From 0a28bb038bb82c2c4ae07433c04ce0f0f79d59bf Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Mon, 12 Aug 2024 17:24:11 -0700
Subject: [PATCH 01/17] Using np.asarray() to support numpy 2.0

---
 astromodels/functions/function.py                | 12 ++++++------
 astromodels/functions/functions_1D/extinction.py |  2 +-
 astromodels/functions/template_model.py          |  4 ++--
 astromodels/xspec/factory.py                     |  2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/astromodels/functions/function.py b/astromodels/functions/function.py
index d58757a1..3ab23b3e 100644
--- a/astromodels/functions/function.py
+++ b/astromodels/functions/function.py
@@ -1479,7 +1479,7 @@ def __call__(self, x):
 
             # Transform the input to an array of floats. If x is a single number, this will be an array of size 1
 
-            new_input = np.array(x, dtype=float, ndmin=1, copy=False)
+            new_input = np.asarray(x, dtype=float)
 
             # Compute the function
 
@@ -1705,8 +1705,8 @@ def __call__(self, x, y, *args, **kwargs):
 
             # Transform the input to an array of floats
 
-            new_x = np.array(x, dtype=float, ndmin=1, copy=False)
-            new_y = np.array(y, dtype=float, ndmin=1, copy=False)
+            new_x = np.asarray(x, dtype=float)
+            new_y = np.asarray(y, dtype=float)
 
             # Compute the function
 
@@ -1876,9 +1876,9 @@ def __call__(self, x, y, z):
             # This is either a single number or a list
             # Transform the input to an array of floats
 
-            new_x = np.array(x, dtype=float, ndmin=1, copy=False)
-            new_y = np.array(y, dtype=float, ndmin=1, copy=False)
-            new_z = np.array(z, dtype=float, ndmin=1, copy=False)
+            new_x = np.asarray(x, dtype=float)
+            new_y = np.asarray(y, dtype=float)
+            new_z = np.asarray(z, dtype=float)
 
             # Compute the function
 
diff --git a/astromodels/functions/functions_1D/extinction.py b/astromodels/functions/functions_1D/extinction.py
index 3c55d5c6..0be335fd 100644
--- a/astromodels/functions/functions_1D/extinction.py
+++ b/astromodels/functions/functions_1D/extinction.py
@@ -89,7 +89,7 @@ def evaluate(self, x, e_bmv, rv, redshift):
 
         if isinstance(x, astropy_units.Quantity):
 
-            _x = np.array(x.to("keV").value, ndmin=1, copy=False, dtype=float)
+            _x = np.asarray(x.to("keV").value, dtype=float)
 
             _unit = astropy_units.cm**2
             _y_unit = astropy_units.dimensionless_unscaled
diff --git a/astromodels/functions/template_model.py b/astromodels/functions/template_model.py
index 5861da0f..e351e384 100644
--- a/astromodels/functions/template_model.py
+++ b/astromodels/functions/template_model.py
@@ -760,8 +760,8 @@ def _interpolate(self, energies, scale, parameters_values):
             # a dimensionless quantity (actually we take the .value property) because otherwise
             # the logarithm below will fail.
 
-            energies = np.array(
-                energies.to("keV").value, ndmin=1, copy=False, dtype=float
+            energies = np.asarray(
+                energies.to("keV").value, dtype=float
             )
 
             # Same for the scale
diff --git a/astromodels/xspec/factory.py b/astromodels/xspec/factory.py
index edef7d3e..405be7f0 100644
--- a/astromodels/xspec/factory.py
+++ b/astromodels/xspec/factory.py
@@ -486,7 +486,7 @@ def evaluate(self, x, $PARAMETERS_NAMES$):
 
         if isinstance(x, u.Quantity):
 
-            x = np.array(x.to('keV').value, ndmin=1, copy=False, dtype=float)
+            x = np.asarray(x.to('keV').value, dtype=float)
 
             quantity = True
 

From e3a13ba5a1472371abe7335aa6e917dde28ef0e9 Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Mon, 12 Aug 2024 18:01:05 -0700
Subject: [PATCH 02/17] Reverting to np.array() with copy=None

---
 astromodels/functions/function.py                | 12 ++++++------
 astromodels/functions/functions_1D/extinction.py |  2 +-
 astromodels/functions/template_model.py          |  4 ++--
 astromodels/xspec/factory.py                     |  2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/astromodels/functions/function.py b/astromodels/functions/function.py
index 3ab23b3e..bbe57ad9 100644
--- a/astromodels/functions/function.py
+++ b/astromodels/functions/function.py
@@ -1479,7 +1479,7 @@ def __call__(self, x):
 
