Update test run (#1340)

holoviz · May 30, 2024 · 0cdbd43 · 0cdbd43
1 parent d6cbacf
commit 0cdbd43
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Showing 6 changed files with 9 additions and 135 deletions.
diff --git a/.coveragerc b/.coveragerc
diff --git a/.github/codecov.yml b/.github/codecov.yml
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -159,11 +159,6 @@ jobs:
           conda activate test-environment
           python -c "import numba; print('Numba', numba.__version__)"
           python -c "import numpy; print('Numpy', numpy.__version__)"
-      - name: doit test_lint
-        if: runner.os == 'Linux'
-        run: |
-          conda activate test-environment
-          doit test_lint
       - name: download data
         run: |
           conda activate test-environment
@@ -182,59 +177,6 @@ jobs:
         run: |
           conda activate test-environment
           doit test_examples
-      - name: codecov
-        run: |
-          conda activate test-environment
-          codecov
-
-  test_pip:
-    name: Pip tests on ${{ matrix.os }} with Python ${{ matrix.python-version }}
-    needs: [pre_commit]
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ['ubuntu-latest', 'macos-latest']
-        python-version: ["3.12"]
-    steps:
-      - name: Checkout source
-        uses: actions/checkout@v3
+      - uses: codecov/codecov-action@v4
         with:
-          fetch-depth: 0
-      - name: Install Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Update setuptools
-        run: |
-          pip install --upgrade setuptools
-      - name: Install pyctdev
-        run: |
-          pip install pyctdev
-      - name: doit develop_install
-        run: |
-          doit ecosystem=pip develop_install -o tests -o examples
-      - name: download data
-        run: |
-          python scripts/download_data.py
-      - name: doit env_capture
-        run: |
-          doit ecosystem=pip env_capture
-      - name: doit test_lint
-        if: runner.os == 'Linux'
-        run: |
-          doit ecosystem=pip test_lint
-      - name: doit test_unit
-        run: |
-          doit ecosystem=pip test_unit
-      - name: doit test_unit_nojit
-        run: |
-          doit ecosystem=pip test_unit_nojit
-        env:
-          NUMBA_DISABLE_JIT: 1
-      - name: doit test_examples
-        run: |
-          doit ecosystem=pip test_examples
-      - name: codecov
-        run: |
-          codecov
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/examples/conftest.py b/examples/conftest.py
@@ -1,7 +1,5 @@
 from importlib.util import find_spec
 
-import platform
-
 collect_ignore_glob = [
     "tiling.ipynb",
 ]
@@ -16,21 +14,3 @@
         "user_guide/7_Networks.ipynb",
         "user_guide/8_Polygons.ipynb",
     ]
-
-# 2023-07-21 with following error:
-# nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 300 seconds.
-# Here is a preview of the cell contents:
-# -------------------
-# import holoviews.operation.datashader as hd
-# import holoviews as hv
-# hv.extension("bokeh")
-# circle = hv.Graph(edges, label='Bokeh edges').opts(node_size=5)
-# hnodes = circle.nodes.opts(size=5)
-# dscirc = (hd.spread(hd.datashade(circle))*hnodes).relabel("Datashader edges")
-# circle + dscirc
-# ------------------------------ Captured log call ------------------------------
-# ERROR    traitlets:client.py:841 Timeout waiting for execute reply (300s).
-if platform.system() == "Windows":
-    collect_ignore_glob += [
-        "user_guide/7_Networks.ipynb",
-    ]
diff --git a/setup.py b/setup.py
@@ -65,18 +65,13 @@
     # 'spatialpandas',
 
