Source: python-pybedtools
Version: 0.8.0-5
Severity: wishlist
Tags: patch
User: reproducible-bui...@lists.alioth.debian.org
Usertags: filesystem
X-Debbugs-Cc: reproducible-b...@lists.alioth.debian.org
Hi,
Whilst working on the Reproducible Builds effort [0] we noticed that
python-pybedtools could not be built reproducibly.
This is because it includes output inherited from non-deterministic
filesystem ordering:
/usr/lib/python3/dist-packages/pybedtools/cbedtools.cpp:
│ │ │ │ @@ -16,17 +16,17 @@
│ │ │ │ "z"
│ │ │ │ ],
│ │ │ │ "name": "pybedtools.cbedtools",
│ │ │ │ "sources": [
│ │ │ │ "pybedtools/cbedtools.pyx",
│ │ │ │ - "pybedtools/include/fileType.cpp",
│ │ │ │ "pybedtools/include/bedFile.cpp",
│ │ │ │ - "pybedtools/include/gzstream.cpp"
│ │ │ │ + "pybedtools/include/gzstream.cpp",
│ │ │ │ + "pybedtools/include/fileType.cpp"
│ │ │ │ ]
│ │ │ │ },
│ │ │ │ "module_name": "pybedtools.cbedtools"
│ │ │ │ }
Patch attached that sorts these entries in setup.py.
[0] https://reproducible-builds.org/
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` la...@debian.org / chris-lamb.co.uk
`-
--- a/debian/patches/reproducible-builds.patch 1970-01-01 01:00:00.000000000
+0100
--- b/debian/patches/reproducible-builds.patch 2021-09-28 16:37:45.666272543
+0100
@@ -0,0 +1,24 @@
+Description: Make the build reproducible
+Author: Chris Lamb <la...@debian.org>
+Last-Update: 2021-09-28
+
+--- python-pybedtools-0.8.0.orig/setup.py
++++ python-pybedtools-0.8.0/setup.py
+@@ -199,7 +199,7 @@ extensions = [
+ depends=glob.glob('pybedtools/include/*h'),
+ libraries=['stdc++', 'z'],
+ include_dirs=['pybedtools/include/'],
+- sources=['pybedtools/cbedtools' + EXT] +
glob.glob('pybedtools/include/*.cpp'),
++ sources=['pybedtools/cbedtools' + EXT] +
sorted(glob.glob('pybedtools/include/*.cpp')),
+ language='c++'),
+
+ Extension(
+@@ -207,7 +207,7 @@ extensions = [
+ depends=glob.glob('pybedtools/include/*h'),
+ libraries=['stdc++', 'z'],
+ include_dirs=['pybedtools/include/'],
+- sources=['pybedtools/featurefuncs' + EXT] +
glob.glob('pybedtools/include/*.cpp'),
++ sources=['pybedtools/featurefuncs' + EXT] +
sorted(glob.glob('pybedtools/include/*.cpp')),
+ language='c++'),
+ ]
+
--- a/debian/patches/series 2021-09-28 16:33:12.425681025 +0100
--- b/debian/patches/series 2021-09-28 16:37:44.886270948 +0100
@@ -8,3 +8,4 @@
remove_badges_from_documentation.patch
parseDebianVersions.patch
add_missing_shebang.patch
+reproducible-builds.patch
