[med-svn] [Git][med-team/python-cooler][master] 3 commits: Upstream is now testing the extra requirement if ipytree (see ITP #985001). ...

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / python-cooler


Commits:
f9222b3a by Andreas Tille at 2021-12-09T08:25:17+01:00
Upstream is now testing the extra requirement if ipytree (see ITP #985001).  The tests are excluded for the moment.

- - - - -
aa39846c by Andreas Tille at 2021-12-09T08:27:05+01:00
Close bug

- - - - -
4a1885f9 by Andreas Tille at 2021-12-09T08:29:57+01:00
routine-update: Ready to upload to unstable

- - - - -


5 changed files:

- + debian/README.Debian
- debian/changelog
- debian/control
- + debian/patches/exclude_tests_in_need_of_ipytree.patch
- + debian/patches/series


Changes:

=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,14 @@
+cooler for Debian
+=================
+
+Upstream declares ipytree (see ITP #985001) as "extra requirement".
+Since it is hard to package due to lots of JS scripts it can not be
+installed as Debian package for the moment and tests using iptree
+are ignored.
+
+In case you need this functionality please run
+
+   pip install ipytree
+
+ -- Andreas Tille <tille at debian.org>  Thu, 09 Dec 2021 08:19:05 +0100
+


=====================================
debian/changelog
=====================================
@@ -1,18 +1,18 @@
-python-cooler (0.8.11-1) UNRELEASED; urgency=medium
+python-cooler (0.8.11-1) unstable; urgency=medium
 
   [ Andreas Tille ]
   * New upstream version
+    Closes: #1000814
   * Fix watchfile to detect new versions on github
   * Standards-Version: 4.6.0 (routine-update)
-  TODO ipytree: A Tree Widget using Jupyter-widgets protocol and jsTree
-       https://github.com/martinRenou/ipytree
-       (probably a hard one due to JS issues
-       see ITP #985001
+  * Upstream is testing the extra requirement if ipytree (see ITP #985001).
+    These tests are excluded for the moment.
+    Closes: #979625
 
   [ Nilesh Patra ]
   * Make Build Reproducible (Closes: #965361)
 
- -- Andreas Tille <tille at debian.org>  Thu, 30 Sep 2021 11:58:23 +0200
+ -- Andreas Tille <tille at debian.org>  Thu, 09 Dec 2021 08:27:41 +0100
 
 python-cooler (0.8.8-1) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -43,6 +43,7 @@ Depends: ${python3:Depends},
          python3-yaml,
          python3-simplejson
 Recommends: python3-dask
+Suggests: python3-pip
 Description: library for a sparse, compressed, binary persistent storage
  Cooler is a support library for a sparse, compressed, binary persistent
  storage format, also called cooler, used to store genomic interaction


=====================================
debian/patches/exclude_tests_in_need_of_ipytree.patch
=====================================
@@ -0,0 +1,45 @@
+Description: Upstream is now testing the extra requirement if ipytree (see ITP #985001).
+ The tests are excluded in this patch since ipytree is pretty hard to package
+ and the dependency is declared as "extra" so the main functionality of the
+ package seems not be affected.
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 09 Dec 2021 08:19:05 +0100
+
+--- a/tests/test_cli_export.py
++++ b/tests/test_cli_export.py
+@@ -7,7 +7,7 @@ import pandas as pd
+ from _common import cooler_cmp
+ from click.testing import CliRunner
+ import cooler
+-# import pytest
++import pytest
+ 
+ 
+ ### EXPORT ###
+@@ -107,7 +107,7 @@ def test_dump():
+         lower2 = pd.read_csv(StringIO(result.output), sep="\t")
+         assert np.allclose(lower1, lower2)
+ 
+-
++ at pytest.mark.skip("Test needs (implicitly) ipytree which is not yet packaged for Debian ... skipped")
+ def test_show():
+     runner = CliRunner()
+     with runner.isolated_filesystem():
+--- a/tests/test_fileops.py
++++ b/tests/test_fileops.py
+@@ -3,6 +3,7 @@ import os.path as op
+ import shutil
+ 
+ import h5py
++import pytest
+ 
+ from _common import isolated_filesystem, cooler_cmp
+ from cooler import fileops
+@@ -142,6 +143,7 @@ def test_ln():
+         cooler_cmp(test_file + "::resolutions/2", dst_file + "::abc/d")
+ 
+ 
++ at pytest.mark.skip("Test needs ipytree which is not yet packaged for Debian ... skipped")
+ def test_print_trees():
+     src_file = op.join(testdir, "data", "toy.symm.upper.2.mcool")
+     fileops.pprint_attr_tree(src_file, level=3)


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+exclude_tests_in_need_of_ipytree.patch



View it on GitLab: https://salsa.debian.org/med-team/python-cooler/-/compare/0cf2a59d50d6bc20f5a9249a72620137168abad1...4a1885f9336a43d33fe8e5244ac35a37b728d7eb

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-cooler/-/compare/0cf2a59d50d6bc20f5a9249a72620137168abad1...4a1885f9336a43d33fe8e5244ac35a37b728d7eb
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