[med-svn] [Git][med-team/q2-taxa][master] 6 commits: New upstream version 2024.5.0+dfsg
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Jun 26 13:28:04 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / q2-taxa
Commits:
38843b85 by Michael R. Crusoe at 2024-06-26T13:26:52+02:00
New upstream version 2024.5.0+dfsg
- - - - -
9437a6b2 by Michael R. Crusoe at 2024-06-26T13:26:52+02:00
routine-update: New upstream version
- - - - -
50f68de7 by Michael R. Crusoe at 2024-06-26T13:26:53+02:00
Update upstream source from tag 'upstream/2024.5.0+dfsg'
Update to upstream version '2024.5.0+dfsg'
with Debian dir b8f4f8216d936156ff8ca7ac2cf7ab780ef88fbc
- - - - -
5abb1da0 by Michael R. Crusoe at 2024-06-26T13:27:13+02:00
routine-update: Regenerate debian/control from debian/control.in
- - - - -
d441b0bb by Michael R. Crusoe at 2024-06-26T13:28:01+02:00
d/patches/configparser.patch: copy from qiime
- - - - -
ca0590d7 by Michael R. Crusoe at 2024-06-26T13:33:40+02:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- + debian/patches/configparser.patch
- − debian/patches/pandas2.0.patch
- debian/patches/series
- q2_taxa/_method.py
- q2_taxa/_version.py
- q2_taxa/plugin_setup.py
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+q2-taxa (2024.5.0+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Regenerate debian/control from debian/control.in (routine-update)
+ * d/patches/configparser.patch: copy from qiime
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 26 Jun 2024 13:32:53 +0200
+
q2-taxa (2024.2.0+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -12,9 +12,9 @@ Build-Depends: debhelper-compat (= 13),
python3-pytest-cov,
python3-pandas,
nodejs,
- qiime (>= 2024.2),
- q2templates (>= 2024.2),
- q2-types (>= 2024.2),
+ qiime (>= 2024.5),
+ q2templates (>= 2024.5),
+ q2-types (>= 2024.5),
webpack (>= 5.0~),
node-terser-webpack-plugin,
node-babel-loader,
@@ -34,9 +34,9 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3-pandas,
- qiime (>= 2024.2),
- q2templates (>= 2024.2),
- q2-types (>= 2024.2),
+ qiime (>= 2024.5),
+ q2templates (>= 2024.5),
+ q2-types (>= 2024.5),
node-d3-scale-chromatic,
node-natural-sort,
node-thenby
=====================================
debian/patches/configparser.patch
=====================================
@@ -0,0 +1,27 @@
+From: Athos Ribeiro <athos.ribeiro at canonical.com>
+Date: Mon, 3 Jun 2024 11:31:54 -0300
+Subject: Use ConfigParser instead of SafeConfigParser
+
+The configparser's SafeConfigParser has been renamed to ConfigParser in
+Python 3.2 [1]. It was finally removed in Python 3.12 [2].
+
+[1] https://docs.python.org/dev/whatsnew/3.2.html#configparser
+[2] https://docs.python.org/3/whatsnew/3.12.html#configparser
+
+Last-Update: 2024-06-03
+Forwarded: not-needed, see https://github.com/qiime2/q2-sample-classifier/pull/229
+
+--- q2-types.orig/versioneer.py
++++ q2-types/versioneer.py
+@@ -340,9 +340,9 @@
+ # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
+ # the top of versioneer.py for instructions on writing your setup.cfg .
+ setup_cfg = os.path.join(root, "setup.cfg")
+- parser = configparser.SafeConfigParser()
++ parser = configparser.ConfigParser()
+ with open(setup_cfg, "r") as f:
+- parser.readfp(f)
++ parser.read_file(f)
+ VCS = parser.get("versioneer", "VCS") # mandatory
+
+ def get(parser, name):
=====================================
debian/patches/pandas2.0.patch deleted
=====================================
@@ -1,16 +0,0 @@
-Description: Patch for Pandas 2.0
-Bug-Debian: https://bugs.debian.org/1053943
-Author: s3v <c0llapsed at yahoo.it>)
-Last-Update: Sat, 17 Feb 2024 19:31:48 +0100
-
---- a/q2_taxa/_method.py
-+++ b/q2_taxa/_method.py
-@@ -79,7 +79,7 @@
- # becomes an issue, this is a target for refactoring.
- ids_to_keep -= set(taxonomy.get_ids(where=query))
-
-- return ids_to_keep
-+ return list(ids_to_keep)
-
-
- def filter_table(table: pd.DataFrame, taxonomy: qiime2.Metadata,
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,3 @@
+configparser.patch
0001-make-compatible-with-webpack5.patch
0002-skip-tests-needing-internet.patch
-pandas2.0.patch
=====================================
q2_taxa/_method.py
=====================================
@@ -79,7 +79,7 @@ def _ids_to_keep_from_taxonomy(feature_ids, taxonomy, include, exclude,
# becomes an issue, this is a target for refactoring.
ids_to_keep -= set(taxonomy.get_ids(where=query))
- return ids_to_keep
+ return list(ids_to_keep)
def filter_table(table: pd.DataFrame, taxonomy: qiime2.Metadata,
=====================================
q2_taxa/_version.py
=====================================
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (tag: 2024.2.0, Release-2024.2)"
- git_full = "2f8e51958e1cc9f334a5535550b788c03bb5f45a"
- git_date = "2024-02-16 21:57:06 +0000"
+ git_refnames = " (tag: 2024.5.0, Release-2024.5)"
+ git_full = "5a46cfbf681cac8c7717df871547f5323c29865e"
+ git_date = "2024-05-29 04:18:32 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_taxa/plugin_setup.py
=====================================
@@ -16,6 +16,7 @@ from q2_types.feature_table import FeatureTable, Frequency, PresenceAbsence
from . import barplot, collapse, filter_table, filter_seqs
import q2_taxa._examples as ex
+T1 = qiime2.plugin.TypeMatch([Frequency, PresenceAbsence])
plugin = qiime2.plugin.Plugin(
name='taxa',
@@ -67,7 +68,7 @@ plugin.methods.register_function(
function=filter_table,
inputs={
'taxonomy': FeatureData[Taxonomy],
- 'table': FeatureTable[Frequency]
+ 'table': FeatureTable[T1]
},
parameters={'include': qiime2.plugin.Str,
'exclude': qiime2.plugin.Str,
@@ -75,7 +76,7 @@ plugin.methods.register_function(
qiime2.plugin.Str % qiime2.plugin.Choices(
['exact', 'contains']),
'query_delimiter': qiime2.plugin.Str},
- outputs=[('filtered_table', FeatureTable[Frequency])],
+ outputs=[('filtered_table', FeatureTable[T1])],
input_descriptions={
'taxonomy': ('Taxonomic annotations for features in the provided '
'feature table. All features in the feature table must '
View it on GitLab: https://salsa.debian.org/med-team/q2-taxa/-/compare/a284f247246f176c114793339683d173c9ee346d...ca0590d74cf053c639423f8f8df73e01173df7c4
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View it on GitLab: https://salsa.debian.org/med-team/q2-taxa/-/compare/a284f247246f176c114793339683d173c9ee346d...ca0590d74cf053c639423f8f8df73e01173df7c4
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