Add markdown linter to style check (CI)

This adds configuration files for markdownlint, reformats markdown files
and also updated the configuration of the CI.

.gitlab-ci.yml

-#image: dumux-precice:3.3git-iterative-pr-2.2.0
-#image: dumux-precice:3.3-2.2.1
-#image: ajaust/style-check:clang-10
-image: ajaust/style-check:0.1
+image: ajaust/style-check:0.2
 
 stages:
     - check
@@ -11,9 +8,8 @@ stages:
 check-style-clang-10:
     stage: check
     script:
-        - ./scripts/format/run-clang-format.sh
-        - git diff > style-patch.diff
-        - if [ -s style-patch.diff ]; then echo "Download the style patch as artifact and apply it or run ./scripts/format/run-clang-format.sh and commit again."; false; fi
+        - ./scripts/format/run-clang-format.sh > clang-format-output.txt
+        - if [ -s clang-format-output.txt ]; then cat clang-format-output.txt; echo "Some files need reformatting. Check the output and run ./scripts/format/run-clang-format.sh and commit again."; false; fi
     needs: []
     artifacts:
         when: on_failure
@@ -24,17 +20,16 @@ check-style-clang-10:
 check-style-black:
     stage: check
     script:
-        - sudo apt-get update && sudo apt-get install -y python3 python3-distutils python-is-python3 wget
-        - wget https://bootstrap.pypa.io/get-pip.py && python get-pip.py && rm get-pip.py && ln -sf ${HOME}/.local/bin/pip3 ${HOME}/.local/bin/pip && export PATH="${HOME}/.local/bin":"${PATH}" && pip install black
+        - pip install --user black
         - black .
-        - git diff > python-style-patch.diff
-        - if [ -s python-style-patch.diff ]; then echo "Download the style patch as artifact and apply it or run black . and commit again."; false; fi
     needs: []
-    artifacts:
-        when: on_failure
-        paths:
-            - python-style-patch.diff
-        expire_in: 2 days
+
+check-style-markdownlint:
+    stage: check
+    script:
+        - sudo gem install mdl
+        - mdl .
+    needs: []
 
 .build_template: &build-tests
   stage: build

.mdl.rb

+# Enable all rules by default
+all
+
+######################################################
+# Deactivated/excluded rules
+######################################################
+
+
+######################################################
+# Adapted rules
+######################################################
+
+# Enforce dashes as symvol in lists
+rule 'MD004', :style => :dash
+# Enforce indent with four space characters. This helps with
+# mixing ordered and unordered lists
+rule 'MD007', :indent => 4
+# Extend line length for text.
+# This will complain for overly wide tables and code blocks.
+rule 'MD013', :line_length => 99999
+
+# Nested lists should be indented with four spaces.
+# Modification: Question marks should be allowed
+rule 'MD026', :punctuation => '.,;:!'
+
+# Ordered lists must have prefix that increases in order
+rule 'MD029', :style => :ordered

.mdlrc

+# Load style file (ruby script)
+style '.mdl.rb'
\ No newline at end of file

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 ## Not released yet
 
+- 2022-05-17: Added configuation for Markdown linter `markdownlint` and added it to CI. The linter can be called locally by typing `mdl .` from the root of the repository. This also led to an updated configuration of the CI.
+- 2022-05-17: Add some more documentation on how to install the adapter to the `README.md`.
 - 2022-02-18: Updated CI to use images from account `ajaust` from Dockerhub. Changed tolerance for partitioned tests to 5e-5 due to minimal changes in the solution with the new images on a new VM.
 - 2022-02-09: Made sure all private member of the adapter are suffixed with an underscore.
 - 2022-02-01: Add some extra information on the documentation in the `README.md`. Removed old/out-of-date mkdocs documentation from `doc/mkdocs`.
@@ -13,10 +15,10 @@
 - 2022-01-25: Added [description templates](https://docs.gitlab.com/ee/user/project/description_templates.html) for merge requests and issues.
 - 2022-01-12: The repository has been restructured. The main changes are:
 
