[med-svn] [Git][med-team/snakemake][debian_for_upstream_5.14.0_which_requires_conda] 4 commits: move python3 fixes to a single patch
Rebecca N. Palmer
gitlab at salsa.debian.org
Thu Apr 9 17:30:09 BST 2020
Rebecca N. Palmer pushed to branch debian_for_upstream_5.14.0_which_requires_conda at Debian Med / snakemake
Commits:
56367974 by Rebecca N. Palmer at 2020-04-09T17:15:09+01:00
move python3 fixes to a single patch
- - - - -
e9fcd301 by Rebecca N. Palmer at 2020-04-09T17:18:45+01:00
Disable buggy test (upstream 322) and tests needing conda or docker.
- - - - -
925c7493 by Rebecca N. Palmer at 2020-04-09T17:20:29+01:00
Delete unused patches.
- - - - -
1cf3a516 by Rebecca N. Palmer at 2020-04-09T17:21:38+01:00
Use boto3 (like upstream) not boto.
- - - - -
12 changed files:
- debian/changelog
- debian/control
- − debian/patches/0004-drop_test_symlink_time_handling.patch
- − debian/patches/0005-drop_test_symlink_temp.patch
- − debian/patches/0007-noop-rate-limiter.patch
- − debian/patches/0010-skip-test-without-rmarkdown.patch
- − debian/patches/boto3_is_just_boto
- − debian/patches/py3_subprocess.patch
- debian/patches/python3 → debian/patches/python3.patch
- debian/patches/series
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -10,6 +10,9 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium
[ Rebecca N. Palmer ]
* Use Python 3 in subprocess calls.
+ * Disable buggy test (upstream 322) and tests needing conda or docker.
+ * Delete unused patches.
+ * Use boto3 (like upstream) not boto.
-- Rebecca N. Palmer <rebecca_palmer at zoho.com> Thu, 09 Apr 2020 14:57:00 +0100
=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: ca-certificates,
imagemagick,
python3,
python3-biopython,
- python3-boto,
+ python3-boto3,
python3-botocore,
python3-configargparse,
python3-datrie,
@@ -71,7 +71,7 @@ Depends: ca-certificates,
Recommends: cwltool,
imagemagick,
python3-biopython,
- python3-boto,
+ python3-boto3,
python3-botocore,
python3-dropbox,
python3-flask,
=====================================
debian/patches/0004-drop_test_symlink_time_handling.patch deleted
=====================================
@@ -1,20 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 13 Dec 2016 16:05:05 +0100
-Bug-Debian: https://bugs.debian.org/845737
-Description: Ignore failures of test that might happpen in pbuilder
-
---- a/tests/tests.py
-+++ b/tests/tests.py
-@@ -371,7 +371,11 @@ def test_input_generator():
- def test_symlink_time_handling():
- #See Snakefile for notes on why this fails on some systems
- if os.utime in os.supports_follow_symlinks:
-- run(dpath("test_symlink_time_handling"))
-+ try:
-+ run(dpath("test_symlink_time_handling"))
-+ except:
-+ # skip this test that might fail when building in a pbuilder chroot
-+ pass
-
-
- def test_issue328():
=====================================
debian/patches/0005-drop_test_symlink_temp.patch deleted
=====================================
@@ -1,21 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 13 Dec 2016 16:05:05 +0100
-Bug-Debian: https://bugs.debian.org/848820
-Description: Ignore failures of test that might happpen in pbuilder
- .
- According to upstream this is fixed in commit d697f23
- so the patch is deactivated
-
---- a/tests/tests.py
-+++ b/tests/tests.py
-@@ -308,10 +308,6 @@
- cluster_sync="./qsub")
-
-
--def test_symlink_temp():
-- run(dpath("test_symlink_temp"), shouldfail=True)
--
--
- def test_empty_include():
- run(dpath("test_empty_include"))
-
=====================================
debian/patches/0007-noop-rate-limiter.patch deleted
=====================================
@@ -1,36 +0,0 @@
-Author: Christian Amsüss <chrysn at fsfe.org>
-Last-Update: Tue, 14 Nov 2017 09:28:21 CET +0100
-Description: Temporary workaround for missing ratelimiter package (#880661).
