Rename ewels/MegaQC -> MultiQC/MegaQC

CHANGELOG.rst

@@ -19,9 +19,9 @@ Development
    * Fix a bug in pytest where we used `scope` as a positional argument
    * Update the SubFactoryList to a new version that works with newer FactoryBoy versions
 
-.. _[#430]: https://github.com/ewels/MegaQC/issues/430
-.. _[#440]: https://github.com/ewels/MegaQC/pull/440
-.. _[#433]: https://github.com/ewels/MegaQC/pull/433
+.. _[#430]: https://github.com/MultiQC/MegaQC/issues/430
+.. _[#440]: https://github.com/MultiQC/MegaQC/pull/440
+.. _[#433]: https://github.com/MultiQC/MegaQC/pull/433
 
 =======
 
@@ -87,12 +87,12 @@ Internal Changes
 -  Many and more dependency updates
 
 
-.. _[#69]:  https://github.com/ewels/MegaQC/issues/69
-.. _[#138]: https://github.com/ewels/MegaQC/issues/138
-.. _[#139]: https://github.com/ewels/MegaQC/issues/139
-.. _[#140]: https://github.com/ewels/MegaQC/issues/140
-.. _[#148]: https://github.com/ewels/MegaQC/issues/148
-.. _[#156]: https://github.com/ewels/MegaQC/issues/156
-.. _[#170]: https://github.com/ewels/MegaQC/issues/170
-.. _[#194]: https://github.com/ewels/MegaQC/issues/194
-.. _[#443]: https://github.com/ewels/MegaQC/pull/443
+.. _[#69]:  https://github.com/MultiQC/MegaQC/issues/69
+.. _[#138]: https://github.com/MultiQC/MegaQC/issues/138
+.. _[#139]: https://github.com/MultiQC/MegaQC/issues/139
+.. _[#140]: https://github.com/MultiQC/MegaQC/issues/140
+.. _[#148]: https://github.com/MultiQC/MegaQC/issues/148
+.. _[#156]: https://github.com/MultiQC/MegaQC/issues/156
+.. _[#170]: https://github.com/MultiQC/MegaQC/issues/170
+.. _[#194]: https://github.com/MultiQC/MegaQC/issues/194
+.. _[#443]: https://github.com/MultiQC/MegaQC/pull/443

README.rst

@@ -20,7 +20,7 @@ MegaQC is a web application that you can install and run on your own
 network. It collects and visualises data parsed by MultiQC across multiple runs.
 The MegaQC home page looks something like this:
 
-.. figure:: https://raw.githubusercontent.com/ewels/MegaQC/master/docs/source/images/megaqc_homepage.png
+.. figure:: https://raw.githubusercontent.com/MultiQC/MegaQC/master/docs/source/images/megaqc_homepage.png
    :alt: MegaQC homepage
 
    Screenshot of the MegaQC home page.
@@ -37,7 +37,7 @@ to learn how to install, deploy and use MegaQC.
 .. _MultiQC website: http://multiqc.info
 .. _GitHub repository: https://github.com/ewels/MultiQC
 
-.. |MegaQC| image:: https://raw.githubusercontent.com/ewels/MegaQC/master/megaqc/static/img/MegaQC_logo.png
+.. |MegaQC| image:: https://raw.githubusercontent.com/MultiQC/MegaQC/master/megaqc/static/img/MegaQC_logo.png
 .. |Docker| image:: https://img.shields.io/docker/automated/ewels/megaqc.svg?style=flat-square
    :target: https://hub.docker.com/r/ewels/megaqc/
 .. |Build Status| image:: https://travis-ci.org/ewels/MegaQC.svg?branch=master

docs/source/_templates/index.html

@@ -27,7 +27,7 @@ <h1><a href="index.html"><img src="_static/images/MegaQC_logo_darkbg.svg" title=
 									<li><a href="docs/index.html" title="Read the MegaQC documentation">Docs</a></li>
 									<li><a href="http://multiqc.info/" target="_blank" title="Find out more about MultiQC, which MegaQC relies upon">MultiQC</a></li>
 									<li><a href="https://gitter.im/ewels/MegaQC" target="_blank" title="Get help by chatting with the developers">Gitter</a></li>
-									<li><a href="https://github.com/ewels/MegaQC" target="_blank" title="View the code on GitHub">GitHub</a></li>
+									<li><a href="https://github.com/MultiQC/MegaQC" target="_blank" title="View the code on GitHub">GitHub</a></li>
 								</ul>
 							</nav>
 
