[med-svn] [Git][med-team/multiqc][master] 13 commits: Cleanup d/copyright and fix bootstrap.min.css
Andreas Tille
gitlab at salsa.debian.org
Thu Mar 26 18:03:27 GMT 2020
Andreas Tille pushed to branch master at Debian Med / multiqc
Commits:
fa4e80a4 by Andreas Tille at 2020-03-26T18:10:18+01:00
Cleanup d/copyright and fix bootstrap.min.css
- - - - -
acd21c05 by Andreas Tille at 2020-03-26T18:13:41+01:00
New upstream version 1.8+dfsg
- - - - -
4c7aabca by Andreas Tille at 2020-03-26T18:13:42+01:00
Update upstream source from tag 'upstream/1.8+dfsg'
Update to upstream version '1.8+dfsg'
with Debian dir 2ef923243da576c02c9e9e6466a0394550e3bcd4
- - - - -
7f0e81ab by Andreas Tille at 2020-03-26T18:15:16+01:00
Remove some cruft
- - - - -
23563178 by Andreas Tille at 2020-03-26T18:15:26+01:00
New upstream version 1.8+dfsg
- - - - -
950c768f by Andreas Tille at 2020-03-26T18:15:27+01:00
Update upstream source from tag 'upstream/1.8+dfsg'
Update to upstream version '1.8+dfsg'
with Debian dir a08daafb4e635be1d30e8ea2f3991615373da621
- - - - -
b105befa by Andreas Tille at 2020-03-26T18:17:05+01:00
DEP3
- - - - -
429a7751 by Andreas Tille at 2020-03-26T18:27:32+01:00
Fetch sources of jquery.toast.css
- - - - -
8630a7f9 by Andreas Tille at 2020-03-26T18:29:49+01:00
Remove jquery.toast.css which is now in debian/missing-sources
- - - - -
365794f0 by Andreas Tille at 2020-03-26T18:30:26+01:00
New upstream version 1.8+dfsg
- - - - -
7482f7cb by Andreas Tille at 2020-03-26T18:30:28+01:00
Update upstream source from tag 'upstream/1.8+dfsg'
Update to upstream version '1.8+dfsg'
with Debian dir d0e1a56fbb4a93590c16619543e408c0490e784b
- - - - -
4fba4a73 by Andreas Tille at 2020-03-26T18:44:53+01:00
MIT license
- - - - -
2eaac639 by Andreas Tille at 2020-03-26T19:03:02+01:00
Create dir first
- - - - -
17 changed files:
- − .github/CONTRIBUTING.md
- − .github/ISSUE_TEMPLATE/bug_report.md
- − .github/ISSUE_TEMPLATE/feature_request.md
- − .github/ISSUE_TEMPLATE/module-request.md
- − .github/PULL_REQUEST_TEMPLATE.md
- − .github/RELEASE_CHECKLIST.md
- − .gitignore
- debian/copyright
- + debian/missing-sources/jquery-toast-plugin/get
- + debian/missing-sources/jquery-toast-plugin/jquery.toast.css
- + debian/missing-sources/jquery-toast-plugin/jquery.toast.min.css
- debian/multiqc.links
- debian/patches/removeHighcharts.patch
- debian/rules
- − multiqc/templates/default/assets/css/bootstrap.min.css
- − multiqc/templates/default/assets/css/jquery.toast.css
- − multiqc/templates/geo/assets/css/bootstrap.min.css
Changes:
=====================================
.github/CONTRIBUTING.md deleted
=====================================
@@ -1,43 +0,0 @@
-# MultiQC Contributing Guidelines
-
-Hi there! Many thanks for taking an interest in improving MultiQC.
-
-I try to manage the required tasks for MultiQC using GitHub issues, you probably came to this page when creating one. Most issues come in two flavours - either reporting a problem or requesting a feature. Please use the template prefilled into new issues when this is the case as it saves time. The most common reason for long-running issues is module requests without any example log files for example.
