[med-svn] [Git][med-team/python-cobra][master] 7 commits: Build-Depends: python3-importlib-resources
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Aug 25 14:36:57 BST 2022
Andreas Tille pushed to branch master at Debian Med / python-cobra
Commits:
a148e24c by Andreas Tille at 2022-08-25T14:01:41+02:00
Build-Depends: python3-importlib-resources
- - - - -
d0c08fda by Andreas Tille at 2022-08-25T14:01:55+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
31a38ef6 by Andreas Tille at 2022-08-25T14:06:00+02:00
Update patches
- - - - -
4bb929ac by Andreas Tille at 2022-08-25T14:08:34+02:00
Build-Depends: python3-pytest-mock
- - - - -
76ff0f74 by Andreas Tille at 2022-08-25T15:00:51+02:00
Reactivate test_show_versions patch
- - - - -
b5ed468e by Andreas Tille at 2022-08-25T15:01:39+02:00
Ignore tests accessing remote locations
- - - - -
dbe74dbb by Andreas Tille at 2022-08-25T15:23:58+02:00
Reflect move of data directory inside upstream source
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/ignore_tests.patch
- − debian/patches/no_importlib_resources_for_test.patch
- debian/patches/series
- debian/patches/xfail_test_show_versions.patch
- debian/python-cobra-data.install
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,13 @@
python-cobra (0.25.0-1) UNRELEASED; urgency=medium
+ [ Étienne Mollier ]
* Team upload.
* New upstream version
-TODO: package importlib_resources as it seems now needed to import cobra..
+
+ [ Andreas Tille ]
+ * Build-Depends: python3-importlib-resources, python3-pytest-mock
+ * Standards-Version: 4.6.1 (routine-update)
+ * Ignore tests accessing remote locations
-- Étienne Mollier <emollier at debian.org> Wed, 04 May 2022 21:27:29 +0200
=====================================
debian/control
=====================================
@@ -11,6 +11,7 @@ Build-Depends: debhelper-compat (= 13),
python3-setuptools,
python3-depinfo,
python3-future,
+ python3-importlib-resources,
python3-numpy,
python3-optlang,
python3-ruamel.yaml,
@@ -25,6 +26,7 @@ Build-Depends: debhelper-compat (= 13),
cython3,
python3-pytest <!nocheck>,
python3-pytest-benchmark <!nocheck>,
+ python3-pytest-mock <!nocheck>,
python3-jsonschema <!nocheck>,
libsbml5 <!nocheck>,
python3-matplotlib <!nocheck>,
@@ -33,7 +35,7 @@ Build-Depends: debhelper-compat (= 13),
python3-httpx <!nocheck>,
python3-pydantic <!nocheck>,
python3-rich <!nocheck>
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/python-cobra
Vcs-Git: https://salsa.debian.org/med-team/python-cobra.git
Homepage: https://opencobra.github.io/cobrapy/
=====================================
debian/patches/ignore_tests.patch
=====================================
@@ -0,0 +1,31 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 25 Aug 2022 14:49:24 +0200
+Description: Ignore test accessing online resources
+
+--- a/tests/test_io/test_web/test_load.py
++++ b/tests/test_io/test_web/test_load.py
+@@ -41,7 +41,7 @@ def test_biomodels_access(biomodels):
+ load_model("BIOMD0000000633", cache=False, repositories=[biomodels])
+ biomodels.get_sbml.assert_called_once_with(model_id="BIOMD0000000633")
+
+-
++ at pytest.mark.skip(reason="Do not test in Debian since build is offline")
+ def test_unknown_model():
+ """Expect that a not found error is raised (e2e)."""
