c):
 
         for key in overfluctuation_fraction:
             # define a gamma function to fit the overfluctuation fraction vs injection scale
-            y_vals = overfluctuation_fraction[key]
+            y_vals: np.ndarray = overfluctuation_fraction[key]
 
             best_f = None
 
@@ -822,15 +823,12 @@ def best_f(x):
                     discovery_trial_fraction, best_a, best_b, best_c
                 )
 
-                # "disc_potential" and "disc_potential_25" attributes are set here
-                # use of `setattr` makes the code a bit obscure and could be improved
-                # TODO: properly propagate to result!
-                setattr(self, out_list[i], k_to_flux(sol))
+                discovery_potential_flux[key] = k_to_flux(sol)
 
             except RuntimeError as e:
                 logger.warning(f"RuntimeError for discovery potential!: {e}")
 
-            # Now we plot something.
+            # Now we plot stuff.
             xrange = np.linspace(0.0, 1.1 * max(x), 1000)
 
             # Need to define a sensible output naming scheme.
@@ -862,22 +860,27 @@ def best_f(x):
             fig.savefig(savepath)
             plt.close()
 
+        # we store the output in the result attribute
+        # having these hardcoded keys is a bit ugly
+        self.result.discovery_potential_3sigma_value = discovery_potential_flux[
+            "3 sigma"
+        ]
+        self.result.discovery_potential_5sigma_value = discovery_potential_flux[
+            "5 sigma"
+        ]
+        self.result.discovery_potential_TS25_value = discovery_potential_flux[
+            "5 sigma (Wilks)"
+        ]
+
         if self.result.discovery_potential_5sigma_value > max(x_flux):
             self.extrapolated_disc = True
 
-        msg = ""
-
-        if self.extrapolated_disc:
-            msg = "EXTRAPOLATED "
+        msg = "EXTRAPOLATED " if self.extrapolated_disc else ""
 
         logger.info(
-            "{0}Discovery potential is {1:.3g}".format(
-                msg, self.result.discovery_potential_5sigma_value
-            )
-        )
-        logger.info(
-            "Discovery potential (TS = 25) is {0:.3g}".format(self.disc_potential_25)
+            f"{msg}Discovery potential is {self.result.discovery_potential_5sigma_value:.3g}"
         )
+        logger.info(f"Discovery potential (Wilks, TS = 25) is {disc_potential_25:.3g}")
 
     def noflare_plots(self, scale):
         ts_array = np.array(self.results[scale]["TS"])
diff --git a/flarestack/core/ts_distributions.py b/flarestack/core/ts_distributions.py
index 2612312e..c5d3da80 100644
--- a/flarestack/core/ts_distributions.py
+++ b/flarestack/core/ts_distributions.py
@@ -293,7 +293,7 @@ def filter_nan(values: list) -> np.ndarray:
 
 
 def fit_background(
-    ts_values: list, ts_type: str = "standard"
+    ts_values: np.ndarray, ts_type: str = "standard"
 ) -> Optional[BackgroundFit]:
     """Wrapper around fit_background_ts
 
@@ -328,11 +328,11 @@ class DiscoverySpec(BaseModel):
     wilks: Optional[bool] = False
 
     @property
-    def name(self):
+    def name(self) -> str:
         if self.wilks:
             return f"{self.significance} sigma (Wilks)"
         else:
-            return f"{self.significance}"
+            return f"{self.significance} sigma"
 
     # @property
     # def cdf_threshold(self):
@@ -365,7 +365,7 @@ def calc_ts_threshold(bg_fit: BackgroundFit, significance: float) -> DiscoverySp
 
 
 def plot_ts_distribution(
-    ts_values: list,
+    ts_values: np.ndarray,
     bg_fit: BackgroundFit,
     significances: list[DiscoverySpec],
     path: Path,

From 773fbedcf813a3424110b3984ebecf845439e453 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 00:02:58 +0200
Subject: [PATCH 28/53] mypy compliance

---
 flarestack/data/icecube/ic_season.py | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/flarestack/data/icecube/ic_season.py b/flarestack/data/icecube/ic_season.py
index 3fb66ef7..abb20c68 100644
--- a/flarestack/data/icecube/ic_season.py
+++ b/flarestack/data/icecube/ic_season.py
@@ -16,7 +16,7 @@
 
 logger = logging.getLogger(__name__)
 