-
-However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)
-
-> _If you need help using MultiQC then the best place to go is the Gitter chatroom where you can ask me questions directly: https://gitter.im/ewels/MultiQC_
-
-## Contribution workflow
-If you'd like to write some code for MultiQC, the standard workflow
-is as follows:
-
-1. Check that there isn't already an issue about your idea in the
- [MultiQC issues](https://github.com/ewels/MultiQC/issues) to avoid
- duplicating work.
- * Feel free to add a new issue here for the same reason.
-2. Fork the MultiQC repository to your GitHub account
-3. Make the necessary changes / additions within your forked repository
-4. Submit a Pull Request and wait for the code to be reviewed and merged..
-
-If you're not used to this workflow with git, you can start with some [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/) or even their [excellent interactive tutorial](https://try.github.io/).
-
-When it comes to MultiQC, please consult the [MultiQC documentation](http://multiqc.info/docs/) and don't hesitate to get in touch on [gitter](https://gitter.im/ewels/MultiQC) for help and feedback.
-
-A few pointers to bear in mind:
-
-* New modules should be _fast_
- * MultiQC modules parse log files, they _don't_ calculating new metrics (typically).
-* New modules must scale well
- * Try to imagine what will happen if someone runs your module with 5000 samples
-* Code must run on both Python 2 and 3
-
-### Review workflow
-Once you've submitted a new pull request, here's what you can expect from me:
-
-* I usually don't look at your code at all until the automated tests pass
- * The tests use example data in the [MultiQC_TestData](https://github.com/ewels/MultiQC_TestData) repository, so you'll need some files there before the PR will go any further.
- * You can set up [Travis](https://travis-ci.org) to run the same tests on your fork really easily - just enable the repo.
-* First pass - I go through and give feedback just by reading the code
-* Second pass - I download and run your code, usually more feedback
-* Merge! Once we're both happy, I merge into the main codebase.
=====================================
.github/ISSUE_TEMPLATE/bug_report.md deleted
=====================================
@@ -1,27 +0,0 @@
----
-name: Bug report
-about: MultiQC is breaking / not behaving in the way you expect
-
----
-
-**Description of bug:**
-A clear and concise description of what the bug is.
-
-**MultiQC Error log:**
-```
-Please paste your MultiQC error log here.
-Use the triple backticks for code formatting (use a blank line before and after your log)
-```
-
-**File that triggers the error:**
-Please drag and drop (and upload to the GitHub issue) an input file that I can use to replicate the error.
-
-**MultiQC run details (please complete the following):**
- - Command used to run MultiQC: [eg. `multiqc .`]
- - MultiQC Version: [eg. MultiQC v1.1]
- - Operating System: [eg. macOS Sierra 10.12.5]
- - Python Version: [eg. Python 2.7.12]
- - Method of MultiQC installation: [eg. pip, conda, manual]
-
- **Additional context**
- Add any other context about the problem here.
=====================================
.github/ISSUE_TEMPLATE/feature_request.md deleted
=====================================
@@ -1,17 +0,0 @@
----
-name: Feature request
-about: Suggest an idea for MultiQC
-
----
-
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
-
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
-
-**Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
-
-**Additional context**
-Add any other context or screenshots about the feature request here.
=====================================
.github/ISSUE_TEMPLATE/module-request.md deleted
=====================================
@@ -1,21 +0,0 @@
----
-name: Module request
-about: Request support for a new bioinformatics tool in MultiQC
-
----
-
-**Tool Details**
- - Name of tool: [eg. My Tool]
- - Tool homepage: [eg. http://www.github/me/mytool]
- - Tool description: [eg. My Tool is a really excellent tool that does what no other tool can do]
- - Data suitable for MultiQC plot(s): [eg. amazing Histogram]
- - Most interesting data for General Stats table: [eg. Interesting Metric number 14]
-
-**Tool output:**
- - Log filename pattern: [eg. `*_mytool.txt`]
- * Only for file that contains information interesting to MultiQC.
- * Only if standardised by the tool and NOT specified by user (eg. consistent for all runs of tool by whoever)
- - File contents
- * Please drag and drop a file to upload to the issue, or submit as a pull-request to https://github.com/ewels/MultiQC_TestData
- * _Please don't just paste contents._ GitHub can alter whitespace and formatting. Instead, please attach a file by dragging and dropping onto the issue.