-  - The adapter is now called `CouplingAdapter` and resides in `dumux-precice/`. The build process has been adapted accordingly.
-  - Tests case reside in `test/` directory and there in the corresponding subdirectory depending on whether it is a `monolithic`ly or `partitioned`ly coupled test case.
-  - Other example cases reside in the directory `examples/`. This is mainly the directory called `appl/` before, but with a new folder structure.
-  - The configuration of tests has been changed such that it is possible to build all tests using the `build_tests` target.
+    - The adapter is now called `CouplingAdapter` and resides in `dumux-precice/`. The build process has been adapted accordingly.
+    - Tests case reside in `test/` directory and there in the corresponding subdirectory depending on whether it is a `monolithic`ly or `partitioned`ly coupled test case.
+    - Other example cases reside in the directory `examples/`. This is mainly the directory called `appl/` before, but with a new folder structure.
+    - The configuration of tests has been changed such that it is possible to build all tests using the `build_tests` target.
 
   For details check out the merge request [!18 Restructure repository and tests](https://git.iws.uni-stuttgart.de/dumux-appl/dumux-precice/-/merge_requests/18)
 - 2022-01-10: Add license file. The code is licensed under GPLv3 without template exception.

README.md

@@ -21,12 +21,12 @@ The DuMuX-preCICE adapter is a DUNE module named `dumux-precice` which can be bu
 
 - DuMuX **newer** than 3.2
 
-  - Builds using the current `master` branch of DuMuX might fail.
-  - If you run into trouble with a new DuMuX release, please open an issue in the repository and add the error message that you receive.
+    - Builds using the current `master` branch of DuMuX might fail.
+    - If you run into trouble with a new DuMuX release, please open an issue in the repository and add the error message that you receive.
 
 - preCICE >=2.0.0
 
-  - The adapter is build via the DUNE build system that is based on CMake. Thus, the CMake [link instructions for preCICE](https://precice.org/installation-linking.html#cmake) apply.
+    - The adapter is build via the DUNE build system that is based on CMake. Thus, the CMake [link instructions for preCICE](https://precice.org/installation-linking.html#cmake) apply.
 
 - `wget` or `git` to download the DuMuX-preCICE adapter.
 - Optional: [`dune-subgrid`](https://www.dune-project.org/modules/dune-subgrid/) allows for modified grid geometries.
@@ -124,4 +124,4 @@ There is no publication related to this code available yet.
 ### Publications using dumux-precice
 
 - Jaust A., Weishaupt K., Mehl M., Flemisch B. (2020) Partitioned Coupling Schemes for Free-Flow and Porous-Media Applications with Sharp Interfaces. In: Klöfkorn R., Keilegavlen E., Radu F., Fuhrmann J. (eds) Finite Volumes for Complex Applications IX - Methods, Theoretical Aspects, Examples. FVCA 2020. Springer Proceedings in Mathematics & Statistics, vol 323. Springer, Cham. <https://doi.org/10.1007/978-3-030-43651-3_57>
-  - Code can be found at: <https://git.iws.uni-stuttgart.de/dumux-pub/jaust2020a>
+    - Code can be found at: <https://git.iws.uni-stuttgart.de/dumux-pub/jaust2020a>

scripts/format/run-clang-format.sh

 #!/usr/bin/env sh
 set -e
 # Runs clang-format on all *.cc and *.hh files
-find dumux-precice/ -regex '.*\.\(cc\|hh\)' -exec clang-format-10 -style=file -i {} \;
-find examples/ -regex '.*\.\(cc\|hh\)' -exec clang-format-10 -style=file -i {} \;
-find postprocessing/ -regex '.*\.\(cc\|hh\|hpp\|cpp\)' -exec clang-format-10 -style=file -i {} \;
+find dumux-precice/ -regex '.*\.\(cc\|hh\)' -exec clang-format-10 --dry-run -style=file -i {} \;
+find examples/ -regex '.*\.\(cc\|hh\)' -exec clang-format-10 --dry-run -style=file -i {} \;
+find postprocessing/ -regex '.*\.\(cc\|hh\|hpp\|cpp\)' -exec clang-format-10 --dry-run -style=file -i {} \;