Move to Github actions (#102)

* Add GitHub actions workflow
* Make tests executable from top-level directory.
* Add codecov to install script.
* Remove Travis configuration file.

.travis-data/install_script.sh → .ci/install_script.sh

@@ -5,9 +5,8 @@
 # Be verbose, and stop with error as soon there's one
 set -ev
 
-cd ${TRAVIS_BUILD_DIR}
-
-pip install -U pip
+pip install codecov
+pip install -U pip setuptools wheel
 
 case "$INSTALL_TYPE" in
     dev)
@@ -17,4 +16,8 @@ case "$INSTALL_TYPE" in
         python setup.py sdist
         ls -1 dist/ | xargs -I % pip install dist/%[dev]
         ;;
+    dev_bdist_wheel)
+        python setup.py bdist_wheel
+        ls -1 dist/ | xargs -I % pip install dist/%[dev]
+        ;;
 esac

.coveragerc

@@ -0,0 +1,7 @@
+[run]
+source = z2pack
+
+[report]
+exclude_lines =
+    # Ignore lines used only for mypy runs
+    if ty\.TYPE_CHECKING:

.github/workflows/ci.yml

@@ -0,0 +1,121 @@
+name: Continuous Integration
+
+on: [push, pull_request]
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+        install-type: [dev]
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Install apt dependencies
+      run: |
+        sudo apt update -qq
+        sudo apt install -qq graphviz
+
+    - uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: pip-${{ matrix.python-version }}-${{ matrix.install-type }}-${{ hashFiles('**/setup.json')
+          }}
+        restore-keys: pip-${{ matrix.python-version }}-${{ matrix.install-type }}
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install the python project
+      env:
+        INSTALL_TYPE: ${{ matrix.install-type }}
+      run: .ci/install_script.sh
+
+    - name: Build documentation
+      env:
+        READTHEDOCS: 'True'
+      run: SPHINXOPTS='-nW' make -C doc html
+    - uses: actions/upload-artifact@v2
+      with:
+        name: doc-build
+        path: doc/build/html
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+        install-type: [dev]
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Install apt dependencies
+      run: |
+        sudo apt update -qq
+        sudo apt install -qq graphviz
+
+    - uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: pip-${{ matrix.python-version }}-${{ matrix.install-type }}-${{ hashFiles('**/setup.json')
+          }}
+        restore-keys: pip-${{ matrix.python-version }}-${{ matrix.install-type }}
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install the python project
+      env:
+        INSTALL_TYPE: ${{ matrix.install-type }}
+      run: .ci/install_script.sh
+
+    - name: Run pre-commit
+      run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1
+        )
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+        install-type: [dev]
+        include:
+        - python-version: 3.8
+          install-type: dev_sdist
+        - python-version: 3.8
+          install-type: dev_bdist_wheel
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Install apt dependencies
+      run: |
+        sudo apt update -qq
+        sudo apt install -qq graphviz
+
+    - uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: pip-${{ matrix.python-version }}-${{ matrix.install-type }}-${{ hashFiles('**/setup.json')
+          }}
+        restore-keys: pip-${{ matrix.python-version }}-${{ matrix.install-type }}
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install the python project
+      env:
+        INSTALL_TYPE: ${{ matrix.install-type }}
+      run: .ci/install_script.sh
+
+    - name: Run pytest
+      run: pytest --cov=z2pack --cov-config=.coveragerc
+    - name: Run codecov
+      run: codecov

.github/workflows_source/ci.yml

@@ -0,0 +1,91 @@
+name: Continuous Integration
+
+on: [push, pull_request]
+
+_anchors:
+  checkout: &CHECKOUT
+    name: Checkout code
+    uses: actions/checkout@v2
+
+  apt-dependencies: &APT_DEPENDENCIES
+    name: Install apt dependencies
+    run: |
+      sudo apt update -qq
+      sudo apt install -qq graphviz
+
+  pip-cache: &PIP_CACHE
+    uses: actions/cache@v2
+    with:
+      path: ~/.cache/pip
+      key: pip-${{ matrix.python-version }}-${{ matrix.install-type }}-${{ hashFiles('**/setup.json') }}
+      restore-keys: pip-${{ matrix.python-version }}-${{ matrix.install-type }}
+
+  python-setup: &PYTHON_SETUP
+    name: Set up Python
+    uses: actions/setup-python@v2
+    with:
+      python-version: ${{ matrix.python-version }}
+
+  install-project: &INSTALL_PROJECT
+    name: Install the python project
+    env:
+      INSTALL_TYPE: ${{ matrix.install-type }}
+    run: .ci/install_script.sh
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+        install-type: [dev]
+    steps:
+      - *CHECKOUT
+      - *APT_DEPENDENCIES
+      - *PIP_CACHE
+      - *PYTHON_SETUP
+      - *INSTALL_PROJECT
+      - name: Build documentation
+        env:
+          READTHEDOCS: "True"
+        run: SPHINXOPTS='-nW' make -C doc html
+      - uses: actions/upload-artifact@v2
+        with:
+          name: doc-build
+          path: doc/build/html
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+        install-type: [dev]
+    steps:
+      - *CHECKOUT
+      - *APT_DEPENDENCIES
+      - *PIP_CACHE
+      - *PYTHON_SETUP
+      - *INSTALL_PROJECT
+      - name: Run pre-commit
+        run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+        install-type: [dev]
+        include:
+          - python-version: 3.8
+            install-type: dev_sdist
+          - python-version: 3.8
+            install-type: dev_bdist_wheel
+    steps:
+      - *CHECKOUT
+      - *APT_DEPENDENCIES
+      - *PIP_CACHE
+      - *PYTHON_SETUP
+      - *INSTALL_PROJECT
+      - name: Run pytest
+        run: pytest --cov=z2pack --cov-config=.coveragerc
+      - name: Run codecov
+        run: codecov