             # Transform the input to an array of floats. If x is a single number, this will be an array of size 1
 
-            new_input = np.asarray(x, dtype=float)
+            new_input = np.array(x, dtype=float, ndmin=1, copy=None)
 
             # Compute the function
 
@@ -1705,8 +1705,8 @@ def __call__(self, x, y, *args, **kwargs):
 
             # Transform the input to an array of floats
 
-            new_x = np.asarray(x, dtype=float)
-            new_y = np.asarray(y, dtype=float)
+            new_x = np.array(x, dtype=float, ndmin=1, copy=None)
+            new_y = np.array(y, dtype=float, ndmin=1, copy=None)
 
             # Compute the function
 
@@ -1876,9 +1876,9 @@ def __call__(self, x, y, z):
             # This is either a single number or a list
             # Transform the input to an array of floats
 
-            new_x = np.asarray(x, dtype=float)
-            new_y = np.asarray(y, dtype=float)
-            new_z = np.asarray(z, dtype=float)
+            new_x = np.array(x, dtype=float, ndmin=1, copy=None)
+            new_y = np.array(y, dtype=float, ndmin=1, copy=None)
+            new_z = np.array(z, dtype=float, ndmin=1, copy=None)
 
             # Compute the function
 
diff --git a/astromodels/functions/functions_1D/extinction.py b/astromodels/functions/functions_1D/extinction.py
index 0be335fd..f75d535e 100644
--- a/astromodels/functions/functions_1D/extinction.py
+++ b/astromodels/functions/functions_1D/extinction.py
@@ -89,7 +89,7 @@ def evaluate(self, x, e_bmv, rv, redshift):
 
         if isinstance(x, astropy_units.Quantity):
 
-            _x = np.asarray(x.to("keV").value, dtype=float)
+            _x = np.array(x.to("keV").value, ndmin=1, copy=None, dtype=float)
 
             _unit = astropy_units.cm**2
             _y_unit = astropy_units.dimensionless_unscaled
diff --git a/astromodels/functions/template_model.py b/astromodels/functions/template_model.py
index e351e384..d8b55917 100644
--- a/astromodels/functions/template_model.py
+++ b/astromodels/functions/template_model.py
@@ -760,8 +760,8 @@ def _interpolate(self, energies, scale, parameters_values):
             # a dimensionless quantity (actually we take the .value property) because otherwise
             # the logarithm below will fail.
 
-            energies = np.asarray(
-                energies.to("keV").value, dtype=float
+            energies = np.array(
+                energies.to("keV").value, ndmin=1, copy=None, dtype=float
             )
 
             # Same for the scale
diff --git a/astromodels/xspec/factory.py b/astromodels/xspec/factory.py
index 405be7f0..401e6808 100644
--- a/astromodels/xspec/factory.py
+++ b/astromodels/xspec/factory.py
@@ -486,7 +486,7 @@ def evaluate(self, x, $PARAMETERS_NAMES$):
 
         if isinstance(x, u.Quantity):
 
-            x = np.asarray(x.to('keV').value, dtype=float)
+            x = np.array(x.to('keV').value, ndmin=1, copy=None, dtype=float)
 
             quantity = True
 

From d2c9c242cb79db547ccbaac1f3465f2ffe1c78aa Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 13 Aug 2024 12:26:34 -0700
Subject: [PATCH 03/17] Adding copy_if_needed argument.

---
 astromodels/functions/function.py                | 13 +++++++------
 astromodels/functions/functions_1D/extinction.py |  3 ++-
 astromodels/functions/template_model.py          |  3 ++-
 astromodels/utils/file_utils.py                  |  8 +++++++-
 astromodels/xspec/factory.py                     |  3 ++-
 5 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/astromodels/functions/function.py b/astromodels/functions/function.py
index bbe57ad9..d9b4b6f4 100644
--- a/astromodels/functions/function.py
+++ b/astromodels/functions/function.py
@@ -24,6 +24,7 @@
 from astromodels.utils.logging import setup_logger
 from astromodels.utils.pretty_list import dict_to_list
 from astromodels.utils.table import dict_to_table
+from astromodels.utils.file_utils import copy_if_needed
 from yaml.reader import ReaderError
 
 log = setup_logger(__name__)
@@ -1479,7 +1480,7 @@ def __call__(self, x):
 
