Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake
Commits: 2316ca65 by Rebecca N. Palmer at 2026-07-01T21:32:36+01:00 Fix config schema loading from local files. (Closes: #1141070) - - - - - 4 changed files: - debian/changelog - debian/patches/series - + debian/patches/urljoin_slashes.patch - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,6 +1,7 @@ snakemake (7.32.4-12) UNRELEASED; urgency=medium * Re-enable R/rpy2 tests. + * Fix config schema loading from local files. (Closes: #1141070) -- Rebecca N. Palmer <[email protected]> Wed, 01 Jul 2026 19:45:01 +0100 ===================================== debian/patches/series ===================================== @@ -23,3 +23,4 @@ test_extra_time.patch no_pkg_resources.patch numpy2compat.patch graphviz_compat.patch +urljoin_slashes.patch ===================================== debian/patches/urljoin_slashes.patch ===================================== @@ -0,0 +1,17 @@ +Description: Include the /// in file: config URLs + +Author: Rebecca N. Palmer <[email protected]> +Bug-Debian: https://bugs.debian.org/1141070 +Forwarded: no + +--- snakemake-7.32.4.orig/snakemake/utils.py ++++ snakemake-7.32.4/snakemake/utils.py +@@ -68,7 +68,7 @@ def validate(data, schema, set_default=T + schema = _load_configfile(source, filetype="Schema") + if isinstance(schemafile, LocalSourceFile): + resolver = RefResolver( +- urljoin("file:", schemafile.get_path_or_uri()), ++ urljoin("file://", schemafile.get_path_or_uri()), + schema, + handlers={ + "file": lambda uri: _load_configfile(re.sub("^file://", "", uri)) ===================================== debian/rules ===================================== @@ -47,7 +47,9 @@ export SPHINXBUILD=/usr/share/sphinx/scripts/python3/sphinx-build dh $@ --with sphinxdoc --buildsystem=pybuild # LC_ALL is for reproducibility +# the first python3 is a test related to #1141070 (in trixie/python3.13, both of these get a triple slash) execute_after_dh_auto_build: + python3 -c "import urllib.parse;print(urllib.parse.urljoin('file:','/b/a.html'),urllib.parse.urljoin('file://','/b/a.html'))" PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) \ cd docs && LC_ALL=C.UTF-8 LANGUAGE=C.UTF-8 make html View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/2316ca65fe222a35f23ab26ae1799e0ba6e31824 -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/2316ca65fe222a35f23ab26ae1799e0ba6e31824 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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