Prepare v1.0.1 (#357)

* Fix README

* Fix zenodo contributor list

* Add Singularity instruction to README

* Copy Python frontend module to build dir always

Fixes #317

* Fix NMR

* Add NMR note in manual

* Add doc strings for H_... interation operators

* Add warning for complex NMR tensor eigenvalues

* Fix typo

* Check for NaN in NMR tensor

* Handle missing MW guess orbitals, fixes #338 (#341)

* Simplify GHA workflow

* Create mrchem-gha.yml

* Move code coverage job to GHA

* Move Minazo linting to GHA

* Install clang-format with APT

* Clean up

* Say bye to Travis

* Danger lints

* Simple

* Remove Travis CI badge

* Update DANGER_GITHUB_API_TOKEN

* Scramble formatting to check Minazo works

* Appease Minazo, the mighty bot

* Fix runtime failure while reading basis set for SAD guess (#344)

* Debug issue with the conda package

* Perfect trimming of string

* Token

* Try with GITHUB_TOKEN

* Refactor Danger action

* Try to fix Minazo

* Try to heal Minazo, part N

* Update Gemfile.lock

* Fix precision issue with chk initial guess (#347)

* Change fetch-depth (#348)

* Change fetch-depth

See here: danger/danger#1103 (comment)

* Check if GITHUB_TOKEN is necessary

* Giggles

* Which one do I  need?

* Tokens

* Stupid tokens

* Token in the wild

* Don't know

* Try something else

* Remove conditional

* back to pull_request

* Make it stop

* Revert

* Clean up actions (#350)

* Clean up actions

* Fix YAML syntax

* Fix MPI deadlock for shared-mem with bank

* Update token in Minazo workflow

* Use v1 of checkout action

* Limit Eigen to single thread (#352)

Threading lead to highly unpredictable results
for large matrix-matrix multiplications.

* Change clone command to https version (#353)

* Change clone command to https version

* Change clone command to https version

* Misc fixes for v1.0.1 (#355)

* Minor fixes in printed output

- Print orbital norms regardless of MPI ownership.
- Use proper absolute threshold for printed status
  of energy convergergence.

* Fix README error in Singluarity command

* Remove non-existing git version from tools/betzy.env

* Force grid refinement on HydrogenFunction, closes #354

* Decommission Minazo (#356)

* Bump version 1.0.1

Co-authored-by: Roberto Di Remigio <[email protected]>
Co-authored-by: Roberto Di Remigio <[email protected]>
Co-authored-by: Luca Frediani <[email protected]>

.github/mrchem-codecov.yml

@@ -0,0 +1,12 @@
+name: mrchem-codecov
+channels:
+  - conda-forge
+dependencies:
+  - cmake
+  - cxx-compiler
+  - eigen
+  - lcov
+  - mrcpp
+  - ninja
+  - nlohmann_json
+  - xcfun

.github/mrchem-gha.yml

@@ -0,0 +1,11 @@
+name: mrchem-gha
+channels:
+  - conda-forge
+dependencies:
+  - cmake
+  - cxx-compiler
+  - eigen
+  - mrcpp
+  - ninja
+  - nlohmann_json
+  - xcfun

.github/workflows/build-test.yml

@@ -26,28 +26,37 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.6
-      uses: actions/setup-python@v2
+    - name: Cache conda
+      uses: actions/cache@v1
+      env:
+        CACHE_NUMBER: 0  # Increase this value to reset cache if .github/mrchem-gha.yml has not changed
       with:
-        python-version: 3.6
+        path: ~/conda_pkgs_dir
+        key:
+          ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/mrchem-gha.yml') }}
+
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+          auto-update-conda: true
+          auto-activate-base: false
+          activate-environment: mrchem-gha
+          environment-file: .github/mrchem-gha.yml
+          channel-priority: true
+          python-version: 3.6
+          use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
 
-    - name: Install dependencies
-      run: |
-        sudo chown -R $USER $CONDA
-        $CONDA/bin/conda create --name mrchem python=3.6 eigen mrcpp xcfun nlohmann_json ninja -c conda-forge
     - name: Configure
-      shell: bash
+      shell: bash -l {0}
       run: |
-        source $CONDA/bin/activate mrchem
-        python ./setup --type=$BUILD_TYPE --omp --arch-flags=false --generator=Ninja --prefix=$GITHUB_WORKSPACE/Software/MRChem build --cmake-options="-DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DPYTHON_EXECUTABLE=$CONDA_PREFIX/bin/python"
+        python ./setup --type=$BUILD_TYPE --omp --arch-flags=false --generator=Ninja --prefix=$GITHUB_WORKSPACE/Software/MRChem build
+        
     - name: Build
-      shell: bash
+      shell: bash -l {0}
       run: |
-        source $CONDA/bin/activate mrchem
         cmake --build build --config $BUILD_TYPE --target install -- -v -d stats
+        
     - name: Test
-      shell: bash
+      shell: bash -l {0}
       run: |
         cd build
-        source $CONDA/bin/activate mrchem
         ctest -C $BUILD_TYPE --output-on-failure --verbose

.github/workflows/code-coverage.yml

@@ -0,0 +1,54 @@
+name: Compute code coverage for MRChem
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+env:
+  BUILD_TYPE: Debug
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up environment
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+          auto-update-conda: true
+          auto-activate-base: false
+          activate-environment: mrchem-codecov
+          environment-file: .github/mrchem-codecov.yml
+          channel-priority: true
+          python-version: 3.6
+
+    - name: Configure
+      shell: bash -l {0}
+      run: |
+        python ./setup --type=$BUILD_TYPE --arch-flags=false --coverage --generator=Ninja --prefix=$GITHUB_WORKSPACE/Software/MRChem build
+  
+    - name: Build
+      shell: bash -l {0}
+      run: |
+        cmake --build build --config $BUILD_TYPE --target install -- -v -d stats
+    
+    - name: Test MRChem and generate coverage report
+      shell: bash -l {0}
+      run: |
+        cd build
+        ctest -C $BUILD_TYPE --output-on-failure --verbose
+        lcov --version
+        lcov --directory . --capture --output-file coverage.info
+        lcov --remove coverage.info '/usr/*' --output-file coverage.info
+        lcov --remove coverage.info 'external/*' --output-file coverage.info
+        lcov --remove coverage.info 'test/*' --output-file coverage.info
+        lcov --list coverage.info
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1