             # Transform the input to an array of floats. If x is a single number, this will be an array of size 1
 
-            new_input = np.array(x, dtype=float, ndmin=1, copy=None)
+            new_input = np.array(x, dtype=float, ndmin=1, copy=copy_if_needed)
 
             # Compute the function
 
@@ -1705,8 +1706,8 @@ def __call__(self, x, y, *args, **kwargs):
 
             # Transform the input to an array of floats
 
-            new_x = np.array(x, dtype=float, ndmin=1, copy=None)
-            new_y = np.array(y, dtype=float, ndmin=1, copy=None)
+            new_x = np.array(x, dtype=float, ndmin=1, copy=copy_if_needed)
+            new_y = np.array(y, dtype=float, ndmin=1, copy=copy_if_needed)
 
             # Compute the function
 
@@ -1876,9 +1877,9 @@ def __call__(self, x, y, z):
             # This is either a single number or a list
             # Transform the input to an array of floats
 
-            new_x = np.array(x, dtype=float, ndmin=1, copy=None)
-            new_y = np.array(y, dtype=float, ndmin=1, copy=None)
-            new_z = np.array(z, dtype=float, ndmin=1, copy=None)
+            new_x = np.array(x, dtype=float, ndmin=1, copy=copy_if_needed)
+            new_y = np.array(y, dtype=float, ndmin=1, copy=copy_if_needed)
+            new_z = np.array(z, dtype=float, ndmin=1, copy=copy_if_needed)
 
             # Compute the function
 
diff --git a/astromodels/functions/functions_1D/extinction.py b/astromodels/functions/functions_1D/extinction.py
index f75d535e..c5fac1d4 100644
--- a/astromodels/functions/functions_1D/extinction.py
+++ b/astromodels/functions/functions_1D/extinction.py
@@ -9,6 +9,7 @@
 
 from astromodels.functions.function import Function1D, FunctionMeta
 from astromodels.utils.logging import setup_logger
+from astromodels.utils.file_utils import copy_if_needed
 
 log = setup_logger(__name__)
 
@@ -89,7 +90,7 @@ def evaluate(self, x, e_bmv, rv, redshift):
 
         if isinstance(x, astropy_units.Quantity):
 
-            _x = np.array(x.to("keV").value, ndmin=1, copy=None, dtype=float)
+            _x = np.array(x.to("keV").value, ndmin=1, copy=copy_if_needed, dtype=float)
 
             _unit = astropy_units.cm**2
             _y_unit = astropy_units.dimensionless_unscaled
diff --git a/astromodels/functions/template_model.py b/astromodels/functions/template_model.py
index d8b55917..a42ef75f 100644
--- a/astromodels/functions/template_model.py
+++ b/astromodels/functions/template_model.py
@@ -21,6 +21,7 @@
 from astromodels.functions.function import Function1D, FunctionMeta
 from astromodels.utils import get_user_data_path
 from astromodels.utils.logging import setup_logger
+from astromodels.utils.file_utils import copy_if_needed
 
 log = setup_logger(__name__)
 
@@ -761,7 +762,7 @@ def _interpolate(self, energies, scale, parameters_values):
             # the logarithm below will fail.
 
             energies = np.array(
-                energies.to("keV").value, ndmin=1, copy=None, dtype=float
+                energies.to("keV").value, ndmin=1, copy=copy_if_needed, dtype=float
             )
 
             # Same for the scale
diff --git a/astromodels/utils/file_utils.py b/astromodels/utils/file_utils.py
index 5c16a394..b70415fe 100644
--- a/astromodels/utils/file_utils.py
+++ b/astromodels/utils/file_utils.py
@@ -3,11 +3,17 @@
 
 import os
 from pathlib import Path
-
+import numpy as np
 import pkg_resources
 
 _custom_config_path = os.environ.get("ASTROMODELS_CONFIG")
 
+copy_if_needed: Optional[bool]
+
+if np.lib.NumpyVersion(np.__version__) >= "2.0.0":
+    copy_if_needed = None
+else:
+    copy_if_needed = False
 
 def _get_data_file_path(data_file: str) -> Path:
     """
diff --git a/astromodels/xspec/factory.py b/astromodels/xspec/factory.py
index 401e6808..0adddfb1 100644
--- a/astromodels/xspec/factory.py
+++ b/astromodels/xspec/factory.py
@@ -431,6 +431,7 @@ def get_models(model_dat_path):
 from astromodels.functions.function import FunctionMeta, Function1D
 import numpy as np
 import astropy.units as u
+from astromodels.utils.file_utils import copy_if_needed
 from astromodels.xspec import _xspec
 import six
 
