Your message dated Fri, 06 Sep 2019 04:07:05 +0000
with message-id <[email protected]>
and subject line Bug#932116: fixed in snakemake 5.5.4-1
has caused the Debian Bug report #932116,
regarding snakemake: please make the build reproducible
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
932116: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=932116
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: snakemake
Version: 5.5.3-1
Severity: wishlist
Tags: patch
User: [email protected]
Usertags: buildpath
X-Debbugs-Cc: [email protected]
Hi,
Whilst working on the Reproducible Builds effort [0], we noticed
that snakemake could not be built reproducibly.
This is because it encoded the absolute buildpath in a Python keyword
argument which, when rendered in the documention, made the package
contents change when built from different locations.
Patch attached.
[0] https://reproducible-builds.org/
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` [email protected] / chris-lamb.co.uk
`-
--- a/debian/patches/0012-reproducible-build.patch 1969-12-31
21:00:00.000000000 -0300
--- b/debian/patches/0012-reproducible-build.patch 2019-07-15
09:24:36.994818005 -0300
@@ -0,0 +1,40 @@
+Description: Make the build reproducible
+Author: Chris Lamb <[email protected]>
+Last-Update: 2019-07-15
+
+--- snakemake-5.5.3.orig/snakemake/report/__init__.py
++++ snakemake-5.5.3/snakemake/report/__init__.py
+@@ -98,10 +98,12 @@ def data_uri_from_file(file, defaultenc=
+
+
+ def report(text, path,
+- stylesheet=os.path.join(os.path.dirname(__file__), "report.css"),
++ stylesheet=None,
+ defaultenc="utf8",
+ template=None,
+ metadata=None, **files):
++ if stylesheet is None:
++ stylesheet = os.path.join(os.path.dirname(__file__), "report.css")
+ outmime, _ = mimetypes.guess_type(path)
+ if outmime != "text/html":
+ raise ValueError("Path to report output has to be an HTML file.")
+--- snakemake-5.5.3.orig/snakemake/utils.py
++++ snakemake-5.5.3/snakemake/utils.py
+@@ -189,7 +189,7 @@ def makedirs(dirnames):
+
+
+ def report(text, path,
+- stylesheet=os.path.join(os.path.dirname(__file__), "report.css"),
++ stylesheet=None,
+ defaultenc="utf8",
+ template=None,
+ metadata=None, **files):
+@@ -233,6 +233,8 @@ def report(text, path,
+ metadata (str): E.g. an optional author name or email address.
+
+ """
++ if stylesheet is None:
++ stylesheet = os.path.join(os.path.dirname(__file__), "report.css")
+ try:
+ import snakemake.report
+ except ImportError:
--- a/debian/patches/series 2019-07-15 09:11:32.053668609 -0300
--- b/debian/patches/series 2019-07-15 09:24:34.722883985 -0300
@@ -9,3 +9,4 @@
0009-skip-test-without-google-cloud-sdk.patch
# 0010-skip-test-without-rmarkdown.patch
0011-fix-privacy-breach.patch
+0012-reproducible-build.patch
--- End Message ---
--- Begin Message ---
Source: snakemake
Source-Version: 5.5.4-1
We believe that the bug you reported is fixed in the latest version of
snakemake, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <[email protected]> (supplier of updated snakemake
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 31 Jul 2019 11:24:24 +0200
Source: snakemake
Architecture: source
Version: 5.5.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 932116 933527
Changes:
snakemake (5.5.4-1) unstable; urgency=medium
.
[ Dylan Aïssi ]
* Apply patch from Chris Lamb to make the build reproducible
(Closes: #932116).
.
[ Michael R. Crusoe ]
* New upstream release
* debian/control: Add missing build-deps (as shown in errors during the
documentation building)
* debian/README.source: Document missing (optional?) dependencies
* debian/rules: Fix test invocation, as almost all tests were missed;
Document what is known about the skipped tests
* Apply patch from upstream to fix duplicated argument (Closes: #933527)
.
[ Andreas Tille ]
* debhelper-compat 12
* Standards-Version: 4.4.0
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
* Remove obsolete fields Name, Contact from debian/upstream/metadata.
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