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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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