@@ -486,7 +487,7 @@ def evaluate(self, x, $PARAMETERS_NAMES$):
 
         if isinstance(x, u.Quantity):
 
-            x = np.array(x.to('keV').value, ndmin=1, copy=None, dtype=float)
+            x = np.array(x.to('keV').value, ndmin=1, copy=copy_if_needed, dtype=float)
 
             quantity = True
 

From 831f979d7879a2ffb0c30569fe26798c385df6b2 Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 13 Aug 2024 12:33:13 -0700
Subject: [PATCH 04/17] Minor.

---
 astromodels/utils/file_utils.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/astromodels/utils/file_utils.py b/astromodels/utils/file_utils.py
index b70415fe..33cb13de 100644
--- a/astromodels/utils/file_utils.py
+++ b/astromodels/utils/file_utils.py
@@ -3,6 +3,7 @@
 
 import os
 from pathlib import Path
+from typing import Optional
 import numpy as np
 import pkg_resources
 

From 734fa78bb8e5d48026fe883e80b2d76f8eb50d84 Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 13 Aug 2024 12:39:06 -0700
Subject: [PATCH 05/17] Minor.

---
 astromodels/utils/file_utils.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/astromodels/utils/file_utils.py b/astromodels/utils/file_utils.py
index 33cb13de..f4dfda58 100644
--- a/astromodels/utils/file_utils.py
+++ b/astromodels/utils/file_utils.py
@@ -16,6 +16,7 @@
 else:
     copy_if_needed = False
 
+
 def _get_data_file_path(data_file: str) -> Path:
     """
     Returns the absolute path to the required data files.

From 936cf7781fb0d25f9a43d57a0bc704b81e2512d8 Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Mon, 9 Sep 2024 14:29:24 -0400
Subject: [PATCH 06/17] Trying to remove architecture.

---
 .github/workflows/deploy.yml | 6 +++---
 .github/workflows/docs.yml   | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 6f1cc34f..09ef669c 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -98,7 +98,7 @@ jobs:
               with:
                   activate-environment: "test_env"
                   auto-activate-base: false
-                  architecture: "x64"
+                  #architecture: "x64"
                   miniforge-variant: Mambaforge
                   #miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
@@ -174,7 +174,7 @@ jobs:
         runs-on: ${{ matrix.os }}
         strategy:
             matrix:
-                os: [ubuntu-latest, macos-latest]
+                os: [ubuntu-latest, macos-latest, macos-12]
                 python-version: [3.9]
 
         steps:
@@ -195,7 +195,7 @@ jobs:
               with:
                   activate-environment: "test_env"
                   auto-activate-base: false
-                  architecture: "x64"
+                  #architecture: "x64"
                   miniforge-variant: Mambaforge
                   #miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index e375bf1a..ea72b77b 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -48,7 +48,8 @@ jobs:
       - name: Execute the notebooks
         #shell: bash -l {0}
         run: |
-
+          # Make sure we fail in case of error
+          set -e
           # Download an example file
           
           wget https://www.astropy.org/astropy-data/photometry/spitzer_example_image.fits

From 7c7904a48053248462abe7e56bdca031511f2233 Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Mon, 9 Sep 2024 14:41:44 -0400
Subject: [PATCH 07/17] Trying to remove architecture.

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

diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
index 0e17e96c..d6ecbcca 100644
--- a/.github/workflows/test_and_build.yml
+++ b/.github/workflows/test_and_build.yml
@@ -119,7 +119,7 @@ jobs:
               with:
                   activate-environment: "test_env"
                   auto-activate-base: false
-                  architecture: "x64"
+                  #architecture: "x64"
                   #mamba-version: "*"
                   miniforge-version: latest
                   python-version: ${{ matrix.python-version }}

From 47e782ccf92e5cb37580d02232da81cc080dac1a Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 10 Sep 2024 09:41:46 -0400
Subject: [PATCH 08/17] First import.

