build: release on push to main; sdist, wheels and pypi publish (#26)

* build: release on push to main; sdist, wheels and pypi publish * build: use setup-micromamba with bash shell and pip * test: mv input-data > data ; win-compatible paths in tests * fix: catch TypeError in try/except for non-path `masks` in windows * build: run all py versions in ubuntu; only latest in mac/win
martibosch · Aug 11, 2023 · 8151caf · 8151caf
1 parent 5bf543f
commit 8151caf
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -2,11 +2,78 @@ name: release
 
 on:
   push:
-    tags:
-      - "v*"
+    branches:
+      - main
 
 jobs:
+  make_sdist:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.11"
+
+      - name: install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: build wheels and source tarball
+        run: |
+          python -m build --sdist
+          twine check --strict dist/*
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+  build_wheels:
+    name: wheel on ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: pypa/cibuildwheel@v2
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          path: wheelhouse/*.whl
+
+  publish_dev_build:
+    needs: [make_sdist, build_wheels]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://pypi.org/p/pylandstats
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: publish to test pypi
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
+
   release:
+    if: startsWith(github.event.ref, "refs/tags/v")
+    needs: [publish_dev_build]
     name: create release
     runs-on: ubuntu-latest
     environment:
@@ -17,9 +84,6 @@ jobs:
       id-token: write
       # see https://github.com/softprops/action-gh-release/issues/236
       contents: write
-    strategy:
-      matrix:
-        python-versions: ["3.10"]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -39,23 +103,6 @@ jobs:
           sinceTag: v0.1.0
           output: RELEASE-CHANGELOG.md
 
-      - uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-versions }}
-
-      - name: install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install build twine
-
-      - name: build wheels and source tarball
-        run: |
-          python -m build
-          twine check --strict dist/*
-
-      - name: show temporary files
-        run: ls -l
-
       - name: create github release
         uses: softprops/action-gh-release@v1
         with:

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -9,23 +9,28 @@ jobs:
   test:
     strategy:
       matrix:
-        python-versions: ["3.8", "3.9", "3.10", "3.11"]
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         include:
-          - miniforge-variant: Mambaforge
-            miniforge-version: 4.11.0-4
+          - os: macos-latest
+            python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.11"
+
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
       - uses: actions/checkout@v2
 
-      - name: setup conda environment with mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          use-mamba: true
-          python-version: ${{ matrix.python-version }}
-          miniforge-variant: ${{ matrix.miniforge-variant }}
-          miniforge-version: ${{ matrix.miniforge-version }}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pip
 
       - name: install dependencies
         run: pip install tox tox-gh-actions

diff --git a/pylandstats/zonal.py b/pylandstats/zonal.py
@@ -148,13 +148,16 @@ def __init__(
                 elif not isinstance(masks, gpd.GeoDataFrame):
                     try:
                         masks = gpd.read_file(masks)
-                    except AttributeError:
+                    except (AttributeError, TypeError):
                         # AttributeError: 'list'/'numpy.ndarray' object has no
                         # attribute 'startswith'
                         # we assume that `masks` is a list-like of numpy
                         # arrays or a numpy array, in which case we rename the
                         # variable to `masks_arr` so that it is properly used
                         # below
+                        # TypeError: in windows, fiona will try to read `masks` as a
+                        # regular expression and raise a TypeError (see
+                        # https://github.com/Toblerity/Fiona/blob/master/fiona/path.py)
                         masks_arr = masks
 
                 # at this point, `masks` can either be a GeoDataFrame (in

diff --git a/tests/input-data/gmb-lausanne.gpkg → tests/data/gmb-lausanne.gpkg b/tests/input-data/gmb-lausanne.gpkg → tests/data/gmb-lausanne.gpkg
diff --git a/tests/input-data/ls100_06.npy → tests/data/ls100_06.npy b/tests/input-data/ls100_06.npy → tests/data/ls100_06.npy
diff --git a/tests/input-data/ls100_06.tif → tests/data/ls100_06.tif b/tests/input-data/ls100_06.tif → tests/data/ls100_06.tif
diff --git a/tests/input-data/ls100_12.npy → tests/data/ls100_12.npy b/tests/input-data/ls100_12.npy → tests/data/ls100_12.npy
diff --git a/tests/input-data/ls100_12.tif → tests/data/ls100_12.tif b/tests/input-data/ls100_12.tif → tests/data/ls100_12.tif
diff --git a/tests/input-data/ls250_06.npy → tests/data/ls250_06.npy b/tests/input-data/ls250_06.npy → tests/data/ls250_06.npy
diff --git a/tests/input-data/ls250_06.tif → tests/data/ls250_06.tif b/tests/input-data/ls250_06.tif → tests/data/ls250_06.tif
diff --git a/tests/input-data/ls250_12.npy → tests/data/ls250_12.npy b/tests/input-data/ls250_12.npy → tests/data/ls250_12.npy
diff --git a/tests/input-data/ls250_12.tif → tests/data/ls250_12.tif b/tests/input-data/ls250_12.tif → tests/data/ls250_12.tif
diff --git a/tests/input-data/masks_arr.npy → tests/data/masks_arr.npy b/tests/input-data/masks_arr.npy → tests/data/masks_arr.npy
diff --git a/tests/test_pylandstats.py b/tests/test_pylandstats.py
@@ -18,6 +18,9 @@
 plt.switch_backend("agg")  # only for testing purposes
 geom_crs = "epsg:4326"
 