-flarestack_dataset_dir: str = os.environ.get("FLARESTACK_DATASET_DIR")
+flarestack_dataset_dir: Optional[str] = os.environ.get("FLARESTACK_DATASET_DIR")
 
 """
 Source data on the WIPAC cluster.
@@ -50,14 +50,18 @@
 
     icecube_dataset_dir = Path(flarestack_dataset_dir)
 
-    ref_dir_7yr = icecube_dataset_dir / mirror_7yr_dirname
-    if not ref_dir_7yr.is_dir():
-        logger.warning(f"No 7yr sensitivity directory found at {ref_dir_7yr}")
+    ref_7yr_path: Path = icecube_dataset_dir / mirror_7yr_dirname
+    if ref_7yr_path.is_dir():
+        ref_dir_7yr: Optional[Path] = ref_7yr_path
+    else:
+        logger.warning(f"No 7yr sensitivity directory found at {ref_7yr_path}")
         ref_dir_7yr = None
 
-    ref_10yr = icecube_dataset_dir / ref_10yr_filename
-    if not ref_10yr.is_file():
-        logger.warning(f"No 10yr sensitivity found at {ref_10yr}")
+    ref_10yr_path: Path = icecube_dataset_dir / ref_10yr_filename
+    if ref_10yr_path.is_file():
+        ref_10yr: Optional[Path] = ref_10yr_path
+    else:
+        logger.warning(f"No 10yr sensitivity found at {ref_10yr_path}")
         ref_10yr = None
 else:
     logger.info(
@@ -98,7 +102,7 @@ def get_dataset_dir() -> str:
     return dataset_dir
 
 
-def get_published_sens_ref_dir() -> tuple[Path]:
+def get_published_sens_ref_dir() -> tuple[Path, Path]:
     """
     Returns the paths to reference sensitivities.
     """

From c51cf8038ae5abb6d1390d714a9c0c0753d0fe25 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 00:06:09 +0200
Subject: [PATCH 29/53] comment acknowledging this still needs a rework

---
 flarestack/data/icecube/ic_season.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/flarestack/data/icecube/ic_season.py b/flarestack/data/icecube/ic_season.py
index abb20c68..358254bf 100644
--- a/flarestack/data/icecube/ic_season.py
+++ b/flarestack/data/icecube/ic_season.py
@@ -45,6 +45,7 @@
 """
 mirror_7yr_dirname = "mirror-7year-PS-sens"  # expected identical at all mirrors
 
+# NOTE: the following block is somehow convoluted and the logic should be restructured.
 if flarestack_dataset_dir is not None:
     logger.info(f"Loading datasets from {flarestack_dataset_dir} (local)")
 

From 59f6254321cecc22838693eb369f22e6c0ae46ac Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 00:22:00 +0200
Subject: [PATCH 30/53] type annotation for subclasses

---
 flarestack/core/llh.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flarestack/core/llh.py b/flarestack/core/llh.py
index 4789c2f9..0e5197b6 100644
--- a/flarestack/core/llh.py
+++ b/flarestack/core/llh.py
@@ -80,7 +80,7 @@ def read_llh_dict(llh_dict):
 class LLH(object):
     """Base class LLH."""
 
-    subclasses = {}
+    subclasses: dict[str, object] = {}
 
     def __init__(self, season, sources, llh_dict):
         self.season = season

From 319bd3f1bf03473c33da0ef636e26f4911b10d91 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 00:36:22 +0200
Subject: [PATCH 31/53] mypy compliance

---
 flarestack/core/llh.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/flarestack/core/llh.py b/flarestack/core/llh.py
index 0e5197b6..493894eb 100644
--- a/flarestack/core/llh.py
+++ b/flarestack/core/llh.py
@@ -1394,13 +1394,17 @@ def find_significant_events(self, coincident_data, source):
     return FlareLLH(season, sources, llh_dict)
 
 
+# NOTE: `mypy` allowed to find some deprecations in the following __main__ block that were never noticed before, because the block is not part of any testing routine. It should be checked whether equivalent code is covered by an unit test, before removing the (now commented) block altogether.
+"""
 if __name__ == "__main__":
+
+
     from flarestack.shared import fs_scratch_dir
     from scipy.interpolate import InterpolatedUnivariateSpline
 
     g = EnergyPDF.create({"energy_pdf_name": "PowerLaw", "gamma": 2.2})
 
