[med-svn] [Git][med-team/snakemake][debian-v7] Fix config schema loading from local files. (Closes: #1141070)

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

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 <rebecca_palmer at zoho.com>  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 <rebecca_palmer at zoho.com>
+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
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