[med-svn] [Git][med-team/qiime][master] 3 commits: Build-Depends newly packages python3-parsl
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Jan 25 10:41:17 GMT 2024
Andreas Tille pushed to branch master at Debian Med / qiime
Commits:
9a2fd860 by Andreas Tille at 2024-01-25T11:25:26+01:00
Build-Depends newly packages python3-parsl
- - - - -
2cf24376 by Andreas Tille at 2024-01-25T11:27:45+01:00
Depends: python3-tomlkit
- - - - -
6c3a90a7 by Andreas Tille at 2024-01-25T11:40:33+01:00
Attempt to work on bug #1060965
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/bibtexparser.patch
- debian/patches/python3.10.patch
- debian/patches/python3.8.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -2,8 +2,8 @@ qiime (2023.9.2-1) UNRELEASED; urgency=medium
* New upstream version
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
- * Build-Depends: python3-appdirs
- TODO: https://github.com/Parsl/parsl
+ * Build-Depends: python3-appdirs, python3-parsl
+ * Depends: python3-tomlkit
-- Andreas Tille <tille at debian.org> Mon, 20 Nov 2023 14:03:56 +0100
=====================================
debian/control
=====================================
@@ -16,6 +16,7 @@ Build-Depends: debhelper-compat (= 13),
python3-decorator <!nocheck>,
python3-dill <!nocheck>,
python3-pandas <!nocheck>,
+ python3-parsl <!nocheck>,
python3-tzlocal <!nocheck>,
python3-yaml <!nocheck>,
python3-networkx <!nocheck>
@@ -34,6 +35,7 @@ Depends: ${shlibs:Depends},
python3-decorator,
python3-dill,
python3-pandas,
+ python3-tomlkit,
python3-tzlocal,
python3-yaml,
python3-pyparsing,
=====================================
debian/patches/bibtexparser.patch
=====================================
@@ -0,0 +1,12 @@
+Bug-Debian: https://bugs.debian.org/1060965
+
+--- a/qiime2/core/cite.py
++++ b/qiime2/core/cite.py
+@@ -23,6 +23,7 @@ class Citations(collections.OrderedDict)
+ root = os.path.abspath(root)
+ path = os.path.join(root, path)
+
++# This attribute does not exist any more in bibtexparser 2.0
+ parser = bp.bparser.BibTexParser()
+ # Downstream tooling is much easier with unicode. For actual latex
+ # users, use the modern biber backend instead of bibtex
=====================================
debian/patches/python3.10.patch
=====================================
@@ -7,9 +7,9 @@ Forwarded: no
Last-Update: 2022-09-03
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- qiime.orig/qiime2/sdk/tests/test_method.py
-+++ qiime/qiime2/sdk/tests/test_method.py
-@@ -209,15 +209,15 @@
+--- a/qiime2/sdk/tests/test_method.py
++++ b/qiime2/sdk/tests/test_method.py
+@@ -210,15 +210,15 @@ class TestMethod(unittest.TestCase):
kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
exp_parameters = [
('ints1', inspect.Parameter(
@@ -30,7 +30,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
]
self.assertEqual(parameters, exp_parameters)
-@@ -234,9 +234,9 @@
+@@ -235,9 +235,9 @@ class TestMethod(unittest.TestCase):
kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
exp_parameters = [
('mapping1', inspect.Parameter(
@@ -42,8 +42,8 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
]
self.assertEqual(parameters, exp_parameters)
---- qiime.orig/qiime2/sdk/tests/test_visualizer.py
-+++ qiime/qiime2/sdk/tests/test_visualizer.py
+--- a/qiime2/sdk/tests/test_visualizer.py
++++ b/qiime2/sdk/tests/test_visualizer.py
@@ -6,6 +6,7 @@
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
@@ -52,7 +52,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
import concurrent.futures
import inspect
import os.path
-@@ -181,13 +182,13 @@
+@@ -181,13 +182,13 @@ class TestVisualizer(unittest.TestCase,
kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
exp_parameters = [
('mapping1', inspect.Parameter(
@@ -70,7 +70,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
]
self.assertEqual(parameters, exp_parameters)
-@@ -205,7 +206,7 @@
+@@ -205,7 +206,7 @@ class TestVisualizer(unittest.TestCase,
kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
exp_parameters = [
('ints', inspect.Parameter(
@@ -79,9 +79,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
]
self.assertEqual(parameters, exp_parameters)
---- qiime.orig/qiime2/sdk/tests/test_pipeline.py
-+++ qiime/qiime2/sdk/tests/test_pipeline.py
-@@ -61,13 +61,13 @@
+--- a/qiime2/sdk/tests/test_pipeline.py
++++ b/qiime2/sdk/tests/test_pipeline.py
+@@ -61,13 +61,13 @@ class TestPipeline(unittest.TestCase):
kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
exp_parameters = [
('int_sequence', inspect.Parameter(
=====================================
debian/patches/python3.8.patch
=====================================
@@ -7,7 +7,7 @@ Last-Update: 2020-11-30
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/qiime2/core/path.py
+++ b/qiime2/core/path.py
-@@ -155,6 +155,14 @@ class InternalDirectory(_ConcretePath):
+@@ -154,6 +154,14 @@ class InternalDirectory(_ConcretePath):
# Same reasoning as truediv
return _ConcretePath(path, str(self))
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ python3.8.patch
python3.9.patch
enable_decorator_5.patch
python3.10.patch
+bibtexparser.patch
View it on GitLab: https://salsa.debian.org/med-team/qiime/-/compare/6c10866dba702116e55ca91c69f4321ad7dc0f48...6c3a90a79ae5759005d8f410bd19f15401e0c96b
--
View it on GitLab: https://salsa.debian.org/med-team/qiime/-/compare/6c10866dba702116e55ca91c69f4321ad7dc0f48...6c3a90a79ae5759005d8f410bd19f15401e0c96b
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