@@ -186,7 +186,7 @@ <h2>Still not sure?</h2>
               <ul class="actions">
                 <li><a href="docs/index.html" class="button style2">Read the docs</a></li>
                 <li><a href="#" class="button style1">Try a live demo</a></li>
-                <li><a href="https://github.com/ewels/MegaQC" target="_blank" class="button style2">See the code</a></li>
+                <li><a href="https://github.com/MultiQC/MegaQC" target="_blank" class="button style2">See the code</a></li>
               </ul>
 						</header>
 

docs/source/conf.py

@@ -98,4 +98,4 @@ def find_source():
     tag = "master"
     # TODO use this after the first release: tag = 'master' if 'dev' in release else ('v' + release)
 
-    return "https://github.com/ewels/megaqc/blob/%s/%s" % (tag, filename)
+    return "https://github.com/MultiQC/MegaQC/blob/%s/%s" % (tag, filename)

docs/source/docs/dev/backend.rst

@@ -13,7 +13,7 @@ will likely be SQLite.
 
 Database models are located in `model/models.py`_ and `user/models.py`_.
 
-Database schema migrations 
+Database schema migrations
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 You need to generate a new migration whenever the database schema (ie
@@ -61,16 +61,16 @@ be done inside `test_api.py`_, which tests all REST API endpoints.
 
 .. _flask: https://www.palletsprojects.com/p/flask/
 .. _SQLAlchemy: https://docs.sqlalchemy.org/
-.. _model/models.py: https://github.com/ewels/MegaQC/blob/master/megaqc/model/models.py
-.. _user/models.py: https://github.com/ewels/MegaQC/blob/master/megaqc/user/models.py
-.. _megaqc/api: https://github.com/ewels/MegaQC/tree/master/megaqc/api
-.. _megaqc/rest_api: https://github.com/ewels/MegaQC/tree/master/megaqc/rest_api
-.. _views.py: https://github.com/ewels/MegaQC/blob/master/megaqc/rest_api/views.py
+.. _model/models.py: https://github.com/MultiQC/MegaQC/blob/master/megaqc/model/models.py
+.. _user/models.py: https://github.com/MultiQC/MegaQC/blob/master/megaqc/user/models.py
+.. _megaqc/api: https://github.com/MultiQC/MegaQC/tree/master/megaqc/api
+.. _megaqc/rest_api: https://github.com/MultiQC/MegaQC/tree/master/megaqc/rest_api
+.. _views.py: https://github.com/MultiQC/MegaQC/blob/master/megaqc/rest_api/views.py
 .. _flapison: https://github.com/TMiguelT/flapison
-.. _schemas.py: https://github.com/ewels/MegaQC/tree/master/megaqc/rest_api/schemas.py
-.. _public/views.py: https://github.com/ewels/MegaQC/tree/master/megaqc/public/views.py
-.. _user/views.py: https://github.com/ewels/MegaQC/tree/master/megaqc/user/views.py
+.. _schemas.py: https://github.com/MultiQC/MegaQC/tree/master/megaqc/rest_api/schemas.py
+.. _public/views.py: https://github.com/MultiQC/MegaQC/tree/master/megaqc/public/views.py
+.. _user/views.py: https://github.com/MultiQC/MegaQC/tree/master/megaqc/user/views.py
 .. _Jinja2: https://jinja.palletsprojects.com/en/2.11.x/
 .. _frontend: ./frontend.md
-.. _python_tests: https://github.com/ewels/MegaQC/tree/master/tests
-.. _test_api.py: https://github.com/ewels/MegaQC/tree/master/megaqc/api/test_api.py
+.. _python_tests: https://github.com/MultiQC/MegaQC/tree/master/tests
+.. _test_api.py: https://github.com/MultiQC/MegaQC/tree/master/megaqc/api/test_api.py

