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 <[email protected]> Thu, 22 Aug 2024 18:44:37 +0200 + -- Étienne Mollier <[email protected]> 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 This package is no longer maintained, except for exceptional + 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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