diff --git a/.github/workflows/publish_docs.yaml b/.github/workflows/publish_docs.yaml index ecf92113..49c195be 100644 --- a/.github/workflows/publish_docs.yaml +++ b/.github/workflows/publish_docs.yaml @@ -41,7 +41,7 @@ jobs: # TODO: We could also build latex & PDF documentation and upload them as artifacts - name: Deploy - if: ${{ github.ref == 'refs/heads/master' }} + if: ${{ github.ref == 'refs/heads/main' }} uses: peaceiris/actions-gh-pages@v3 with: github_token: ${{ secrets.GITHUB_TOKEN }} diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 2ddae3d6..4a1594f3 100644 --- a/CHANGELOG.rst +++ b/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 diff --git a/README.rst b/README.rst index 1d430cb1..a3033879 100644 --- a/README.rst +++ b/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/main/docs/source/images/megaqc_homepage.png :alt: MegaQC homepage Screenshot of the MegaQC home page. @@ -37,11 +37,9 @@ 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 -.. |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 - :target: https://travis-ci.org/ewels/MegaQC +.. |MegaQC| image:: https://raw.githubusercontent.com/MultiQC/MegaQC/main/megaqc/static/img/MegaQC_logo.png +.. |Docker| image:: https://img.shields.io/docker/automated/multiqc/megaqc.svg?style=flat-square + :target: https://hub.docker.com/r/multiqc/megaqc/ .. |Gitter| image:: https://img.shields.io/badge/gitter-%20join%20chat%20%E2%86%92-4fb99a.svg?style=flat-square :target: https://gitter.im/ewels/MegaQC .. |Documentation| image:: https://img.shields.io/badge/Documentation-passing-passing diff --git a/deployment/docker-compose.yml b/deployment/docker-compose.yml index 5ad7539a..0542e0a8 100644 --- a/deployment/docker-compose.yml +++ b/deployment/docker-compose.yml @@ -2,7 +2,7 @@ version: "3.7" services: megaqc: - image: ewels/megaqc + image: multiqc/megaqc build: .. volumes: # Share the static files via a volume diff --git a/docs/source/_templates/index.html b/docs/source/_templates/index.html index 63521763..0bfcef58 100644 --- a/docs/source/_templates/index.html +++ b/docs/source/_templates/index.html @@ -26,8 +26,8 @@

Home
  • Docs
  • MultiQC
    • -
  • Gitter
    • -
  • GitHub
    • +
  • Gitter
    • +
  • GitHub
    • @@ -186,7 +186,7 @@

    Still not sure?