---
 ci/environment_noxspec.yml | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 ci/environment_noxspec.yml

diff --git a/ci/environment_noxspec.yml b/ci/environment_noxspec.yml
new file mode 100644
index 00000000..16b332f5
--- /dev/null
+++ b/ci/environment_noxspec.yml
@@ -0,0 +1,27 @@
+name: test_env
+
+channels:
+  - conda-forge
+  - defaults
+  
+dependencies:
+  - python
+  - numpy
+  - pyyaml>=5.1
+  - astropy
+  - scipy
+  - numdifftools
+  - hdf5
+  - pytables
+  - pandas>=0.23
+  - dill
+  - wcslib
+  - future
+  - numba
+  - h5py
+  - interpolation>=2.2.3
+  - libgfortran
+  - omegaconf
+  - colorama
+  - rich
+  - joblib

From 62b74d38dd178548582acae525c1d420480de232 Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 10 Sep 2024 09:42:18 -0400
Subject: [PATCH 09/17] Removing xspec-modelsonly installation for
 macos-latest.

---
 .github/workflows/deploy.yml         | 32 +++++++++++++++++-----------
 .github/workflows/test_and_build.yml |  6 +++++-
 2 files changed, 24 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 09ef669c..89a0fc89 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -75,7 +75,10 @@ jobs:
             matrix:
                 os: [ubuntu-latest, macos-latest, macos-12]
                 python-version: [3.9]
-
+                include:
+                  - environment: ci/environment.yml
+                  - environment:  ci/environment_noxspec.yml
+                    os: macos-latest
         steps:
             - name: Checkout
               uses: actions/checkout@v4
@@ -103,7 +106,7 @@ jobs:
                   #miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
-                  environment-file: ci/environment.yml
+                  environment-file: ${{ matrix.environment }}
                   use-only-tar-bz2: true
                   channel-priority: true
                   channels: conda-forge, xspecmodels, threeml
@@ -176,20 +179,23 @@ jobs:
             matrix:
                 os: [ubuntu-latest, macos-latest, macos-12]
                 python-version: [3.9]
-
+                include:
+                  - environment: ci/environment.yml
+                  - environment:  ci/environment_noxspec.yml
+                    os: macos-latest
         steps:
             - name: Checkout
               uses: actions/checkout@v4
               with:
                   fetch-depth: 0
-            - name: Cache conda
-              uses: actions/cache@v4
-              env:
-                # Increase this value to reset cache if etc/example-environment.yml has not changed
-                CACHE_NUMBER: 0
-              with:
-                  path: ~/conda_pkgs_dir
-                  key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }}
+            #- name: Cache conda
+            #  uses: actions/cache@v4
+            #  env:
+            #    # Increase this value to reset cache if etc/example-environment.yml has not changed
+            #    CACHE_NUMBER: 0
+            #  with:
+            #      path: ~/conda_pkgs_dir
+            #      key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }}
             - name: Add conda ${{ matrix.python-version }} to system path
               uses: conda-incubator/setup-miniconda@v3
               with:
@@ -200,7 +206,7 @@ jobs:
                   #miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
-                  environment-file: ci/environment.yml
+                  environment-file: ${{ matrix.environment }}
                   use-only-tar-bz2: true
                   channel-priority: true
                   channels: conda-forge, xspecmodels, threeml
@@ -254,7 +260,7 @@ jobs:
                   LABEL="--label dev"
 
                   fi
-
+.github/workflows/test_and_build.yml
                   if [[ ${{matrix.os}} == ubuntu-latest ]];
                   then
 
diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
index d6ecbcca..796d3ea4 100644
--- a/.github/workflows/test_and_build.yml
+++ b/.github/workflows/test_and_build.yml
@@ -102,6 +102,10 @@ jobs:
             matrix:
                 os: ["ubuntu-latest", "macos-latest", "macos-12"]
                 python-version: [3.9]
+                include:
+                  - environment: ci/environment.yml
+                  - environment:  ci/environment_noxspec.yml
+                    os: macos-latest
         runs-on: ${{ matrix.os }}
         steps:
             - name: Checkout
@@ -124,7 +128,7 @@ jobs:
                   miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
-                  environment-file: ci/environment.yml
+                  environment-file: ${{ matrix.environment }}
                   use-only-tar-bz2: true
                   channel-priority: strict
                   channels: conda-forge, xspecmodels

From 17968b00b7a5fde41500f56cc58c525a384b254a Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 10 Sep 2024 09:43:30 -0400
Subject: [PATCH 10/17] Removing xspec-modelsonly installation for
 macos-latest.

---
 .github/workflows/deploy.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 89a0fc89..f2f49d8e 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -260,7 +260,6 @@ jobs:
                   LABEL="--label dev"
 
                   fi
-.github/workflows/test_and_build.yml
                   if [[ ${{matrix.os}} == ubuntu-latest ]];
                   then
 

From 8f0ae00f22e38226198d18ba6f460dff05d7f845 Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 10 Sep 2024 10:08:19 -0400
Subject: [PATCH 11/17] Second attempt to remove xspec-modelsonly for
 macos-latest.

