[med-svn] [Git][med-team/toil][master] 2 commits: d/patches/setting_version.patch: update for Python 3.12

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / toil


Commits:
e349225a by Michael R. Crusoe at 2024-11-15T01:41:17+01:00
d/patches/setting_version.patch: update for Python 3.12

- - - - -
26e4087e by Michael R. Crusoe at 2024-11-15T01:41:19+01:00
WIP

- - - - -


5 changed files:

- debian/changelog
- + debian/patches/fix_tests
- debian/patches/series
- debian/patches/setting_version.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -9,6 +9,7 @@ toil (7.0.0-1) UNRELEASED; urgency=medium
   * d/patches/needs_aws-proxyfix: Fix build due to purposely invalid
     proxy configuration.
   * d/rules: skip online tests
+  * d/patches/setting_version.patch: update for Python 3.12
 
  -- Michael R. Crusoe <crusoe at debian.org>  Mon, 27 May 2024 08:45:55 +0200
 


=====================================
debian/patches/fix_tests
=====================================
@@ -0,0 +1,11 @@
+--- toil.orig/src/toil/test/provisioners/clusterTest.py
++++ toil/src/toil/test/provisioners/clusterTest.py
+@@ -34,7 +34,7 @@
+ class AbstractClusterTest(ToilTest):
+     def __init__(self, methodName: str) -> None:
+         super().__init__(methodName=methodName)
+-        self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa'
++        self.keyName = os.getenv('TOIL_AWS_KEYNAME', 'id_rsa').strip()
+         self.clusterName = f'aws-provisioner-test-{uuid4()}'
+         self.leaderNodeType = 't2.medium'
+         self.clusterType = 'mesos'


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+fix_tests
 needs_aws-proxyfix
 skip-mypy-boto3
 soften-configargparser-deps


=====================================
debian/patches/setting_version.patch
=====================================
@@ -15,12 +15,12 @@ copy/update that field manually
 +baseVersion = '7.0.0'
 +cgcloudVersion = '1.6.0a1.dev393'
 +version = '7.0.0-d569ea5711eb310ffd5703803f7250ebf7c19576'
-+cacheTag = 'cache-local-py3.11'
-+mainCacheTag = 'cache-master-py3.11'
++cacheTag = 'cache-local-py3.12'
++mainCacheTag = 'cache-master-py3.12'
 +distVersion = '7.0.0'
 +exactPython = 'python3.12'
 +python = 'python3.12'
-+dockerTag = '7.0.0-d569ea5711eb310ffd5703803f7250ebf7c19576-py3.11'
++dockerTag = '7.0.0-d569ea5711eb310ffd5703803f7250ebf7c19576-py3.12'
 +currentCommit = 'd569ea5711eb310ffd5703803f7250ebf7c19576'
 +dockerRegistry = 'quay.io/ucsc_cgl'
 +dockerName = 'toil'


=====================================
debian/rules
=====================================
@@ -23,7 +23,7 @@ override_dh_auto_install:
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	PYBUILD_SYSTEM=custom \
-		PYBUILD_TEST_ARGS='TOIL_SKIP_ONLINE=true HOME={home_dir} {interpreter} setup.py develop --user && PYTHONPATH={dir}/src:$$PYTHONPATH PATH={home_dir}/.local/bin/:$$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True {interpreter} -m pytest -n auto --dist loadscope -vv -W ignore --ignore src/toil/test/lib/aws/test_s3.py --ignore src/toil/test/provisioners/aws/awsProvisionerTest.py --ignore src/toil/test/wdl/wdltoil_test.py --ignore src/toil/test/cwl/cwlTest.py --ignore src/toil/test/src/promisedRequirementTest.py --ignore src/toil/test/lib/test_ec2.py --ignore src/toil/test/batchSystems/batchSystemTest.py --ignore src/toil/test/lib/aws/test_iam.py -k "not (test_bioconda or test_run_conformance or testImportFtpFile or ToilWdlIntegrationTest or SortTest or testCwlexample or testVirtualEnv or ToilDocumentationTest or test_cwl_toil_kill or testImportReadFileCompatibility or CleanWorkDirTest or DeferredFunctionTest or WdlToilTest or test_cactus_integration)" {dir}/src/toil/test' \
+		PYBUILD_TEST_ARGS='TOIL_SKIP_ONLINE=true HOME={home_dir} {interpreter} setup.py develop --user && PYTHONPATH={dir}/src:$$PYTHONPATH PATH={home_dir}/.local/bin/:$$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True {interpreter} -m pytest -n auto --dist loadscope -vv -W ignore --ignore src/toil/test/lib/aws/test_s3.py --ignore src/toil/test/provisioners/aws/awsProvisionerTest.py --ignore src/toil/test/wdl/wdltoil_test.py --ignore src/toil/test/cwl/cwlTest.py --ignore src/toil/test/src/promisedRequirementTest.py --ignore src/toil/test/lib/test_ec2.py --ignore src/toil/test/batchSystems/batchSystemTest.py --ignore src/toil/test/lib/aws/test_iam.py --ignore  src/toil/test/provisioners/clusterTest.py --ignore src/toil/test/wdl/wdltoil_test_kubernetes.py --ignore src/toil/test/cactus/test_cactus_integration.py -k "not (test_bioconda or test_run_conformance or testImportFtpFile or ToilWdlIntegrationTest or SortTest or testCwlexample or testVirtualEnv or ToilDocumentationTest or test_cwl_toil_kill or testImportReadFileCompatibility or CleanWorkDirTest or DeferredFunctionTest or WdlToilTest or ToilKillTestWithAWSJobStore)" {dir}/src/toil/test' \
 		dh_auto_test
 endif
 



View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/839d3645fc477d9ea7357672b1ccfa5eb47f7de6...26e4087ef6787c28061336c77ed51ac6b36d36ce

-- 
View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/839d3645fc477d9ea7357672b1ccfa5eb47f7de6...26e4087ef6787c28061336c77ed51ac6b36d36ce
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