Release version 1.2

.github/codecov.yml

@@ -0,0 +1,15 @@
+codecov:
+  require_ci_to_pass: yes
+  notify:
+    after_n_builds: 3   # allow regression + unit tests + pylbo to pass before notification
+
+comment:
+  require_changes: true
+  layout: "diff, flags"
+
+coverage:
+  status:
+    patch: off
+    project:
+      default:
+        threshold: 2%

.github/issue_template.md

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+## Issue description
+<!-- A short description of the issue. Also add label(s) indicating if it is a feature request, bug report or something else.
+Feel free to delete sections that are not applicable. -->
+
+## Feature request
+<!-- What would you like to see added to the code?
+If you want start a discussion instead, feel free to open a discussion in the corresponding repository tab or ask us through Slack. -->
+
+
+## Bug report
+**Minimal example for reproduction**
+<!-- Paste your code between the quotation marks below. -->
+```
+
+```
+
+**Actual result**
+<!-- Result obtained when the above piece of code is run. This can be a description, screenshot, console statements etc. -->
+
+**Expected result**
+<!-- Which result do you expect instead? -->
+
+**Version info**
+- Legolas version:
+- Pylbo version:
+- Python version:
+- Version of relevant libraries (matplotlib, numpy, etc.):

.github/pull_request_template.md

@@ -1,42 +1,19 @@
-Hi, thanks for the pull request! To make sure everything stays nice and consistent, here is a default template which you can use.
-It also includes a checklist of small things that are usually forgotten or overlooked. You may remove parts that are not applicable to the current PR
-(including these sentences).
-
-Cheers,
-
-Legolas dev team
-
 ## PR description
-
-> fill or delete
+<!-- A short description of the pull request. Feel free to delete sections that are not applicable.-->
 
 ## New features
+**Legolas**
+-
 
-> fill or delete
+**Pylbo**
+-
 
 ## Bugfixes
+**Legolas**
+-
 
-> fill or delete
-
+**Pylbo**
+-
 ## Checklist
-
-**Source code stuff**
-- [ ] everything is nicely formatted using [Black-like code style](https://black.readthedocs.io/en/stable/the_black_code_style.html)
-- [ ] use-statements should use `use mod_xxx, only:` as much as possible
-- [ ] things that can go in a separate module, should go in a separate module
-- [ ] code additions|changes are also added|changed in the docstrings
-
-**Testing stuff**
-- [ ] all tests pass
-- [ ] in case of new features, new tests are added
-
-**Website stuff**
-- [ ] relevant pages on the website are edited, if relevant
-- [ ] on the edited pages, the `last_modified_at` frontmatter key is updated
-- [ ] all links render as they should, check through a local `bundle exec jekyll serve` in the `docs` directory
-- [ ] additions to the parfile are also added to `parameters_file.md`
-
-**Release stuff**
-(only if this is a merge-in-master release)
-- [ ] bump version number
-- [ ] changelog pages on the website are updated
+- [ ] all tests pass (and for new features, new tests are added)
+- [ ] documentation has been updated (if applicable)

.github/workflows/docs.yml

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+name: docs
+
+on:
+  push:
+    branches: [ master, develop ]
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  develop:
+    runs-on: ubuntu-latest
+
+    # only run on PR or push to develop, skip on master
+    if: ${{ contains(github.base_ref, 'develop') || contains(github.ref, 'refs/heads/develop') }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install ford graphviz
+        sudo apt-get install graphviz
+        pip install -U sphinx
+        pip install numpydoc sphinx-rtd-theme lazy-object-proxy==1.4 sphinx-autoapi
+
+    - name: Generate documentation
+      run: |
+        cd docs
+        python generate_docs.py develop
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: ${{ contains(github.ref, 'refs/heads/develop') }}
+      with:
+          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+          external_repository: n-claes/legolas.science-dev
+          publish_branch: main
+          publish_dir: ./docs
+          cname: dev.legolas.science
+          enable_jekyll: true
+          full_commit_message: 'dev: deploy n-claes/legolas@${{ github.sha }}'
+
+  stable:
+    runs-on: ubuntu-latest
+
+    # only run on push to master, skip for develop
+    if: ${{ contains(github.ref, 'refs/heads/master') }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install ford graphviz
+        sudo apt-get install graphviz
+        pip install -U sphinx
+        pip install numpydoc sphinx-rtd-theme lazy-object-proxy==1.4 sphinx-autoapi
+
+    - name: Generate documentation
+      run: |
+        cd docs
+        python generate_docs.py stable
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY_STABLE }}
+          external_repository: n-claes/legolas.science-stable
+          publish_branch: main
+          publish_dir: ./docs
+          cname: legolas.science
+          enable_jekyll: true
+          full_commit_message: 'stable: deploy n-claes/legolas@${{ github.sha }}'

