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commit 8634cb3e6ec42e46ce672d4aba57bb86f67c2a8b Author: Kevin Murray <[email protected]> Date: Wed Jan 18 11:18:34 2017 +1100 Backport bugfix for dynamic rule crash --- debian/changelog | 8 +++++++- .../0007-Backport-bugfix-for-dynamic-rules.patch | 22 ++++++++++++++++++++++ debian/patches/series | 1 + 3 files changed, 30 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 77c0815..d6c44c6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,10 @@ -snakemake (3.9.1-2) UNRELEASED; urgency=medium +snakemake (3.9.1-3) unstable; urgency=medium + + * Backport fix for crash with dynamic rules (from bitbucket PR #168). + + -- Kevin Murray <[email protected]> Wed, 18 Jan 2017 00:20:04 +0000 + +snakemake (3.9.1-2) unstable; urgency=medium * Future-proof patch to work-around missing snakemake binary when running tests before installation diff --git a/debian/patches/0007-Backport-bugfix-for-dynamic-rules.patch b/debian/patches/0007-Backport-bugfix-for-dynamic-rules.patch new file mode 100644 index 0000000..d729216 --- /dev/null +++ b/debian/patches/0007-Backport-bugfix-for-dynamic-rules.patch @@ -0,0 +1,22 @@ +From: Kevin Murray <[email protected]> +Date: Wed, 18 Jan 2017 11:17:46 +1100 +Subject: Backport bugfix for dynamic rules + +>From https://bitbucket.org/snakemake/snakemake/pull-requests/168 +--- + snakemake/io.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/snakemake/io.py b/snakemake/io.py +index d60a055..ae38f14 100644 +--- a/snakemake/io.py ++++ b/snakemake/io.py +@@ -758,7 +758,7 @@ class Namedlist(list): + add = len(items) - 1 + for name, (i, j) in self._names.items(): + if i > index: +- self._names[name] = (i + add, j + add) ++ self._names[name] = (i + add, None if j is None else j + add) + elif i == index: + self.set_name(name, i, end=i + len(items)) + diff --git a/debian/patches/series b/debian/patches/series index 1bf9663..f6364e5 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -4,3 +4,4 @@ 0004-drop_test_symlink_time_handling.patch 0005-drop_test_symlink_temp.patch 0006-restore-bin.patch +0007-Backport-bugfix-for-dynamic-rules.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snakemake.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
