Coverage notebooks (#299)

CI Setup
=======
* use full pip install for asdf schema tests
* use two jobs for sphinx
* use nbval in test action
* only run coverage and notebooks on ubuntu/3.8


General
======
* use settings from setup.cfg
* added pyproject.toml to allow install setuptools_scm etc in one shot
* [setup] declare test deps as extra-deps
* use pip install -e .[test] to install everything in one shot
* min req. python in recipe


Coverage measuring
===============

* remove "weldx/visualization/*" from codecov ignore
* remove some # pragma: no cover
* removed some "no cover" pragmas due to notebook cov

Co-authored-by: Cagtay Fabry <[email protected]>

.github/workflows/pytest.yml

@@ -41,14 +41,23 @@ jobs:
             ${{ runner.os }}-pip-
 
       - name: pip installs
-        run: |
-          pip install pytest pytest-cov pytest-xdist setuptools_scm
-          pip install -e .
+        run: pip install -e .[test]
+
       - name: run pytest
         run: |
-          pytest --runslow -n2
+          pytest -n 2 --runslow tests/
+          echo "Exited with '$?'"
+
+      - name: run pytest on notebooks (append coverage)
+        if: (matrix.os == 'ubuntu-latest') && (matrix.py == '3.8')
+        run: |
+          pytest -n 2 --dist loadscope --nbval --current-env --cov=weldx --cov-append tutorials/
           echo "Exited with '$?'"
-          coverage xml
+
+      - name: coverage xml (combination is performed by pytest-cov)
+        if: (matrix.os == 'ubuntu-latest') && (matrix.py == '3.8')
+        run: coverage xml
 
       - name: codecov.io
+        if: (matrix.os == 'ubuntu-latest') && (matrix.py == '3.8')
         uses: codecov/codecov-action@v1

.github/workflows/pytest_asdf.yml

@@ -16,8 +16,7 @@ jobs:
           python-version: ${{ matrix.py }}
       - name: pip installs
         run: |
-          pip install pytest pytest-cov setuptools_scm
-          pip install .
+          pip install -e .[test]
       - name: run pytest
         run: |
           pytest --asdf-tests --ignore=tests/ --no-cov

.typo-ci.yml

@@ -31,6 +31,8 @@ excluded_words:
   - functools
   - boltons
   - meshio
+  - pytest-xdist
+  - nbval
   # matplotlib ----------------------------------
   - gca
   - mpl
@@ -151,6 +153,7 @@ excluded_words:
   - quickstart
   - nsecond
   - iterutils
+  - pyproject
   # German ---------------------------------------
   - Bundesanstalt
   - für

codecov.yml

@@ -25,4 +25,3 @@ coverage:
 ignore:
   - "tests"
   - "*__init__.py"
-  - "weldx/visualization/*"

conda.recipe/meta.yaml

@@ -8,17 +8,17 @@ source:
     path: ..
 
 build:
-  script: python setup.py install --single-version-externally-managed --record=record.txt
+  script: pip install . -v
   number: 0
   noarch: python
 
 requirements:
-    build:
-        - python
-        - setuptools
+    host:
+        - python >=3.8
+        - pip
         - setuptools_scm
     run:
-        - python
+        - python >=3.8
         # dependencies are defined in setup.py
         {% for dep in data['install_requires'] %}
         - {{ dep.lower() }}
@@ -27,6 +27,7 @@ requirements:
 test:
     imports:
         - weldx
+        - weldx.visualization
 
 about:
     home: www.bam.de/weldx

environment.yml

@@ -27,6 +27,8 @@ dependencies:
   - pydocstyle=5
   - pytest
   - pytest-cov
+  - pytest-xdist
+  - nbval
   # Plotting
   - ipykernel
   - ipympl

pyproject.toml

@@ -0,0 +1,8 @@
+[build-system]
+requires = [
+  "wheel",
+  "setuptools >= 40.9.0",
+  "setuptools_scm",
+  "numpy",  # for bottleneck
+]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -31,7 +31,7 @@ project_urls =
     Changelog = https://github.com/BAMweldx/weldx/blob/master/CHANGELOG.md
 
 [options]
-packages = weldx
+packages = find:
 python_requires = >=3.8
 setup_requires =
     setuptools >=38.3.0
@@ -53,6 +53,13 @@ install_requires =
     k3d
     meshio
 
+[options.extras_require]
+test =
+    pytest
+    pytest-cov
+    pytest-xdist
+    nbval
+
 include_package_data = True
 
 [options.entry_points]

weldx/asdf/util.py

@@ -113,7 +113,7 @@ def write_read_buffer(
     return read_buffer(buffer, open_kwargs)
 
 
-def get_yaml_header(file) -> str:  # pragma: no cover
+def get_yaml_header(file) -> str:
     """Read the YAML header part (excluding binary sections) of an ASDF file.
 
