[med-svn] [Git][med-team/python-cogent][master] 3 commits: Ignore some tests that try to access network
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Sep 29 10:10:29 BST 2022
Andreas Tille pushed to branch master at Debian Med / python-cogent
Commits:
612e7d3f by Andreas Tille at 2022-09-29T10:58:51+02:00
Ignore some tests that try to access network
- - - - -
c10ca666 by Andreas Tille at 2022-09-29T11:00:42+02:00
Drop outdated debian/README.source and README.Debian
- - - - -
c582a134 by Andreas Tille at 2022-09-29T11:10:02+02:00
Upload to unstable
- - - - -
6 changed files:
- − debian/README.Debian
- − debian/README.source
- debian/changelog
- + debian/patches/ignore_tests_accessing_network.patch
- debian/patches/remove-jupyter-sphinx.patch
- debian/patches/series
Changes:
=====================================
debian/README.Debian deleted
=====================================
@@ -1,65 +0,0 @@
-PyCogent for Debian
--------------------
-
-Note that not all unit tests are working. At package build time only
-those tests are ran that do not fail. The test results are reflected
-in the package dependencies: If a test runs the tested tool is listed
-as Recommends - otherwise the tool is only Suggested (since not tested).
-
-There is some work left to fix the tests for all tools. It is suspected
-that the tools just evolved and changed their interface. Volunteers to
-adapt the tests are welcome.
-
-
-The following external tools are supported by PyCogent but not yet
-packaged for Debian:
-
-
-blat: http://anonscm.debian.org/gitweb/?p=debian-med/blat.git
- Packaging prepared but licensing issues
-
-carnac: http://bioinfo.lifl.fr/carnac/
- Asket upstream about versioned tarball
-
-cmfinder: http://bio.cs.washington.edu/yzizhen/CMfinder/
- registration page
-
-comrna: http://stormo.wustl.edu/comRNA/
- needs contact about license: If you are a commercial user or want to commercialize it, please contact the authors.
-
-contrafold: http://contra.stanford.edu/contrafold/
- http://bioinformatics.oxfordjournals.org/content/22/14/e90.abstract
- Packaging prepared at https://anonscm.debian.org/git/debian-med/contrafold.git
-
-covea: not sure - may be part of (non-free) trnascan-se
- https://anonscm.debian.org/git/debian-med/trnascan-se.git
-
-dynalign: http://rna.urmc.rochester.edu/dynalign.html
- Mathews DH, Turner DH (2002). "Dynalign: an algorithm for finding the secondary structure common to two RNA sequences". J. Mol. Biol. 317 (2): 191–203. doi:10.1006/jmbi.2001.5351. PMID 11902836.
- Note that Dynalign is now fully incorporated into the RNAstructure package
- --> http://rna.urmc.rochester.edu/RNAstructure.html<->(GPL, but registration)
-
-foldalign: http://rth.dk/resources/foldalign/
- http://bioinformaticsreview.com/20160413/foldalign-a-tool-for-secondary-structure-alignment-of-rna/
- == https://www.ncbi.nlm.nih.gov/pubmed/26704597
-
-guppy: https://staff.aist.go.jp/yutaka.ueno/guppy/
-
-ilm: ???
-
-knetfold: http://knetfold.abcc.ncifcrf.gov/
-
-mfold: http://mfold.rna.albany.edu/?q=mfold/download-mfold
-
-msms: ???
-
-pplacer: http://www.mybiosoftware.com/phylogenetic-analysis/5069
-
-Fold.out ???
-
-PETfold: http://rth.dk/resources/petfold/download.html
- (findphyl)
-
-pknotsRG: http://www.hsls.pitt.edu/obrc/index.php?page=URL1212590768
-
-rnaview: http://www.mybiosoftware.com/rna-analysis/1141
=====================================
debian/README.source deleted
=====================================
@@ -1,62 +0,0 @@
-Unfortunately the development of cogent seems to have stoped and there
-are a few weak points in the code of certain architectures. I decided
-to rather document these failed tests that became obvious on
-autobuilders than to drop the architecture at all. Past package
-versions went without the testing at all - now we have at least some
-documentation about failures.
-
-armel:
-======
- https://buildd.debian.org/status/fetch.php?pkg=python-cogent&arch=armel&ver=1.5.3-6&stamp=1450913833
- ...
-
-======================================================================
-FAIL: test__div_ (test_core.test_profile.ProfileTests)
-__div__ and __truediv__: always true division b/c __future__.division
-----------------------------------------------------------------------
-Traceback (most recent call last):
- File "/«PKGBUILDDIR»/tests/test_core/test_profile.py", line 336, in test__div_
- self.assertRaises(ProfileError, p1.__div__, p3)
-AssertionError: ProfileError not raised
-
-======================================================================
-FAIL: test_reduce_operators (test_core.test_profile.ProfileTests)
-reduce: should work fine with different operators
-----------------------------------------------------------------------
-Traceback (most recent call last):
- File "/«PKGBUILDDIR»/tests/test_core/test_profile.py", line 278, in test_reduce_operators
- normalize_input=True,normalize_output=False)
-AssertionError: ProfileError not raised
-
-----------------------------------------------------------------------
-Ran 3502 tests in 1767.832s
-
-FAILED (failures=2)
-
-
-
-ppc64el / mips64el / ppc64
-==========================
- https://buildd.debian.org/status/fetch.php?pkg=python-cogent&arch=ppc64el&ver=1.5.3-6&stamp=1450911552
- ...