docs/source/docs/dev/documentation.rst

@@ -10,8 +10,8 @@ Building the documentation locally
 The MegaQC documentation requires
 
 1. An installation of MegaQC to fetch the API endpoints and the Click commands.
-2. All dependencies specified in the `docs requirements.txt <https://github.com/ewels/MegaQC/blob/master/docs/requirements.txt>`_.
-   Install them by invoking: ``pip install -r docs/requirements.txt``. 
+2. All dependencies specified in the `docs requirements.txt <https://github.com/MultiQC/MegaQC/blob/master/docs/requirements.txt>`_.
+   Install them by invoking: ``pip install -r docs/requirements.txt``.
 
 After having installed all requirements run ``make api-docs && make html`` in the ``docs`` directory.
 The generated ``html`` files are found in the ``docs/_build/html`` subfolder.
@@ -23,4 +23,4 @@ Publishing the documentation
 On pushes to the ``master`` branch, the documentation is automatically built and pushed
 to the ``gh-pages`` branch. The static html files on this branch are then deployed
 to Github Pages and displayed to the outside world.
-All of this is done with the `Publish Docs Github Actions workflow <https://github.com/ewels/MegaQC/blob/master/.github/workflows/publish_docs.yaml>`.
+All of this is done with the `Publish Docs Github Actions workflow <https://github.com/MultiQC/MegaQC/blob/master/.github/workflows/publish_docs.yaml>`.

docs/source/docs/dev/frontend.rst

@@ -22,7 +22,7 @@ Note that all new pages going forward should be written using React, to
 improve the maintainability of the frontend.
 
 .. _React: https://reactjs.org/
-.. _templates: https://github.com/ewels/MegaQC/tree/master/megaqc/templates
-.. _static: https://github.com/ewels/MegaQC/tree/master/megaqc/static
-.. _react.html: https://github.com/ewels/MegaQC/tree/master/megaqc/templates/public/react.html
-.. _src: https://github.com/ewels/MegaQC/tree/master/src
+.. _templates: https://github.com/MultiQC/MegaQC/tree/master/megaqc/templates
+.. _static: https://github.com/MultiQC/MegaQC/tree/master/megaqc/static
+.. _react.html: https://github.com/MultiQC/MegaQC/tree/master/megaqc/templates/public/react.html
+.. _src: https://github.com/MultiQC/MegaQC/tree/master/src

docs/source/docs/index.rst

@@ -23,4 +23,4 @@ Indices and tables
 * :ref:`modindex`
 * :ref:`search`
 
-.. |MegaQC| image:: https://raw.githubusercontent.com/ewels/MegaQC/master/megaqc/static/img/MegaQC_logo.png
+.. |MegaQC| image:: https://raw.githubusercontent.com/MultiQC/MegaQC/master/megaqc/static/img/MegaQC_logo.png

docs/source/docs/installation/installation_dev.rst

@@ -17,7 +17,7 @@ If you’re doing development work, you need access to the source code
 
 .. code:: bash
 
-   git clone https://github.com/ewels/MegaQC
+   git clone https://github.com/MultiQC/MegaQC/
 
