Source: snakemake
Version: 6.9.1+dfsg1-3
Severity: wishlist
Tags: patch
User: reproducible-bui...@lists.alioth.debian.org
Usertags: randomness
X-Debbugs-Cc: reproducible-b...@lists.alioth.debian.org
Hi,
Whilst working on the Reproducible Builds effort [0] we noticed that
snakemake could not be built reproducibly.
This is because it generates and ships a Graphviz .dot file during the
tests and this file has a non-deterministic ordering. Also, the PDF
file generated from this very .dot file contains a created date in its
headers.
Patch attached that fixes the non-determinism in the .dot file
generation and prevents the Debian packaging from shipping the
non-deterministic PDF version.
[0] https://reproducible-builds.org/
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` la...@debian.org / chris-lamb.co.uk
`-
--- a/debian/patches/reproducible-build.patch 1970-01-01 01:00:00.000000000
+0100
--- b/debian/patches/reproducible-build.patch 2021-10-22 09:09:22.433645939
+0100
@@ -0,0 +1,33 @@
+Description: Make the build reproducible
+Author: Chris Lamb <la...@debian.org>
+Last-Update: 2021-10-22
+
+--- snakemake-6.9.1+dfsg1.orig/snakemake/dag.py
++++ snakemake-6.9.1+dfsg1/snakemake/dag.py
+@@ -1781,7 +1781,7 @@ class DAG:
+ huefactor = 2 / (3 * len(self.rules))
+ rulecolor = {
+ rule: "{:.2f} 0.6 0.85".format(i * huefactor)
+- for i, rule in enumerate(self.rules)
++ for i, rule in sorted(enumerate(self.rules))
+ }
+
+ # markup
+@@ -1850,7 +1850,7 @@ class DAG:
+ huefactor = 2 / (3 * len(self.rules))
+ rulecolor = {
+ rule: hsv_to_htmlhexrgb(i * huefactor, 0.6, 0.85)
+- for i, rule in enumerate(self.rules)
++ for i, rule in sorted(enumerate(self.rules))
+ }
+
+ def resolve_input_functions(input_files):
+@@ -1956,7 +1956,7 @@ class DAG:
+ {items}
+ }}\
+ """
+- ).format(items="\n".join(nodes + edges))
++ ).format(items="\n".join(sorted(nodes) + sorted(edges)))
+
+ def summary(self, detailed=False):
+ if detailed:
--- a/debian/patches/series 2021-10-22 09:05:53.731764374 +0100
--- b/debian/patches/series 2021-10-22 09:09:21.661639882 +0100
@@ -9,3 +9,4 @@
fix_test_pytest.patch
python2to3.patch
hack-around-connectionpool.patch
+reproducible-build.patch
--- a/debian/rules 2021-10-22 09:05:53.731764374 +0100
--- b/debian/rules 2021-10-22 09:06:22.120052643 +0100
@@ -28,7 +28,7 @@
# Skipped in build due to network use, but run in autopkgtest: test_ancient
# Tests marked @connected skip themselves in this case
-export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests
{dir}/tests/test_filegraph/.snakemake/ {dir}/tests/linting/*/.snakemake/
+export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests
{dir}/tests/test_filegraph/.snakemake/ {dir}/tests/linting/*/.snakemake/
{dir}/tests/test_filegraph/fg.pdf
export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name
$(PYBUILD_NAME))/bin:$(PATH)