- * If the file is many MBs then it's ok to truncate it, though please leave a few lines of data in so that it's clear what the format is.
=====================================
.github/PULL_REQUEST_TEMPLATE.md deleted
=====================================
@@ -1,21 +0,0 @@
-Many thanks to contributing to MultiQC!
-
-Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things I request on pull requests (PRs).
-
-## If this PR is _not_ a new module
- - [ ] This comment contains a description of changes (with reason)
- - [ ] `CHANGELOG.md` has been updated
- - [ ] (optional but recommended): https://github.com/ewels/MultiQC_TestData contains test data for this change
-
-## If this PR is for a new module
- - [ ] There is example tool output for tools in the https://github.com/ewels/MultiQC_TestData repository
- - [ ] Code is tested and works locally (including with `--lint` flag)
- - [ ] `CHANGELOG.md` is updated
- - [ ] `README.md` is updated
- - [ ] `docs/README.md` is updated with link to below
- - [ ] `docs/modulename.md` is created
- - [ ] Everything that can be represented with a plot instead of a table is a plot
- - [ ] Report sections have a description and help text (with `self.add_section`)
- - [ ] There aren't any huge tables with > 6 columns (explain reasoning if so)
- - [ ] Each table column has a different colour scale to its neighbour, which relates to the data (eg. if high numbers are bad, they're red)
- - [ ] Module does not do any significant computational work
=====================================
.github/RELEASE_CHECKLIST.md deleted
=====================================
@@ -1,69 +0,0 @@
-# Release checklist
-This checklist is for my own reference, as I forget the steps every time..
-
-1. Check that everything is up to date and ready to go
-2. Figure out what this release should be called
-3. Update version numbers in code: `setup.py`, `CHANGELOG.md`
-4. Link the changelog subheading to the as yet non-existant release URL. Add date.
-5. Install the package again in `install` mode:
- ```bash
- python setup.py install
- ```
- * This removes the commit hash from the version number when MultiQC runs
-6. Run using test data
- * Check for any command line or javascript errors
- * Check version numbers are printed correctly
-7. Create new demo reports for the website and upload.
- * Spot any previously unnoticed bugs and fix
-8. Release on PyPI:
- ```bash
- rm -rf dist/
- python setup.py sdist bdist_wheel
- twine upload dist/*.tar.gz
- ```
-9. Test that it pip installs:
- ```bash
- conda create --name testing --yes python pip && source activate testing
- pip install multiqc
- multiqc .
- source deactivate && conda remove --name testing --all --yes && conda clean --all --yes
- ```
-10. Commit and push version updates
-11. Make a [release](https://github.com/ewels/MultiQC/releases) on GitHub - paste changelog section.
-12. Check that [PyPI listing page](https://pypi.python.org/pypi/multiqc/) looks sane
-13. Make a new release on `bioconda`:
- ```bash
- # Update to latest bioconda
- cd ../bioconda-recipes
- git checkout master
- git pull upstream master
- git push
- git branch -D multiqc
- # Build new conda recipe from PyPI to automatically collect new dependencies
- git checkout -b multiqc
- cd recipes
- # Do the conda skeleton to copy the dependencies
- mkdir mqctemp && cd mqctemp && atom .
- conda skeleton pypi multiqc
- # Update with new release header - see https://goo.gl/ZfRnmj
- cd ../multiqc && atom .
- # Get the sha256sum of the release
- curl -OL https://github.com/ewels/MultiQC/archive/v1.5.tar.gz
- shasum --algorithm 256 v1.5.tar.gz
- # Switch out download for GitHub release and remove all other cruft
- # commit changes
- cd ../../
- git commit -am "MultiQC version 1.5 release"
- # Test locally
- docker pull bioconda/bioconda-utils-build-env
- circleci build
- # Push updates
- git push -u origin multiqc
- # Submit a Pull Request and merge
- ```
-14. Tell UPPMAX about the new version and ask for the module system to be updated.