- This removes functionality and should not be left in for the package for a
- released version, but eases fixing the build failures.
-
---- a/snakemake/executors.py
-+++ b/snakemake/executors.py
-@@ -405,7 +405,11 @@
- exec_job=None,
- assume_shared_fs=True,
- max_status_checks_per_second=1):
-- from ratelimiter import RateLimiter
-+
-+ import contextlib
-+ @contextlib.contextmanager
-+ def _cm(): yield
-+ RateLimiter = lambda *args, **wkargs: _cm()
-
- local_input = local_input or []
- super().__init__(workflow, dag,
---- a/snakemake/scheduler.py
-+++ b/snakemake/scheduler.py
-@@ -61,7 +61,11 @@
- force_use_threads=False,
- assume_shared_fs=True):
- """ Create a new instance of KnapsackJobScheduler. """
-- from ratelimiter import RateLimiter
-+
-+ import contextlib
-+ @contextlib.contextmanager
-+ def _cm(): yield
-+ RateLimiter = lambda *args, **wkargs: _cm()
-
- self.cluster = cluster
- self.cluster_config = cluster_config
=====================================
debian/patches/0010-skip-test-without-rmarkdown.patch deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/patches/boto3_is_just_boto deleted
=====================================
@@ -1,35 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: In Debian, boto3 is just boto
---- snakemake.orig/snakemake/remote/S3.py
-+++ snakemake/snakemake/remote/S3.py
-@@ -16,7 +16,7 @@
-
- try:
- # third-party modules
-- import boto3
-+ import boto as boto3
- import botocore
- except ImportError as e:
- raise WorkflowError(
---- snakemake.orig/snakemake/remote/S3Mocked.py
-+++ snakemake/snakemake/remote/S3Mocked.py
-@@ -22,7 +22,7 @@
-
- try:
- # third-party
-- import boto3
-+ import boto as boto3
- from moto import mock_s3
- except ImportError as e:
- raise WorkflowError(
---- snakemake.orig/tests/test_static_remote/S3MockedForStaticTest.py
-+++ snakemake/tests/test_static_remote/S3MockedForStaticTest.py
-@@ -20,7 +20,7 @@
-
- try:
- # third-party
-- import boto3
-+ import boto as boto3
- from moto import mock_s3
- import filechunkio
- except ImportError as e:
=====================================
debian/patches/py3_subprocess.patch deleted
=====================================
@@ -1,29 +0,0 @@
-Description: Use Python 3 in subprocess calls
-
-TODO - are any of the ones in snakemake/script.py:execute_script a problem?
-
-Author: Rebecca N. Palmer <rebecca_palmer at zoho.com>
-Forwarded: no
-
---- snakemake-5.14.0.orig/tests/test_linting.py
-+++ snakemake-5.14.0/tests/test_linting.py
-@@ -18,7 +18,7 @@ def test_lint(lint, case):
- out = (
- sp.check_output(
- [
-- "python",
-+ "python3",
- "-m",
- "snakemake",
- "--lint",
---- snakemake-5.14.0.orig/tests/test_tibanna.py
-+++ snakemake-5.14.0/tests/test_tibanna.py
-@@ -8,7 +8,7 @@ from common import *
- # run tibanna test before any moto-related tests because they apparently render AWS environment variables invalid or uneffective.