+tests_dir = "tests"
+tests_data_dir = path.join(tests_dir, "data")
+
 
 class TestImports(unittest.TestCase):
     def test_base_imports(self):
@@ -29,9 +32,11 @@ def test_geo_imports(self):
 
 class TestLandscape(unittest.TestCase):
     def setUp(self):
-        self.ls_arr = np.load("tests/input-data/ls250_06.npy", allow_pickle=True)
+        self.ls_arr = np.load(
+            path.join(tests_data_dir, "ls250_06.npy"), allow_pickle=True
+        )
         self.ls = pls.Landscape(self.ls_arr, res=(250, 250))
-        self.landscape_fp = "tests/input-data/ls250_06.tif"
+        self.landscape_fp = path.join(tests_data_dir, "ls250_06.tif")
 
     def test_io(self):
         # test that if we provide a ndarray, we also need to provide the
@@ -330,7 +335,7 @@ def test_metrics_value_ranges(self):
         # TODO: assert 0 < ls.interspersion_juxtaposition_index() <= 100
 
     def test_transonic(self):
-        ls_arr = np.load("tests/input-data/ls250_06.npy", allow_pickle=True)
+        ls_arr = np.load(path.join(tests_data_dir, "ls250_06.npy"), allow_pickle=True)
         ls = pls.Landscape(ls_arr, res=(250, 250))
         adjacency_df = ls._adjacency_df
         self.assertIsInstance(adjacency_df, pd.DataFrame)
@@ -367,17 +372,17 @@ def setUp(self):
 
         self.landscapes = [
             pls.Landscape(
-                np.load("tests/input-data/ls100_06.npy", allow_pickle=True),
+                np.load(path.join(tests_data_dir, "ls100_06.npy"), allow_pickle=True),
                 res=(100, 100),
             ),
             pls.Landscape(
-                np.load("tests/input-data/ls250_06.npy", allow_pickle=True),
+                np.load(path.join(tests_data_dir, "ls250_06.npy"), allow_pickle=True),
                 res=(250, 250),
             ),
         ]
         self.landscape_fps = [
-            "tests/input-data/ls100_06.tif",
-            "tests/input-data/ls250_06.tif",
+            path.join(tests_data_dir, "ls100_06.tif"),
+            path.join(tests_data_dir, "ls250_06.tif"),
         ]
         self.attribute_name = "resolution"
         self.attribute_values = [100, 250]
@@ -672,8 +677,8 @@ def setUp(self):
         # between passing `Landscape` objects or filepaths is already tested
         # in `TestMultiLandscape`
         self.landscape_fps = [
-            "tests/input-data/ls250_06.tif",
-            "tests/input-data/ls250_12.tif",
+            path.join(tests_data_dir, "ls250_06.tif"),
+            path.join(tests_data_dir, "ls250_12.tif"),
         ]
         self.dates = [2006, 2012]
         self.inexistent_class_val = 999
@@ -774,21 +779,23 @@ def test_spatiotemporalanalysis_plot_metrics(self):
 
 class TestZonaAlnalysis(unittest.TestCase):
     def setUp(self):
-        self.masks_arr = np.load("tests/input-data/masks_arr.npy", allow_pickle=True)
+        self.masks_arr = np.load(
+            path.join(tests_data_dir, "masks_arr.npy"), allow_pickle=True
+        )
         self.landscape = pls.Landscape(
-            np.load("tests/input-data/ls250_06.npy", allow_pickle=True),
+            np.load(path.join(tests_data_dir, "ls250_06.npy"), allow_pickle=True),
             res=(250, 250),
         )
-        self.landscape_fp = "tests/input-data/ls250_06.tif"
+        self.landscape_fp = path.join(tests_data_dir, "ls250_06.tif")
         with rio.open(self.landscape_fp) as src:
             self.landscape_transform = src.transform
             self.landscape_crs = src.crs
-        self.masks_fp = "tests/input-data/gmb-lausanne.gpkg"
+        self.masks_fp = path.join(tests_data_dir, "gmb-lausanne.gpkg")
         # for buffer analysis
         self.geom = geometry.Point(6.6327025, 46.5218269)
         self.buffer_dists = [10000, 15000, 20000]
 
-        self.tmp_dir = path.join("tests/tmp")
+        self.tmp_dir = path.join(tests_dir, "tmp")
         os.mkdir(self.tmp_dir)
 
     def tearDown(self):
@@ -1179,8 +1186,8 @@ def test_grid_init(self):
 class TestSpatioTemporalBufferAnalysis(unittest.TestCase):
     def setUp(self):
         self.landscape_fps = [
-            "tests/input-data/ls250_06.tif",
-            "tests/input-data/ls250_12.tif",
+            path.join(tests_data_dir, "ls250_06.tif"),
+            path.join(tests_data_dir, "ls250_12.tif"),
         ]
         self.dates = [2006, 2012]
         self.base_mask = gpd.GeoSeries(