-    e_range = np.logspace(0, 7, 1e3)
+    e_range = np.logspace(start=0, stop=7, num=1000)
 
     f = InterpolatedUnivariateSpline(e_range, np.log(g.f(e_range)))
 
@@ -1440,3 +1444,4 @@ def find_significant_events(self, coincident_data, source):
 
     for i in np.linspace(0.0, 10.0, 21):
         print(i, f([i], weights))
+"""

From 1d6e058b4b741a024c8fb2132524f85cfedf8d22 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 00:48:00 +0200
Subject: [PATCH 32/53] format string / mypy compliance

---
 flarestack/utils/asimov_estimator.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/flarestack/utils/asimov_estimator.py b/flarestack/utils/asimov_estimator.py
index f1d1733f..3333e7f7 100644
--- a/flarestack/utils/asimov_estimator.py
+++ b/flarestack/utils/asimov_estimator.py
@@ -162,9 +162,7 @@ def signalness(sig_over_background):
 
             if len(source_mc) == 0:
                 logging.warning(
-                    "Warning, no MC found for dummy source at declinbation ".format(
-                        np.arcsin(lower), np.arcsin(upper)
-                    )
+                    f"Warning, no MC found for dummy source at declination {np.arcsin(lower)} {np.arcsin(upper)}"
                 )
                 ts_vals.append(0.0)
                 n_sigs.append(0.0)

From 198671286f4c8dde4ebff9b61180d41537cdfc09 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 00:56:00 +0200
Subject: [PATCH 33/53] comment out double definition of a class

---
 flarestack/core/angular_error_modifier.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/flarestack/core/angular_error_modifier.py b/flarestack/core/angular_error_modifier.py
index 298611ac..2479470c 100644
--- a/flarestack/core/angular_error_modifier.py
+++ b/flarestack/core/angular_error_modifier.py
@@ -34,7 +34,7 @@
 
 
 class BaseFloorClass(object):
-    subclasses = {}
+    subclasses: dict[str, object] = {}
 
     def __init__(self, floor_dict):
         self.floor_dict = floor_dict
@@ -149,7 +149,7 @@ def __init__(self, floor_dict):
         if not os.path.isfile(self.pickle_name):
             self.create_pickle()
         else:
-            logger.debug("Loading from".format(self.pickle_name))
+            logger.debug(f"Loading from {self.pickle_name}")
 
         with open(self.pickle_name, "r") as f:
             pickled_data = Pickle.load(f)
@@ -182,6 +182,9 @@ def create_function(self, pickled_array):
         return lambda data, params: np.array([func(params) for _ in data])
 
 
+"""
+# This class has been commented out since its name is redefined below.
+# However, it seems QuantileFloor1D is never explicitly called in the code and is hence likely untested.
 @BaseFloorClass.register_subclass("quantile_floor_1d")
 class QuantileFloor1D(BaseQuantileFloor, BaseStaticFloor):
     def create_pickle(self):
@@ -190,6 +193,7 @@ def create_pickle(self):
     def create_function(self, pickled_array):
         func = interp1d(pickled_array[0], pickled_array[1])
         return lambda data, params: func(data["logE"])
+"""
 
 
 @BaseFloorClass.register_subclass("quantile_floor_1d_e")
@@ -245,7 +249,7 @@ def create(
         e_pdf_dict,
         floor_name="static_floor",
         aem_name="no_modifier",
-        **kwargs
+        **kwargs,
     ):
         pull_dict = dict()
         pull_dict["season"] = season

From aeea9308656eba1b7d852e214ec5fac6a2cfdc59 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 01:09:31 +0200
Subject: [PATCH 34/53] cosmetics

---
 flarestack/core/llh.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/flarestack/core/llh.py b/flarestack/core/llh.py
index 493894eb..73cdebe9 100644
--- a/flarestack/core/llh.py
+++ b/flarestack/core/llh.py
@@ -1394,8 +1394,9 @@ def find_significant_events(self, coincident_data, source):
     return FlareLLH(season, sources, llh_dict)
 
 
-# NOTE: `mypy` allowed to find some deprecations in the following __main__ block that were never noticed before, because the block is not part of any testing routine. It should be checked whether equivalent code is covered by an unit test, before removing the (now commented) block altogether.
 """
+# NOTE: `mypy` allowed to find some deprecations in the following __main__ block that were never noticed before, because the block is not part of any testing routine. It should be checked whether equivalent code is covered by an unit test, before removing the (now commented) block altogether.
+
 if __name__ == "__main__":
 
