[med-svn] [Git][med-team/snakemake][debian_for_upstream_5.14.0_which_requires_conda] Privacy: use local dagre-d3, add missing Javascript dependencies,
Rebecca N. Palmer
gitlab at salsa.debian.org
Sat Apr 11 11:24:25 BST 2020
Rebecca N. Palmer pushed to branch debian_for_upstream_5.14.0_which_requires_conda at Debian Med / snakemake
Commits:
e7d154fa by Rebecca N. Palmer at 2020-04-11T11:24:08+01:00
Privacy: use local dagre-d3, add missing Javascript dependencies,
don't appear to show live status when we don't.
- - - - -
16 changed files:
- debian/README.source
- debian/changelog
- debian/control
- − debian/patches/0011-fix-privacy-breach.patch
- debian/patches/0003-Use-debian-s-mathjax-package.patch → debian/patches/local_javascript.patch
- debian/patches/series
- debian/snakemake.install
- − debian/svg/get-svgs
- − debian/svg/install_with-bioconda-brightgreen.svg
- − debian/svg/johanneskoester_follow.svg
- − debian/svg/master.svg
- − debian/svg/pyversions_snakemake.svg
- − debian/svg/snakemake.svg
- − debian/svg/snakemake_gt_3.5.2-brightgreen.svg
- − debian/svg/stack-overflow-orange.svg
- − debian/svg/status.svg
Changes:
=====================================
debian/README.source
=====================================
@@ -1,18 +1,8 @@
-The documentation for snakemake contains potential privacy breach issues
-since it is refering to external active code. Most of these are dealt
-with in 0011-fix-privacy-breach.patch. Here are the remaining issues:
+Use of external Javascript etc (privacy issue):
- 1. Package python3-theano contains
- /usr/lib/python3/dist-packages/theano/d3viz/js/dagre-d3.min.js
- which could be used to replace
- http://cpettitt.github.io/project/dagre-d3/v0.1.5/dagre-d3.js
- However, simply adding a python3-theano dependency sounds obscure. So
- rather https://github.com/cpettitt/dagre-d3 should be packaged seprately.
- 2. JavaScript library
- https://silviomoreto.github.io/bootstrap-select/
- should be packaged to solve the two remaining issues.
-
- -- Andreas Tille <tille at debian.org> Tue, 12 Dec 2017 11:32:28 +0100
+- report.html, table.html: several
+- gui.html: mostly fixed but one remains,
+ https://silviomoreto.github.io/bootstrap-select/
Missing (optional) dependencies:
=====================================
debian/changelog
=====================================
@@ -18,6 +18,8 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium
* Update d/copyright, remove no longer needed Files-Excluded.
* Enable verbose test output.
* Update dependencies, add minimal-Depends test.
+ * Privacy: use local dagre-d3, add missing Javascript dependencies,
+ don't appear to show live status when we don't.
-- Rebecca N. Palmer <rebecca_palmer at zoho.com> Thu, 09 Apr 2020 14:57:00 +0100
=====================================
debian/control
=====================================
@@ -54,8 +54,11 @@ Rules-Requires-Root: no
Package: snakemake
Architecture: all
Depends: ca-certificates,
+ libjs-bootstrap,
libjs-d3,
+ libjs-jquery,
libjs-mathjax,
+ node-dagre-d3-renderer,
python3-appdirs,
python3-configargparse,
python3-datrie,
=====================================
debian/patches/0011-fix-privacy-breach.patch deleted
=====================================
@@ -1,61 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Dec 2017 09:02:44 +0100
-Description: Avoid privacy breach
- Remark: The replacement of the icons might lead to kind of outdated
- information in the local copy of the docs. The tradeoff enhanced privacy
- is probably worth it since most probably will read up to date docs
- online anyway.
- .
- This patch does not solve all issues. The remaining ones are discussed
- in debian/README.source.
