move configuration into pyproject.toml (#150)

* move configuration into `pyproject.toml` * update test workflows * formatting * pin `stormevents` version * add `pytest-mock` * also test upon update to `pyproject.toml`
oceanmodeling · Apr 20, 2022 · e1edc14 · e1edc14
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -6,62 +6,19 @@ on:
       - published
 
 jobs:
-  build_wheels:
-    name: build wheel
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ ubuntu-latest ]
-        python-version: [ '3.x' ]
-    steps:
-      - name: checkout repository
-        uses: actions/checkout@v2
-      - name: install Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: load cached Python installation
-        id: cache
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.pythonLocation }}
-          key: build-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml', 'setup.*') }}
-      - name: build wheel
-        run: pip wheel . -w dist --no-deps
-      - name: save wheel
-        uses: actions/upload-artifact@v2
-        with:
-          name: build
-          path: ./dist/*.whl
-  build_sdist:
-    name: package source
+  publish:
+    name: publish package to PyPI
     runs-on: ubuntu-latest
     steps:
       - name: checkout repository
         uses: actions/checkout@v2
-      - name: install Python
-        uses: actions/setup-python@v2
-      - name: install dependencies
+      - name: install Poetry
+        uses: abatilo/actions-poetry@v2.1.3
+      - name: install Dunamai
         run: pip install dunamai
-      - name: package source
-        run: python setup.py sdist
-      - name: save source package
-        uses: actions/upload-artifact@v2
-        with:
-          name: build
-          path: ./dist/*.tar.gz
-  upload_pypi:
-    name: publish to PyPI
-    needs: [ build_wheels, build_sdist ]
-    runs-on: ubuntu-latest
-    steps:
-      - name: retrieve wheel(s) and source
-        uses: actions/download-artifact@v2
-        with:
-          name: build
-          path: dist
-      - name: upload wheel(s) and source
-        uses: pypa/[email protected]
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
+      - name: extract version from VCS
+        run: poetry version $(dunamai from any)
+      - name: build wheel and source
+        run: poetry build
+      - name: upload wheel and source
+        run: poetry publish --username __token__ --password ${{ secrets.PYPI_TOKEN }}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,44 +1,54 @@
 name: tests
 
-on: [ push ]
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - '**.py'
+      - '.github/workflows/tests.yml'
+      - 'pyproject.toml'
+  pull_request:
+    branches:
+      - main
 
 jobs:
   lint:
     name: lint
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [ '3.x' ]
     steps:
       - name: clone repository
         uses: actions/checkout@v2
       - name: install Python
         uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
       - name: load cached Python installation
         id: cache
         uses: actions/cache@v2
         with:
           path: ${{ env.pythonLocation }}
-          key: lint-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml', 'setup.*') }}
-      - name: install dependencies
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: pip install ".[development]"
+          key: lint-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+      - name: install linters
+        run: pip install flake8 oitnb
       - name: lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: lint with oitnb
+        run: oitnb . --check
   test:
     needs: lint
     name: test
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ ubuntu-latest ]
-        python-version: [ '3.6', '3.x' ]
+        os: [ ubuntu-latest, macos-latest ]
+        python-version: [ '3.6', '3.7', '3.8', '3.9', '3.x' ]
+        exclude:
+          - os: macos-latest
+            python-version: '3.x'
     steps:
       - name: clone repository
         uses: actions/checkout@v2
@@ -51,18 +61,33 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ${{ env.pythonLocation }}
-          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml', 'setup.*') }}
+          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
       - name: install dependencies
-        if: steps.cache.outputs.cache-hit != 'true'
         run: pip install ".[testing]"
       - name: run tests
-        if: matrix.python-version != '3.x' || matrix.os != 'ubuntu-latest'
         run: pytest --numprocesses auto
+  test_with_coverage:
+    needs: [ lint, test ]
+    name: test with coverage
+    runs-on: ubuntu-latest
+    steps:
+      - name: clone repository
+        uses: actions/checkout@v2
+      - name: install Python
+        uses: actions/setup-python@v2
+      - name: load cached Python installation
+        id: cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+      - name: install dependencies
+        run: pip install ".[testing]"
       - name: run tests with coverage
-        if: matrix.python-version == '3.x' && matrix.os == 'ubuntu-latest'
         run: pytest --numprocesses auto --cov . --cov-report xml:coverage.xml
+      - name: show coverage report
+        run: coverage report
       - name: upload coverage to Codecov
-        if: matrix.python-version == '3.x' && matrix.os == 'ubuntu-latest'
         uses: codecov/[email protected]
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

