[med-svn] [snakemake] 02/03: Patch test stream readirection to prevent failure

[Kevin Murray]

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daube-guest pushed a commit to branch master
in repository snakemake.

commit 4139c518b6f38b3db6f8f0ac9303fe02a1095c88
Author: Kevin Murray <kdmfoss at gmail.com>
Date:   Fri Dec 2 13:49:17 2016 +1100

    Patch test stream readirection to prevent failure
    
    Seems that `ls >/dev/sterr` does not work, while `ls >&2` does. This
    adds a patch to enforce the latter.
---
 debian/files                                       |  1 +
 debian/patches/0003-Compat-fix.patch               | 30 ++++++++++++++++++++++
 .../0003-Use-debian-s-mathjax-package.patch        |  1 -
 debian/patches/series                              |  1 +
 4 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/debian/files b/debian/files
new file mode 100644
index 0000000..20986cb
--- /dev/null
+++ b/debian/files
@@ -0,0 +1 @@
+snakemake_3.8.2+dfsg-1_source.buildinfo science optional
diff --git a/debian/patches/0003-Compat-fix.patch b/debian/patches/0003-Compat-fix.patch
new file mode 100644
index 0000000..3b7c936
--- /dev/null
+++ b/debian/patches/0003-Compat-fix.patch
@@ -0,0 +1,30 @@
+From: Kevin Murray <kdmfoss at gmail.com>
+Date: Fri, 2 Dec 2016 13:47:22 +1100
+Subject: Compat fix
+
+---
+ tests/test_symlink_time_handling/Snakefile | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/tests/test_symlink_time_handling/Snakefile b/tests/test_symlink_time_handling/Snakefile
+index c878ef1..10fab79 100644
+--- a/tests/test_symlink_time_handling/Snakefile
++++ b/tests/test_symlink_time_handling/Snakefile
+@@ -40,7 +40,7 @@ shell("touch -h -t {} input_link".format(timestr(4)))
+ shell("ln -s input_link output_link")
+ shell("touch -h -t {} output_link".format(timestr(2)))
+ 
+-shell("ls -lR > /dev/stderr")
++shell("ls -lR >&2")
+ 
+ rule main:
+     output: "time_diff.txt"
+@@ -55,7 +55,7 @@ rule main:
+             os.stat("input_file", follow_symlinks=False).st_mtime
+         ) / (60*60) )
+         # I expect the result "4 1"
+-        shell("ls -lR > /dev/stderr")
++        shell("ls -lR >&2")
+         shell("echo {time_diff1} {time_diff2} | tee time_diff.txt 2>&1")
+ 
+ rule make_output:
diff --git a/debian/patches/0003-Use-debian-s-mathjax-package.patch b/debian/patches/0003-Use-debian-s-mathjax-package.patch
index 2782ab2..f3a72a5 100644
--- a/debian/patches/0003-Use-debian-s-mathjax-package.patch
+++ b/debian/patches/0003-Use-debian-s-mathjax-package.patch
@@ -2,7 +2,6 @@ From: Kevin Murray <spam at kdmurray.id.au>
 Date: Mon, 14 Sep 2015 00:12:40 +1000
 Subject: Use local javascript/css as appropriate j
 
-
 Use debian's mathjax package
 ---
  docs/conf.py       | 3 +++
diff --git a/debian/patches/series b/debian/patches/series
index 3f89150..8e43f1d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 0001-Use-the-inbuild-sphinx.ext.napoleon.patch
 0003-Use-debian-s-mathjax-package.patch
+0003-Compat-fix.patch

-- 
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