 

From 2132ded93ce72cd9b5fe754e41b3401a20232254 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 01:09:40 +0200
Subject: [PATCH 35/53] mypy compliance

---
 flarestack/core/angular_error_modifier.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/flarestack/core/angular_error_modifier.py b/flarestack/core/angular_error_modifier.py
index 2479470c..63510aed 100644
--- a/flarestack/core/angular_error_modifier.py
+++ b/flarestack/core/angular_error_modifier.py
@@ -216,7 +216,7 @@ def create_function(self, pickled_array):
 
 
 class BaseAngularErrorModifier(object):
-    subclasses = {}
+    subclasses: dict[str, object] = {}
 
     def __init__(self, pull_dict):
         self.season = pull_dict["season"]
@@ -339,7 +339,7 @@ def __init__(self, pull_dict):
         if not os.path.isfile(self.pull_name):
             self.create_pickle()
         else:
-            logger.debug("Loading from".format(self.pull_name))
+            logger.debug(f"Loading from {self.pull_name}")
 
         with open(self.pull_name, "r") as f:
             self.pickled_data = Pickle.load(f)
@@ -470,6 +470,9 @@ def create_dynamic(self, pickled_array):
         return lambda data: func(data["logE"], data["sinDec"])
 
 
+"""
+# NOTE: `mypy` allowed to find some deprecations in the following __main__ block that were never noticed before, because the block is not part of any testing routine. It should be checked whether equivalent code is covered by an unit test, before removing the (now commented) block altogether.
+
 if __name__ == "__main__":
     from flarestack.data.icecube.ps_tracks.ps_v002_p01 import IC86_1_dict
     from flarestack.analyses.angular_error_floor.plot_bias import (
@@ -534,3 +537,4 @@ def med_pull(data):
 # for gamma in np.linspace(1.0, 4.0, 4):
 #     print data_loader(IC86_1_dict["exp_path"])["logE"][:8]
 #     print np.degrees(x.f(data_loader(IC86_1_dict["exp_path"])[:8], [gamma]))
+"""

From a82376c2caa1f43a8dd63b55f88d95304bab7ecc Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 01:14:48 +0200
Subject: [PATCH 36/53] mypy compliance

---
 flarestack/core/minimisation.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flarestack/core/minimisation.py b/flarestack/core/minimisation.py
index a739bfe0..2fb41865 100644
--- a/flarestack/core/minimisation.py
+++ b/flarestack/core/minimisation.py
@@ -93,10 +93,10 @@ class MinimisationHandler(object):
     the injector and the likelihood.
     """
 
-    subclasses = {}
+    subclasses: dict[str, object] = {}
 
     # Each MinimisationHandler must specify which LLH classes are compatible
-    compatible_llh = []
+    compatible_llh: list[str] = []
     compatible_negative_n_s = False
 
     def __init__(self, mh_dict):

From 91142a9d3e7dd6a99120ac272879a3abde0f8299 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 01:21:54 +0200
Subject: [PATCH 37/53] comment out unused (?) code

---
 flarestack/core/multiprocess_wrapper.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/flarestack/core/multiprocess_wrapper.py b/flarestack/core/multiprocess_wrapper.py
index e0f102f8..115c35a2 100644
--- a/flarestack/core/multiprocess_wrapper.py
+++ b/flarestack/core/multiprocess_wrapper.py
@@ -40,7 +40,9 @@ def add_injector(self, season, sources):
 
 class MultiProcessor:
     queue = None
-    results = dict()
+
+    # this is not used within the class, maybe it can be safely dropped
+    # results = dict()
 
     def __init__(self, n_cpu, **kwargs):
         self.queue = JoinableQueue()

From e8631b6c0d54f3f495132d7d232af0a97e05d6ff Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 01:28:48 +0200
Subject: [PATCH 38/53] cpu_count safeguards

---
 flarestack/core/multiprocess_wrapper.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/flarestack/core/multiprocess_wrapper.py b/flarestack/core/multiprocess_wrapper.py
index 115c35a2..96807382 100644
--- a/flarestack/core/multiprocess_wrapper.py
+++ b/flarestack/core/multiprocess_wrapper.py
@@ -151,9 +151,15 @@ def run_multiprocess(n_cpu, mh_dict):
 
     logging.basicConfig(level=logging.INFO)
 
