Added Coverage (#391)

* coverage

* coverage

* coverage

* update requirements

* coverage xml

* merged

* install cov

* fixed tests

* fixed tests

* fix pip install for PR action

---------

Co-authored-by: Patrick Huck <phuck@lbl.gov>

.github/workflows/pull-request.yml

@@ -28,8 +28,8 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: '**/pyproject.toml'
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
       - name: Install webdriver
         run: sudo apt-get update && sudo apt-get install chromium-chromedriver
       - name: Install dependencies
@@ -38,10 +38,15 @@ jobs:
           python${{ matrix.python-version }} -m pip install `grep numpy== requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt`
           python${{ matrix.python-version }} -m pip install -r requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
           python${{ matrix.python-version }} -m pip install --upgrade pip
-          python${{ matrix.python-version }} -m pip install --no-deps .[server]
+          python${{ matrix.python-version }} -m pip install --no-deps .[server,test]
       - name: Test modules
-        run: python${{ matrix.python-version }} -m pytest tests
+        run: python${{ matrix.python-version }} -m pytest --cov=crystal_toolkit --cov-report=xml tests
       - name: Test example apps
         env:
           PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}
-        run: python${{ matrix.python-version }} -m pytest --color=yes --webdriver Chrome --headless crystal_toolkit/apps/examples/tests/
+        run: python${{ matrix.python-version }} -m pytest --cov=crystal_toolkit --cov-report=xml --color=yes --webdriver Chrome --headless crystal_toolkit/apps/examples/tests/
+      - uses: codecov/codecov-action@v1
+        if: matrix.python-version == 3.10
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml

crystal_toolkit/apps/tests/test_main.py

@@ -20,4 +20,4 @@ def test_main_app_startup(dash_duo: DashDuo):
     dash_duo.take_snapshot("main_app_startup-layout")
 
     logs = dash_duo.get_logs()
-    assert logs is None, f"Unexpected browser {logs=}"
+    assert not logs, f"Unexpected browser {logs=}"

pyproject.toml

@@ -30,6 +30,7 @@ server = ["dash-extensions", "gunicorn[gevent]", "habanero", "hiphive", "redis"]
 robocrys = ["robocrys"]
 temdiff = ["py4DSTEM>=0.13.11"]
 fermi = ["ifermi", "pyfftw"]
+phonon = ["phonopy"]
 vtk = ["dash-vtk"]
 localenv = ["dscribe"]
 figures = ["kaleido"]
@@ -135,3 +136,27 @@ no_implicit_optional = false
 [tool.versioningit.vcs]
 default-tag = "0.0.1"
 method = "git"
+
+[tool.coverage.run]
+branch = true
+include = ["crystal_toolkit/*"]
+omit = ["crystal_toolkit/apps/*",]
+
+[tool.coverage.paths]
+source = ["crystal_toolkit/"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+exclude_also = [
+    "def __repr__",
+    "if self.debug:",
+    "if settings.DEBUG",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if 0:",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+    "class .*\\bProtocol\\):",
+    "@(abc\\.)?abstractmethod",
+    ]

requirements/ubuntu-latest_py3.10.txt

@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
-#    pip-compile --output-file=requirements/ubuntu-latest_py3.10.txt pyproject.toml
+#    pip-compile --output-file=./requirements/ubuntu-latest_py3.10.txt pyproject.toml
 #
 aiofiles==22.1.0
     # via ypy-websocket

requirements/ubuntu-latest_py3.10_extras.txt

@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
-#    pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.10_extras.txt pyproject.toml
+#    pip-compile --all-extras --output-file=./requirements/ubuntu-latest_py3.10_extras.txt pyproject.toml
 #
 aiofiles==22.1.0
     # via ypy-websocket
@@ -284,6 +284,7 @@ h5py==3.11.0
     #   hdf5plugin
     #   hiphive
     #   ncempy
+    #   phonopy
     #   py4dstem
 habanero==1.2.6
     # via crystal_toolkit (pyproject.toml)
@@ -448,6 +449,7 @@ matplotlib==3.9.2
     #   boltztrap2
     #   ifermi
     #   ncempy
+    #   phonopy
     #   py4dstem
     #   pymatgen
     #   vtk
@@ -563,6 +565,7 @@ numpy==1.26.4
     #   numba
     #   numpy-stl
     #   pandas
+    #   phonopy
     #   py4dstem
     #   pyfftw
     #   pylops
@@ -775,6 +778,7 @@ pyyaml==6.0.2
     #   dask
     #   distributed
     #   jupyter-events
+    #   phonopy
     #   pre-commit
     #   pyaml
     #   pybtex
@@ -914,6 +918,7 @@ spglib==2.5.0
     #   boltztrap2
     #   hiphive
     #   ifermi
+    #   phonopy
     #   pymatgen
     #   robocrys
 sphinx==7.4.7

requirements/ubuntu-latest_py3.11.txt

@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
-#    pip-compile --output-file=requirements/ubuntu-latest_py3.11.txt pyproject.toml
+#    pip-compile --output-file=./requirements/ubuntu-latest_py3.11.txt pyproject.toml
 #
 aiofiles==22.1.0
     # via ypy-websocket

requirements/ubuntu-latest_py3.11_extras.txt

@@ -273,6 +273,7 @@ h5py==3.11.0
     #   hdf5plugin
     #   hiphive
     #   ncempy
+    #   phonopy
     #   py4dstem
 habanero==1.2.6
     # via crystal_toolkit (pyproject.toml)
@@ -437,6 +438,7 @@ matplotlib==3.9.2
     #   boltztrap2
     #   ifermi
     #   ncempy
+    #   phonopy
     #   py4dstem
     #   pymatgen
     #   vtk
@@ -552,6 +554,7 @@ numpy==1.26.4
     #   numba
     #   numpy-stl
     #   pandas
+    #   phonopy
     #   py4dstem
     #   pyfftw
     #   pylops
@@ -764,6 +767,7 @@ pyyaml==6.0.2
     #   dask
     #   distributed
     #   jupyter-events
+    #   phonopy
     #   pre-commit
     #   pyaml
     #   pybtex
@@ -903,6 +907,7 @@ spglib==2.5.0
     #   boltztrap2
     #   hiphive
     #   ifermi
+    #   phonopy
     #   pymatgen
     #   robocrys
 sphinx==7.4.7