[med-svn] [Git][med-team/busco][master] 3 commits: Adapt patches to new upstream version
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Oct 21 12:03:09 BST 2026
Andreas Tille pushed to branch master at Debian Med / busco
Commits:
3052f704 by Andreas Tille at 2026-10-21T12:56:11+02:00
Adapt patches to new upstream version
- - - - -
539d8672 by Andreas Tille at 2026-10-21T12:56:18+02:00
Fix dh-python FTBFS caused by tests build directory (Closes: #1151393)
- - - - -
5598c0a6 by Andreas Tille at 2026-10-21T13:00:48+02:00
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/patches/find-bbmap-instead-of-bbtools.patch
- debian/patches/fix-and-disable-tests.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,13 @@
-busco (6.1.0-1) UNRELEASED; urgency=medium
+busco (6.1.0-1) unstable; urgency=medium
- * Packaging update (routine-update)
* New upstream version
+ * Adapt patches to new upstream version.
+ * Do not leave a tests symlink in the pybuild build directory, fixing
+ the dh-python FTBFS.
+ Closes: #1151393
* Remove unused entry from debian/source/include-binaries.
- -- Andreas Tille <tille at debian.org> Wed, 21 Oct 2026 11:49:50 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 21 Oct 2026 12:57:01 +0200
busco (6.0.0-1) unstable; urgency=medium
=====================================
debian/patches/find-bbmap-instead-of-bbtools.patch
=====================================
@@ -1,5 +1,6 @@
Author: Nilesh Patra
-Last-Update: 2022-07-29
+Last-Update: 2026-10-21
+Assisted-By: opencode/deepseek-v4.1-flash-free
Description: use bbmap instead of bbtools
--- a/config/config.ini
@@ -36,7 +37,7 @@ Description: use bbmap instead of bbtools
for line in lines:
--- a/src/busco/BuscoConfig.py
+++ b/src/busco/BuscoConfig.py
-@@ -92,7 +92,7 @@ class BaseConfig(ConfigParser, metaclass
+@@ -101,7 +101,7 @@ class BaseConfig(ConfigParser, metaclass=ABCMeta):
"new_species.pl",
"optimize_augustus.pl",
"hmmsearch",
=====================================
debian/patches/fix-and-disable-tests.patch
=====================================
@@ -1,96 +1,10 @@
-Description: Replace __main__ calls with proper busco imports, skipping test_run_lineages_initializes_BuscoRunner
- for now as this fails with a Mock iterable problem
+Description: Skip tests that cannot work in the Debian build environment
+ test_list_lineages requires network access to download the lineage list and
+ test_direct_download_action_called fails because argparse probes attributes
+ that the autospec Mock does not provide.
Author: Nilesh Patra <nilesh at debian.org>
-Last-Update: 2021-07-02
---- a/tests/unittests/BuscoConfig_unittests.py
-+++ b/tests/unittests/BuscoConfig_unittests.py
-@@ -410,7 +410,7 @@ class TestBuscoConfig(unittest.TestCase)
- self.test_params["evalue"] = 0.001
- self.test_params["lineage_dataset"] = "test"
- with patch(
-- "__main__.BuscoConfig_unittests.BuscoConfig.logger.warning"
-+ "busco.BuscoConfig_unittests.BuscoConfig.logger.warning"
- ) as mock_logger:
- config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)
- config.configure()
-@@ -455,7 +455,7 @@ class TestBuscoConfig(unittest.TestCase)
- )
-
- @patch(
-- "__main__.BuscoConfig_unittests.BuscoConfig.os.path.isdir", return_value=True
-+ "busco.BuscoConfig.os.path.isdir", return_value=True
- )
- def test_batch_mode_true(self, *args):
- config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)
-@@ -465,10 +465,10 @@ class TestBuscoConfig(unittest.TestCase)
- config.set.assert_has_calls(calls)
-
- @patch(
-- "__main__.BuscoConfig_unittests.BuscoConfig.os.path.isdir", return_value=False
-+ "busco.BuscoConfig.os.path.isdir", return_value=False
- )
- @patch(
-- "__main__.BuscoConfig_unittests.BuscoConfig.os.path.isfile", return_value=True
-+ "busco.BuscoConfig.os.path.isfile", return_value=True
