Merged in master

Author: landreman

.coveragerc

@@ -4,6 +4,6 @@ source = simsopt
 
 [paths]
 sources = 
-    /opt/hostedtoolcache/Python/3.7.10/x64/lib/python3.7/site-packages
     /opt/hostedtoolcache/Python/3.8.10/x64/lib/python3.8/site-packages
+    /opt/hostedtoolcache/Python/3.7.10/x64/lib/python3.7/site-packages
     /opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages

.github/workflows/ci.yml

@@ -6,9 +6,14 @@
 # This appears to be a known harmless annoyance:
 # https://gitlab.alpinelinux.org/alpine/aports/-/issues/11122
 
-name: CI
+name: Simple CI
 
-on: [push, pull_request]
+on: 
+  push:
+    branches-ignore: [master]
+    tags-ignore: [v*]
+  pull_request:
+    branches-ignore: [master]
 
 jobs:
   test:
@@ -21,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7.10, 3.8.10, 3.9.5] # To sync with coveragerc
+        python-version: [3.8.10] # To sync with coveragerc
         test-type: [unit, integrated]
 
     steps:
@@ -55,9 +60,7 @@ jobs:
       #  submodules: true
 
     # We must run actions/checkout@v2 before downloading and building VMEC, since checkout deletes the contents of the directory.
-    # For now we use the mattland fork of VMEC. Once changes are pushed to mbkumar's fork, we can use that instead.
     - name: Download the VMEC2000 standalone repository
-      # run: git clone https://gitlab.com/mattland/VMEC2000.git
       run: git clone https://github.com/hiddensymmetries/VMEC2000.git
 
     - name: ls -l again
@@ -84,9 +87,7 @@ jobs:
 
     - name: Install python dependencies
       run: |
-        #pip install wheel numpy scipy jax jaxlib cmake scikit-build ninja f90nml h5py pyoculus qsc sympy
-        pip install wheel numpy f90nml scikit-build cmake qsc sympy
-        # qsc is used for an integrated test.
+        pip install wheel numpy f90nml scikit-build cmake qsc sympy pyevtk
 
     - name: Install booz_xform
       run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform
@@ -164,120 +165,62 @@ jobs:
     - name: ls in VMEC2000/python 1
       run: ls -l VMEC2000/python
 
-    # - name: Configure VMEC2000 module
-    #   run: |
-    #     cd VMEC2000/python
-    #     cp ubuntu.json cmake_config_file.json
-    #     cat cmake_config_file.json
-
-    - name: Configure VMEC2000 module
+    - name: Configure and install VMEC2000 module
       run: |
         cd VMEC2000
         cp python/machines/ubuntu.json cmake_config_file.json
         cat cmake_config_file.json
-
-    - name: Build and install VMEC2000 module
-      run: |
-        # cd VMEC2000/python
-        # python setup.py build_ext
-        cd VMEC2000
         pip install .
 
-    # - name: Install VMEC2000 module
-    #   run: |
-    #     cd VMEC2000/python
-    #     python setup.py install
-
-    # - name: ls in VMEC2000/python 2
-    #   run: ls -l VMEC2000/python
-
     - name: Try importing vmec module
       run: python -c "print(dir()); import vmec; print(dir()); print(dir(vmec)); print('package:', vmec.__package__); print('spec:', vmec.__spec__); print('doc:', vmec.__doc__); print('file:', vmec.__file__); print('path:', vmec.__path__)"
 
     - name: Install simsopt package
-      # if: "contains(matrix.test-type, 'integrated')"
       run: pip install -v .[MPI,SPEC]
 
-    #- name: Run mpi unit tests
-    #  if: "contains(matrix.test-type, 'unit')"
-    #  run: ./run_tests_mpi
-
-    #- name: Run serial unit tests
-    #  if: "contains(matrix.test-type, 'unit')"
-    #  run: |
-    #    cd tests
-    #    python3 -m unittest -v
-    
-    - name: Run examples as integrated tests
-      if: "contains(matrix.test-type, 'integrated')"
+    - name: Run examples as part of integrated tests
+      if: contains(matrix.test-type, 'integrated')
       run: |
         cd examples
-        ./run_examples
+        ./run_serial_examples
+        ./run_spec_examples
+        ./run_vmec_examples
+        ./run_spec_vmec_examples
 
     - name: Install coverage dependencies
-      if: "contains(matrix.test-type, 'unit')"
-      run: pip install coverage # tox tox-gh-actions tox-venv
+      if: contains(matrix.test-type, 'unit')
+      run: pip install coverage
 