+    # os.cpu_count() may return None, deal safely with that
+    cpu_count = os.cpu_count()
+    available_cpus = cpu_count if cpu_count is not None else 1
+    # 1 <= n_cpu <= 32
+    n_cpu = min(max(1, available_cpus - 1), 32)
+
     parser = argparse.ArgumentParser()
     parser.add_argument("-f", "--file", help="Path for analysis pkl_file")
-    parser.add_argument("-n", "--n_cpu", default=min(max(1, os.cpu_count() - 1), 32))
+    parser.add_argument("-n", "--n_cpu", default=n_cpu)
     cfg = parser.parse_args()
 
     logger.info(f"N CPU available {os.cpu_count()}. Using {cfg.n_cpu}")

From e20771f39ccb6ad3da934b5ea9e12aa86107a528 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 01:51:24 +0200
Subject: [PATCH 39/53] mypy compliance

---
 flarestack/cluster/submitter.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/flarestack/cluster/submitter.py b/flarestack/cluster/submitter.py
index 3d1659a3..e30fc105 100644
--- a/flarestack/cluster/submitter.py
+++ b/flarestack/cluster/submitter.py
@@ -22,7 +22,9 @@
 
 
 class Submitter(object):
-    submitter_dict = dict()
+    # in other modules, such attribute is called 'subclass'
+    # is this functionally different?
+    submitter_dict: dict[str, object] = dict()
 
     def __init__(
         self,
@@ -302,7 +304,7 @@ class HTCondorSubmitter(Submitter):
 
     # Log path
     log_path = Path(log_dir)
-    override_log_path = None
+    override_log_path: Optional[Path] = None
 
     def __init__(self, *args, **kwargs):
         """

From e1b0c71a584ff5866c5e993643d308071ff4ca22 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 02:02:18 +0200
Subject: [PATCH 40/53] add typing import and reorder previous imports

---
 flarestack/cluster/submitter.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/flarestack/cluster/submitter.py b/flarestack/cluster/submitter.py
index e30fc105..18667f47 100644
--- a/flarestack/cluster/submitter.py
+++ b/flarestack/cluster/submitter.py
@@ -1,6 +1,15 @@
+import copy
 import json
-import os, subprocess, time, logging, shutil, copy, sys
+import logging
 import numpy as np
+import os
+from pathlib import Path
+import shutil
+import subprocess
+import sys
+import time
+from typing import Optional
+
 from flarestack.shared import (
     fs_dir,
     log_dir,
@@ -15,8 +24,6 @@
 from flarestack.core.minimisation import MinimisationHandler
 from flarestack.core.results import ResultsHandler
 
-from pathlib import Path
-
 
 logger = logging.getLogger(__name__)
 

From 2c20fd696ed72173e3f0131f2ce2df5e9132f418 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 02:10:58 +0200
Subject: [PATCH 41/53] match signature with subclass, drop kwargs support

---
 flarestack/data/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flarestack/data/__init__.py b/flarestack/data/__init__.py
index 818c1f61..95d10e11 100644
--- a/flarestack/data/__init__.py
+++ b/flarestack/data/__init__.py
@@ -188,7 +188,7 @@ def data_background_model(self, **kwargs):
         exp = append_fields(exp, "weight", weight, usemask=False, dtypes=[float]).copy()
         return exp
 
-    def get_background_model(self, **kwargs):
+    def get_background_model(self) -> dict:
         """Generic Function to return background model. This could be
         the experimental data (if the signal contamination is small),
         or a weighted MC dataset. By default, uses data."""

From f26b32aa3271909aa03e5fd5704031e8446f2e4c Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 02:17:56 +0200
Subject: [PATCH 42/53] exclude file

---
 flarestack/utils/percentile_SoB.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/flarestack/utils/percentile_SoB.py b/flarestack/utils/percentile_SoB.py
index 30cea302..c95bfefa 100644
--- a/flarestack/utils/percentile_SoB.py
+++ b/flarestack/utils/percentile_SoB.py
@@ -1,3 +1,10 @@
+# type: ignore
+
+# exclude this file from `mypy` checking since IC86_1_dict can no longer be imported
+# this also implies that this file is currently untested, otherwise such a test would fail
+# if in the future its functionality is restored, remove the `type: ignore` comment
+
+
 import os
 import numpy as np
 import scipy

From ee8073a20b021d282f74ca0ea0d20c1d4fc41e46 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 02:20:06 +0200
Subject: [PATCH 43/53] exclude file from mypy checking