- )
- def test_batch_mode_false_with_file(self, *args):
- config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)
-@@ -476,10 +476,10 @@ class TestBuscoConfig(unittest.TestCase)
- config._check_batch_mode()
-
- @patch(
-- "__main__.BuscoConfig_unittests.BuscoConfig.os.path.isdir", return_value=False
-+ "busco.BuscoConfig.os.path.isdir", return_value=False
- )
- @patch(
-- "__main__.BuscoConfig_unittests.BuscoConfig.os.path.isfile", return_value=False
-+ "busco.BuscoConfig.os.path.isfile", return_value=False
- )
- def test_batch_mode_false_with_error(self, *args):
- config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)
-@@ -498,14 +498,14 @@ class TestBuscoConfig(unittest.TestCase)
- with self.assertRaises(BuscoConfig.BuscoConfigError):
- config._check_required_input_exists()
-
-- @patch("__main__.BuscoConfig_unittests.BuscoConfig.BuscoDownloadManager")
-+ @patch("busco.BuscoConfig.BuscoDownloadManager")
- def test_downloader_initialized(self, mock_downloader):
- config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)
- config.configure()
- config._init_downloader()
- mock_downloader.assert_called()
-
-- @patch("__main__.BuscoConfig_unittests.BuscoConfig.PrettyLog")
-+ @patch("busco.BuscoConfig.PrettyLog")
- def test_log_config(self, mock_pretty_log):
- config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)
- config.configure()
---- a/tests/unittests/ConfigManager_unittests.py
-+++ b/tests/unittests/ConfigManager_unittests.py
-@@ -49,9 +49,9 @@ class TestConfigManager(unittest.TestCas
- config_manager.config_file, os.environ.get("BUSCO_CONFIG_FILE")
- )
-
-- @patch("__main__.ConfigManager_unittests.ConfigManager.logger", autospec=True)
-+ @patch("busco.ConfigManager_unittests.ConfigManager.logger", autospec=True)
- @patch(
-- "__main__.ConfigManager_unittests.ConfigManager.BuscoConfigMain", autospec=True
-+ "busco.ConfigManager_unittests.ConfigManager.BuscoConfigMain", autospec=True
- )
- def test_config_main_configured(self, mock_config, *args):
- config_manager = ConfigManager.BuscoConfigManager(self.params)
-@@ -59,9 +59,9 @@ class TestConfigManager(unittest.TestCas
- config_manager.load_busco_config_main()
- mock_config.return_value.configure.assert_called()
-
-- @patch("__main__.ConfigManager_unittests.ConfigManager.logger", autospec=True)
-+ @patch("busco.ConfigManager_unittests.ConfigManager.logger", autospec=True)
- @patch(
-- "__main__.ConfigManager_unittests.ConfigManager.BuscoConfigMain", autospec=True
-+ "busco.ConfigManager_unittests.ConfigManager.BuscoConfigMain", autospec=True
- )
- def test_config_main_validated(self, mock_config, *args):
- config_manager = ConfigManager.BuscoConfigManager(self.params)
+Last-Update: 2026-10-21
+Assisted-By: opencode/deepseek-v4.1-flash-free
--- a/tests/unittests/run_BUSCO_unittests.py
+++ b/tests/unittests/run_BUSCO_unittests.py
@@ -69,44 +69,6 @@ class TestParams(unittest.TestCase):
=====================================
debian/rules
=====================================
@@ -10,5 +10,5 @@ include /usr/share/dpkg/default.mk
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_test -- --before-test="ln -s $(CURDIR)/tests {build_dir}" --test-custom --test-args 'cd {build_dir}/tests && {interpreter} -m unittest unittests.run_BUSCO_unittests -v'
+ dh_auto_test -- --test-custom --test-args 'cd {build_dir}/tests && {interpreter} -m unittest unittests.run_BUSCO_unittests -v'
endif
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/112f385f352e3b07d88e25c50230673f8f0be026...5598c0a6f7b33c774f52abbfa645ab4a6676ed9c
--
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/112f385f352e3b07d88e25c50230673f8f0be026...5598c0a6f7b33c774f52abbfa645ab4a6676ed9c
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