[med-svn] [snakemake] 01/03: Fix first set of privacy breach issues
Andreas Tille
tille at debian.org
Tue Dec 12 09:05:41 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository snakemake.
commit 06998c947f92d32cd8dea0094a2367253e9f2c77
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 12 09:13:44 2017 +0100
Fix first set of privacy breach issues
---
debian/changelog | 3 ++
debian/control | 1 +
debian/patches/0011-fix-privacy-breach.patch | 58 ++++++++++++++++++++++++
debian/patches/series | 1 +
debian/snakemake.install | 3 +-
debian/svg/get-svgs | 12 +++++
debian/svg/install_with-bioconda-brightgreen.svg | 1 +
debian/svg/johanneskoester_follow.svg | 1 +
debian/svg/pyversions_snakemake.svg | 1 +
debian/svg/snakemake.svg | 1 +
debian/svg/stack-overflow-orange.svg | 1 +
11 files changed, 82 insertions(+), 1 deletion(-)
diff --git a/debian/changelog b/debian/changelog
index 4315e86..bb7ae96 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -16,6 +16,9 @@ snakemake (4.3.1-1) UNRELEASED; urgency=medium
* Patch out test cases with unsatisfied dependencies
* Bump standards version to 4.1.2
+ [ Andreas Tille ]
+ * Avoid privacy breach
+
-- Christian M. Amsüss <chrysn at fsfe.org> Mon, 11 Dec 2017 20:51:06 +0100
snakemake (3.10.0-1) unstable; urgency=medium
diff --git a/debian/control b/debian/control
index b12ee66..4944d66 100644
--- a/debian/control
+++ b/debian/control
@@ -40,6 +40,7 @@ Depends: ${misc:Depends},
python3-wrapt,
python3-yaml,
libjs-mathjax,
+ libjs-d3,
ca-certificates
Recommends: python3-boto,
Description: pythonic workflow management system
diff --git a/debian/patches/0011-fix-privacy-breach.patch b/debian/patches/0011-fix-privacy-breach.patch
new file mode 100644
index 0000000..f334dc4
--- /dev/null
+++ b/debian/patches/0011-fix-privacy-breach.patch
@@ -0,0 +1,58 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 12 Dec 2017 09:02:44 +0100
+Description: Avoid privacy breach
+
+--- a/snakemake/gui.html
++++ b/snakemake/gui.html
+@@ -1,7 +1,7 @@
+ <html>
+ <head>
+ <script type="text/javascript" src="file://usr/share/javascript/jquery/jquery.min.js"></script>
+- <script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/d3/3.4.6/d3.min.js"></script>
++ <script type="text/javascript" src="file:///usr/share/javascript/d3/d3.min.js"></script>
+ <script type="text/javascript" src="file://usr/share/javascript/bootstrap/js/bootstrap.min.js"></script>
+ <script type="text/javascript" src="http://cpettitt.github.io/project/dagre-d3/v0.1.5/dagre-d3.js"></script>
+ <script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.js"></script>
+--- a/docs/project_info/citations.rst
++++ b/docs/project_info/citations.rst
+@@ -45,7 +45,7 @@ The markdown syntax is
+
+ .. sourcecode:: text
+
+- [](https://snakemake.bitbucket.io)
++ [Snakemake](https://snakemake.bitbucket.io)
+
+ Replace the ``3.5.2`` with the minimum required Snakemake version.
+ You can also `change the style <http://shields.io/#styles>`_.
+--- a/docs/index.rst
++++ b/docs/index.rst
+@@ -4,13 +4,13 @@
+ Snakemake
+ =========
+
+-.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
++.. image:: file:///usr/share/doc/snakemake/html/_svg/install_with-bioconda-brightgreen.svg
+ :target: https://bioconda.github.io/recipes/snakemake/README.html
+
+-.. image:: https://img.shields.io/pypi/pyversions/snakemake.svg
++.. image:: file:///usr/share/doc/snakemake/html/_svg/pyversions_snakemake.svg
+ :target: https://www.python.org
+
+-.. image:: https://img.shields.io/pypi/v/snakemake.svg
++.. image:: file:///usr/share/doc/snakemake/html/_svg/snakemake.svg
+ :target: https://pypi.python.org/pypi/snakemake
+
+ .. image:: https://quay.io/repository/snakemake/snakemake/status
+@@ -19,10 +19,10 @@ Snakemake
+ .. image:: https://app.wercker.com/status/5b4faec0485e3b6ed5497f3e8e551b34/s/master
+ :target: https://app.wercker.com/project/byKey/5b4faec0485e3b6ed5497f3e8e551b34
+
+-.. image:: https://img.shields.io/badge/stack-overflow-orange.svg
++.. image:: file:///usr/share/doc/snakemake/html/_svg/stack-overflow-orange.svg
+ :target: http://stackoverflow.com/questions/tagged/snakemake
+
+-.. image:: https://img.shields.io/twitter/follow/johanneskoester.svg?style=social&label=Follow
++.. image:: file:///usr/share/doc/snakemake/html/_svg/johanneskoester_follow.svg
+ :target: https://twitter.com/johanneskoester
+
+ The Snakemake workflow management system is a tool to create **reproducible and scalable** data analyses.