---
 flarestack/misc/plot_data_rate.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/flarestack/misc/plot_data_rate.py b/flarestack/misc/plot_data_rate.py
index 7d403ceb..7f2bfc5e 100644
--- a/flarestack/misc/plot_data_rate.py
+++ b/flarestack/misc/plot_data_rate.py
@@ -1,3 +1,10 @@
+# type: ignore
+
+# exclude this file from `mypy` checking since the attribute "diffuse_8year" can no longer be imported
+# this also implies that this file is currently untested, otherwise such a test would fail
+# if in the future its functionality is restored, remove the `type: ignore` comment
+
+
 import os
 import matplotlib.pyplot as plt
 from flarestack.data.icecube.northern_tracks.nt_v002_p05 import diffuse_8year

From c86e133aa6b42cce959ab37a2df97b65324dfa0c Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 02:22:58 +0200
Subject: [PATCH 44/53] exclude file from mypy checking

---
 .../data/icecube/public/IC86_1/parse_public_IC86_1.py      | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/flarestack/data/icecube/public/IC86_1/parse_public_IC86_1.py b/flarestack/data/icecube/public/IC86_1/parse_public_IC86_1.py
index 84eb2530..c1bf6506 100644
--- a/flarestack/data/icecube/public/IC86_1/parse_public_IC86_1.py
+++ b/flarestack/data/icecube/public/IC86_1/parse_public_IC86_1.py
@@ -1,3 +1,10 @@
+# type: ignore
+
+# exclude this file from `mypy` checking since the attribute IC86_1_dict can no longer be imported
+# this also implies that this file is currently untested, otherwise such a test would fail
+# if in the future its functionality is restored, remove the `type: ignore` comment
+
+
 """Script to convert public data files provided by IceCube for the first year
 of IC86_1 into a format useable for science with flarestack. The data files
 themselves are duplicates of those provided at:

From 563582db7fce8578298358dc3196846d6dcfecf5 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 02:38:12 +0200
Subject: [PATCH 45/53] deprecate function

---
 flarestack/data/dataset_index.py | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/flarestack/data/dataset_index.py b/flarestack/data/dataset_index.py
index 2e9b1a36..ef8403c8 100644
--- a/flarestack/data/dataset_index.py
+++ b/flarestack/data/dataset_index.py
@@ -15,7 +15,7 @@ class DatasetIndex:
 
     def __init__(self) -> None:
         """constructor"""
-        self.index = dict()
+        self.index: dict[str, Dataset] = dict()
 
     def add_dataset(self, dataset: Dataset) -> None:
         """adds a dataset to the index
@@ -26,19 +26,21 @@ def add_dataset(self, dataset: Dataset) -> None:
         """
         self.index[dataset.name] = dataset
 
-    def add_alias(self, alias: str, name: str) -> None:
-        """adds an alias for a dataset
-
-        Args:
-            alias (str): alias name
-            name (str): dataset name
-        """
-        dest = self.index[name]
-        if isinstance(dest, Dataset):
-            self.index[alias] = name
-        else:
-            logger.warning("f{name} is already an alias, aliasing {dest} instead.")
-            self.index[alias] = dest
+    # supporting aliases does not play well with the typing consistency of dataset_index
+    # tentatively comment out this logic, can be removed at a later stage
+    # def add_alias(self, alias: str, name: str) -> None:
+    #     """adds an alias for a dataset
+    #
+    #     Args:
+    #         alias (str): alias name
+    #         name (str): dataset name
+    #     """
+    #     dest = self.index[name]
+    #     if isinstance(dest, Dataset):
+    #         self.index[alias] = name
+    #     else:
+    #         logger.warning("f{name} is already an alias, aliasing {dest} instead.")
+    #         self.index[alias] = dest
 
     def get_dataset(self, name: str) -> Dataset:
         """retrieve a dataset by name

From d02667b138f820ce1e2d709199bff16434842807 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 02:38:24 +0200
Subject: [PATCH 46/53] mypy compliance

---
 flarestack/misc/verify_discovery_potential_estimation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flarestack/misc/verify_discovery_potential_estimation.py b/flarestack/misc/verify_discovery_potential_estimation.py
index b5c16959..fd19f414 100644
--- a/flarestack/misc/verify_discovery_potential_estimation.py
+++ b/flarestack/misc/verify_discovery_potential_estimation.py
@@ -84,7 +84,7 @@
             mask = np.ones_like(sindecs, dtype=bool)
 
         else:
-            mask = [sindecs > -0.05]
+            mask = sindecs > -0.05  # mypy: changed from [sindecs > -0.05]
 
         color = ["r", "blue", "green", "y"][j]
 

