[med-svn] [Git][med-team/busco][master] 2 commits: Fix python3.12 string Closes: #1085372
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Dec 5 16:36:47 GMT 2024
Andreas Tille pushed to branch master at Debian Med / busco
Commits:
cbcc77fb by Andreas Tille at 2024-12-05T17:31:38+01:00
Fix python3.12 string Closes: #1085372
- - - - -
f9cef1e2 by Andreas Tille at 2024-12-05T17:31:59+01:00
Standards-Version: 4.7.0 (routine-update)
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/find-bbmap-instead-of-bbtools.patch
- debian/patches/fix-and-disable-tests.patch
- + debian/patches/python3.12-syntax.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+busco (5.5.0-3) UNRELEASED; urgency=medium
+
+ * Fix python3.12 string
+ Closes: #1085372
+ * Standards-Version: 4.7.0 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Thu, 05 Dec 2024 17:30:17 +0100
+
busco (5.5.0-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 13),
python3-pandas <!nocheck>,
python3-setuptools,
hmmer
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/busco
Vcs-Git: https://salsa.debian.org/med-team/busco.git
Homepage: https://gitlab.com/ezlab/busco
=====================================
debian/patches/find-bbmap-instead-of-bbtools.patch
=====================================
@@ -4,7 +4,7 @@ Description: use bbmap instead of bbtools
--- a/config/config.ini
+++ b/config/config.ini
-@@ -108,6 +108,6 @@
+@@ -108,6 +108,6 @@ command = run_sepp.py
path = /usr/local/bin/
command = prodigal
@@ -14,7 +14,7 @@ Description: use bbmap instead of bbtools
command = stats.sh
--- a/src/busco/busco_tools/bbtools.py
+++ b/src/busco/busco_tools/bbtools.py
-@@ -8,8 +8,8 @@
+@@ -8,8 +8,8 @@ logger = BuscoLogger.get_logger(__name__
class BBToolsRunner(BaseRunner):
@@ -25,7 +25,7 @@ Description: use bbmap instead of bbtools
metrics = {}
def __init__(self):
-@@ -80,7 +80,7 @@
+@@ -80,7 +80,7 @@ class BBToolsRunner(BaseRunner):
def parse_output(self):
@@ -36,7 +36,7 @@ Description: use bbmap instead of bbtools
for line in lines:
--- a/src/busco/BuscoConfig.py
+++ b/src/busco/BuscoConfig.py
-@@ -69,7 +69,7 @@
+@@ -70,7 +70,7 @@ class BaseConfig(ConfigParser, metaclass
"new_species.pl",
"optimize_augustus.pl",
"hmmsearch",
=====================================
debian/patches/fix-and-disable-tests.patch
=====================================
@@ -4,7 +4,7 @@ Author: Nilesh Patra <nilesh at debian.org>
Last-Update: 2021-07-02
--- a/tests/unittests/AutoLineage_unittests.py
+++ b/tests/unittests/AutoLineage_unittests.py
-@@ -45,7 +45,7 @@
+@@ -45,7 +45,7 @@ class TestAutoLineage(unittest.TestCase)
mock_run_lineages_list.assert_has_calls(calls, any_order=True)
@patch("busco.AutoLineage.logger.info")
@@ -13,7 +13,7 @@ Last-Update: 2021-07-02
@patch("busco.ConfigManager.BuscoConfigAuto", autospec=True)
def test_run_lineages_initializes_BuscoConfigAuto(self, mock_config_auto, *args):
config_manager = BuscoConfigManager({})
-@@ -71,9 +71,10 @@
+@@ -71,9 +71,10 @@ class TestAutoLineage(unittest.TestCase)
]
mock_config_auto.assert_has_calls(calls, any_order=True)
@@ -26,7 +26,7 @@ Last-Update: 2021-07-02
def test_run_lineages_initializes_BuscoRunner(
