[med-svn] [Git][med-team/python-pyani][master] 4 commits: disable-namedlist.patch: new: disable use of obsolete module.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / python-pyani


Commits:
bb9fefc9 by Étienne Mollier at 2024-08-24T17:06:35+02:00
disable-namedlist.patch: new: disable use of obsolete module.

- - - - -
3712b0b0 by Étienne Mollier at 2024-08-24T19:21:02+02:00
d/control: tests depend on many additional python3 modules.

- - - - -
b847142d by Étienne Mollier at 2024-08-24T19:21:29+02:00
d/rules: skip test_download_dry_run which needs Internet.

- - - - -
50a6bc02 by Étienne Mollier at 2024-08-24T19:22:44+02:00
Update changelog.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/disable-namedlist.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -4,8 +4,13 @@ python-pyani (0.2.13.1-1) UNRELEASED; urgency=medium
   * pytest.patch: delete: upstream migrated away from nosetest.
   * dataframe_sort.patch: delete: fixed upstream.
   * d/control: declare compliance to standards version 4.7.0.
+  * disable-namedlist.patch: new: disable use of obsolete module.
+  * d/control: tests depend on many additional python3 modules.
+  * d/rules: skip test_download_dry_run which needs Internet.
+ TODO: there are still many test failures that need investigation before
+ the package will be suitable for upload.
 
- -- Étienne Mollier <emollier at debian.org>  Thu, 22 Aug 2024 18:44:37 +0200
+ -- Étienne Mollier <emollier at debian.org>  Sat, 24 Aug 2024 19:21:50 +0200
 
 python-pyani (0.2.12-3) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -9,10 +9,15 @@ Build-Depends: debhelper-compat (= 13),
                python3-all-dev,
                python3-setuptools,
                python3-biopython <!nocheck>,
+               python3-intervaltree <!nocheck>,
+               python3-jinja2 <!nocheck>,
                python3-matplotlib <!nocheck>,
+               python3-networkx <!nocheck>,
                python3-pandas <!nocheck>,
                python3-scipy <!nocheck>,
                python3-seaborn <!nocheck>,
+               python3-sqlalchemy <!nocheck>,
+               python3-tqdm <!nocheck>,
                mummer <!nocheck>,
                ncbi-blast+ <!nocheck>,
                python3-pytest <!nocheck>


=====================================
debian/patches/disable-namedlist.patch
=====================================
@@ -0,0 +1,42 @@
+Description: disable use of namedlist module.
+ python3-namedlist is not available in Debian, and according to
+ pypi.org[1]:
+ > This package is no longer maintained, except for exceptional
+ > cases.  Please use the built-in dataclasses module instead.
+ .
+ [1]: https://pypi.org/project/namedlist/
+
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2024-08-24
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pyani.orig/pyani/download.py
++++ python-pyani/pyani/download.py
+@@ -48,8 +48,6 @@
+ import traceback
+ import urllib.request
+ 
+-from namedlist import namedlist
+-
+ from pathlib import Path
+ from subprocess import CompletedProcess
+ from typing import Any, Dict, List, NamedTuple, Optional, Tuple
+@@ -177,7 +175,7 @@
+     dlfiledata: DLFileData,
+     dltype: str = "RefSeq",
+     disable_tqdm: bool = False,
+-) -> namedlist:
++) -> DLStatus:
+     """Download genome and accompanying MD5 hash from NCBI.
+ 
+     :param args:  Namespace for command-line arguments
+@@ -202,7 +200,7 @@
+     dlstatus = retrieve_genome_and_hash(
+         filestem, dlfiledata.suffix, dlfiledata.ftpstem, outdir, timeout, disable_tqdm
+     )
+-    # Pylint is confused by the content of dlstatus (a namedlist)
++    # Pylint is confused by the content of dlstatus
+     if dlstatus.error is not None:  # pylint: disable=no-member
+         logger.warning(termcolor("%s download failed: skipping!", "magenta"), dltype)
+         logger.debug(


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


=====================================
debian/rules
=====================================
@@ -3,6 +3,9 @@
 DH_VERBOSE := 1
 export PYBUILD_NAME=pyani
 
+# test_download_dry_run looks to need Internet any way.
+export PYBUILD_TEST_ARGS=-k 'not test_download_dry_run'
+
 %:
 	dh $@ --buildsystem=pybuild
 



View it on GitLab: https://salsa.debian.org/med-team/python-pyani/-/compare/6459219843dd44b1809410b745823d03ba36122f...50a6bc02f23a752d7326062374003e4a466fac66

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pyani/-/compare/6459219843dd44b1809410b745823d03ba36122f...50a6bc02f23a752d7326062374003e4a466fac66
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