Move GitHub repository to MultiQC organisation (#2243)

* ewels/MultiQC_TestData -> MultiQC/test-data

* ewels/MultiQC -> MultiQC/MultiQC

* Rename the docker image too

* [automated] Update CHANGELOG.md

* Don't update repo name in the changelog

* [automated] Update CHANGELOG.md

* Rename branch 'master' to 'main'

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>

.github/CONTRIBUTING.md

@@ -14,7 +14,7 @@ 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
+   [MultiQC issues](https://github.com/MultiQC/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
@@ -37,7 +37,7 @@ A few pointers to bear in mind:
 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.
+  - The tests use example data in the [test-data](https://github.com/MultiQC/test-data) repository, so you'll need some files there before the PR will go any further.
   - The tests use [GitHub Actions](https://github.com/features/actions) so should also run automatically on your fork.
 - First pass - I go through and give feedback just by reading the code
 - Second pass - I download and run your code, usually more feedback

.github/PULL_REQUEST_TEMPLATE.md

@@ -7,7 +7,7 @@ Please fill in the appropriate checklist below (delete whatever is not relevant)
 
 <!-- If this PR is for a NEW module - delete if not -->
 
-- [ ] There is example tool output for tools in the <https://github.com/ewels/MultiQC_TestData> repository or attached to this PR
+- [ ] There is example tool output for tools in the <https://github.com/MultiQC/test-data> repository or attached to this PR
 - [ ] Code is tested and works locally (including with `--strict` flag)
 - [ ] `docs/README.md` is updated with link to below
 - [ ] `docs/modulename.md` is created