From 27dc1c8f7c245e5f8f58525a9edb3a6f079c0376 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 10:24:27 +0200
Subject: [PATCH 47/53] exclude file from type checking

---
 flarestack/misc/verify_discovery_potential_estimation.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/flarestack/misc/verify_discovery_potential_estimation.py b/flarestack/misc/verify_discovery_potential_estimation.py
index fd19f414..e887a594 100644
--- a/flarestack/misc/verify_discovery_potential_estimation.py
+++ b/flarestack/misc/verify_discovery_potential_estimation.py
@@ -1,3 +1,9 @@
+# type: ignore
+
+# exclude this file from `mypy` checking since the current implementation of `AsimovEstimator` is not compatible with the syntax used here.
+# this also implies that this file is currently untested, otherwise such a test would fail
+# if in the future its functionality is restored, remove the `type: ignore` comment
+
 import numpy as np
 import os
 from flarestack.data.icecube.ps_tracks.ps_v002_p01 import ps_v002_p01
@@ -84,7 +90,7 @@
             mask = np.ones_like(sindecs, dtype=bool)
 
         else:
-            mask = sindecs > -0.05  # mypy: changed from [sindecs > -0.05]
+            mask = sindecs > -0.05  # after mypy: changed from [sindecs > -0.05]
 
         color = ["r", "blue", "green", "y"][j]
 

From ad61c11e5d78af6a963c84f0ae22c31512f5a1a7 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 11:29:12 +0200
Subject: [PATCH 48/53] avoiding redefinitions makes mypy happy

---
 flarestack/core/llh.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/flarestack/core/llh.py b/flarestack/core/llh.py
index 73cdebe9..61441c95 100644
--- a/flarestack/core/llh.py
+++ b/flarestack/core/llh.py
@@ -900,7 +900,7 @@ def create_kwargs(self, data, pull_corrector, weight_f=None):
 
         return kwargs
 
-    def calculate_test_statistic(self, params, weights, **kwargs):
+    def calculate_test_statistic(self, params, weights, **kwargs) -> float:
         """Calculates the test statistic, given the parameters. Uses numexpr
         for faster calculations.
 
@@ -920,18 +920,18 @@ def calculate_test_statistic(self, params, weights, **kwargs):
         # If n_s if negative, then removes the energy term from the likelihood
 
         for i, n_j in enumerate(all_n_j):
-            SoB_spacetime: list = kwargs["SoB_spacetime_cache"][i]
+            SoB_spacetime_data: list = kwargs["SoB_spacetime_cache"][i]
 
             # Switches off Energy term for negative n_s, which should in theory
             # be a continuous change that does not alter the likelihood for
             # n_s > 0 (as it is not included for n_s=0).
 
-            if len(SoB_spacetime) == 0:
+            if len(SoB_spacetime_data) == 0:
                 x.append(np.array([1.0]))
 
             else:
                 SoB_spacetime = kwargs["pull_corrector"].estimate_spatial(
-                    gamma, SoB_spacetime
+                    gamma, SoB_spacetime_data
                 )
 
                 if n_j < 0:

From d590295e90c0a95a9f96df8ba003d60db3fad227 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 11:29:32 +0200
Subject: [PATCH 49/53] comment out untested and non-working code

---
 flarestack/data/simulate/simcube.py | 32 ++++++++++++++++-------------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/flarestack/data/simulate/simcube.py b/flarestack/data/simulate/simcube.py
index 602195ff..b78e120b 100644
--- a/flarestack/data/simulate/simcube.py
+++ b/flarestack/data/simulate/simcube.py
@@ -236,19 +236,23 @@ def wrapper_f(
 
     simcube_dataset.add_sim_season(name, wrapper_f)
 
