[med-svn] [Git][med-team/multiqc][upstream] 3 commits: New upstream version 1.8+dfsg
Andreas Tille
gitlab at salsa.debian.org
Thu Mar 26 18:03:29 GMT 2020
Andreas Tille pushed to branch upstream at Debian Med / multiqc
Commits:
acd21c05 by Andreas Tille at 2020-03-26T18:13:41+01:00
New upstream version 1.8+dfsg
- - - - -
23563178 by Andreas Tille at 2020-03-26T18:15:26+01:00
New upstream version 1.8+dfsg
- - - - -
365794f0 by Andreas Tille at 2020-03-26T18:30:26+01:00
New upstream version 1.8+dfsg
- - - - -
10 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
- − 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/
=====================================
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/8e0f0a307732297bf290518b06c3be3f48f40f9a...365794f0e4b055aee0129531c30e66aaec21cc5e
--
View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/compare/8e0f0a307732297bf290518b06c3be3f48f40f9a...365794f0e4b055aee0129531c30e66aaec21cc5e
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200326/20bf676c/attachment-0001.html>
More information about the debian-med-commit
mailing list