Documentation urls check

.github/workflows/action.yml

@@ -0,0 +1,29 @@
+name: Documentation URLs Check
+
+on:
+  pull_request:
+  push:
+    branches:
+      - 'release-*'
+      - 'develop'
+      - 'staging'
+      - 'main'
+
+    tags:
+      - 'v*'
+  schedule:
+    # Run everyday at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
+    - cron: "1 2 * * *"
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        base-branch: 'staging'
+        max-depth: -1
+        check-modified-files-only: 'yes'
+        config-file: '.github/workflows/config.json'
+        file-extension: '.md'

.github/workflows/config.json

@@ -0,0 +1,7 @@
+{
+  "ignorePatterns": [
+    {
+      "pattern": "^http://docs.github", "^pkgs.org"
+    }
+  ]
+}

docs/faqs/contributor-faq.md

@@ -11,7 +11,7 @@ The following section provides general information to new contributors.
 
 * Check out the development version of OpenMS (see OpenMS [releases and installers](downloads/releases.md)).
 * Build OpenMS according to the installation instructions.
-* Read the [OpenMS Coding Conventions](https://github.com/OpenMS/OpenMS/wiki/Coding-conventions).
+* Read the [OpenMS Coding Conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html).
 * Read the [OpenMS Tutorial](../tutorials/user-tutorial.md).
 * Create a GitHub account.
 * Subscribe to the [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) or [contact us](../contact-us.md).
@@ -23,14 +23,14 @@ to `TOOLS` if they are stable enough, are fully tested, fully documented, and a
 
 ### I have written a class for OpenMS. What should I do?
 
-Follow the [OpenMS coding conventions]().
+Follow the [OpenMS coding conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html).
 
 Coding style (brackets, variable names, etc.) must conform to the conventions.
 
 * The class and all the members must be documented thoroughly.
 * Check your code with the tool  `tools/checker.php`. Call `php tools/checker.php` for detailed instructions.
 
-Please open a pull request and follow the [pull request guidelines](pull-request-checklist.md).
+Please open a pull request and follow the [pull request guidelines](../additional-resources/pull-request-checklist.md).
 
 ## Troubleshooting
 
@@ -197,4 +197,3 @@ To contribute to a bug fix:
 3. Fix the bug and add a test.
 4. Create a pull request for your branch.
 5. After approval and merge make sure the issue is closed.
-

docs/faqs/developer-faq.md

@@ -11,7 +11,7 @@ The following section provides general information to new contributors.
 
 * Check out the development version of OpenMS (see website).
 * Build OpenMS by following the [installation instructions]() or [from source](../installations/build-openms-from-source.md).
-* Read the [OpenMS Coding Conventions]()
+* Read the [OpenMS Coding Conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html)
 * Read the [OpenMS Tutorial](../tutorials/user-tutorial.md).
 * Create a GitHub account.
 * Subscribe to the [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) or [contact-us](../contact-us.md).
@@ -23,14 +23,14 @@ to `TOOLS` if they are stable enough, are fully tested, fully documented, and a
 
 ### I have written a class for OpenMS. What should I do?
 
-Follow the [OpenMS coding conventions]().
+Follow the [OpenMS coding conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html).
 
 Coding style (brackets, variable names, etc.) must conform to the conventions.
 
 * The class and all the members should be properly documented.
 * Check your code with the tool  `tools/checker.php`. Call `php tools/checker.php` for detailed instructions.
 
-Please open a pull request and follow the [pull request guidelines](pull-request-checklist.md).
+Please open a pull request and follow the [pull request guidelines](../additional-resources/pull-request-checklist.md).
 
 ### Can I use QT designer to create GUI widgets?
 

docs/guides/contributors-quickstart-guide.md

@@ -40,10 +40,10 @@ To create a fork:
 
 ### Coding conventions
 
-See the manual for coding style recommended by OpenMS: [Coding conventions](https://github.com/OpenMS/OpenMS/wiki/Coding-conventions).
+See the manual for coding style recommended by OpenMS: [Coding conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html).
 
 ```{seealso}
-[C++ Guide](https://github.com/OpenMS/OpenMS/wiki/Cpp-Guide).
+[C++ Guide](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/developer_faq.html).
 ```
 
 OpenMS automatically tests for common coding convention violations using a modified version of `cpplint`.

docs/topp-and-utils/toppas.md

@@ -13,7 +13,7 @@ The following figure shows a simple example pipeline that has just been created
 
 ![TOPPAS simple example](../images/topp/TOPPAS_simple_example.png)
 
-More information about TOPPAS can be found in the [TOPPAS tutorial](../tutorials/TOPP/TOPPAS-tutorial.md).
+More information about TOPPAS can be found in the [TOPPAS tutorial](../tutorials/TOPPAS/TOPPAS-tutorial.md).
 
 **The command line parameters of this tool are**: