[med-svn] [Git][med-team/python-cobra][master] patch-out python3-importlib-resources

[Alexandre Detiste (@detiste-guest)]

Alexandre Detiste pushed to branch master at Debian Med / python-cobra


Commits:
587179a9 by Alexandre Detiste at 2025-07-03T00:27:01+02:00
patch-out python3-importlib-resources

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/pr1452.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-cobra (0.29.1-3) unstable; urgency=medium
+
+  * Team upload.
+  * Patch-out dependency on external python3-importlib-resources.
+
+ -- Alexandre Detiste <tchet at debian.org>  Thu, 03 Jul 2025 00:26:36 +0200
+
 python-cobra (0.29.1-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -9,7 +9,6 @@ Build-Depends: debhelper-compat (= 13),
                python3-dev,
                python3-setuptools,
                python3-depinfo,
-               python3-importlib-resources,
                python3-numpy,
                python3-optlang (>= 1.7.0-1~),
                python3-ruamel.yaml,


=====================================
debian/patches/pr1452.patch
=====================================
@@ -0,0 +1,129 @@
+From 61c0bfe738dee0ec76fb8fbffa0b0854ef66b13e Mon Sep 17 00:00:00 2001
+From: Alexandre Detiste <alexandre.detiste at gmail.com>
+Date: Thu, 3 Jul 2025 00:18:34 +0200
+Subject: [PATCH] use the importlib.resources from the standard library, not
+ the external backport
+
+---
+ setup.cfg                              |  1 -
+ src/cobra/io/web/cobrapy_repository.py |  4 ++--
+ tests/conftest.py                      |  4 ++--
+ tests/data/update_pickles.py           | 11 +++++------
+ tests/test_io/test_json.py             |  2 +-
+ tox.ini                                |  1 -
+ 6 files changed, 10 insertions(+), 13 deletions(-)
+
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -56,7 +56,6 @@
+ 	depinfo ~=2.2
+ 	diskcache ~=5.0
+ 	httpx ~=0.24
+-	importlib_resources
+ 	numpy >=1.13
+ 	optlang ~=1.8
+ 	pandas >=1.0,<3.0
+--- a/src/cobra/io/web/cobrapy_repository.py
++++ b/src/cobra/io/web/cobrapy_repository.py
+@@ -1,6 +1,6 @@
+ """Provide functions for loading metabolic models from local package data."""
+ 
+-import importlib_resources
++import importlib.resources
+ 
+ import cobra.data
+ 
+@@ -50,7 +50,7 @@
+             A gzip-compressed, UTF-8 encoded SBML document.
+         """
+         return (
+-            importlib_resources.files(cobra.data)
++            importlib.resources.files(cobra.data)
+             .joinpath(f"{model_id}.xml.gz")
+             .read_bytes()
+         )
+--- a/tests/conftest.py
++++ b/tests/conftest.py
+@@ -1,10 +1,10 @@
+ """Define global fixtures."""
+ 
++import importlib.resources
+ from pathlib import Path
+ from pickle import load as _load
+ from typing import List, Tuple
+ 
+-import importlib_resources
+ import pytest
+ 
+ import cobra
+@@ -14,7 +14,7 @@
+ 
+ 
+ data_dir = Path(__file__).parent / "data"
+-cobra_data_dir = importlib_resources.files(cobra.data)
++cobra_data_dir = importlib.resources.files(cobra.data)
+ 
+ 
+ def create_test_model(model_name: str = "salmonella") -> Model:
+--- a/tests/data/update_pickles.py
++++ b/tests/data/update_pickles.py
+@@ -10,12 +10,11 @@
+ """
+ 
+ 
++import importlib.resources
+ from collections import OrderedDict
+ from json import dump as json_dump
+ from pickle import dump, load
+ 
+-import importlib_resources
+-
+ import cobra
+ from cobra.io import (
+     load_matlab_model,
+@@ -99,16 +98,16 @@
+     # output to various formats
+     with open("mini.pickle", "wb") as outfile:
+         dump(mini, outfile, protocol=2)
+-    save_matlab_model(mini, importlib_resources.files(cobra.data).joinpath("mini.mat"))
++    save_matlab_model(mini, importlib.resources.files(cobra.data).joinpath("mini.mat"))
+     save_json_model(
+-        mini, importlib_resources.files(cobra.data).joinpath("mini.json"), pretty=True
++        mini, importlib.resources.files(cobra.data).joinpath("mini.json"), pretty=True
+     )
+-    save_yaml_model(mini, importlib_resources.files(cobra.data).joinpath("mini.yml"))
++    save_yaml_model(mini, importlib.resources.files(cobra.data).joinpath("mini.yml"))
+     write_sbml_model(mini, "mini_fbc2.xml")
+     write_sbml_model(mini, "mini_fbc2.xml.bz2")
+     write_sbml_model(mini, "mini_fbc2.xml.gz")
+     write_sbml_model(
+-        mini, importlib_resources.files(cobra.data).joinpath("mini_cobra.xml")
++        mini, importlib.resources.files(cobra.data).joinpath("mini_cobra.xml")
+     )
+     raven = load_matlab_model("raven.mat")
+     with open("raven.pickle", "wb") as outfile:
+--- a/tests/test_io/test_json.py
++++ b/tests/test_io/test_json.py
+@@ -1,11 +1,11 @@
+ """Test functionalities of I/O in JSON format."""
+ 
+ import json
++from importlib.resources import files
+ from pathlib import Path
+ from typing import Any, Callable, Dict, Union
+ 
+ import pytest
+-from importlib_resources import files
+ 
+ from cobra import Model
+ from cobra import io as cio
+--- a/tox.ini
++++ b/tox.ini
+@@ -111,7 +111,6 @@
+     diskcache
+     future
+     httpx
+-    importlib_resources
+     libsbml
+     numpy
+     optlang


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ ignore_tests.patch
 no_future_dependency.patch
 remove-appdirs.patch
 a2b9d00a04b85b8c8eb12e4deba29ce2147896cf.patch
+pr1452.patch



View it on GitLab: https://salsa.debian.org/med-team/python-cobra/-/commit/587179a9fbbd2d21f8eb96834ff5782df7bf21be

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-cobra/-/commit/587179a9fbbd2d21f8eb96834ff5782df7bf21be
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