.github/workflows/legolas.yml

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+name: legolas
+
+on:
+  push:
+    branches: [master, develop]
+  pull_request:
+    branches: [master, develop]
+
+env:
+  CC: /usr/bin/gcc-9
+  FC: /usr/bin/gfortran-9
+  PFUNIT_DIR: /home/runner/work/legolas/legolas/tests/pFUnit/build/installed
+  LEGOLASDIR: /home/runner/work/legolas/legolas
+  ARPACK_ROOT: /home/runner/work/legolas/legolas/tests/arpack-ng
+
+jobs:
+  test:
+    name: "${{ matrix.name }}"
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: unit-tests
+            coverage: true
+          - name: regression
+            coverage: true
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        sudo add-apt-repository ppa:ubuntu-toolchain-r/test
+        sudo apt update
+        sudo apt-get install gfortran-9
+        sudo apt-get -y install cmake
+        sudo apt-get install libblas-dev
+        sudo apt-get install liblapack-dev
+        sudo apt-get install lcov
+        gfortran-9 --version
+        cmake --version
+        which gcov
+        which gcov-9
+
+    - name: Install Python dependencies & Pylbo
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest numpy matplotlib f90nml tqdm psutil pytest-mpl
+        cd post_processing
+        python setup.py develop
+
+    - name: Cache pFUnit
+      id: pfunit-cache
+      uses: actions/cache@v1
+      with:
+        path: tests/pFUnit/
+        key: ${{ runner.os }}-pfunitv1
+
+    - name: Build pFUnit
+      if: steps.pfunit-cache.outputs.cache-hit != 'true'
+      run: |
+        cd tests/
+        git clone https://github.com/Goddard-Fortran-Ecosystem/pFUnit.git
+        cd pFUnit
+        mkdir build
+        cd build
+        cmake .. -DSKIP_MPI=YES -DSKIP_OPENMP=YES -DSKIP_FHAMCREST=YES
+        make -j 2 tests
+        make -j 2 install
+
+    - name: Cache ARPACK
+      id: arpack-cache
+      uses: actions/cache@v1
+      with:
+        path: tests/arpack-ng/
+        key: ${{ runner.os }}-arpackv2
+
+    - name: Build ARPACK
+      if: steps.arpack-cache.outputs.cache-hit != 'true'
+      run: |
+        cd tests
+        git clone https://github.com/opencollab/arpack-ng.git
+        cd arpack-ng
+        mkdir build
+        mkdir installed
+        cd build
+        cmake -DEXAMPLES=OFF -DMPI=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=../installed ..
+        make -j 2
+        sudo make -j 2 install
+
+    - name: Compile Legolas
+      run: |
+        mkdir build
+        cd build
+        if [[ "${{ matrix.coverage }}" ]]; then
+          cmake -DCoverage=ON ..
+        else
+          cmake ..
+        fi
+        make -j 2
+
+    - name: Run tests
+      run: |
+        # depending on unit or regression tests we use different coverage options
+        if [[ "${{ matrix.name }}" == "unit-tests" ]]; then
+          cd $LEGOLASDIR/tests/unit_tests
+          mkdir build
+          cd build
+          cmake -DCoverage=ON ..
+          make -j 2
+          cd ..
+          ./test_legolas
+        elif [[ "${{ matrix.name }}" == "regression" ]]; then
+          cd $LEGOLASDIR/tests/regression_tests
+          pytest -v regression.py test*
+        fi
+        if [[ "${{ matrix.coverage }}" ]]; then
+          # generate coverage report
+          cd $LEGOLASDIR
+          mkdir coverage
+          cd coverage
+          lcov --capture --directory $LEGOLASDIR/build \
+             --output-file ${{ matrix.name }}.info \
+             --gcov-tool /usr/bin/gcov-9
+        fi
+        # filter out coverage files
+        find $LEGOLASDIR/build -name '*.gc*' -delete
+
+    - name: Archive failed logs
+      uses: actions/upload-artifact@v2
+      if: failure()
+      with:
+        name: failed_logs
+        path: tests/regression_tests/image_comparisons
+
+    - name: Upload coverage report
+      uses: codecov/codecov-action@v1
+      if: ${{ matrix.coverage }}
+      with:
+        files: ./coverage/${{ matrix.name }}.info
+        flags: legolas