diff --git a/debian/patches/series b/debian/patches/series
index f1e5f3c..96dc7bc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -8,3 +8,4 @@
0008-remove_sphinx.ext.patch
0009-skip-test-without-google-cloud-sdk.patch
0010-skip-test-without-rmarkdown.patch
+0011-fix-privacy-breach.patch
diff --git a/debian/snakemake.install b/debian/snakemake.install
index 57a72ce..12321e8 100644
--- a/debian/snakemake.install
+++ b/debian/snakemake.install
@@ -1 +1,2 @@
-build/sphinx/html usr/share/doc/snakemake
+build/sphinx/html usr/share/doc/snakemake
+debian/svg/*.svg usr/share/doc/snakemake/html/_svg
diff --git a/debian/svg/get-svgs b/debian/svg/get-svgs
new file mode 100755
index 0000000..7846ba7
--- /dev/null
+++ b/debian/svg/get-svgs
@@ -0,0 +1,12 @@
+#!/bin/sh
+# Download some images referenced by the docs locally to avoid
+# potential privacy breaches
+rm *.svg
+wget -q https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
+mv install\ with-bioconda-brightgreen.svg install_with-bioconda-brightgreen.svg
+wget -q https://img.shields.io/pypi/pyversions/snakemake.svg
+mv snakemake.svg pyversions_snakemake.svg
+wget -q https://img.shields.io/pypi/v/snakemake.svg
+wget -q https://img.shields.io/badge/stack-overflow-orange.svg
+wget -q https://img.shields.io/twitter/follow/johanneskoester.svg?style=social\&label=Follow
+mv johanneskoester.svg?style=social\&label=Follow johanneskoester_follow.svg
diff --git a/debian/svg/install_with-bioconda-brightgreen.svg b/debian/svg/install_with-bioconda-brightgreen.svg
new file mode 100644
index 0000000..703fe3e
--- /dev/null
+++ b/debian/svg/install_with-bioconda-brightgreen.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="128" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="128" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h69v20H0z"/><path fill="#4c1" d="M69 0h59v20H69z"/><path fill="url(#b)" d="M0 0h128v20H0z"/></g><g fill="#fff" t [...]
\ No newline at end of file
diff --git a/debian/svg/johanneskoester_follow.svg b/debian/svg/johanneskoester_follow.svg
new file mode 100644
index 0000000..74af79f
--- /dev/null
+++ b/debian/svg/johanneskoester_follow.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="100" height="20"><style>a #llink:hover{fill:url(#b);stroke:#ccc}a #rlink:hover{fill:#4183c4}</style><linearGradient id="a" x2="0" y2="100%"><stop offset="0" stop-color="#fcfcfc" stop-opacity="0"/><stop offset="1" stop-opacity=".1"/></linearGradient><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#ccc" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><g str [...]
\ No newline at end of file
diff --git a/debian/svg/pyversions_snakemake.svg b/debian/svg/pyversions_snakemake.svg
new file mode 100644
index 0000000..8447ff9
--- /dev/null
+++ b/debian/svg/pyversions_snakemake.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="76" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="76" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h49v20H0z"/><path fill="#007ec6" d="M49 0h27v20H49z"/><path fill="url(#b)" d="M0 0h76v20H0z"/></g><g fill="#fff" t [...]
\ No newline at end of file
diff --git a/debian/svg/snakemake.svg b/debian/svg/snakemake.svg
new file mode 100644
index 0000000..20038e9
--- /dev/null
+++ b/debian/svg/snakemake.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="78" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="78" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h33v20H0z"/><path fill="#007ec6" d="M33 0h45v20H33z"/><path fill="url(#b)" d="M0 0h78v20H0z"/></g><g fill="#fff" t [...]
\ No newline at end of file
diff --git a/debian/svg/stack-overflow-orange.svg b/debian/svg/stack-overflow-orange.svg
new file mode 100644
index 0000000..50c5af8
--- /dev/null
+++ b/debian/svg/stack-overflow-orange.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="96" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="96" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h39v20H0z"/><path fill="#fe7d37" d="M39 0h57v20H39z"/><path fill="url(#b)" d="M0 0h96v20H0z"/></g><g fill="#fff" t [...]
\ No newline at end of file
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