     - name: Run tests using coverage
-      if: "contains(matrix.test-type, 'unit')"
+      if: contains(matrix.test-type, 'unit')
       run: | 
         coverage run --source=simsopt -m unittest discover -s tests
+
+    - name: Run tests using coverage
+      if: contains(matrix.test-type, 'unit')
+      run: | 
         mpiexec -n 1 coverage run -m unittest discover -k "mpi" -s tests
         mpiexec -n 2 coverage run -m unittest discover -k "mpi" -s tests
         mpiexec -n 3 coverage run -m unittest discover -k "mpi" -s tests
 
-    - name: Upload uncombined coverage to github
-      if: "contains(matrix.test-type, 'unit')"
-      uses: actions/upload-artifact@v2
-      with:
-        name: gh-actions-parallel-coverage
-        path: .coverage.*
-        if-no-files-found: error
-
-  coverage:
-    runs-on: ubuntu-18.04
-    needs: [ test ]
-    steps:
-
-    - name: Set up Python 
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.7.10
-
-    - name: Install coverage
-      run: pip install coverage
-
-    - name: Checkout simsopt 
-      uses: actions/checkout@v2
-
-    - name: Install simsopt before running coverage
-      run: pip install .
-
-    - name: Download artifact
-      uses: actions/download-artifact@v2
-      with:
-        name: gh-actions-parallel-coverage
-        path: ./
-
-    - name: Display coverage files before combine 
-      run: ls -a
-
     - name: Combine coverage reports
+      if: contains(matrix.test-type, 'unit')
       run: | 
         coverage combine
         coverage report
         coverage xml
 
     - name: Upload coverage to github
+      if: contains(matrix.test-type, 'unit')
       uses: actions/upload-artifact@v2
       with:
         name: tox-gh-actions-coverage
         path: coverage.xml
         if-no-files-found: error
 
     - name: Upload coverage to Codecov
-      # The next line prevents github from trying to upload to Codecov on forks of the repository, avoiding a permissions error
-      if: ${{ github.repository_owner == 'hiddenSymmetries' }}
+      # The last conditional on the next line prevents github from trying to upload to Codecov on forks of the repository, avoiding a permissions error
+      if: contains(matrix.test-type, 'unit') && github.repository_owner == 'hiddenSymmetries'
       uses: codecov/codecov-action@v1
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -290,3 +233,66 @@ jobs:
         fail_ci_if_error: true
         #path_to_write_report: ./coverage/codecov_report.gz
         verbose: true
+
+#    - name: Upload uncombined coverage to github
+#      if: contains(matrix.test-type, 'unit')
+#      uses: actions/upload-artifact@v2
+#      with:
+#        name: gh-actions-parallel-coverage
+#        path: .coverage.*
+#        if-no-files-found: error
+#
+#  coverage:
+#    runs-on: ubuntu-18.04
+#    needs: [ test ]
+#    steps:
+#
+#    - name: Set up Python 
+#      uses: actions/setup-python@v2
+#      with:
+#        python-version: 3.8.10
+#
+#    - name: Install coverage
+#      run: pip install coverage
+#
+#    - name: Checkout simsopt 
+#      uses: actions/checkout@v2
+#
+#    - name: Install simsopt before running coverage
+#      run: pip install .
+#
+#    - name: Download artifact
+#      uses: actions/download-artifact@v2
+#      with:
+#        name: gh-actions-parallel-coverage
+#        path: ./
+#
+#    - name: Display coverage files before combine 
+#      run: ls -a
+#
+#    - name: Combine coverage reports
+#      run: | 
+#        coverage combine
+#        coverage report
+#        coverage xml
+#
+#    - name: Upload coverage to github
+#      uses: actions/upload-artifact@v2
+#      with:
+#        name: tox-gh-actions-coverage
+#        path: coverage.xml
+#        if-no-files-found: error
+#
+#    - name: Upload coverage to Codecov
+#      uses: codecov/codecov-action@v1
+#      with:
+#        token: ${{ secrets.CODECOV_TOKEN }}
+#        file: ./coverage.xml
+#        #files: ./coverage1.xml,./coverage2.xml
+#        #directory: ./coverage/reports/
+#        flags: unittests
+#        env_vars: PYTHON
+#        name: codecov-umbrella
+#        fail_ci_if_error: true
+#        #path_to_write_report: ./coverage/codecov_report.gz
+#        verbose: true