 2. Install Dependencies
 ------------------------------------------------

docs/source/docs/installation/installation_docker.rst

@@ -14,10 +14,10 @@ The MegaQC Docker container
 Overview
 ~~~~~~~~~~
 
-The MegaQC container is based on the `Node container <https://hub.docker.com/_/node>`_ 
+The MegaQC container is based on the `Node container <https://hub.docker.com/_/node>`_
 to compile all Javascript scripts and the `Gunicorn Flask container <https://hub.docker.com/r/tiangolo/meinheld-gunicorn-flask/dockerfile>`_
 providing Gunicorn, Flask and MegaQC preconfigured for production deployments.
-The `Gunicorn Flask <https://hub.docker.com/r/tiangolo/meinheld-gunicorn-flask/dockerfile>`_ container 
+The `Gunicorn Flask <https://hub.docker.com/r/tiangolo/meinheld-gunicorn-flask/dockerfile>`_ container
 is also the one spinning up the final server.
 
 Pulling the docker image from dockerhub
@@ -53,10 +53,10 @@ You can then run MegaQC as described above:
 Configuration
 ~~~~~~~~~~~~~~~
 
-Besides the sections below it is also recommended to read the 
+Besides the sections below it is also recommended to read the
 `Gunicorn Flask container documentation <https://github.com/tiangolo/meinheld-gunicorn-flask-docker>`_,
 which explains how to customize the ``host`` IP where Gunicorn listens
-to requests, the ``port`` the container should listen on and ``bind``, the actual 
+to requests, the ``port`` the container should listen on and ``bind``, the actual
 host and port passed to gunicorn, let alone custom Gunicorn configuration files.
 
 Environment variables
@@ -199,15 +199,15 @@ Overview
 
 The `docker-compose`_ configuration can be accessed in the `deployment folder`_.
 The docker-compose configuration provides the :ref:`megaqc_docker_container`,
-a `postgres container <https://hub.docker.com/_/postgres>`_ for the SQL database 
+a `postgres container <https://hub.docker.com/_/postgres>`_ for the SQL database
 and a `nginx container <https://hub.docker.com/_/nginx>`_ for the reverse proxy setup.
 