diff --git a/.github/workflows/tests_simple.yml b/.github/workflows/tests_simple.yml
@@ -0,0 +1,55 @@
+name: tests
+
+on:
+  push:
+    branches-ignore:
+      - main
+    paths:
+      - '**.py'
+      - '.github/workflows/tests_simple.yml'
+      - 'pyproject.toml'
+
+jobs:
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: clone repository
+        uses: actions/checkout@v2
+      - name: install Python
+        uses: actions/setup-python@v2
+      - name: load cached Python installation
+        id: cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.pythonLocation }}
+          key: lint-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+      - name: install linters
+        run: pip install flake8 oitnb
+      - name: lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: lint with oitnb
+        run: oitnb . --check
+  test:
+    needs: lint
+    name: test
+    runs-on: ubuntu-latest
+    steps:
+      - name: clone repository
+        uses: actions/checkout@v2
+      - name: install Python
+        uses: actions/setup-python@v2
+      - name: load cached Python installation
+        id: cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+      - name: install dependencies
+        run: pip install ".[testing]"
+      - name: run tests
+        run: pytest --numprocesses auto
diff --git a/adcircpy/forcing/winds/best_track.py b/adcircpy/forcing/winds/best_track.py
@@ -23,52 +23,49 @@
 
 class BestTrackForcing(VortexTrack, WindForcing):
     def __init__(
-            self,
-            storm: Union[str, PathLike, DataFrame, io.BytesIO],
-            nws: int = None,
-            interval_seconds: int = None,
-            start_date: datetime = None,
-            end_date: datetime = None,
+        self,
+        storm: Union[str, PathLike, DataFrame, io.BytesIO],
+        nws: int = None,
+        interval_seconds: int = None,
+        start_date: datetime = None,
+        end_date: datetime = None,
     ):
         if nws is None:
             nws = 20
 
         valid_nws_values = [8, 19, 20]
         assert (
-                nws in valid_nws_values
+            nws in valid_nws_values
         ), f'ATCF BestTrack can only use `nws` values in {valid_nws_values}'
 
         if interval_seconds is None:
             interval_seconds = 3600
 
         VortexTrack.__init__(
-                self,
-                storm=storm,
-                start_date=start_date,
-                end_date=end_date,
-                file_deck='b',
-                advisories=['BEST'],
+            self,
+            storm=storm,
+            start_date=start_date,
+            end_date=end_date,
+            file_deck='b',
+            advisories=['BEST'],
         )
         WindForcing.__init__(self, nws=nws, interval_seconds=interval_seconds)
 
     @classmethod
     def from_fort22(
-            cls,
-            fort22: PathLike,
-            nws: int = None,
-            interval_seconds: int = None,
-            start_date: datetime = None,
-            end_date: datetime = None,
+        cls,
+        fort22: PathLike,
+        nws: int = None,
+        interval_seconds: int = None,
+        start_date: datetime = None,
+        end_date: datetime = None,
     ) -> 'WindForcing':
-        instance = cls.from_file(path=fort22, start_date=start_date,
-                                 end_date=end_date)
-        WindForcing.__init__(instance, nws=nws,
-                             interval_seconds=interval_seconds)
+        instance = cls.from_file(path=fort22, start_date=start_date, end_date=end_date)
+        WindForcing.__init__(instance, nws=nws, interval_seconds=interval_seconds)
         return instance
 
