[med-svn] [Git][med-team/snakemake][debian-v7] Tests: put the cache somewhere we're allowed to write to.

[Rebecca N. Palmer (@rnpalmer-guest)]

Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake


Commits:
8c8b0eaa by Rebecca N. Palmer at 2024-08-05T21:42:39+01:00
Tests: put the cache somewhere we're allowed to write to.

- - - - -


3 changed files:

- debian/changelog
- debian/patches/cancelscript_debug.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+snakemake (7.32.4-4+ppa3) unstable; urgency=medium
+
+  * Tests: put the cache somewhere we're allowed to write to.
+
+ -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Mon, 05 Aug 2024 21:41:16 +0100
+
 snakemake (7.32.4-4+ppa2) unstable; urgency=medium
 
   * Tests: ignore nocheck to get a log on riscv64.


=====================================
debian/patches/cancelscript_debug.patch
=====================================
@@ -5,6 +5,16 @@ Description: Extra debug output from test_cluster_cancel*
 Author: Rebecca N. Palmer <rebecca_palmer at zoho.com>
 Forwarded: not-needed
 
+--- a/snakemake/sourcecache.py
++++ b/snakemake/sourcecache.py
+@@ -350,6 +350,7 @@ class SourceCache:
+         self.cache = Path(
+             os.path.join(get_appdirs().user_cache_dir, "snakemake/source-cache")
+         )
++        print("cache path", self.cache)
+         os.makedirs(self.cache, exist_ok=True)
+         if runtime_cache_path is None:
+             runtime_cache_parent = self.cache / "runtime-cache"
 --- a/tests/common.py
 +++ b/tests/common.py
 @@ -204,6 +204,7 @@ def run(


=====================================
debian/rules
=====================================
@@ -51,8 +51,9 @@ export SPHINXBUILD=/usr/share/sphinx/scripts/python3/sphinx-build
 execute_after_dh_auto_build:
 	PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) \
 	cd docs && LC_ALL=C.UTF-8 LANGUAGE=C.UTF-8 make html
+	mkdir $(shell pybuild --print build_dir --interpreter python3)/snakemaketmp000
 	chmod +x $(shell pybuild --print build_dir --interpreter python3)/../../../bin/snakemake; cp -r $(shell pybuild --print build_dir --interpreter python3)/../../../bin $(shell pybuild --print build_dir --interpreter python3)/../../../tests $(shell pybuild --print build_dir --interpreter python3)
-	. /etc/profile.d/modules.sh && python3.12 -m pytest -o faulthandler_timeout=60 -v $(shell pybuild --print build_dir --interpreter python3)/tests/test*.py -k 'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_deploy_hashing and not test_peppy and not test_modules_peppy and not test_report_display_code and not test_wrapper_local_git_prefix and not test_github_issue1396 and not test_az_batch_executor and not test_modules_prefix and not test_ancient and not test_github_issue1062 and not test_symlink_time_handling and not test_env_modules and not test_github_issue1460 and not test_rule_inheritance_globals and not test_prebuilt_conda_script and not test_persistent_dict and not test_issue328' || true
+	. /etc/profile.d/modules.sh && HOME=$(shell pybuild --print build_dir --interpreter python3)/snakemaketmp000 python3.12 -m pytest -o faulthandler_timeout=60 -v $(shell pybuild --print build_dir --interpreter python3)/tests/test*.py -k 'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_deploy_hashing and not test_peppy and not test_modules_peppy and not test_report_display_code and not test_wrapper_local_git_prefix and not test_github_issue1396 and not test_az_batch_executor and not test_modules_prefix and not test_ancient and not test_github_issue1062 and not test_symlink_time_handling and not test_env_modules and not test_github_issue1460 and not test_rule_inheritance_globals and not test_prebuilt_conda_script and not test_persistent_dict and not test_issue328' || true
 
 execute_after_dh_installdocs:
 	find debian -name '__pycache__' -o name '.gitignore' | xargs rm -rf



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/8c8b0eaa387a94736e7279ab05f1ab01cf81fdec

-- 
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/8c8b0eaa387a94736e7279ab05f1ab01cf81fdec
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