-
-FAIL: test_makeTreeArray (test_core.test_tree.TreeNodeTests)
-makeTreeArray maps nodes to the descendants in them
-----------------------------------------------------------------------
-Traceback (most recent call last):
- File "/«PKGBUILDDIR»/tests/test_core/test_tree.py", line 1004, in test_makeTreeArray
- array([[1,1,1,1], [1,1,1,0], [1,1,1,0],[0,0,1,0]]))
- File "/«PKGBUILDDIR»/cogent/util/unit_test.py", line 316, in failUnlessEqual
- (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
-AssertionError: Got array([[ 0., 0., 1., 0.],
- [ 1., 1., 1., 1.],
- [ 1., 1., 1., 0.],
- [ 1., 1., 1., 0.]]), but expected array([[1, 1, 1, 1],
- [1, 1, 1, 0],
- [1, 1, 1, 0],
- [0, 0, 1, 0]])
-
-----------------------------------------------------------------------
-Ran 3502 tests in 84.862s
-
-FAILED (failures=1)
=====================================
debian/changelog
=====================================
@@ -1,8 +1,10 @@
-python-cogent (2022.8.24a1+dfsg-1) UNRELEASED; urgency=medium
+python-cogent (2022.8.24a1+dfsg-1) unstable; urgency=medium
* New upstream version
+ * Ignore some tests that try to access network
+ * Drop outdated debian/README.source and README.Debian
- -- Andreas Tille <tille at debian.org> Thu, 29 Sep 2022 09:27:12 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 29 Sep 2022 11:00:51 +0200
python-cogent (2022.5.25a1+dfsg-1) unstable; urgency=medium
=====================================
debian/patches/ignore_tests_accessing_network.patch
=====================================
@@ -0,0 +1,38 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 29 Sep 2022 09:27:12 +0200
+Description: Ignore some tests that try to access network
+
+--- a/tests/test_util/test_io.py
++++ b/tests/test_util/test_io.py
+@@ -317,6 +317,7 @@ def test_open_zip_multi(tmp_dir):
+ open_(zip_path)
+
+
++ at pytest.mark.skip(reason="Do not test in Debian since offline")
+ @pytest.mark.parametrize(
+ "mode",
+ ("r", "rb", "rt", None),
+@@ -357,6 +358,7 @@ def test_open_url_local():
+ assert remote_data.splitlines() == local_data.splitlines()
+
+
++ at pytest.mark.skip(reason="Do not test in Debian since offline")
+ def test_open_url_compressed():
+ """comparing compressed file handling"""
+ file_name = "formattest.fasta.gz"
+@@ -373,6 +375,7 @@ def test_open_url_compressed():
+ assert remote_data.splitlines() == local_data.splitlines()
+
+
++ at pytest.mark.skip(reason="Do not test in Debian since offline")
+ def test_open_url_write_exceptions():
+ """Test 'w' mode (should raise Exception)"""
+ with pytest.raises(Exception):
+@@ -382,6 +385,7 @@ def test_open_url_write_exceptions():
+ )
+
+
++ at pytest.mark.skip(reason="Do not test in Debian since offline")
+ def test_open_url_exceptions():
+ """non-http(s) address for url (should raise Exception)"""
+ with pytest.raises(Exception):
=====================================
debian/patches/remove-jupyter-sphinx.patch
=====================================
@@ -4,7 +4,7 @@ Forwarded: not-needed
Last-Update: 2022-02-20
--- a/pyproject.toml
+++ b/pyproject.toml
-@@ -51,7 +51,6 @@ doc = ["click",
+@@ -52,7 +52,6 @@ doc = ["click",
"ipykernel",
"ipython",
"ipywidgets",
@@ -12,7 +12,7 @@ Last-Update: 2022-02-20
"jupyter_client",
"jupyterlab",
"jupytext",
-@@ -79,7 +78,6 @@ dev = ["black",
+@@ -80,7 +79,6 @@ dev = ["black",
"ipython",
"ipywidgets",
"isort",
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
sphinx.patch
fix_interpreter.patch
remove-jupyter-sphinx.patch
+ignore_tests_accessing_network.patch
View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/55d3f2d01b5568707e61ba86ae57254c3e971475...c582a1345bb3d1cae7c55527cdd38622403e914c
--
View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/55d3f2d01b5568707e61ba86ae57254c3e971475...c582a1345bb3d1cae7c55527cdd38622403e914c
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