 Usage
 ~~~~~~~~
 
 Inside the `deployment folder`_ the `docker-compose`_ configuration
-together with the associated `.env <https://github.com/ewels/MegaQC/blob/master/deployment/.env>`_ file 
-are found. To spin up all containers simply run from inside the `deployment folder <https://github.com/ewels/MegaQC/blob/master/deployment>`_:
+together with the associated `.env <https://github.com/MultiQC/MegaQC/blob/master/deployment/.env>`_ file
+are found. To spin up all containers simply run from inside the `deployment folder <https://github.com/MultiQC/MegaQC/blob/master/deployment>`_:
 
 .. code:: bash
 
@@ -229,18 +229,18 @@ Environment variables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The default environment variables for MegaQC used when starting the :ref:`megaqc_docker_container`
-are defined inside the `.env <https://github.com/ewels/MegaQC/blob/master/deployment/.env>`_ file.
+are defined inside the `.env <https://github.com/MultiQC/MegaQC/blob/master/deployment/.env>`_ file.
 Simply edit the file and the new environment variables will be passed to the :ref:`megaqc_docker_container`.
 
 Further runtime arguments
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Further runtime arguments can be added to a 
+Further runtime arguments can be added to a
 `command section <https://docs.docker.com/compose/compose-file/#command>`_
 inside the `docker-compose`_ configuration file.
 
-.. _deployment_folder: https://github.com/ewels/MegaQC/blob/master/deployment
-.. _docker-compose: https://github.com/ewels/MegaQC/blob/master/deployment/docker-compose.yml
+.. _deployment_folder: https://github.com/MultiQC/MegaQC/blob/master/deployment
+.. _docker-compose: https://github.com/MultiQC/MegaQC/blob/master/deployment/docker-compose.yml
 .. _dockerhub: https://hub.docker.com/r/ewels/megaqc/
 
 HTTPS
@@ -256,4 +256,4 @@ Then, edit these lines to the full filepath of the respective ``.crt`` and ``.ke
     CRT_PATH=./nginx-selfsigned.crt
     KEY_PATH=./nginx-selfsigned.key
 
-After this, run the stack as described above, and then you should be able to access MegaQC on ``https://your_hostname``.
+After this, run the stack as described above, and then you should be able to access MegaQC on ``https://your_hostname``.

docs/source/docs/installation/installation_prod.rst

@@ -2,8 +2,8 @@ Production
 =============
 
 This section explains how to set up a production environment without
-the usage of container technologies. If you want to run MegaQC in a 
-containerized environment please refer to :ref:`docker_installation`. 
+the usage of container technologies. If you want to run MegaQC in a
+containerized environment please refer to :ref:`docker_installation`.
 
 1. Install the MegaQC package
 -----------------------------
@@ -169,5 +169,5 @@ If you run an older OS, ensure that the package is installed.
 
 .. _Python MySQL connector: https://dev.mysql.com/downloads/connector/python/2.1.html
 .. _PyPI package: https://pypi.python.org/pypi/mysql-connector-python/2.0.4
-.. _create an issue: https://github.com/ewels/MegaQC/issues/new
-.. _deployment_folder: https://github.com/ewels/MegaQC/blob/master/deployment
+.. _create an issue: https://github.com/MultiQC/MegaQC/issues/new
+.. _deployment_folder: https://github.com/MultiQC/MegaQC/blob/master/deployment

docs/source/docs/troubleshooting.rst

@@ -18,9 +18,9 @@ Usage
 
 -  When creating a violin plot I get an error.
 
-   - This is a known issue: https://github.com/ewels/MegaQC/issues/31
+   - This is a known issue: https://github.com/MultiQC/MegaQC/issues/31
 
 -  TypeError: '<' not supported between instances of 'NoneType' and 'float' when trying to compare data
 
-   - This is a known issue: https://github.com/ewels/MegaQC/issues/156
+   - This is a known issue: https://github.com/MultiQC/MegaQC/issues/156
    - Please ensure that your reports do not have missing fields

megaqc/templates/footer.html

@@ -6,7 +6,7 @@
     <p>
         <a href="http://multiqc.info/db" target="_blank">MegaQC v{{ version }}</a>
          - Written by Phil Ewels, Denis Moreno, Michael Milton, Tor Solli-Nowlan and Lukas Heumos,
-        available on <a href="https://github.com/ewels/MegaQC" target="_blank">GitHub</a>.
+        available on <a href="https://github.com/MultiQC/MegaQC" target="_blank">GitHub</a>.
     </p>
     <p>
       MegaQC uses

megaqc/templates/public/home.html

@@ -24,7 +24,7 @@ <h1><img id="megaqc-homepage-title-img" src="{{ url_for('static', filename='img/
   </div>
   <div class="d-xl-none">
     <p class="lead">MegaQC is a web application that collects results from multiple runs of MultiQC and allows bulk visualisation.</p>
-    <p>See the MegaQC GitHub repository for installation instructions and documentation: <a href="https://github.com/ewels/MegaQC" target="_blank">https://github.com/ewels/MegaQC</a></p>
+    <p>See the MegaQC GitHub repository for installation instructions and documentation: <a href="https://github.com/MultiQC/MegaQC" target="_blank">https://github.com/MultiQC/MegaQC/</a></p>
   </div>
 </div>
 

pyproject.toml

@@ -14,7 +14,7 @@ keywords = [
         "quality control",
 ]
 homepage = "https://megaqc.info/"
-repository = "https://github.com/ewels/MegaQC/"
+repository = "https://github.com/MultiQC/MegaQC"
 documentation = "https://megaqc.info/docs/index.html"
 classifiers = [
         "Development Status :: 4 - Beta",

setup.py

@@ -61,7 +61,7 @@
         "quality control",
     ],
     url="https://megaqc.info/",
-    download_url="https://github.com/ewels/MegaQC/releases",
+    download_url="https://github.com/MultiQC/MegaQC/releases",
     license="GPLv3",
     packages=["megaqc"],
     include_package_data=True,