     def summary(
-            self, output: Union[str, os.PathLike] = None,
-            overwrite: bool = False,
+        self, output: Union[str, os.PathLike] = None, overwrite: bool = False,
     ):
         min_storm_speed = numpy.min(self.data['speed'])
         max_storm_speed = numpy.max(self.data['speed'])
@@ -77,8 +74,7 @@ def summary(
         min_central_pressure = numpy.min(self.data['central_pressure'])
         max_wind_speed = numpy.max(self.data['max_sustained_wind_speed'])
         start_loc = (self.data['longitude'][0], self.data['latitude'][0])
-        end_loc = (
-        self.data['longitude'].iloc[-1], self.data['latitude'].iloc[-1])
+        end_loc = (self.data['longitude'].iloc[-1], self.data['latitude'].iloc[-1])
         f = [
             f'Summary of storm: {self.nhc_code}',
             f'min./max. track speed: {min_storm_speed} m/s, {max_storm_speed} m/s',
@@ -144,13 +140,13 @@ def clip_to_bbox(self, bbox, bbox_crs):
         msg = f'bbox must be a {Bbox} instance.'
         assert isinstance(bbox, Bbox), msg
         bbox_pol = Polygon(
-                [
-                    [bbox.xmin, bbox.ymin],
-                    [bbox.xmax, bbox.ymin],
-                    [bbox.xmax, bbox.ymax],
-                    [bbox.xmin, bbox.ymax],
-                    [bbox.xmin, bbox.ymin],
-                ]
+            [
+                [bbox.xmin, bbox.ymin],
+                [bbox.xmax, bbox.ymin],
+                [bbox.xmax, bbox.ymax],
+                [bbox.xmin, bbox.ymax],
+                [bbox.xmin, bbox.ymin],
+            ]
         )
         _switch = True
         unique_dates = numpy.unique(self.data['datetime'])
@@ -167,8 +163,7 @@ def clip_to_bbox(self, bbox, bbox_crs):
             transformer = Transformer.from_crs(df_crs, utm_crs, always_xy=True)
             p = Point(*transformer.transform(lon, lat))
             pol = p.buffer(radii)
-            transformer = Transformer.from_crs(utm_crs, bbox_crs,
-                                               always_xy=True)
+            transformer = Transformer.from_crs(utm_crs, bbox_crs, always_xy=True)
             pol = ops.transform(transformer.transform, pol)
             if _switch is True:
                 if not pol.intersects(bbox_pol):
@@ -187,16 +182,15 @@ def clip_to_bbox(self, bbox, bbox_crs):
                     break
 
         if _found_start_date is False:
-            raise Exception(
-                f'No data within mesh bounding box for storm {self.storm_id}.')
+            raise Exception(f'No data within mesh bounding box for storm {self.storm_id}.')
 
     def plot_track(
-            self,
-            axis: Axis = None,
-            show: bool = False,
-            color: str = 'k',
-            coastline: bool = True,
-            **kwargs,
+        self,
+        axis: Axis = None,
+        show: bool = False,
+        color: str = 'k',
+        coastline: bool = True,
+        **kwargs,
     ):
         kwargs.update({'color': color})
         if axis is None:
@@ -210,7 +204,7 @@ def plot_track(
             axis.quiver(row['longitude'], row['latitude'], U, V, **kwargs)
             if i % 6 == 0:
                 axis.annotate(
-                        row['datetime'], (row['longitude'], row['latitude']),
+                    row['datetime'], (row['longitude'], row['latitude']),
                 )
         if show:
             axis.axis('scaled')
@@ -224,6 +218,6 @@ def plot_wind_swath(self, isotach: int, segments: int = 91):
         plot_polygons(isotachs)
         plot_polygons(swath)
         pyplot.suptitle(
-                f'{self.nhc_code} - isotach {isotach} kt ({self.start_date} - {self.end_date})'
+            f'{self.nhc_code} - isotach {isotach} kt ({self.start_date} - {self.end_date})'
         )
         pyplot.show()