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Replace deprecated pkg_resources #667

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Replace deprecated pkg_resources #667

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4f71fef
Replace deprecated pkg_resources
rzats Jan 4, 2024
2b94ee1
Fix linting
rzats Jan 4, 2024
f764427
Less strict version
rzats Jan 23, 2024
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6 changes: 3 additions & 3 deletions Python-packages/covidcast-py/covidcast/covidcast.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,12 @@
from datetime import timedelta, date
from functools import reduce
from typing import Union, Iterable, Tuple, List
from importlib.metadata import version, PackageNotFoundError

import pandas as pd
import numpy as np
from delphi_epidata import Epidata
from delphi_epidata.delphi_epidata import _HEADERS
from pkg_resources import get_distribution, DistributionNotFound
from epiweeks import Week

from .errors import NoDataWarning
Expand All @@ -18,8 +18,8 @@
Epidata.BASE_URL = "https://api.covidcast.cmu.edu/epidata"
# Prepend to Epidata client's user agent to specify this package and version
try:
_ver = get_distribution("covidcast").version
except DistributionNotFound:
_ver = version("covidcast")
except PackageNotFoundError:
_ver = "0.0.0"
_HEADERS['user-agent'] = f"covidcast/{_ver} " + _HEADERS['user-agent']

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21 changes: 13 additions & 8 deletions Python-packages/covidcast-py/covidcast/geography.py
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Expand Up @@ -4,14 +4,19 @@
from typing import Union, Iterable

import pandas as pd
import pkg_resources

COUNTY_CENSUS = pd.read_csv(
pkg_resources.resource_filename(__name__, "geo_mappings/county_census.csv"), dtype=str)
MSA_CENSUS = pd.read_csv(
pkg_resources.resource_filename(__name__, "geo_mappings/msa_census.csv"), dtype=str)
STATE_CENSUS = pd.read_csv(
pkg_resources.resource_filename(__name__, "geo_mappings/state_census.csv"), dtype=str)
import importlib_resources

county_census = importlib_resources.files(__name__) / 'geo_mappings' / 'county_census.csv'
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since this is the top-level namespace for this sub-package, we should either prefix this variable name with an underscore or avoid creating the variable in the first place. this is especially true because its name is the lowercase version of the name of a constant, so maybe make the name more descriptive if you want to keep it around.

Suggested change
county_census = importlib_resources.files(__name__) / 'geo_mappings' / 'county_census.csv'
_county_census_file_path = importlib_resources.files(__name__) / 'geo_mappings' / 'county_census.csv'

with importlib_resources.as_file(county_census) as path:
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does this context manager afford us anything? it looks like pd.read_csv() should be able to accept the county_census variable directly.

COUNTY_CENSUS = pd.read_csv(path, dtype=str)

msa_census = importlib_resources.files(__name__) / 'geo_mappings' / 'msa_census.csv'
with importlib_resources.as_file(msa_census) as path:
MSA_CENSUS = pd.read_csv(path, dtype=str)

state_census = importlib_resources.files(__name__) / 'geo_mappings' / 'state_census.csv'
with importlib_resources.as_file(state_census) as path:
STATE_CENSUS = pd.read_csv(path, dtype=str)

# Filter undesired rows from CSVs.
# They're not removed from the files to keep them identical to rda files.
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12 changes: 7 additions & 5 deletions Python-packages/covidcast-py/covidcast/plotting.py
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Expand Up @@ -9,7 +9,7 @@
import imageio
import numpy as np
import pandas as pd
import pkg_resources
import importlib_resources
from matplotlib import pyplot as plt
from matplotlib import figure, axes
from tqdm import tqdm
Expand Down Expand Up @@ -182,8 +182,9 @@ def get_geo_df(data: pd.DataFrame,
raise ValueError("Unsupported geography type; "
"only `state`, `county`, `hrr`, and `msa` supported.")

shapefile_path = pkg_resources.resource_filename(__name__, SHAPEFILE_PATHS[geo_type])
geo_info = gpd.read_file(shapefile_path)
shapefile = importlib_resources.files(__name__) / SHAPEFILE_PATHS[geo_type]
with importlib_resources.as_file(shapefile) as shapefile_path:
geo_info = gpd.read_file(shapefile_path)

if geo_type == "state":
output = _join_state_geo_df(data, geo_value_col, geo_info, join_type)
Expand Down Expand Up @@ -294,8 +295,9 @@ def _plot_background_states(figsize: tuple) -> tuple:
"""
fig, ax = plt.subplots(1, figsize=figsize)
ax.axis("off")
state_shapefile_path = pkg_resources.resource_filename(__name__, SHAPEFILE_PATHS["state"])
state = gpd.read_file(state_shapefile_path)
state_shapefile = importlib_resources.files(__name__) / SHAPEFILE_PATHS["state"]
with importlib_resources.as_file(state_shapefile) as state_shapefile_path:
state = gpd.read_file(state_shapefile_path)
for state in _project_and_transform(state, "STATEFP"):
state.plot(color="0.9", ax=ax, edgecolor="0.8", linewidth=0.5)
ax.set_xlim(plt.xlim())
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3 changes: 2 additions & 1 deletion Python-packages/covidcast-py/setup.py
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Expand Up @@ -30,7 +30,8 @@
"imageio-ffmpeg",
"imageio",
"tqdm",
"epiweeks"
"epiweeks",
"importlib_resources==6.1.1",
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Should we be pinning the exact version? I'd assume we just want a compatible version, as in importlib_resources~=6.1, or something like that. Or is there a reason we need this exact version?

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It definitely makes sense for this to less rigid than requiring an exact version, particularly since the other packages are specified with open-ended constraints (or none at all). Based on the last comment linked gitlab issue, it looks like this could be:

Suggested change
"importlib_resources==6.1.1",
"importlib_resources>=1.3",

Backports are nice for functionality but potentially headache-inducing w.r.t. dependency complexity... We could make the requirement "importlib_resources>=1.3;python_version<"3.9"" but that requires the code to know when it should use importlib_resources vs importlib.resources

],
package_data={"covidcast": ["shapefiles/*/*", "geo_mappings/*"]}
)
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