.gitignore

@@ -51,6 +51,7 @@ tests/.pytest_cache
 .pytest_cache/v/cache
 .coverage
 .coverage*
+!.coveragerc
 htmlcov
 
 # editors

.pre-commit-config.yaml

@@ -5,9 +5,22 @@ repos:
   - id: yapf
     language: system
 
-- repo: git://github.com/guykisel/prospector-mirror
-  rev: 7ff847e779347033ebbd9e3b88279e7f3a998b45
+- repo: local
   hooks:
-  - id: prospector
+  - id: pylint
+    name: pylint
+    entry: pylint
     language: system
-    exclude: '^(doc/)|(examples/)|(futures/)'
+    types: [python]
+    exclude: '^(doc/)|(examples/)|(futures/)|(utils/)'
+
+  - id: interpolate-workflows
+    name: Interpolate Github workflows
+    entry: python ./utils/interpolate_yaml_anchors.py
+    language: system
+    files: |
+      (?x)^(
+        .github/(.)*|
+        utils/interpolate_yaml_anchors.py
+      )$
+    pass_filenames: false

.pylintrc

@@ -50,7 +50,7 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-disable=too-few-public-methods,too-many-public-methods,bad-continuation,wrong-import-position,line-too-long,locally-disabled,wildcard-import,locally-enabled,too-many-instance-attributes,cyclic-import
+disable=too-few-public-methods,too-many-public-methods,bad-continuation,wrong-import-position,line-too-long,locally-disabled,wildcard-import,locally-enabled,too-many-instance-attributes,cyclic-import,duplicate-code
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 46.4.0", "wheel"]
+build-backend = "setuptools.build_meta"

setup.py

@@ -24,10 +24,8 @@
     'plot': ['matplotlib'],
     'tb': ['tbmodels>=1.1.1'],
     'doc': ['sphinx', 'sphinx-rtd-theme', 'sphinx-pyreverse', 'pylint==2.4.4'],
-    'dev': [
-        'prospector==1.2.0', 'pytest~=6.0', 'pytest-cov', 'yapf==0.29',
-        'pre-commit', 'pylint==2.4.4'
-    ],
+    'dev':
+    ['pytest~=6.0', 'pytest-cov', 'yapf==0.29', 'pre-commit', 'pylint==2.4.4'],
 }
 EXTRAS['dev'] += EXTRAS['plot'] + EXTRAS['tb'] + EXTRAS['doc']
 

tests/fp/test_vasp.py

@@ -34,13 +34,14 @@ def inner(build_dir):
 
 
 @pytest.fixture
-def vasp_system_no_potcar():
+def vasp_system_no_potcar(sample):
     """
     Create a VASP system without the POTCAR file.
     """
     def inner(build_dir):
+        samples_dir = sample('vasp')
         input_files = [
-            'samples/vasp/' + name
+            os.path.join(samples_dir, name)
             for name in ['CHGCAR', 'INCAR', 'POSCAR', 'wannier90.win']
         ]
         return z2pack.fp.System(

tests/local_config.yml

@@ -0,0 +1 @@
+local_config.yml.example

tests/monkeypatch_data.py

@@ -27,7 +27,7 @@ def patch_surface_data(monkeypatch):
     """
     Monkeypatch the SurfaceData class so that it can be set from a nested list of WCC and list of t-values.
     """
-    def __init__(self, wcc_list, t_list=None):  # noqa
+    def __init__(self, wcc_list, t_list=None):
         if t_list is None:
             t_list = np.linspace(0, 1, len(wcc_list))
         self.lines = SortedList(key=lambda x: x.t)

tests/plottest_helpers.py

@@ -32,7 +32,11 @@ def assert_image_equal(disable_diff_save, pytestconfig):
     Save the current figure to a temporary file and check that it's the same as the reference image of the given name.
     """
     def inner(name, tol=1e-6):
-        path = './reference_plots/' + name + '.png'
+        path = os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), 'reference_plots',
+            name + '.png'
+        )
+
         if not os.path.exists(path):
             plt.savefig(path)
             raise ValueError('Reference plot did not exist.')

tests/test_read_mmn.py

@@ -7,10 +7,10 @@
 import z2pack
 
 
-def test_read(compare_data):
+def test_read(compare_data, sample):
     compare_data(
         lambda x, y: np.equal(x, y).all(),
-        z2pack.fp._read_mmn.get_m('samples/mmn/bi.mmn')
+        z2pack.fp._read_mmn.get_m(sample('mmn/bi.mmn'))
     )