-15. Describe new release on [SeqAnswers thread](http://seqanswers.com/forums/showthread.php?p=195831#post195831)
-16. Tweet that new version is released
-17. Update version numbers to new dev version in `setup.py`
-18. Add a new section in the changelog for the development version
-19. Commit and push. Continue making more awesome :metal:
=====================================
.gitignore deleted
=====================================
@@ -1,32 +0,0 @@
-
-# MultiQC files
-multiqc_config.yaml
-multiqc_report.html
-multiqc_data
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-
-# Distribution / packaging
-.Python
-develop-eggs/
-eggs/
-.eggs/
-*.egg-info/
-.installed.cfg
-*.egg
-build/
-dist/
-tmp/
-
-# OS generated files
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
-
-.idea/
=====================================
debian/copyright
=====================================
@@ -1,24 +1,12 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: MultiQC
Source: https://github.com/ewels/MultiQC/
-Files-Excluded: .eggs
- multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.*
- multiqc/templates/default/assets/js/packages/bootstrap.min.js
- multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
- multiqc/templates/default/assets/js/packages/jquery-ui.min.js
- multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
- multiqc/templates/default/assets/js/packages/highcharts.offline-exporting.js
- multiqc/templates/default/assets/js/packages/highcharts.export-csv.js
- multiqc/templates/default/assets/js/packages/highcharts.exporting.js
- multiqc/templates/default/assets/js/packages/highcharts.js
- multiqc/templates/default/assets/js/packages/highcharts.heatmap.js
- multiqc/templates/default/assets/js/packages/
- multiqc/templates/default/assets/js/packages/lz-string.min.js
- multiqc/templates/default/assets/js/packages/jquery.toast.min.js
- multiqc/templates/default/assets/js/packages/FileSaver.min.js
- multiqc/templates/default/assets/js/packages/clipboard.min.js
-
-
+Files-Excluded: */glyphicons-halflings-regular.*
+ */bootstrap.min.*
+ */assets/js/packages/
+ */jquery.toast.css
+ */.github
+ */.gitignore
# ./multiqc/templates/default/assets/js/packages/jquery.toast.min.js - not in Debian
@@ -26,40 +14,33 @@ Files: *
Copyright: 2015-2019 Phil Ewels <phil.ewels at scilifelab.se>
License: GPL-3.0+
-# Removed from source tree and now referenced directly from the generated files
-#Files: multiqc/templates/default/assets/js/packages/highcharts*
-#Copyright: 2009-2016 Torstein Honsi
-#License: Highcharts_non-free
-# http://www.highcharts.com/license
-#
-# Removed from source tree to be sym linking to Debian package
-#Files:
-# ./multiqc/templates/default/assets/js/packages/bootstrap.min.js
-# other jquery links
-#
-# Removed from source tree and substitute with links to online repository
-# ./multiqc/templates/default/assets/js/packages/jquery.toast.min.js
-# ./multiqc/templates/default/assets/js/packages/highcharts.heatmap.js
-#
-# /*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/FileSaver.js */
-# ./multiqc/templates/default/assets/js/packages/FileSaver.min.js
-#
-# clipboard.js v1.5.16
-# Files: ./multiqc/templates/default/assets/js/packages/clipboard.min.js
-# Author: Zeno Rocha
-# URL: https://zenorocha.github.io/clipboard.js
-# Copyright: MIT
-
-
-Files: multiqc/templates/default/assets/js/packages/clipboard.min.js
-Copyright: Zeno Rocha <https://zenorocha.github.io/clipboard.js>
-License: MIT
-
Files: debian/*
Copyright: 2019 Andreas Tille <tilla at debian.org>
Steffen Moeller <moeller at debian.org>
License: GPL-3.0+
+Files: debian/missing-sources/jquery-toast-plugin/*
+Copyright: 2014 Kamran Ahmed
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