+ with pytest.raises(
+@@ -50,6 +50,7 @@ def test_unknown_model():
+ load_model("MODELWHO?", cache=False)
+
+
++ at pytest.mark.skip(reason="Do not test in Debian since build is offline")
+ @pytest.mark.parametrize(
+ "model_id, num_metabolites, num_reactions",
+ [("e_coli_core", 72, 95), ("BIOMD0000000633", 50, 35)],
+@@ -61,6 +62,7 @@ def test_remote_load(model_id: str, num_
+ assert len(model.reactions) == num_reactions
+
+
++ at pytest.mark.skip(reason="Do not test in Debian since build is offline")
+ def test_cache(monkeypatch, tmp_path, bigg_models, biomodels):
+ """Test that remote models are properly cached."""
+ config = Configuration()
=====================================
debian/patches/no_importlib_resources_for_test.patch deleted
=====================================
@@ -1,61 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 29 Sep 2020 12:43:02 +0200
-Description: importlib_resources is not packaged for Debian thus ignore the test that needs this module
-
---- a/setup.cfg
-+++ b/setup.cfg
-@@ -57,7 +57,6 @@
- diskcache ~=5.0
- future
- httpx ~=0.14
-- importlib_resources
- numpy ~=1.13
- optlang ~=1.5
- pandas ~=1.0
---- a/src/cobra/test/test_io/test_json.py
-+++ b/src/cobra/test/test_io/test_json.py
-@@ -8,19 +8,19 @@
- from os.path import join
-
- import pytest
--from importlib_resources import open_text
-+#from importlib_resources import open_text
-
- from cobra import io as cio
- from cobra.test.test_io.conftest import compare_models
-
--
-- at pytest.fixture(scope="module")
--def json_schema_v1():
-- with open_text(cio, "schema_v1.json") as handle:
-- schema_v1 = json.load(handle)
-- return schema_v1
-+#@pytest.fixture(scope="module")
-+#def json_schema_v1():
-+# with open_text(cio, "schema_v1.json") as handle:
-+# schema_v1 = json.load(handle)
-+# return schema_v1
-
-
-+ at pytest.mark.skip(reason="importlib_resources not packaged for Debian")
- def test_validate_json(data_directory, json_schema_v1):
- """Validate file according to JSON-schema."""
- jsonschema = pytest.importorskip("jsonschema")
-@@ -35,6 +35,7 @@
- assert compare_models(mini_model, json_model) is None
-
-
-+ at pytest.mark.skip(reason="importlib_resources not packaged for Debian")
- def test_save_json_model(tmpdir, mini_model, json_schema_v1):
- """Test the writing of JSON model."""
- jsonschema = pytest.importorskip("jsonschema")
---- a/tox.ini
-+++ b/tox.ini
-@@ -94,7 +94,6 @@
- known_third_party =
- depinfo
- future
-- importlib_resources
- libsbml
- numpy
- optlang
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,3 @@
mathjax.patch
-no_importlib_resources_for_test.patch
xfail_test_show_versions.patch
+ignore_tests.patch
=====================================
debian/patches/xfail_test_show_versions.patch
=====================================
@@ -3,8 +3,8 @@ The corresponding files aren't installed during build time. This simple xpass du
Author: Nilesh Patra <npatra974 at gmail.com>
Forwarded: not-needed
Last-Update: 2020-11-05
---- a/src/cobra/test/test_util/test_util.py
-+++ b/src/cobra/test/test_util/test_util.py
+--- a/tests/test_util/test_util.py
++++ b/tests/test_util/test_util.py
@@ -34,6 +34,7 @@
assert test_data["c"]["d"] == 2
=====================================
debian/python-cobra-data.install
=====================================
@@ -1 +1 @@
-src/cobra/test/data usr/share/python-cobra
+tests/data usr/share/python-cobra
View it on GitLab: https://salsa.debian.org/med-team/python-cobra/-/compare/1415ae8f9106263849047b512e6a01e4110297d8...dbe74dbbc0d816ad1e9471139decd5a4b1dacc4c
--
View it on GitLab: https://salsa.debian.org/med-team/python-cobra/-/compare/1415ae8f9106263849047b512e6a01e4110297d8...dbe74dbbc0d816ad1e9471139decd5a4b1dacc4c
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220825/5d38d746/attachment-0001.htm>
More information about the debian-med-commit
mailing list