- def test_tibanna():
- workdir = dpath("test_tibanna")
-- subprocess.check_call(["python", "cleanup.py"], cwd=workdir)
-+ subprocess.check_call(["python3", "cleanup.py"], cwd=workdir)
-
- os.environ["TEST_ENVVAR1"] = "test"
- os.environ["TEST_ENVVAR2"] = "test"
=====================================
debian/patches/python3 → debian/patches/python3.patch
=====================================
@@ -1,5 +1,10 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
-Subject: Use python3 instead of python
+Description: Use Python 3 in subprocess calls
+
+TODO - are any of the ones in snakemake/script.py:execute_script a problem?
+
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>, Rebecca N. Palmer <rebecca_palmer at zoho.com>
+Forwarded: no
+
--- a/tests/test_delete_all_output/Snakefile
+++ b/tests/test_delete_all_output/Snakefile
@@ -8,9 +8,9 @@ rule delete_all_output:
@@ -59,3 +64,25 @@ Subject: Use python3 instead of python
shell:
- "python -m snakemake --cores 1 --profile . -s Snakefile.internal"
+ "python3 -m snakemake --cores 1 --profile . -s Snakefile.internal"
+--- a/tests/test_linting.py
++++ b/tests/test_linting.py
+@@ -18,7 +18,7 @@ def test_lint(lint, case):
+ out = (
+ sp.check_output(
+ [
+- "python",
++ "python3",
+ "-m",
+ "snakemake",
+ "--lint",
+--- a/tests/test_tibanna.py
++++ b/tests/test_tibanna.py
+@@ -8,7 +8,7 @@ from common import *
+ # run tibanna test before any moto-related tests because they apparently render AWS environment variables invalid or uneffective.
+ def test_tibanna():
+ workdir = dpath("test_tibanna")
+- subprocess.check_call(["python", "cleanup.py"], cwd=workdir)
++ subprocess.check_call(["python3", "cleanup.py"], cwd=workdir)
+
+ os.environ["TEST_ENVVAR1"] = "test"
+ os.environ["TEST_ENVVAR2"] = "test"
=====================================
debian/patches/series
=====================================
@@ -1,15 +1,9 @@
0001-Use-the-inbuild-sphinx.ext.napoleon.patch
0003-Use-debian-s-mathjax-package.patch
0003-Compat-fix.patch
-# 0004-drop_test_symlink_time_handling.patch
-# 0005-drop_test_symlink_temp.patch - should be fixed in commit d697f23
0006-restore-bin.patch
-# 0007-noop-rate-limiter.patch - broken and obsolete with https://bugs.debian.org/880661
0008-remove_sphinx.ext.patch
0009-skip-test-without-google-cloud-sdk.patch
-# 0010-skip-test-without-rmarkdown.patch
0011-fix-privacy-breach.patch
-boto3_is_just_boto
-python3
+python3.patch
workaround_sphinx_issue.patch
-py3_subprocess.patch
=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@ export HOME=$(CURDIR)/fakehome
export PYBUILD_NAME=snakemake
export PYBUILD_DESTDIR_python3=debian/snakemake
export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}
-export PYBUILD_TEST_ARGS=python{version} -m pytest tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules'
+export PYBUILD_TEST_ARGS=python{version} -m pytest tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_cluster_sync'
# test_report
# test_ancient
@@ -19,6 +19,9 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest tests/test*.py -n auto -k 'no
# test_issue1093 fails due to conda usage; commenting that out and installing bwa produces a different ordering than desired
# test_default_resources and test_remote needs moto to be packaged https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=777089
# test_env_modules relies on "module load" which is not packaged for Debian
+# test_archive uses conda
+# test_container uses docker://bash
+# test_cluster_sync is broken (https://github.com/snakemake/snakemake/issues/322)
export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests {dir}/tests/test_filegraph/.snakemake/
=====================================
debian/tests/run-unit-test
=====================================
@@ -17,5 +17,5 @@ cd "${AUTOPKGTEST_TMP}"
export HOME="${AUTOPKGTEST_TMP}"
-python3 -m pytest ${ROOT}/tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules'
+python3 -m pytest ${ROOT}/tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_cluster_sync'
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46
--
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46
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