---
 .github/workflows/test_and_build.yml | 10 ++++++++++
 conda-dist/recipe/meta.yaml          | 22 +++++++++++-----------
 2 files changed, 21 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
index 796d3ea4..854eafca 100644
--- a/.github/workflows/test_and_build.yml
+++ b/.github/workflows/test_and_build.yml
@@ -172,6 +172,16 @@ jobs:
 
             - name: Test conda install
               shell: bash -l {0}
+              run: python -m pytest -vv --cov=astromodels --cov-report=xml
+              if: ${{matrix.os}} == "macos-latest"
+              env:
+                OMP_NUM_THREADS: 1
+                MKL_NUM_THREADS: 1
+                NUMEXPR_NUM_THREADS: 1
+                MPLBACKEND: "Agg"
+            - name: Test conda install
+              shell: bash -l {0}
+              if: ${{matrix.os}} != "macos-latest" 
               run: |
               
                   echo "======>  importing XSPEC..."
diff --git a/conda-dist/recipe/meta.yaml b/conda-dist/recipe/meta.yaml
index bf055a51..9e072ca5 100644
--- a/conda-dist/recipe/meta.yaml
+++ b/conda-dist/recipe/meta.yaml
@@ -13,10 +13,10 @@ requirements:
     - {{ compiler('c') }} # [linux]
     - {{ compiler('cxx') }} # [linux]
     - {{ compiler('fortran') }} # [linux]
-    - xspec-modelsonly
-    - cfitsio
-    - ccfits
-    - wcslib
+    - xspec-modelsonly #[not arm64]
+    - cfitsio # [not arm64]
+    - ccfits # [not arm64]
+    - wcslib # [not arm64]
 
   host:
     - python
@@ -25,10 +25,10 @@ requirements:
     - numpy
     - pyyaml>=5.1
     - pandas>=0.23
-    - cfitsio
-    - ccfits
-    - wcslib
-    - xspec-modelsonly
+    - cfitsio # [not arm64]
+    - ccfits # [not arm64]
+    - wcslib # [not arm64]
+    - xspec-modelsonly # [not arm64]
     - future
     - numba>=0.54
     - h5py
@@ -46,9 +46,9 @@ requirements:
     - pytables
     - pandas>=0.23
     - dill
-    - cfitsio
-    - ccfits
-    - wcslib
+    - cfitsio # [not arm64]
+    - ccfits # [not arm64]
+    - wcslib # [not arm64]
     - future
     - numba>=0.54
     - h5py

From 5b4a5689336559d284bbd8cfbcbc5d87625262df Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 10 Sep 2024 10:28:27 -0400
Subject: [PATCH 12/17] Trying again.

---
 .github/workflows/test_and_build.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
index 854eafca..ceebdf89 100644
--- a/.github/workflows/test_and_build.yml
+++ b/.github/workflows/test_and_build.yml
@@ -171,17 +171,17 @@ jobs:
                   flake8
 
             - name: Test conda install
+              if: matrix.os == 'macos-latest'
               shell: bash -l {0}
               run: python -m pytest -vv --cov=astromodels --cov-report=xml
-              if: ${{matrix.os}} == "macos-latest"
               env:
                 OMP_NUM_THREADS: 1
                 MKL_NUM_THREADS: 1
                 NUMEXPR_NUM_THREADS: 1
                 MPLBACKEND: "Agg"
             - name: Test conda install
+              if: matrix.os != 'macos-latest' 
               shell: bash -l {0}
-              if: ${{matrix.os}} != "macos-latest" 
               run: |
               
                   echo "======>  importing XSPEC..."

From 138a525ed90161333a8d74bc0c375efcfe92ed75 Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 10 Sep 2024 11:15:06 -0400
Subject: [PATCH 13/17] Actions updated.