     # [tests]
-    'codecov',
     'geodatasets',
-    'flake8',
-    'nbconvert',
-    'nbformat',
-    'nbsmoke[verify] >0.5',
     'netcdf4',
     'nbval',
     'psutil',
     'pytest-xdist',
     # 'pyarrow',
-    'pytest <8',  # Fails lint with IPynbFile is deprecated
+    'pytest',
     'pytest-benchmark',
     'pytest-cov',
     # 'rasterio',
@@ -88,16 +83,11 @@
 
 extras_require = {
     'tests': geopandas + [
-        'codecov',
         'geodatasets',
-        'flake8',
-        'nbconvert',
-        'nbformat',
-        'nbsmoke[verify] >0.5',
         'nbval',
         'netcdf4',
         'pyarrow',
-        'pytest <8',  # Fails lint with IPynbFile is deprecated
+        'pytest',
         'pytest-benchmark',
         'pytest-cov',
         'psutil',

diff --git a/tox.ini b/tox.ini
@@ -3,22 +3,14 @@
 
 [tox]
 #          python version                     test group                     extra envs  extra commands
-envlist = {py39,py310,py311,py312}-{lint,unit,unit_nojit,unit_deploy,examples,all,examples_extra}-{default}-{dev,pkg}
+envlist = {py39,py310,py311,py312}-{unit,unit_nojit,unit_deploy,examples,all,examples_extra}-{default}-{dev,pkg}
 build = wheel
 
-[_lint]
-description = Flake check python and notebooks, and verify notebooks
-deps = .[tests]
-# verify takes quite a long time - maybe split into flakes and lint?
-commands = flake8
-           pytest --nbsmoke-lint -k ".ipynb" examples
-           pytest --nbsmoke-verify -k ".ipynb" examples
-
 [_unit]
 description = Run unit tests
 deps = .[tests]
-commands = pytest datashader -n logical --dist loadgroup --cov=./datashader --cov-append --benchmark-skip
-           pytest datashader --benchmark --cov=./datashader --cov-append
+commands = pytest datashader -n logical --dist loadgroup --cov=./datashader --cov-report=xml --cov-append --benchmark-skip
+           pytest datashader --benchmark --cov=./datashader --cov-report=xml --cov-append
 
 [_unit_deploy]
 description = Run unit tests without coverage
@@ -28,7 +20,7 @@ commands = pytest datashader
 [_unit_nojit]
 description = Run select unit tests with numba jit disabled
 deps = .[tests]
-commands = pytest datashader -k "not test_tiles" -n logical --dist loadgroup --cov=./datashader --cov-append --benchmark-skip
+commands = pytest datashader -k "not test_tiles" -n logical --dist loadgroup --cov=./datashader --cov-report=xml --cov-append --benchmark-skip
 
 [_examples]
 description = Test that default examples run
@@ -44,8 +36,7 @@ commands = pytest --nbsmoke-run -k ".ipynb" --ignore-nbsmoke-skip-run
 [_all]
 description = Run all tests (but only including default examples)
 deps = .[examples, tests]
-commands = {[_lint]commands}
-           {[_unit_deploy]commands}
+commands = {[_unit_deploy]commands}
            {[_examples]commands}
 
 [_pkg]
@@ -58,23 +49,13 @@ commands = pkg: {[_pkg]commands}
            unit: {[_unit]commands}
            unit_nojit: {[_unit_nojit]commands}
            unit_deploy: {[_unit_deploy]commands}
-           lint: {[_lint]commands}
            examples: {[_examples]commands}
            examples_extra: {[_examples_extra]commands}
            all: {[_all]commands}
 
 deps = unit: {[_unit]deps}
        unit_nojit: {[_unit_nojit]deps}
        unit_deploy: {[_unit_deploy]deps}
-       lint: {[_lint]deps}
        examples: {[_examples]deps}
        examples_extra: {[_examples_extra]deps}
        all: {[_all]deps}
-
-[flake8]
-include = *.py
-# run_tests.py is generated by conda build, which appears to have a
-# bug resulting in code being duplicated a couple of times.
-exclude = .git,__pycache__,.tox,.eggs,*.egg,doc,dist,build,_build,.ipynb_checkpoints,run_test.py
-ignore = E,
-         W