-
---- snakemake.orig/snakemake/gui.html
-+++ snakemake/snakemake/gui.html
-@@ -3,7 +3,7 @@
- <head>
- <title>Snakemake</title>
- <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>
---- snakemake.orig/docs/index.rst
-+++ snakemake/docs/index.rst
-@@ -4,13 +4,13 @@
- Snakemake
- =========
-
--.. image:: https://img.shields.io/conda/dn/bioconda/snakemake.svg?label=Bioconda
-+.. 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://img.shields.io/docker/cloud/build/snakemake/snakemake
-@@ -19,7 +19,7 @@
- .. image:: https://github.com/snakemake/snakemake/workflows/CI/badge.svg?branch=master
- :target: https://github.com/snakemake/snakemake/actions?query=branch%3Amaster+workflow%3ACI
-
--.. image:: https://img.shields.io/badge/stack-overflow-orange.svg
-+.. image:: file:///usr/share/doc/snakemake/html/_svg/stack-overflow-orange.svg
- :target: https://stackoverflow.com/questions/tagged/snakemake
-
- .. image:: https://img.shields.io/twitter/follow/johanneskoester.svg?style=social&label=Follow
---- snakemake.orig/docs/project_info/citations.rst
-+++ snakemake/docs/project_info/citations.rst
-@@ -38,7 +38,7 @@
-
- If you publish a Snakemake workflow, consider to add this badge to your project page:
-
--.. image:: https://img.shields.io/badge/snakemake-≥5.6.0-brightgreen.svg?style=flat
-+.. image:: file:///usr/share/doc/snakemake/html/_svg/snakemake_gt_3.5.2-brightgreen.svg
- :target: https://snakemake.readthedocs.io
-
- The markdown syntax is
=====================================
debian/patches/0003-Use-debian-s-mathjax-package.patch → debian/patches/local_javascript.patch
=====================================
@@ -1,12 +1,12 @@
-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
+Description: Use local Javascript etc for privacy
-Use debian's mathjax package
----
- docs/conf.py | 3 +++
- snakemake/gui.html | 6 +++---
- 2 files changed, 6 insertions(+), 3 deletions(-)
+Some of the badge images legally could be replaced with local copies,
+but this would appear to be a live status when it isn't
+(or a per-version status that is easy to forget to update),
+so use text links instead
+
+Author: Kevin Murray <spam at kdmurray.id.au>, Andreas Tille <tille at debian.org>, Rebecca N. Palmer <rebecca_palmer at zoho.com>
+Forwarded: no
--- snakemake.orig/docs/conf.py
+++ snakemake/docs/conf.py
@@ -28,13 +28,73 @@ Use debian's mathjax package
<title>Snakemake</title>
- <script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
+ <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="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="http://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.1.1/js/bootstrap.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://cpettitt.github.io/project/dagre-d3/v0.1.5/dagre-d3.js"></script>
++ <script type="text/javascript" src="file:///usr/share/nodejs/dagre-d3/dist/dagre-d3.min.js"></script>
<script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.js"></script>
- <link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.1.1/css/bootstrap.min.css"/>
+ <link rel="stylesheet" type="text/css" href="file:///usr/share/javascript/bootstrap/css/bootstrap.min.css"/>
<link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.css"/>
<style>
body {
+--- a/docs/index.rst
++++ b/docs/index.rst
+@@ -4,33 +4,14 @@
+ Snakemake
+ =========
+
+-.. image:: https://img.shields.io/conda/dn/bioconda/snakemake.svg?label=Bioconda
+- :target: https://bioconda.github.io/recipes/snakemake/README.html
+-
+-.. image:: https://img.shields.io/pypi/pyversions/snakemake.svg
+- :target: https://www.python.org
+-
+-.. image:: https://img.shields.io/pypi/v/snakemake.svg
+- :target: https://pypi.python.org/pypi/snakemake
+-
+-.. image:: https://img.shields.io/docker/cloud/build/snakemake/snakemake
+- :target: https://hub.docker.com/r/snakemake/snakemake
+-
+-.. image:: https://github.com/snakemake/snakemake/workflows/CI/badge.svg?branch=master
+- :target: https://github.com/snakemake/snakemake/actions?query=branch%3Amaster+workflow%3ACI
+-
+-.. image:: https://img.shields.io/badge/stack-overflow-orange.svg
+- :target: https://stackoverflow.com/questions/tagged/snakemake
+-
+-.. image:: https://img.shields.io/twitter/follow/johanneskoester.svg?style=social&label=Follow
+- :target: https://twitter.com/search?l=&q=%23snakemake%20from%3Ajohanneskoester
+-
+-.. image:: https://img.shields.io/github/stars/snakemake/snakemake?style=social
+- :alt: GitHub stars
+- :target: https://github.com/snakemake/snakemake/stargazers
+-
+-.. .. raw:: html
+- <span class="__dimensions_badge_embed__" data-doi="https://doi.org/10.1093/bioinformatics/bts480" data-legend="always" data-style="large_rectangle"></span><script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>
++`Bioconda <https://bioconda.github.io/recipes/snakemake/README.html>`_
++`PyPI <https://pypi.python.org/pypi/snakemake>`_
++`Docker <https://hub.docker.com/r/snakemake/snakemake>`_
++`CI status <https://github.com/snakemake/snakemake/actions?query=branch%3Amaster+workflow%3ACI>`_
++`Stack Overflow <https://stackoverflow.com/questions/tagged/snakemake>`_
++`Twitter <https://twitter.com/search?l=&q=%23snakemake%20from%3Ajohanneskoester>`_
++`GitHub stars <https://github.com/snakemake/snakemake/stargazers>`_
++`Paper <https://doi.org/10.1093/bioinformatics/bts480>`_
+
+ The Snakemake workflow management system is a tool to create **reproducible and scalable** data analyses.
+ Workflows are described via a human readable, Python based language.
