[med-svn] [Git][med-team/qiime][master] 3 commits: unfuzz python3.8.patch.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Sep 3 11:41:44 BST 2022
Étienne Mollier pushed to branch master at Debian Med / qiime
Commits:
8b102f5d by Étienne Mollier at 2022-09-01T23:05:22+02:00
unfuzz python3.8.patch.
- - - - -
90a4180c by Étienne Mollier at 2022-09-03T12:04:28+02:00
python3.10.patch: added; fix autopkgtest with python3.10.
- - - - -
fc41dee3 by Étienne Mollier at 2022-09-03T12:08:15+02:00
ready to upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/python3.10.patch
- debian/patches/python3.8.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,13 +1,16 @@
-qiime (2022.8.1-1) UNRELEASED; urgency=medium
+qiime (2022.8.1-1) unstable; urgency=medium
- * Team upload.
+ [ Nilesh Patra ]
* New upstream version 2022.8.1
* d/t/run-unit-test: Skip tests on 32-bit
arch (Closes: #1014100)
* Switch from nose to pytest (Closes: #1018609)
- TODO: Fix autopkgtests
- -- Nilesh Patra <nilesh at debian.org> Mon, 29 Aug 2022 20:41:39 +0530
+ [ Étienne Mollier ]
+ * python3.8.patch: unfuzz.
+ * python3.10.patch: added; fix autopkgtest with python3.10.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 03 Sep 2022 12:05:26 +0200
qiime (2022.2.1-2) unstable; urgency=medium
=====================================
debian/patches/python3.10.patch
=====================================
@@ -0,0 +1,101 @@
+Description: adjust test suite for python3.10.
+ This patch adjusts expected results after inspect.Signature.from_callable
+ since this function changed behavior between python3.9 and python3.10. This
+ may be more of a work around than a genuine proper fix.
+Author: Étienne Mollier <emollier at debian.org>
+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 @@
+ kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
+ exp_parameters = [
+ ('ints1', inspect.Parameter(
+- 'ints1', kind, annotation=IntSequence1 | IntSequence2)),
++ 'ints1', kind, annotation=list)),
+ ('ints2', inspect.Parameter(
+- 'ints2', kind, annotation=IntSequence1)),
++ 'ints2', kind, annotation=list)),
+ ('ints3', inspect.Parameter(
+- 'ints3', kind, annotation=IntSequence2)),
++ 'ints3', kind, annotation=list)),
+ ('int1', inspect.Parameter(
+- 'int1', kind, annotation=Int)),
++ 'int1', kind, annotation=int)),
+ ('int2', inspect.Parameter(
+- 'int2', kind, annotation=Int))
++ 'int2', kind, annotation=int))
+ ]
+
+ self.assertEqual(parameters, exp_parameters)
+@@ -234,9 +234,9 @@
+ kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
+ exp_parameters = [
+ ('mapping1', inspect.Parameter(
+- 'mapping1', kind, annotation=Mapping)),
++ 'mapping1', kind, annotation=dict)),
+ ('mapping2', inspect.Parameter(
+- 'mapping2', kind, annotation=Mapping))
++ 'mapping2', kind, annotation=dict))
+ ]
+
+ self.assertEqual(parameters, exp_parameters)
+--- qiime.orig/qiime2/sdk/tests/test_visualizer.py
++++ qiime/qiime2/sdk/tests/test_visualizer.py
+@@ -6,6 +6,7 @@
+ # The full license is in the file LICENSE, distributed with this software.
+ # ----------------------------------------------------------------------------
+
++import collections
+ import concurrent.futures
+ import inspect
+ import os.path
+@@ -181,13 +182,13 @@
+ kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
+ exp_parameters = [
+ ('mapping1', inspect.Parameter(
+- 'mapping1', kind, annotation=Mapping)),
++ 'mapping1', kind, annotation=dict)),
+ ('mapping2', inspect.Parameter(
+- 'mapping2', kind, annotation=Mapping)),
++ 'mapping2', kind, annotation=dict)),
+ ('key_label', inspect.Parameter(
+- 'key_label', kind, annotation=Str)),
++ 'key_label', kind, annotation=str)),
+ ('value_label', inspect.Parameter(
+- 'value_label', kind, annotation=Str))
++ 'value_label', kind, annotation=str))
+ ]
+
+ self.assertEqual(parameters, exp_parameters)
+@@ -205,7 +206,7 @@
+ kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
+ exp_parameters = [
+ ('ints', inspect.Parameter(
+- 'ints', kind, annotation=IntSequence1 | IntSequence2))
++ 'ints', kind, annotation=collections.Counter))
+ ]
+
+ self.assertEqual(parameters, exp_parameters)
+--- qiime.orig/qiime2/sdk/tests/test_pipeline.py
++++ qiime/qiime2/sdk/tests/test_pipeline.py
+@@ -61,13 +61,13 @@
+ kind = inspect.Parameter.POSITIONAL_OR_KEYWORD
+ exp_parameters = [
+ ('int_sequence', inspect.Parameter(
+- 'int_sequence', kind, annotation=IntSequence1)),
++ 'int_sequence', kind)),
+ ('mapping', inspect.Parameter(
+- 'mapping', kind, annotation=Mapping)),
++ 'mapping', kind)),
+ ('do_extra_thing', inspect.Parameter(
+- 'do_extra_thing', kind, annotation=Bool)),
++ 'do_extra_thing', kind)),
+ ('add', inspect.Parameter(
+- 'add', kind, default=1, annotation=Int))
++ 'add', kind, default=1))
+ ]
+
+ for callable_attr in '__call__', 'asynchronous':
=====================================
debian/patches/python3.8.patch
=====================================
@@ -5,11 +5,9 @@ Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=950842
Last-Update: 2020-11-30
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
-Index: qiime/qiime2/core/path.py
-===================================================================
--- qiime.orig/qiime2/core/path.py
+++ qiime/qiime2/core/path.py
-@@ -145,6 +145,14 @@ class InternalDirectory(_ConcretePath):
+@@ -147,6 +147,14 @@
# Same reasoning as truediv
return _ConcretePath(path, str(self))
@@ -24,11 +22,9 @@ Index: qiime/qiime2/core/path.py
class ArchivePath(InternalDirectory):
DEFAULT_PREFIX = 'qiime2-archive-'
-Index: qiime/qiime2/core/type/parse.py
-===================================================================
--- qiime.orig/qiime2/core/type/parse.py
+++ qiime/qiime2/core/type/parse.py
-@@ -93,6 +93,9 @@ def _convert_literals(expr):
+@@ -93,6 +93,9 @@
if node is ast.Name and expr.id == 'inf':
return float('inf')
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ python3.8.patch
python3.9.patch
32-bits.patch
enable_decorator_5.patch
+python3.10.patch
View it on GitLab: https://salsa.debian.org/med-team/qiime/-/compare/ae5b21b9c43323038dd3563fe7ee049531d8a180...fc41dee3fe1c5bf89f1da9b0a10ec2a15137762d
--
View it on GitLab: https://salsa.debian.org/med-team/qiime/-/compare/ae5b21b9c43323038dd3563fe7ee049531d8a180...fc41dee3fe1c5bf89f1da9b0a10ec2a15137762d
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