License: GPL-3.0+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
=====================================
debian/missing-sources/jquery-toast-plugin/get
=====================================
@@ -0,0 +1,3 @@
+#!/bin/sh
+wget -q -N https://raw.githubusercontent.com/kamranahmedse/jquery-toast-plugin/master/src/jquery.toast.css
+yui-compressor jquery.toast.css > jquery.toast.min.css
=====================================
debian/missing-sources/jquery-toast-plugin/jquery.toast.css
=====================================
@@ -0,0 +1,28 @@
+/**
+ * jQuery toast plugin created by Kamran Ahmed copyright MIT license 2014
+ */
+.jq-toast-wrap { display: block; position: fixed; width: 250px; pointer-events: none !important; margin: 0; padding: 0; letter-spacing: normal; z-index: 9000 !important; }
+.jq-toast-wrap * { margin: 0; padding: 0; }
+
+.jq-toast-wrap.bottom-left { bottom: 20px; left: 20px; }
+.jq-toast-wrap.bottom-right { bottom: 20px; right: 40px; }
+.jq-toast-wrap.top-left { top: 20px; left: 20px; }
+.jq-toast-wrap.top-right { top: 20px; right: 40px; }
+
+.jq-toast-single { display: block; width: 100%; padding: 10px; margin: 0px 0px 5px; border-radius: 4px; font-size: 12px; font-family: arial, sans-serif; line-height: 17px; position: relative; pointer-events: all !important; background-color: #444444; color: white; }
+
+.jq-toast-single h2 { font-family: arial, sans-serif; font-size: 14px; margin: 0px 0px 7px; background: none; color: inherit; line-height: inherit; letter-spacing: normal; }
+.jq-toast-single a { color: #eee; text-decoration: none; font-weight: bold; border-bottom: 1px solid white; padding-bottom: 3px; font-size: 12px; }
+
+.jq-toast-single ul { margin: 0px 0px 0px 15px; background: none; padding:0px; }
+.jq-toast-single ul li { list-style-type: disc !important; line-height: 17px; background: none; margin: 0; padding: 0; letter-spacing: normal; }
+
+.close-jq-toast-single { position: absolute; top: 3px; right: 7px; font-size: 14px; cursor: pointer; }
+
+.jq-toast-loader { display: block; position: absolute; top: -2px; height: 5px; width: 0%; left: 0; border-radius: 5px; background: red; }
+.jq-toast-loaded { width: 100%; }
+.jq-has-icon { padding: 10px 10px 10px 50px; background-repeat: no-repeat; background-position: 10px; }
+.jq-icon-info { background-image: url('data:image/png;base64,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'); background-color: #31708f; color: #d9edf7; border-color: #bce8f1; }
+.jq-icon-warning { background-image: url('data:image/png;base64,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'); background-color: #8a6d3b; color: #fcf8e3; border-color: #faebcc; }
+.jq-icon-error { background-image: url('data:image/png;base64,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'); background-color: #a94442; color: #f2dede; border-color: #ebccd1; }
+.jq-icon-success { background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABgAAAAYCAYAAADgdz34AAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsMAAA7DAcdvqGQAAADsSURBVEhLY2AYBfQMgf///3P8+/evAIgvA/FsIF+BavYDDWMBGroaSMMBiE8VC7AZDrIFaMFnii3AZTjUgsUUWUDA8OdAH6iQbQEhw4HyGsPEcKBXBIC4ARhex4G4BsjmweU1soIFaGg/WtoFZRIZdEvIMhxkCCjXIVsATV6gFGACs4Rsw0EGgIIH3QJYJgHSARQZDrWAB+jawzgs+Q2UO49D7jnRSRGoEFRILcdmEMWGI0cm0JJ2QpYA1RDvcmzJEWhABhD/pqrL0S0CWuABKgnRki9lLseS7g2AlqwHWQSKH4oKLrILpRGhEQCw2LiRUIa4lwAAAABJRU5ErkJggg=='); color: #dff0d8; background-color: #3c763d; border-color: #d6e9c6; }
\ No newline at end of file
=====================================
debian/missing-sources/jquery-toast-plugin/jquery.toast.min.css
=====================================
@@ -0,0 +1 @@
