ci: automatically check markdown links

.github/workflows/build.yml

@@ -1,7 +1,7 @@
 name: build
 
 on:
-  # Trigger analysis when pushing in master or pull requests, and when creating
+  # Trigger analysis when pushing in main or pull requests, and when creating
   # a pull request. 
   push:
     branches:

.github/workflows/fair-software.yml

@@ -1,6 +1,11 @@
 name: fair-software
 
-on: push
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+      types: [opened, synchronize, reopened]
 
 jobs:
   verify:

.github/workflows/markdown-link-check.yml

@@ -0,0 +1,20 @@
+name: markdown-link-check
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+
+  markdown-link-check:
+    name: Check markdown links
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        config-file: '.mlc-config.json'

.mlc-config.json

@@ -0,0 +1,37 @@
+{
+    "_comment": "Markdown Link Checker configuration, see https://github.com/gaurav-nelson/github-action-markdown-link-check and https://github.com/tcort/markdown-link-check",
+    "ignorePatterns": [
+        {
+            "pattern": "^http://localhost"
+        },
+        {
+          "pattern": "^https://doi.org/<replace-with-created-DOI>"
+        },
+        {
+          "pattern": "^https://github.com/.*/settings/secrets/actions$"
+        },
+        {
+          "pattern": "^https://github.com/organizations/.*/repositories/new"
+        },
+        {
+          "pattern": "^https://test.pypi.org"
+        },
+        {
+          "pattern": "git@github.com:DeepRank/deeprank-core/*"
+        },
+        {
+          "pattern": "^https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>"
+        },
+        {
+          "pattern": "^https://readthedocs.org/dashboard/import.*"
+        },
+        {
+          "pattern": "^https://opensource.org/license/*",
+          "//comment": "for some reason this is flagged as a broken link even though it is not."
+        }
+    ],
+    "replacementPatterns": [
+    ],
+    "retryOn429": true,
+    "timeout": "20s"
+}

CONTRIBUTING.rst

@@ -34,7 +34,7 @@ You want to make some kind of change to the code base
 
 #. (**important**) announce your plan to the rest of the community *before you start working*. This announcement should be in the form of a (new) issue;
 #. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
-#. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest master commit. While working on your feature branch, make sure to stay up to date with the master branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions `here <https://help.github.com/articles/configuring-a-remote-for-a-fork/>`__ and `here <https://help.github.com/articles/syncing-a-fork/>`__);
+#. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest main commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions `here <https://help.github.com/articles/configuring-a-remote-for-a-fork/>`__ and `here <https://help.github.com/articles/syncing-a-fork/>`__);
 #. make sure the existing tests still work by running ``python setup.py test``;
 #. add your own tests (if necessary);
 #. update or expand the documentation;

README.md

@@ -6,7 +6,7 @@
 | **package** |  [![PyPI version](https://badge.fury.io/py/deeprankcore.svg)](https://badge.fury.io/py/deeprankcore) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/f3f98b2d1883493ead50e3acaa23f2cc)](https://app.codacy.com/gh/DeepRank/deeprank-core?utm_source=github.com&utm_medium=referral&utm_content=DeepRank/deeprank-core&utm_campaign=Badge_Grade) |
 | **docs** | [![Documentation Status](https://readthedocs.org/projects/deeprankcore/badge/?version=latest)](https://deeprankcore.readthedocs.io/en/latest/?badge=latest) [![DOI](https://zenodo.org/badge/450496579.svg)](https://zenodo.org/badge/latestdoi/450496579) |
 | **tests** | [![Build Status](https://github.com/DeepRank/deeprank-core/actions/workflows/build.yml/badge.svg)](https://github.com/DeepRank/deeprank-core/actions) ![Linting status](https://github.com/DeepRank/deeprank-core/actions/workflows/linting.yml/badge.svg?branch=main) [![Coverage Status](https://coveralls.io/repos/github/DeepRank/deeprank-core/badge.svg?branch=main)](https://coveralls.io/github/DeepRank/deeprank-core?branch=main) |
-| **license** |  [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)  |
+| **license** |  [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/license/apache-2-0/)  |
 
 
 ## Overview