     Parameters
@@ -145,7 +145,7 @@ def get_yaml_header(file) -> str:  # pragma: no cover
 _write_read_buffer = write_read_buffer
 
 
-def notebook_fileprinter(file, lexer="YAML"):  # pragma: no cover
+def notebook_fileprinter(file, lexer="YAML"):
     """Print the code from file/BytesIO  to notebook cell with syntax highlighting.
 
     Parameters
@@ -178,7 +178,7 @@ def notebook_fileprinter(file, lexer="YAML"):  # pragma: no cover
     )
 
 
-def asdf_json_repr(file, path: Tuple = None, **kwargs):  # pragma: no cover
+def asdf_json_repr(file, path: Tuple = None, **kwargs):
     """Display YAML header using IPython JSON display repr.
 
     This function works in JupyterLab.

weldx/geometry.py

@@ -1671,9 +1671,7 @@ def rasterize(self, raster_width):
         return np.hstack([raster_data, last_point])
 
     @UREG.wraps(None, (None, _DEFAULT_LEN_UNIT, None, None, None), strict=False)
-    def plot(
-        self, raster_width=1, axes=None, fmt=None, axes_equal=False
-    ):  # pragma: no cover
+    def plot(self, raster_width=1, axes=None, fmt=None, axes_equal=False):
         """Plot the trace.
 
         Parameters
@@ -2218,7 +2216,7 @@ def plot(
         color: Union[int, Tuple[int, int, int], Tuple[float, float, float]] = None,
         label: str = None,
         show_wireframe: bool = True,
-    ) -> matplotlib.axes.Axes:  # pragma: no cover
+    ) -> matplotlib.axes.Axes:
         """Plot the geometry.
 
         Parameters

weldx/measurement.py

@@ -97,7 +97,7 @@ def _add_node(
         if parent_node is not None:
             graph.add_edge(parent_node, node)
 
-    def plot(self, axes=None):  # pragma: no cover
+    def plot(self, axes=None):
         """Plot the measurement chain.
 
         Parameters

weldx/transformations/cs_manager.py

@@ -1752,7 +1752,7 @@ def plot(
         show_traces: bool = True,
         show_vectors: bool = True,
         show_wireframe: bool = False,
-    ):  # pragma: no cover
+    ):
         """Plot the coordinate systems of the coordinate system manager.
 
         Parameters

weldx/transformations/local_cs.py

@@ -840,7 +840,7 @@ def plot(
         show_origin: bool = True,
         show_trace: bool = True,
         show_vectors: bool = True,
-    ):  # pragma: no cover
+    ):
         """Plot the coordinate system.
 
         Parameters

weldx/util.py

@@ -161,7 +161,7 @@ def sine(
     amp: pint.Quantity,
     bias: pint.Quantity = None,
     phase: pint.Quantity = Q_(0, "rad"),
-) -> TimeSeries:  # pragma: no cover
+) -> TimeSeries:
     """Create a simple sine TimeSeries from quantity parameters.
 
     f(t) = amp*sin(f*t+phase)+bias
@@ -192,7 +192,7 @@ def sine(
 
 def lcs_coords_from_ts(
     ts: TimeSeries, time: Union[pd.DatetimeIndex, pint.Quantity]
-) -> xr.DataArray:  # pragma: no cover
+) -> xr.DataArray:
     """Create translation coordinates from a TimeSeries at specific timesteps.
 
     Parameters
@@ -1128,7 +1128,7 @@ def __init__(self, xarray_obj):
         """Construct a WeldX xarray object."""
         self._obj = xarray_obj
 
-    def interp_like(self, da, *args, **kwargs) -> xr.DataArray:  # pragma: no cover
+    def interp_like(self, da, *args, **kwargs) -> xr.DataArray:
         """Interpolate DataArray along dimensions of another DataArray.
 
         Provides some utility options for handling out of range values and broadcasting.