self, mock_runner, mock_config_auto, *args
):
-@@ -89,7 +90,7 @@
+@@ -89,7 +90,7 @@ class TestAutoLineage(unittest.TestCase)
@patch("busco.AutoLineage.logger.info")
@patch("busco.BuscoConfig.BuscoConfigAuto", autospec=True)
@patch("busco.ConfigManager.BuscoConfigManager")
@@ -35,7 +35,7 @@ Last-Update: 2021-07-02
def test_run_lineages_runs_analysis(self, mock_runner, mock_config_manager, *args):
asl = AutoLineage.AutoSelectLineage(mock_config_manager.config_main)
test_lineages = ["a", "b", "c"]
-@@ -103,7 +104,7 @@
+@@ -103,7 +104,7 @@ class TestAutoLineage(unittest.TestCase)
@patch("busco.AutoLineage.logger.info")
@patch("busco.BuscoConfig.BuscoConfigAuto", autospec=True)
@patch("busco.ConfigManager.BuscoConfigManager")
@@ -44,7 +44,7 @@ Last-Update: 2021-07-02
def test_run_lineages_returns_runners(
self, mock_runner, mock_config_manager, *args
):
-@@ -123,7 +124,7 @@
+@@ -123,7 +124,7 @@ class TestAutoLineage(unittest.TestCase)
@patch("busco.AutoLineage.logger.info")
@patch("busco.BuscoConfig.BuscoConfigAuto", autospec=True)
@@ -53,7 +53,7 @@ Last-Update: 2021-07-02
@patch("busco.ConfigManager.BuscoConfigManager")
def test_record_results_first_run(self, mock_config_manager, *args):
asl = AutoLineage.AutoSelectLineage(mock_config_manager.config_main)
-@@ -137,7 +138,7 @@
+@@ -137,7 +138,7 @@ class TestAutoLineage(unittest.TestCase)
@patch("busco.AutoLineage.logger.info")
@patch("busco.BuscoConfig.BuscoConfigAuto", autospec=True)
@@ -62,7 +62,7 @@ Last-Update: 2021-07-02
@patch("busco.ConfigManager.BuscoConfigManager")
def test_record_results_multiple_runs(self, mock_config_manager, *args):
asl = AutoLineage.AutoSelectLineage(mock_config_manager.config_main)
-@@ -261,7 +262,7 @@
+@@ -261,7 +262,7 @@ class TestAutoLineage(unittest.TestCase)
@patch("busco.AutoLineage.logger.info")
@patch("busco.BuscoRunner.AnalysisRunner.set_parent_dataset")
@patch("busco.AutoLineage.AutoSelectLineage.cleanup_disused_runs")
@@ -73,7 +73,7 @@ Last-Update: 2021-07-02
self, mock_config_manager, fake_modedict, mock_cleanup, *args
--- a/tests/unittests/BuscoConfig_unittests.py
+++ b/tests/unittests/BuscoConfig_unittests.py
-@@ -400,7 +400,7 @@
+@@ -403,7 +403,7 @@ class TestBuscoConfig(unittest.TestCase)
config.configure()
config._check_evalue()
@@ -82,7 +82,7 @@ Last-Update: 2021-07-02
def test_evalue_default(self, mock_logger):
self.test_params["evalue"] = 0.001
self.test_params["lineage_dataset"] = "test"
-@@ -447,7 +447,7 @@
+@@ -450,7 +450,7 @@ class TestBuscoConfig(unittest.TestCase)
)
@patch(
@@ -91,7 +91,7 @@ Last-Update: 2021-07-02
)
def test_batch_mode_true(self, *args):
config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)
-@@ -457,10 +457,10 @@
+@@ -460,10 +460,10 @@ class TestBuscoConfig(unittest.TestCase)
config.set.assert_has_calls(calls)
@patch(
@@ -104,7 +104,7 @@ Last-Update: 2021-07-02
)
def test_batch_mode_false_with_file(self, *args):
config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)
-@@ -468,10 +468,10 @@
+@@ -471,10 +471,10 @@ class TestBuscoConfig(unittest.TestCase)
config._check_batch_mode()
@patch(
@@ -117,7 +117,7 @@ Last-Update: 2021-07-02
)
def test_batch_mode_false_with_error(self, *args):