+.jq-toast-wrap{display:block;position:fixed;width:250px;pointer-events:none !important;margin:0;padding:0;letter-spacing:normal;z-index:9000 !important}.jq-toast-wrap *{margin:0;padding:0}.jq-toast-wrap.bottom-left{bottom:20px;left:20px}.jq-toast-wrap.bottom-right{bottom:20px;right:40px}.jq-toast-wrap.top-left{top:20px;left:20px}.jq-toast-wrap.top-right{top:20px;right:40px}.jq-toast-single{display:block;width:100%;padding:10px;margin:0 0 5px;border-radius:4px;font-size:12px;font-family:arial,sans-serif;line-height:17px;position:relative;pointer-events:all !important;background-color:#444;color:white}.jq-toast-single h2{font-family:arial,sans-serif;font-size:14px;margin:0 0 7px;background:0;color:inherit;line-height:inherit;letter-spacing:normal}.jq-toast-single a{color:#eee;text-decoration:none;font-weight:bold;border-bottom:1px solid white;padding-bottom:3px;font-size:12px}.jq-toast-single ul{margin:0 0 0 15px;background:0;padding:0}.jq-toast-single ul li{list-style-type:disc !important;line-height:17px;background:0;margin:0;padding:0;letter-spacing:normal}.close-jq-toast-single{position:absolute;top:3px;right:7px;font-size:14px;cursor:pointer}.jq-toast-loader{display:block;position:absolute;top:-2px;height:5px;width:0;left:0;border-radius:5px;background:red}.jq-toast-loaded{width:100%}.jq-has-icon{padding:10px 10px 10px 50px;background-repeat:no-repeat;background-position:10px}.jq-icon-info{background-image:url('data:image/png;base64,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');background-color:#31708f;color:#d9edf7;border-color:#bce8f1}.jq-icon-warning{background-image:url('data:image/png;base64,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');background-color:#8a6d3b;color:#fcf8e3;border-color:#faebcc}.jq-icon-error{background-image:url('data:image/png;base64,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');background-color:#a94442;color:#f2dede;border-color:#ebccd1}.jq-icon-success{background-image:url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABgAAAAYCAYAAADgdz34AAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsMAAA7DAcdvqGQAAADsSURBVEhLY2AYBfQMgf///3P8+/evAIgvA/FsIF+BavYDDWMBGroaSMMBiE8VC7AZDrIFaMFnii3AZTjUgsUUWUDA8OdAH6iQbQEhw4HyGsPEcKBXBIC4ARhex4G4BsjmweU1soIFaGg/WtoFZRIZdEvIMhxkCCjXIVsATV6gFGACs4Rsw0EGgIIH3QJYJgHSARQZDrWAB+jawzgs+Q2UO49D7jnRSRGoEFRILcdmEMWGI0cm0JJ2QpYA1RDvcmzJEWhABhD/pqrL0S0CWuABKgnRki9lLseS7g2AlqwHWQSKH4oKLrILpRGhEQCw2LiRUIa4lwAAAABJRU5ErkJggg==');color:#dff0d8;background-color:#3c763d;border-color:#d6e9c6}
\ No newline at end of file
=====================================
debian/multiqc.links
=====================================
@@ -14,4 +14,5 @@ usr/share/javascript/jquery-ui/jquery-ui.min.js usr/lib/python3/dist-packages/mu
usr/share/javascript/jquery-tablesorter/jquery.tablesorter.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
# bootstrap
-/usr/share/javascript/bootstrap/js/bootstrap.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/bootstrap.min.js
+/usr/share/javascript/bootstrap/js/bootstrap.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/bootstrap.min.js
+/usr/share/javascript/bootstrap/css/bootstrap.min.css usr/lib/python3/dist-packages/multiqc/templates/default/assets/css/bootstrap.min.css
=====================================
debian/patches/removeHighcharts.patch
=====================================
@@ -1,3 +1,9 @@
+Author: Steffen Moeller
+Last-Update: 2019-08-26 14:41:16 +0200
+Description: Remove hicharts
+ Otherwise package would be non-free due to usage of Highcharts. See
+ https://github.com/ewels/MultiQC/issues/800
+
Index: multiqc/multiqc/templates/default/includes.html
===================================================================
--- multiqc.orig/multiqc/templates/default/includes.html
=====================================
debian/rules