    diff --git a/docs/source/conf.py b/docs/source/conf.py index ba5cd031..5073d5aa 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -67,9 +67,9 @@ "display_github": True, # Set the following variables to generate the resulting github URL for each page. # Format Template: https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/blob/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ suffix }} - "github_user": "ewels", + "github_user": "MultiQC", "github_repo": "MegaQC", - "github_version": "master/docs", + "github_version": "main/docs", "conf_py_path": "/source/", } @@ -95,7 +95,7 @@ def find_source(): filename = "megaqc/%s#L%d-L%d" % find_source() except Exception: filename = info["module"].replace(".", "/") + ".py" - tag = "master" - # TODO use this after the first release: tag = 'master' if 'dev' in release else ('v' + release) + tag = "main" + # TODO use this after the first release: tag = 'main' 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) diff --git a/docs/source/docs/dev/backend.rst b/docs/source/docs/dev/backend.rst index 1b796032..27cba9a4 100644 --- a/docs/source/docs/dev/backend.rst +++ b/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/main/megaqc/model/models.py +.. _user/models.py: https://github.com/MultiQC/MegaQC/blob/main/megaqc/user/models.py +.. _megaqc/api: https://github.com/MultiQC/MegaQC/tree/main/megaqc/api +.. _megaqc/rest_api: https://github.com/MultiQC/MegaQC/tree/main/megaqc/rest_api +.. _views.py: https://github.com/MultiQC/MegaQC/blob/main/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/main/megaqc/rest_api/schemas.py +.. _public/views.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/public/views.py +.. _user/views.py: https://github.com/MultiQC/MegaQC/tree/main/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/main/tests +.. _test_api.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/api/test_api.py diff --git a/docs/source/docs/dev/documentation.rst b/docs/source/docs/dev/documentation.rst index 6bc8dcca..b1b2fc3f 100644 --- a/docs/source/docs/dev/documentation.rst +++ b/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 `_. - Install them by invoking: ``pip install -r docs/requirements.txt``. +2. All dependencies specified in the `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. @@ -20,7 +20,7 @@ Simply open a generated ``html`` file in your favorite browser to read the docum Publishing the documentation --------------------------------- -On pushes to the ``master`` branch, the documentation is automatically built and pushed +On pushes to the ``main`` 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 `. +All of this is done with the `Publish Docs Github Actions workflow `. diff --git a/docs/source/docs/dev/frontend.rst b/docs/source/docs/dev/frontend.rst index 8ac647c4..23c83c5e 100644 --- a/docs/source/docs/dev/frontend.rst +++ b/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 \ No newline at end of file +.. _templates: https://github.com/MultiQC/MegaQC/tree/main/megaqc/templates +.. _static: https://github.com/MultiQC/MegaQC/tree/main/megaqc/static +.. _react.html: https://github.com/MultiQC/MegaQC/tree/main/megaqc/templates/public/react.html +.. _src: https://github.com/MultiQC/MegaQC/tree/main/src diff --git a/docs/source/docs/index.rst b/docs/source/docs/index.rst index 0801d53f..7ec46e76 100644 --- a/docs/source/docs/index.rst +++ b/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/main/megaqc/static/img/MegaQC_logo.png diff --git a/docs/source/docs/installation/installation_dev.rst b/docs/source/docs/installation/installation_dev.rst index 76457f1b..86149404 100644 --- a/docs/source/docs/installation/installation_dev.rst +++ b/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 ------------------------------------------------ diff --git a/docs/source/docs/installation/installation_docker.rst b/docs/source/docs/installation/installation_docker.rst index f6933906..38b8e4dc 100644 --- a/docs/source/docs/installation/installation_docker.rst +++ b/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 `_ +The MegaQC container is based on the `Node container `_ to compile all Javascript scripts and the `Gunicorn Flask container `_ providing Gunicorn, Flask and MegaQC preconfigured for production deployments. -The `Gunicorn Flask `_ container +The `Gunicorn Flask `_ container is also the one spinning up the final server. Pulling the docker image from dockerhub @@ -27,7 +27,7 @@ To run MegaQC with docker, simply use the following command: .. code:: bash - docker run -p 80:80 ewels/megaqc + docker run -p 80:80 multiqc/megaqc This will pull the latest image from `dockerhub`_ and run MegaQC on port 80. @@ -42,21 +42,21 @@ MegaQC code from GitHub. Simply cd to the MegaQC root directory and run .. code:: bash - docker build . -t ewels/megaqc + docker build . -t multiqc/megaqc You can then run MegaQC as described above: .. code:: bash - docker run -p 80:80 ewels/megaqc + docker run -p 80:80 multiqc/megaqc 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 `_, 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 @@ -83,21 +83,21 @@ Running MegaQC for example with a custom database password works as follows: .. code-block:: bash - docker run -e DB_PASS=someotherpassword ewels/megaqc + docker run -e DB_PASS=someotherpassword multiqc/megaqc Furthermore, be aware that the default latest tag will typically be a development version and may not be very stable. You can specify a tagged version to run a release instead: .. code:: bash - docker run -p 80:80 ewels/megaqc:v0.1 + docker run -p 80:80 multiqc/megaqc:v0.2.0 Also note that docker will use a local version of the image if it exists. To pull the latest version of MegaQC use the following command: .. code:: bash - docker pull ewels/megaqc + docker pull multiqc/megaqc Using persistent data ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -117,13 +117,13 @@ To create or re-use a docker volume named ``pg_data``: .. code:: bash - docker run -p 80:80 -v pg_data:/usr/local/lib/postgresql ewels/megaqc + docker run -p 80:80 -v pg_data:/usr/local/lib/postgresql multiqc/megaqc The same can be done for a log directory volume called ``pg_logs`` .. code:: bash - docker run -p 80:80 -v pg_data:/usr/local/lib/postgresql -v pg_logs:/var/log/postgresql ewels/megaqc + docker run -p 80:80 -v pg_data:/usr/local/lib/postgresql -v pg_logs:/var/log/postgresql multiqc/megaqc If you did not specify a volume name, docker will have given it a long hex string as a unique name. If you do not use volumes frequently, you @@ -181,7 +181,7 @@ on ``localhost:5432``, looks as follows: .. code:: bash - docker run --network="host" -p 5432 ewels/megaqc + docker run --network="host" -p 5432 multiqc/megaqc Note that by default ``localhost=127.0.0.1``. @@ -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 `_ for the SQL database +a `postgres container `_ for the SQL database and a `nginx container `_ for the reverse proxy setup. Usage ~~~~~~~~ Inside the `deployment folder`_ the `docker-compose`_ configuration -together with the associated `.env `_ file -are found. To spin up all containers simply run from inside the `deployment folder `_: +together with the associated `.env `_ file +are found. To spin up all containers simply run from inside the `deployment folder `_: .. code:: bash @@ -229,19 +229,19 @@ Environment variables ^^^^^^^^^^^^^^^^^^^^^^^^^^ The default environment variables for MegaQC used when starting the :ref:`megaqc_docker_container` -are defined inside the `.env `_ file. +are defined inside the `.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 `_ 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 -.. _dockerhub: https://hub.docker.com/r/ewels/megaqc/ +.. _deployment_folder: https://github.com/MultiQC/MegaQC/blob/main/deployment +.. _docker-compose: https://github.com/MultiQC/MegaQC/blob/main/deployment/docker-compose.yml +.. _dockerhub: https://hub.docker.com/r/multiqc/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``. \ No newline at end of file +After this, run the stack as described above, and then you should be able to access MegaQC on ``https://your_hostname``. diff --git a/docs/source/docs/installation/installation_prod.rst b/docs/source/docs/installation/installation_prod.rst index 89354cf2..4039d24d 100644 --- a/docs/source/docs/installation/installation_prod.rst +++ b/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/main/deployment diff --git a/docs/source/docs/troubleshooting.rst b/docs/source/docs/troubleshooting.rst index 52095665..4327a39e 100644 --- a/docs/source/docs/troubleshooting.rst +++ b/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 diff --git a/megaqc/templates/footer.html b/megaqc/templates/footer.html index dc482720..9c7add40 100644 --- a/megaqc/templates/footer.html +++ b/megaqc/templates/footer.html @@ -6,7 +6,7 @@