config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)
-@@ -489,14 +489,14 @@
+@@ -492,14 +492,14 @@ class TestBuscoConfig(unittest.TestCase)
with self.assertRaises(BuscoConfig.BatchFatalError):
config._check_required_input_exists()
@@ -136,7 +136,7 @@ Last-Update: 2021-07-02
config.configure()
--- a/tests/unittests/ConfigManager_unittests.py
+++ b/tests/unittests/ConfigManager_unittests.py
-@@ -49,18 +49,18 @@
+@@ -49,18 +49,18 @@ class TestConfigManager(unittest.TestCas
config_manager.config_file, os.environ.get("BUSCO_CONFIG_FILE")
)
@@ -161,7 +161,7 @@ Last-Update: 2021-07-02
config_manager = ConfigManager.BuscoConfigManager(self.params)
--- a/tests/unittests/run_BUSCO_unittests.py
+++ b/tests/unittests/run_BUSCO_unittests.py
-@@ -58,31 +58,6 @@
+@@ -58,31 +58,6 @@ class TestParams(unittest.TestCase):
sys.stdout = sys.__stdout__
self.assertEqual(cm.exception.code, 0)
@@ -195,7 +195,7 @@ Last-Update: 2021-07-02
correct_parse = {
--- a/tests/unittests/GenomeAnalysis_unittests.py
+++ b/tests/unittests/GenomeAnalysis_unittests.py
-@@ -63,7 +63,7 @@
+@@ -61,7 +61,7 @@ class TestConfigManager(unittest.TestCas
"busco.analysis.GenomeAnalysis.BuscoAnalysis.config.get",
return_value="euk_genome_met",
)
@@ -204,7 +204,7 @@ Last-Update: 2021-07-02
@patch("busco.analysis.GenomeAnalysis.BBToolsRunner")
@patch("busco.analysis.GenomeAnalysis.MetaeukRunner")
@patch("busco.analysis.BuscoAnalysis.HMMERRunner")
-@@ -81,7 +81,7 @@
+@@ -80,7 +80,7 @@ class TestConfigManager(unittest.TestCas
"busco.analysis.GenomeAnalysis.BuscoAnalysis.config.get",
return_value="prok_genome",
)
@@ -213,7 +213,7 @@ Last-Update: 2021-07-02
@patch("busco.analysis.GenomeAnalysis.BBToolsRunner")
@patch("busco.analysis.GenomeAnalysis.ProdigalRunner")
@patch("busco.analysis.BuscoAnalysis.HMMERRunner")
-@@ -99,7 +99,7 @@
+@@ -99,7 +99,7 @@ class TestConfigManager(unittest.TestCas
"busco.analysis.GenomeAnalysis.BuscoAnalysis.config.get",
return_value="euk_genome_met",
)
=====================================
debian/patches/python3.12-syntax.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Fix python3.12 string
+Bug-Debian: https://bugs.debian.org/1085372
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2024-12-05
+
+--- a/src/busco/busco_tools/miniprot.py
++++ b/src/busco/busco_tools/miniprot.py
+@@ -197,7 +197,7 @@ class MiniprotAlignRunner(MiniprotRunner
+ frameshift_events, frameshift_lengths = self.decode_cigar(self.cigar_seq)
+ sta_line = gff.readline()
+ sta_seq = sta_line.strip().split("\t")[1]
+- self.ata_seq = re.sub("\*", "", sta_seq.upper())
++ self.ata_seq = re.sub(r"\*", "", sta_seq.upper())
+
+ self.busco_matches[busco_id].add(gene_id)
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
fix-and-disable-tests.patch
find-bbmap-instead-of-bbtools.patch
+python3.12-syntax.patch
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/da9ea3ce9f51a4c9eb2aa454f82f216625e7f447...f9cef1e20e1e95c71cd80c2552ac3005326bd842
--
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/da9ea3ce9f51a4c9eb2aa454f82f216625e7f447...f9cef1e20e1e95c71cd80c2552ac3005326bd842
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