=====================================
@@ -17,3 +17,8 @@ endif
override_dh_auto_clean:
dh_auto_clean
rm -rf multiqc.egg-info/
+
+override_dh_install:
+ dh_install
+ mkdir -p debian/$(PYBUILD_NAME)/usr/lib/python3/dist-packages/multiqc/templates/default/assets/css/
+ cp -a debian/missing-sources/jquery-toast-plugin/jquery.toast.min.css debian/$(PYBUILD_NAME)/usr/lib/python3/dist-packages/multiqc/templates/default/assets/css/jquery.toast.css
=====================================
multiqc/templates/default/assets/css/bootstrap.min.css deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
multiqc/templates/default/assets/css/jquery.toast.css deleted
=====================================
@@ -1 +0,0 @@
-.jq-toast-wrap,.jq-toast-wrap *{margin:0;padding:0}.jq-toast-wrap{display:block;position:fixed;width:250px;pointer-events:none!important;letter-spacing:normal;z-index:9000!important}.jq-toast-wrap.bottom-left{bottom:20px;left:20px}.jq-toast-wrap.bottom-right{bottom:20px;right:40px}.jq-toast-wrap.top-left{top:20px;left:20px}.jq-toast-wrap.top-right{top:20px;right:40px}.jq-toast-single{display:block;width:100%;padding:10px;margin:0 0 5px;border-radius:4px;font-size:12px;font-family:arial,sans-serif;line-height:17px;position:relative;pointer-events:all!important;background-color:#444;color:#fff}.jq-toast-single h2{font-family:arial,sans-serif;font-size:14px;margin:0 0 7px;background:0 0;color:inherit;line-height:inherit;letter-spacing:normal}.jq-toast-single a{color:#eee;text-decoration:none;font-weight:700;border-bottom:1px solid #fff;padding-bottom:3px;font-size:12px}.jq-toast-single ul{margin:0 0 0 15px;background:0 0;padding:0}.jq-toast-single ul li{list-style-type:disc!important;line-height:17px;background:0 0;margin:0;padding:0;letter-spacing:normal}.close-jq-toast-single{position:absolute;top:3px;right:7px;font-size:14px;cursor:pointer}.jq-toast-loader{display:block;position:absolute;top:-2px;height:5px;width:0;left:0;border-radius:5px;background:red}.jq-toast-loaded{width:100%}.jq-has-icon{padding:10px 10px 10px 50px;background-repeat:no-repeat;background-position:10px}.jq-icon-info{background-image:url(data:image/png;base64,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);background-color:#31708f;color:#d9edf7;border-color:#bce8f1}.jq-icon-warning{background-image:url(data:image/png;base64,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);background-color:#8a6d3b;color:#fcf8e3;border-color:#faebcc}.jq-icon-error{background-image:url(data:image/png;base64,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);background-color:#a94442;color:#f2dede;border-color:#ebccd1}.jq-icon-success{background-image:url(data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABgAAAAYCAYAAADgdz34AAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsMAAA7DAcdvqGQAAADsSURBVEhLY2AYBfQMgf///3P8+/evAIgvA/FsIF+BavYDDWMBGroaSMMBiE8VC7AZDrIFaMFnii3AZTjUgsUUWUDA8OdAH6iQbQEhw4HyGsPEcKBXBIC4ARhex4G4BsjmweU1soIFaGg/WtoFZRIZdEvIMhxkCCjXIVsATV6gFGACs4Rsw0EGgIIH3QJYJgHSARQZDrWAB+jawzgs+Q2UO49D7jnRSRGoEFRILcdmEMWGI0cm0JJ2QpYA1RDvcmzJEWhABhD/pqrL0S0CWuABKgnRki9lLseS7g2AlqwHWQSKH4oKLrILpRGhEQCw2LiRUIa4lwAAAABJRU5ErkJggg==);color:#dff0d8;background-color:#3c763d;border-color:#d6e9c6}
=====================================
multiqc/templates/geo/assets/css/bootstrap.min.css deleted
=====================================
The diff for this file was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/compare/77b52c550a417b0a09b382b281f4ea24ab1be69d...2eaac6391b38b75213e045773aa3cb9b076457e8
--
View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/compare/77b52c550a417b0a09b382b281f4ea24ab1be69d...2eaac6391b38b75213e045773aa3cb9b076457e8
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