+--- a/docs/project_info/citations.rst
++++ b/docs/project_info/citations.rst
+@@ -36,10 +36,7 @@ And my PhD thesis which describes all algorithmic details:
+ Project Pages
+ =============
+
+-If you publish a Snakemake workflow, consider to add this badge to your project page:
+-
+-.. image:: https://img.shields.io/badge/snakemake-≥5.6.0-brightgreen.svg?style=flat
+- :target: https://snakemake.readthedocs.io
++If you publish a Snakemake workflow, consider adding a link to `the documentation <https://snakemake.readthedocs.io>`_ with `this badge <https://img.shields.io/badge/snakemake-≥5.6.0-brightgreen.svg?style=flat>`_ to your project page.
+
+ The markdown syntax is
+
=====================================
debian/patches/series
=====================================
@@ -1,9 +1,8 @@
0001-Use-the-inbuild-sphinx.ext.napoleon.patch
-0003-Use-debian-s-mathjax-package.patch
+local_javascript.patch
0003-Compat-fix.patch
0006-restore-bin.patch
0008-remove_sphinx.ext.patch
0009-skip-test-without-google-cloud-sdk.patch
-0011-fix-privacy-breach.patch
python3.patch
workaround_sphinx_issue.patch
=====================================
debian/snakemake.install
=====================================
@@ -1,2 +1 @@
build/sphinx/html usr/share/doc/snakemake
-debian/svg/*.svg usr/share/doc/snakemake/html/_svg
=====================================
debian/svg/get-svgs deleted
=====================================
@@ -1,12 +0,0 @@
-#!/bin/sh
-# Download some images referenced by the docs locally to avoid
-# potential privacy breaches
-rm -f *.svg
-wget -q https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg -O install_with-bioconda-brightgreen.svg
-wget -q https://img.shields.io/pypi/pyversions/snakemake.svg -O 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 -O johanneskoester_follow.svg
-wget -q https://img.shields.io/badge/snakemake-≥3.5.2-brightgreen.svg?style=flat-square -O snakemake_gt_3.5.2-brightgreen.svg
-wget -q https://quay.io/repository/snakemake/snakemake/status -O status.svg
-wget -q https://circleci.com/bb/snakemake/snakemake/tree/master.svg?style=shield -O master.svg
=====================================
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-<svg xmlns="http://www.w3.org/2000/svg" width="102" 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><mask id="a"><rect width="102" height="20" rx="3" fill="#fff"/></mask><g mask="url(#a)"><path fill="#555" d="M0 0h49v20H0z"/><path fill="#4c1" d="M49 0h53v20H49z"/><path fill="url(#b)" d="M0 0h102v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="11"><text x="24.5" y="15" fill="#010101" fill-opacity=".3">circleci</text><text x="24.5" y="14">circleci</text><text x="74.5" y="15" fill="#010101" fill-opacity=".3">passing</text><text x="74.5" y="14">passing</text></g></svg>
\ No newline at end of file
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=====================================
@@ -1 +0,0 @@
-<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" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><text x="255" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="390">python</text><text x="255" y="140" transform="scale(.1)" textLength="390">python</text><text x="615" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="170">3.5</text><text x="615" y="140" transform="scale(.1)" textLength="170">3.5</text></g> </svg>
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-<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" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><text x="175" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="230">pypi</text><text x="175" y="140" transform="scale(.1)" textLength="230">pypi</text><text x="545" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="350">v4.3.1</text><text x="545" y="140" transform="scale(.1)" textLength="350">v4.3.1</text></g> </svg>
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-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="120" height="20"><g shape-rendering="crispEdges"><path fill="#555" d="M0 0h73v20H0z"/><path fill="#4c1" d="M73 0h47v20H73z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><text x="375" y="140" transform="scale(.1)" textLength="630">snakemake</text><text x="955" y="140" transform="scale(.1)" textLength="370">≥3.5.2</text></g> </svg>
\ No newline at end of file
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=====================================
@@ -1 +0,0 @@
-<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" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><text x="205" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="290">stack</text><text x="205" y="140" transform="scale(.1)" textLength="290">stack</text><text x="665" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="470">overflow</text><text x="665" y="140" transform="scale(.1)" textLength="470">overflow</text></g> </svg>
\ No newline at end of file
=====================================
debian/svg/status.svg deleted
=====================================
@@ -1 +0,0 @@
-<svg xmlns="http://www.w3.org/2000/svg" width="106" 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><mask id="a"><rect width="106" height="20" rx="3" fill="#fff"/></mask><g mask="url(#a)"><path fill="#555" d="M0 0h63v20H0z"/><path fill="#97CA00" d="M63 0h43v20H63z"/><path fill="url(#b)" d="M0 0h106v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="11"><text x="32.5" y="15" fill="#010101" fill-opacity=".3">container</text><text x="32.5" y="14">container</text><text x="83.5" y="15" fill="#010101" fill-opacity=".3">ready</text><text x="83.5" y="14">ready</text></g></svg>
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/e7d154fa5c24b5873740cbdafc72920f1660f3c9
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View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/e7d154fa5c24b5873740cbdafc72920f1660f3c9
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