---
 .github/workflows/deploy.yml         | 34 +++++-----------------------
 .github/workflows/test_and_build.yml | 33 ++++-----------------------
 2 files changed, 11 insertions(+), 56 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index f2f49d8e..2eb63b66 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -84,26 +84,12 @@ jobs:
               uses: actions/checkout@v4
               with:
                   fetch-depth: 0
-            # - name: Set up Python
-            #   uses: actions/setup-python@v5
-            #   with:
-            #       python-version: ${{ matrix.python-version }}
-            # - name: Cache conda
-            #   uses: actions/cache@v4
-            #   env:
-            #     # Increase this value to reset cache if etc/example-environment.yml has not changed
-            #     CACHE_NUMBER: 0
-            #   with:
-            #       path: ~/conda_pkgs_dir
-            #       key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }}
             - name: Add conda ${{ matrix.python-version }} to system path
               uses: conda-incubator/setup-miniconda@v3
               with:
                   activate-environment: "test_env"
                   auto-activate-base: false
-                  #architecture: "x64"
                   miniforge-variant: Mambaforge
-                  #miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
                   environment-file: ${{ matrix.environment }}
@@ -158,13 +144,13 @@ jobs:
 
                   #conda install --use-local astromodels
                   conda install -c ${CONDA}/envs/test_env/conda-bld/ astromodels
-            - name: Test conda build
+            - name: Test import xspec
+              if: matrix.os != 'macos-latest'
               shell: bash -l {0}
-              run: |
-                  cd astromodels/tests
-                  echo "======>  importing XSPEC..."
-                  python -c "import astromodels.xspec"
-                  python -m pytest -vv --cov=astromodels --cov-report=xml
+              run: python -c "import astromodels.xspec"
+            - name: Test astromodels
+              shell: bash -l {0}
+              run: python -m pytest -vv --cov=astromodels --cov-report=xml
               env:
                   OMP_NUM_THREADS: 1
                   MKL_NUM_THREADS: 1
@@ -188,14 +174,6 @@ jobs:
               uses: actions/checkout@v4
               with:
                   fetch-depth: 0
-            #- name: Cache conda
-            #  uses: actions/cache@v4
-            #  env:
-            #    # Increase this value to reset cache if etc/example-environment.yml has not changed
-            #    CACHE_NUMBER: 0
-            #  with:
-            #      path: ~/conda_pkgs_dir
-            #      key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }}
             - name: Add conda ${{ matrix.python-version }} to system path
               uses: conda-incubator/setup-miniconda@v3
               with:
diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
index ceebdf89..9020170c 100644
--- a/.github/workflows/test_and_build.yml
+++ b/.github/workflows/test_and_build.yml
@@ -110,21 +110,11 @@ jobs:
         steps:
             - name: Checkout
               uses: actions/checkout@v4
-            # - name: Cache conda
-            #   uses: actions/cache@v4
-            #   env:
-            #     # Increase this value to reset cache if etc/example-environment.yml has not changed
-            #     CACHE_NUMBER: 0
-            #   with:
-            #       path: ~/conda_pkgs_dir
-            #       key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }}
             - name: Add conda ${{ matrix.python-version }} to system path
               uses: conda-incubator/setup-miniconda@v3
               with:
                   activate-environment: "test_env"
                   auto-activate-base: false
-                  #architecture: "x64"
-                  #mamba-version: "*"
                   miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
@@ -132,8 +122,6 @@ jobs:
                   use-only-tar-bz2: true
                   channel-priority: strict
                   channels: conda-forge, xspecmodels
-              
-
             - name: Init Env
               shell: bash -l {0}
               run: |
@@ -170,24 +158,13 @@ jobs:
                   # stop the build if there are Python syntax errors or undefined names
                   flake8
 
-            - name: Test conda install
-              if: matrix.os == 'macos-latest'
+            - name: Test import xspec
+              if: matrix.os != 'macos-latest'
               shell: bash -l {0}
-              run: python -m pytest -vv --cov=astromodels --cov-report=xml
-              env:
-                OMP_NUM_THREADS: 1
-                MKL_NUM_THREADS: 1
-                NUMEXPR_NUM_THREADS: 1
-                MPLBACKEND: "Agg"
-            - name: Test conda install
-              if: matrix.os != 'macos-latest' 
+              run: python -c "import astromodels.xspec"
+            - name: Test astromodels
               shell: bash -l {0}
-              run: |
-              
-                  echo "======>  importing XSPEC..."
-                  python -c "import astromodels.xspec"
-                  python -m pytest -vv --cov=astromodels --cov-report=xml
-
+              run: python -m pytest -vv --cov=astromodels --cov-report=xml
               env:
                   OMP_NUM_THREADS: 1
                   MKL_NUM_THREADS: 1

From 5ab76e94a08efeb9249113c1b270af86a872546c Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 10 Sep 2024 11:32:40 -0400
Subject: [PATCH 14/17] Minor fix.