.github/RELEASE_CHECKLIST.md

@@ -50,12 +50,12 @@ This checklist is for my own reference, as I forget the steps every time.
 8. Commit and push version updates
 9. Generate new rich-codex screenshots
    - On github.com, make a new branch using the branch dropdown called `rich-codex` (or whatever).
-   - Go to _Actions_ and then [_Docs screenshots_](https://github.com/ewels/MultiQC/actions/workflows/screenshots.yml)
+   - Go to _Actions_ and then [_Docs screenshots_](https://github.com/MultiQC/MultiQC/actions/workflows/screenshots.yml)
    - Click _Run Workflow_ top right, and **select your new branch**
    - Click Run. Wait for the action to complete.
-   - Make a PR from this branch to `master` and check that the new screenshot looks ok. Merge if so.
+   - Make a PR from this branch to `main` and check that the new screenshot looks ok. Merge if so.
 10. Make sure that all tests are passing
-11. Make a [release](https://github.com/ewels/MultiQC/releases) on GitHub - paste changelog section.
+11. Make a [release](https://github.com/MultiQC/MultiQC/releases) on GitHub - paste changelog section.
 12. Check that [PyPI listing page](https://pypi.python.org/pypi/multiqc/) looks sane
 13. Update version numbers to new dev version in `setup.py` + a new section in the changelog for the development version
 14. Commit and push version bump
@@ -76,8 +76,8 @@ Instructions for complete rebuild of BioConda:
 ```bash
 # Update to latest bioconda
 cd ../bioconda-recipes
-git checkout master
-git pull upstream master
+git checkout main
+git pull upstream main
 git push
 git branch -D multiqc
 # Build new conda recipe from PyPI to automatically collect new dependencies
@@ -88,7 +88,7 @@ conda skeleton pypi multiqc
 # Update with new release header - see https://goo.gl/ZfRnmj
 cd ../multiqc && code .
 # Get the sha256sum of the release
-curl -OL https://github.com/ewels/MultiQC/archive/v1.5.tar.gz
+curl -OL https://github.com/MultiQC/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

.github/workflows/changelog.py

@@ -4,16 +4,16 @@
 
 Adds a line into the CHANGELOG.md:
 * If a PR title starts with "New module: ", checks that a single module is added,
- and appends an entry under the ""### New modules" section. 
+ and appends an entry under the ""### New modules" section.
 * If a single module was modified, checks that the PR starts with a name of the
  modified module (e.g. "FastQC: new stuff") and adds a line under "### Module updates".
 * All other change will go under the "### MultiQC updates" section.
 * If an entry for the PR is already added, will replace it.
 
 Other assumptions:
-- CHANGELOG.md has a running section for an ongoing "dev" version 
+- CHANGELOG.md has a running section for an ongoing "dev" version
 (i.e. titled "## MultiQC vX.Ydev").
-- Under that section, there are sections "### MultiQC updates", "### New modules" 
+- Under that section, there are sections "### MultiQC updates", "### New modules"
 and "### Module updates".
 - For module's info, checks the file multiqc/modules/<module_name>/<module_name>.py.
 """
@@ -26,7 +26,7 @@
 
 import yaml
 
-REPO_URL = "https://github.com/ewels/MultiQC"
+REPO_URL = "https://github.com/MultiQC/MultiQC"
 MODULES_DIR = Path("multiqc/modules")
 
 # Assumes the environment is set by the GitHub action.
@@ -161,7 +161,7 @@ def _load_file_content_after_pr(path) -> str:
     _run_cmd(f"cd {workspace_path} && gh pr checkout {pr_number}")
     with (workspace_path / path).open() as f:
         text = f.read()
-    _run_cmd(f"cd {workspace_path} && git checkout master")
+    _run_cmd(f"cd {workspace_path} && git checkout main")
     return text
 
 
@@ -329,7 +329,7 @@ def _skip_existing_entry_for_this_pr(line, same_section=True):
         updated_lines.append(line)
 
         # Parse version from the line ## MultiQC v1.10dev or
-        # ## [MultiQC v1.15](https://github.com/ewels/MultiQC/releases/tag/v1.15) ...
+        # ## [MultiQC v1.15](https://github.com/MultiQC/MultiQC/releases/tag/v1.15) ...
         if not (m := re.match(r".*MultiQC (v\d+\.\d+(dev)?).*", line)):
             print(f"Cannot parse version from line {line.strip()}.", file=sys.stderr)
             sys.exit(1)

.github/workflows/changelog.yml

@@ -11,7 +11,7 @@ jobs:
     # Run if comment is on a PR with the main repo, and if it contains the magic keywords.
     # Or run on PR creation, unless asked otherwise in the title.
     if: |
-      github.repository_owner == 'ewels' && (
+      github.repository_owner == 'MultiQC' && (
         github.event_name == 'pull_request_target' ||
         github.event.issue.pull_request && startsWith(github.event.comment.body, '@multiqc-bot changelog')
       )

.github/workflows/deploy-pypi.yml

@@ -25,12 +25,12 @@ jobs:
         run: python setup.py sdist bdist_wheel
 
       - name: Publish MultiQC to PyPI
-        if: github.repository == 'ewels/MultiQC'
+        if: github.repository == 'MultiQC/MultiQC'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}
 #      - name: Tweet
-#        if: github.repository == 'ewels/MultiQC'
+#        if: github.repository == 'MultiQC/MultiQC'
 #        uses: snow-actions/tweet@v1.3.0
 #        with:
 #          status: |

.github/workflows/docker.yml

@@ -2,13 +2,13 @@ name: Publish Docker image
 
 on:
   push:
-    branches: [master]
+    branches: [main]
   release:
     types: [published]
 
 jobs:
   push_to_registry:
-    if: github.repository == 'ewels/MultiQC'
+    if: github.repository == 'MultiQC/MultiQC'
