Ananthu C V pushed to branch master at Debian Med / python-dendropy
Commits: b2cb087f by Ananthu C V at 2024-12-01T18:22:51+05:30 Add patch to drop runtime dependency on pkg_resources (Closes: #1083625) - - - - - d625a792 by Ananthu C V at 2024-12-01T18:23:11+05:30 Bump standards version to 4.7.0 (no changes needed) - - - - - a7f49c44 by Ananthu C V at 2024-12-01T18:23:12+05:30 Correct patch header metadata - - - - - f9626b86 by Ananthu C V at 2024-12-01T18:23:13+05:30 Recreate and improve dendropy-format manpage - - - - - 6d0528ef by Ananthu C V at 2024-12-01T18:35:11+05:30 Point homepage to the package documentation - - - - - 51d6ad7b by Ananthu C V at 2024-12-01T18:35:12+05:30 Upload to unstable - - - - - 6 changed files: - debian/changelog - debian/control - debian/dendropy-format.1 - debian/patches/do_not_try_running_non-existing_testsuite.patch - + debian/patches/remove-pkg-resources-usage.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +python-dendropy (4.6.1-2) unstable; urgency=medium + + * Team upload. + * Add patch to drop runtime dependency on pkg_resources (Closes: #1083625) + * Bump standards version to 4.7.0 (no changes needed) + * Correct patch header metadata + * Recreate and improve dendropy-format manpage + * Point homepage to the package documentation + + -- Ananthu C V <[email protected]> Sun, 01 Dec 2024 18:23:25 +0530 + python-dendropy (4.6.1-1) unstable; urgency=medium [ Lance Lin ] ===================================== debian/control ===================================== @@ -8,10 +8,10 @@ Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools -Standards-Version: 4.6.2 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/python-dendropy Vcs-Git: https://salsa.debian.org/med-team/python-dendropy.git -Homepage: https://dendropy.org/ +Homepage: https://jeetsukumaran.github.io/DendroPy Rules-Requires-Root: no Package: python3-dendropy ===================================== debian/dendropy-format.1 ===================================== @@ -1,10 +1,9 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16. -.TH USAGE: "1" "November 2020" "usage: cat SRC-FILE | dendropy-format --from [FORMAT] --to [FORMAT] [OPTIONS] > DEST-FILE" "User Commands" +.TH dendropy-format "1" "December 2024" "usage: dendropy-format --from [FORMAT] --to [FORMAT] [OPTIONS] <SOURCE-FILE> > DEST-FILE" "User Commands" .SH NAME -usage: \- manual page for usage: cat SRC-FILE | dendropy-format --from [FORMAT] --to [FORMAT] [OPTIONS] > DEST-FILE +dendropy-format - convert files from one format to another .SH DESCRIPTION -usage: cat SRC\-FILE | dendropy\-format \fB\-\-from\fR [FORMAT] \fB\-\-to\fR [FORMAT] [OPTIONS] > DEST\-FILE -.SS "optional arguments:" +usage: dendropy\-format \fB\-\-from\fR [FORMAT] \fB\-\-to\fR [FORMAT] [OPTIONS] <SOURCE\-FILE> > DEST\-FILE +.SS "options:" .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit @@ -22,5 +21,10 @@ Type of data .TP \fB\-t\fR FORMAT, \fB\-\-to\fR FORMAT Format of data source. -.PP -dendropy\-format: error: the following arguments are required: source_file +.TP +\fB\-u\fR, \fB\-\-unquoted\-underscores\fR +[NEXUS/Newick:] Do not quote labels with undescores. +.TP +\fB\-\-recode\-uncertain\fR {missing,gap} +Recode ambiguous or uncertain characters as missing +('?') or gaps ('\-') ===================================== debian/patches/do_not_try_running_non-existing_testsuite.patch ===================================== @@ -1,6 +1,6 @@ Author: Andreas Tille <[email protected]> Forwarded: not-needed -Last-Update: Tue, 08 Oct 2019 09:01:44 +0200 +Last-Update: 2019-10-08 Description: There is no test suite to run - just data see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=937698#17 ===================================== debian/patches/remove-pkg-resources-usage.patch ===================================== @@ -0,0 +1,21 @@ +Description: use importlib instead of deprecated pkg_resources +Author: Ananthu C V <[email protected]> +Bug-Debian: https://bugs.debian.org/1083625 +Last-Update: 2024-12-01 +--- a/setup.py ++++ b/setup.py +@@ -95,3 +95,2 @@ + EXTRA_KWARGS = dict( +- install_requires = ['setuptools'], + include_package_data = True, +--- a/src/dendropy/utility/libexec/__init__.py ++++ b/src/dendropy/utility/libexec/__init__.py +@@ -28,6 +28,6 @@ + try: +- import pkg_resources ++ from importlib.resources import files + # note that this creates a temporary file with the contents of the + # filename if the package is in an egg +- filepath = pkg_resources.resource_filename("dendropy", "utility/libexec/{}".format(filename)) ++ filepath = files("dendropy") / "utility/libexec/{}".format(filename) + # print("-->{}".format(filepath)) ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ do_not_try_running_non-existing_testsuite.patch +remove-pkg-resources-usage.patch View it on GitLab: https://salsa.debian.org/med-team/python-dendropy/-/compare/875d851f0ac2322801488c4aaa921f602a70850f...51d6ad7b8a951d858b750fcd14b04726d1de0263 -- View it on GitLab: https://salsa.debian.org/med-team/python-dendropy/-/compare/875d851f0ac2322801488c4aaa921f602a70850f...51d6ad7b8a951d858b750fcd14b04726d1de0263 You're receiving this email because of your account on salsa.debian.org.
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