---
 .github/workflows/deploy.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 2eb63b66..023cfd2b 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -147,7 +147,9 @@ jobs:
             - name: Test import xspec
               if: matrix.os != 'macos-latest'
               shell: bash -l {0}
-              run: python -c "import astromodels.xspec"
+              run: |
+                  cd astromodels/tests
+                  python -c "import astromodels.xspec"
             - name: Test astromodels
               shell: bash -l {0}
               run: python -m pytest -vv --cov=astromodels --cov-report=xml

From 948ec0eb4f8521f151d4b4b216534b79f7b16e9e Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Tue, 10 Sep 2024 16:15:07 -0400
Subject: [PATCH 15/17] Upload fixed.

---
 .github/workflows/deploy.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 023cfd2b..90e12cd6 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -245,6 +245,11 @@ jobs:
 
                   anaconda -v --show-traceback -t $UPLOAD_TOKEN upload -u threeml ${CONDA}/envs/test_env/conda-bld/linux-64/*.tar.bz2 --force $LABEL
 
+                  elif [[ ${{matrix.os}} == macos-latest ]];
+                  then
+
+                  anaconda -v --show-traceback -t $UPLOAD_TOKEN upload -u threeml ${CONDA}/envs/test_env/conda-bld/osx-arm64/*.tar.bz2 --force $LABEL
+
                   else
 
                   anaconda -v --show-traceback -t $UPLOAD_TOKEN upload -u threeml ${CONDA}/envs/test_env/conda-bld/osx-64/*.tar.bz2 --force $LABEL

From 6325d78b0341350324cb4ba4c3dd4cb6a685ccad Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Fri, 31 Jan 2025 15:45:59 -0800
Subject: [PATCH 16/17] Replacing macos-12 and mambaforge.

---
 .github/workflows/deploy.yml         | 8 ++++----
 .github/workflows/test_and_build.yml | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 90e12cd6..4ac4e14c 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -73,7 +73,7 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                os: [ubuntu-latest, macos-latest, macos-12]
+                os: [ubuntu-latest, macos-latest, macos-13]
                 python-version: [3.9]
                 include:
                   - environment: ci/environment.yml
@@ -89,7 +89,7 @@ jobs:
               with:
                   activate-environment: "test_env"
                   auto-activate-base: false
-                  miniforge-variant: Mambaforge
+                  miniforge-variant: Miniforge3
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
                   environment-file: ${{ matrix.environment }}
@@ -165,7 +165,7 @@ jobs:
         runs-on: ${{ matrix.os }}
         strategy:
             matrix:
-                os: [ubuntu-latest, macos-latest, macos-12]
+                os: [ubuntu-latest, macos-latest, macos-13]
                 python-version: [3.9]
                 include:
                   - environment: ci/environment.yml
@@ -182,7 +182,7 @@ jobs:
                   activate-environment: "test_env"
                   auto-activate-base: false
                   #architecture: "x64"
-                  miniforge-variant: Mambaforge
+                  miniforge-variant: Miniforge3
                   #miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
index 9020170c..a32a82b3 100644
--- a/.github/workflows/test_and_build.yml
+++ b/.github/workflows/test_and_build.yml
@@ -37,7 +37,7 @@ jobs:
             fail-fast: false
             matrix:
                 python-version: ["3.9", "3.10", "3.11"]
-                os: ["ubuntu-latest", "macos-latest", "macos-12"]
+                os: ["ubuntu-latest", "macos-latest", "macos-13"]
         runs-on: ${{ matrix.os }}
         steps:
             - name: Checkout
@@ -100,7 +100,7 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                os: ["ubuntu-latest", "macos-latest", "macos-12"]
+                os: ["ubuntu-latest", "macos-latest", "macos-13"]
                 python-version: [3.9]
                 include:
                   - environment: ci/environment.yml

From feeffd21a0aa0a9d013f36747d24f04e7e99a7fd Mon Sep 17 00:00:00 2001
From: ndilalla <niccolo.dilalla@stanford.edu>
Date: Fri, 31 Jan 2025 15:51:47 -0800
Subject: [PATCH 17/17] Minor.

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

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 4ac4e14c..40c46a51 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -107,7 +107,7 @@ jobs:
                       
                       miniconda_os=Linux
                       compilers="gcc_linux-64 gxx_linux-64 gfortran_linux-64"
-                  else  # osx
+                  else
                       
                       miniconda_os=MacOSX
                       compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"