     name: Build + Push Docker image
     runs-on: ubuntu-latest
     steps:
@@ -47,8 +47,8 @@ jobs:
           platforms: linux/amd64,linux/arm64
           push: true
           tags: |
-            ewels/multiqc:dev
-            ghcr.io/ewels/multiqc:dev
+            multiqc/multiqc:dev
+            ghcr.io/multiqc/multiqc:dev
 
       - name: Push release image
         uses: docker/build-push-action@v3
@@ -60,7 +60,7 @@ jobs:
           platforms: linux/amd64,linux/arm64
           push: true
           tags: |
-            ewels/multiqc:${{ github.event.release.tag_name }}
-            ewels/multiqc:latest
-            ghcr.io/ewels/multiqc:${{ github.event.release.tag_name }}
-            ghcr.io/ewels/multiqc:latest
+            multiqc/multiqc:${{ github.event.release.tag_name }}
+            multiqc/multiqc:latest
+            ghcr.io/multiqc/multiqc:${{ github.event.release.tag_name }}
+            ghcr.io/multiqc/multiqc:latest

.github/workflows/docs_deploy.yml

@@ -3,7 +3,7 @@ name: Docs - Netlify deploy
 on:
   push:
     branches:
-      - master
+      - main
     paths:
       - "docs/**"
       - ".github/workflows/docs_deploy.yml"
@@ -15,7 +15,7 @@ jobs:
   deploy:
     name: "Request deployment"
     runs-on: ubuntu-latest
-    if: github.repository == 'ewels/MultiQC'
+    if: github.repository == 'MultiQC/MultiQC'
     steps:
       - name: Curl request
         run: curl -X POST -d {} ${{ secrets.NETLIFY_BUILD_HOOK }}

.github/workflows/docs_preview.yml

@@ -8,7 +8,7 @@ jobs:
   deploy:
     name: "Deploy preview"
     runs-on: ubuntu-latest
-    if: github.repository == 'ewels/MultiQC'
+    if: github.repository == 'MultiQC/MultiQC'
     defaults:
       run:
         working-directory: ./MultiQC_website

.github/workflows/fix-linting.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
-      github.repository_owner == 'ewels' &&
+      github.repository_owner == 'MultiQC' &&
       github.event.issue.pull_request &&
       startsWith(github.event.comment.body, '@multiqc-bot fix linting')
 

.github/workflows/lint_code.yml

@@ -1,7 +1,7 @@
 name: Lint Code Base
 on:
   push:
-    branches: [master]
+    branches: [main]
   pull_request:
 
 jobs:

.github/workflows/multiqc.yml

@@ -2,7 +2,7 @@ name: "MultiQC"
 on:
   push:
     branches:
-      - master
+      - main
     paths-ignore:
       - "docs/**"
       - "*.md"
@@ -78,7 +78,7 @@ jobs:
       - name: Download test data
         uses: actions/checkout@v3
         with:
-          repository: ewels/MultiQC_TestData
+          repository: MultiQC/test-data
           path: test_data
 
       # Run all of the tests!
@@ -179,10 +179,10 @@ jobs:
       # NB: Download zip file instead of git clone, as Windows complains about reserved filenames and certain characters
       - name: Download test data
         run: |
-          curl -fsSL https://github.com/ewels/MultiQC_TestData/archive/master.zip -o test_data.zip
+          curl -fsSL https://github.com/MultiQC/test-data/archive/main.zip -o test_data.zip
           7z x test_data.zip -y -o"test_data"
-          dir test_data\MultiQC_TestData-master
+          dir test_data\test-data-main
 
       # Run all of the tests! Remember the BACKslash path separator!
       - name: All modules / Custom report filename
-        run: multiqc ${{ needs.changes.outputs.single_module }} --strict test_data\MultiQC_TestData-master\data\modules\ --filename full_report.html
+        run: multiqc ${{ needs.changes.outputs.single_module }} --strict test_data\test-data-main\data\modules\ --filename full_report.html

.github/workflows/screenshots.yml

@@ -17,9 +17,9 @@ jobs:
 
       - name: Download test data
         run: |
-          wget https://github.com/ewels/MultiQC_TestData/archive/refs/heads/master.zip
-          unzip master.zip
-          mv MultiQC_TestData-master/ test_data/
+          wget https://github.com/MultiQC/test-data/archive/refs/heads/main.zip
+          unzip main.zip
+          mv test-data-main/ test_data/
 
       - name: Generate terminal images with rich-codex
         uses: ewels/rich-codex@v1

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "tests"]
 	path = tests
-	url = https://github.com/ewels/MultiQC_TestData.git
+	url = https://github.com/MultiQC/test-data.git

CHANGELOG.md

@@ -4,6 +4,8 @@
 
 ### MultiQC updates
 
+- Move GitHub repository to `MultiQC` organisation ([#2243](https://github.com/MultiQC/MultiQC/pull/2243))
+
 ### New modules
 
 ### Module updates

CITATION.cff

@@ -13,7 +13,7 @@ title: "MultiQC: summarize analysis results for multiple tools and samples in a
 version: 1.12
 doi: 10.1093/bioinformatics/btw354
 date-released: 2022-02-08
-url: "https://github.com/ewels/MultiQC"
+url: "https://github.com/MultiQC/MultiQC"
 preferred-citation:
   type: article
   authors:

README.md

@@ -25,7 +25,7 @@ A very large number of Bioinformatics tools are supported by MultiQC. Please see
 MultiQC can also easily parse data from custom scripts, if correctly formatted / configured - a feature called [Custom Content](https://multiqc.info/docs/custom_content/).
 
 More modules are being written all of the time. Please suggest any ideas as a new
-[issue](https://github.com/ewels/MultiQC/issues) _(please include example log files)_.
+[issue](https://github.com/MultiQC/MultiQC/issues) _(please include example log files)_.
 
 ## Installation
 
@@ -46,7 +46,7 @@ conda install multiqc
 If you would like the development version from GitHub instead, you can install it with `pip`:
 