-bkg_time_pdf_dict = {
-    "time_pdf_name": "fixed_ref_box",
-    "fixed_ref_time_mjd": 50000,
-    "pre_window": 0.0,
-    "post_window": 500.0,
-}
-
-simcube_season = simcube_dataset.set_sim_params(
-    name="IC86-2012",
-    bkg_time_pdf_dict=bkg_time_pdf_dict,
-    bkg_flux_norm=1e8,
-    bkg_e_pdf_dict=bkg_e_pdf_dict,
-)
+# after mypy: it seems the following block of code is not compatible with the current syntax of `simcube_dataset.set_sim_params()`
+# - error: Missing positional argument "bkg_flux_model" in call to "set_sim_params"  [call-arg]
+# this implies this module is likely untested, otherwise such a test would fail
+# the following is commented out, for the time being
+
+# bkg_time_pdf_dict = {
+#     "time_pdf_name": "fixed_ref_box",
+#     "fixed_ref_time_mjd": 50000,
+#     "pre_window": 0.0,
+#     "post_window": 500.0,
+# }
+#
+# simcube_season = simcube_dataset.set_sim_params(
+#     name="IC86-2012",
+#     bkg_time_pdf_dict=bkg_time_pdf_dict,
+#     bkg_flux_norm=1e8,
+#     bkg_e_pdf_dict=bkg_e_pdf_dict,
+# )
 
 # nicecube_10year = SimCubeSeason(0, 100, 1., e_pdf_dict)
-#

From bfeee335cf9f2fe46a32949a385690820e0b62d1 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 13:27:42 +0200
Subject: [PATCH 50/53] del temp variable

---
 flarestack/misc/flare_llh_plots.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/flarestack/misc/flare_llh_plots.py b/flarestack/misc/flare_llh_plots.py
index 986e1b28..3218873c 100644
--- a/flarestack/misc/flare_llh_plots.py
+++ b/flarestack/misc/flare_llh_plots.py
@@ -108,6 +108,7 @@ def energy_ratio(e):
     s_t_list.append((t + float(i)) * 25)
 
 s_t = np.array(s_t_list)
+del st_list
 
 bkg_t = np.random.uniform(0, 1.0, n_bkg) * 100
 

From 4116757c4d30469065aeac174d5a579939e00fc3 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 13:28:26 +0200
Subject: [PATCH 51/53] del temp variable

---
 flarestack/misc/flare_llh_plots.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flarestack/misc/flare_llh_plots.py b/flarestack/misc/flare_llh_plots.py
index 3218873c..e606ca75 100644
--- a/flarestack/misc/flare_llh_plots.py
+++ b/flarestack/misc/flare_llh_plots.py
@@ -108,7 +108,7 @@ def energy_ratio(e):
     s_t_list.append((t + float(i)) * 25)
 
 s_t = np.array(s_t_list)
-del st_list
+del s_t_list
 
 bkg_t = np.random.uniform(0, 1.0, n_bkg) * 100
 

From 188fd107ff69d510c34471317c0ea2b2352e7bbb Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 13:30:03 +0200
Subject: [PATCH 52/53] undo unnecessary update

---
 flarestack/misc/plot_data_rate.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/flarestack/misc/plot_data_rate.py b/flarestack/misc/plot_data_rate.py
index 7f2bfc5e..8bb3e423 100644
--- a/flarestack/misc/plot_data_rate.py
+++ b/flarestack/misc/plot_data_rate.py
@@ -1,13 +1,12 @@
 # type: ignore
 
-# exclude this file from `mypy` checking since the attribute "diffuse_8year" can no longer be imported
+# exclude this file from `mypy` checking since the dataset "nt_v002_p01" can no longer be imported
 # this also implies that this file is currently untested, otherwise such a test would fail
-# if in the future its functionality is restored, remove the `type: ignore` comment
-
+# if in the future this script is updated to use a new data set, remove the `type: ignore` comment
 
 import os
 import matplotlib.pyplot as plt
-from flarestack.data.icecube.northern_tracks.nt_v002_p05 import diffuse_8year
+from flarestack.data.icecube.northern_tracks.nt_v002_p01 import diffuse_8year
 from flarestack.shared import plots_dir
 from flarestack.icecube_utils.dataset_loader import data_loader, grl_loader
 

From b46b7f48fdd07f127601f7638c7bb9f7225d73f9 Mon Sep 17 00:00:00 2001
From: Massimiliano Lincetto <m.lincetto@gmail.com>
Date: Tue, 22 Aug 2023 13:32:48 +0200
Subject: [PATCH 53/53] update python version specs

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index bcddf15b..27910f65 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,13 +17,13 @@ classifiers = [
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.8, <3.12"
+python = ">=3.9, <3.12"
 astropy = "^5.1"
 black = "^23"
 coveralls = "^3.3.1"