    MegaQC v{{ version }} - Written by Phil Ewels, Denis Moreno, Michael Milton, Tor Solli-Nowlan and Lukas Heumos, - available on GitHub. + available on GitHub.

    MegaQC uses diff --git a/megaqc/templates/nav.html b/megaqc/templates/nav.html index 69e76ce5..4fd953a9 100644 --- a/megaqc/templates/nav.html +++ b/megaqc/templates/nav.html @@ -19,7 +19,7 @@ About{%- if request.path == "/home" %} (current){% endif %}

  • - Get Help + Get Help
    • diff --git a/megaqc/templates/public/home.html b/megaqc/templates/public/home.html index 68c7ae4c..e632f6d2 100644 --- a/megaqc/templates/public/home.html +++ b/megaqc/templates/public/home.html @@ -24,7 +24,7 @@

    MegaQC is a web application that collects results from multiple runs of MultiQC and allows bulk visualisation.

    -

    See the MegaQC GitHub repository for installation instructions and documentation: https://github.com/ewels/MegaQC

    +

    See the MegaQC GitHub repository for installation instructions and documentation: https://github.com/MultiQC/MegaQC/

    diff --git a/pyproject.toml b/pyproject.toml index 111a008c..4d0a2cce 100644 --- a/pyproject.toml +++ b/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", diff --git a/setup.py b/setup.py index 903eab11..cfc93c21 100644 --- a/setup.py +++ b/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,