 ```bash
-pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git
+pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC.git
 ```
 
 MultiQC is also available via Docker and Singularity images, Galaxy wrappers, and
@@ -104,10 +104,10 @@ Please consider citing MultiQC if you use it in your analysis.
 ## Contributions & Support
 
 Contributions and suggestions for new features are welcome, as are bug reports!
-Please create a new [issue](https://github.com/ewels/MultiQC/issues) for any
+Please create a new [issue](https://github.com/MultiQC/MultiQC/issues) for any
 of these, including example reports where possible.
 Pull-requests for fixes and additions are very welcome.
-Please see the [contributing notes](https://github.com/ewels/MultiQC/blob/master/.github/CONTRIBUTING.md) for more information about how the process works.
+Please see the [contributing notes](https://github.com/MultiQC/MultiQC/blob/main/.github/CONTRIBUTING.md) for more information about how the process works.
 
 MultiQC has extensive [documentation](http://multiqc.info/docs/development/)
 describing how to write new modules, plugins and templates.
@@ -121,6 +121,6 @@ MultiQC is developed and maintained by Phil Ewels ([@ewels](https://github.com/e
 It was originally written at the [National Genomics Infrastructure](https://ngisweden.scilifelab.se/), part of [SciLifeLab](https://www.scilifelab.se/) in Sweden.
 
 A huge thank you to all code contributors - there are a lot of you!
-See the [Contributors Graph](https://github.com/ewels/MultiQC/graphs/contributors) for details.
+See the [Contributors Graph](https://github.com/MultiQC/MultiQC/graphs/contributors) for details.
 
 MultiQC is released under the GPL v3 or later licence.

docs/README.md

@@ -7,7 +7,7 @@ of common tools.
 These docs can be read in any of three ways:
 
 - On the MultiQC Website: <http://multiqc.info>
-- On GitHub: <https://github.com/ewels/MultiQC/>
+- On GitHub: <https://github.com/MultiQC/MultiQC/>
 - As part of the distributed source code (in `/docs/`)
 
 If you're curious how the website works, check out the
@@ -19,4 +19,4 @@ If you write a module which could be of use to others, it would be great to
 merge those changes back into the core MultiQC project.
 
 For instructions on how best to do this, please see the
-[contributing instructions](https://github.com/ewels/MultiQC/blob/master/.github/CONTRIBUTING.md).
+[contributing instructions](https://github.com/MultiQC/MultiQC/blob/main/.github/CONTRIBUTING.md).

docs/core/custom_content/index.md

@@ -16,7 +16,7 @@ Custom content parsing is a little more restricted than standard modules. Specif
 - Plot customisation is more limited
 
 All plot types can be generated using custom content - see the
-[test files](https://github.com/ewels/MultiQC_TestData/tree/master/data/custom_content)
+[test files](https://github.com/MultiQC/test-data/tree/main/data/custom_content)
 for examples of how data should be structured.
 
 :::note
@@ -147,7 +147,7 @@ description: 'This section is created using a custom HTML file'
 
 If no configuration is given, MultiQC will do its best to guess how to visualise your data appropriately.
 To see examples of typical file structures which are understood, see the
-[test data](https://github.com/ewels/MultiQC_TestData/tree/master/data/custom_content/no_config)
+[test data](https://github.com/MultiQC/test-data/tree/main/data/custom_content/no_config)
 used to develop this code. Something will be probably be shown, but it may produce unexpected results.
 
 :::note
@@ -257,7 +257,7 @@ custom_data:
   example_files:
     file_format: "tsv"
     section_name: "Coverage Decay"
-    description: "This plot comes from files acommpanied by a mutliqc_config.yaml file for configuration"
+    description: "This plot comes from files acommpanied by a multiqc_config.yaml file for configuration"
     plot_type: "linegraph"
     pconfig:
       id: "example_coverage_lineplot"
@@ -294,7 +294,7 @@ custom_data:
 
 If no configuration is given, MultiQC will do its best to guess how to visualise
 your data appropriately. To see examples of typical file structures which are understood, see the
-[test data](https://github.com/ewels/MultiQC_TestData/tree/master/data/custom_content/no_config)
+[test data](https://github.com/MultiQC/test-data/tree/main/data/custom_content/no_config)
 used to develop this code.
 
 # Configuration
@@ -446,7 +446,7 @@ Probably the best way to get to grips with Custom Content is to see some example
 The MultiQC automated testing runs with a bunch of different files, and I try to add to
 these all the time.
 
-You can see these examples here: <https://github.com/ewels/MultiQC_TestData/tree/master/data/custom_content>
+You can see these examples here: <https://github.com/MultiQC/test-data/tree/main/data/custom_content>
 
 For example, to see a file which generates a table in a report by itself, you can
-have a look at `embedded_config/table_headers_mqc.txt` ([link](https://github.com/ewels/MultiQC_TestData/blob/master/data/custom_content/embedded_config/table_headers_mqc.txt)).
+have a look at `embedded_config/table_headers_mqc.txt` ([link](https://github.com/MultiQC/test-data/blob/main/data/custom_content/embedded_config/table_headers_mqc.txt)).

docs/core/development/plugins.md

@@ -55,7 +55,7 @@ to MultiQC:
 
 Any python program can create entry points with the same name, once installed
 MultiQC will find these and run them accordingly. For an example of this in
-action, see the [MultiQC_NGI](https://github.com/ewels/MultiQC_NGI/blob/master/setup.py)
+action, see the [MultiQC_NGI](https://github.com/MultiQC/MultiQC_NGI/blob/master/setup.py)
 setup file:
 
 ```python