Testing in Github Actions for 3 OSs (ActivitySim#2)

* fix for using mamba
* self install to get _version
* strategy on three os
* matrix test
* require dask
* require networkx
* required libs for tests only
* required zarr for tests only
* remove version flag in doctests
* get missing DIST skims into zarr

.github/workflows/run-tests.yml

@@ -8,12 +8,15 @@ on:
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.9]
-
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.9"]
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -23,13 +26,20 @@ jobs:
       - name: Install dependencies
         uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: testing-env
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          use-mamba: true
           environment-file: envs/testing.yml
           python-version: ${{ matrix.python-version }}
+          activate-environment: testing-env
           auto-activate-base: false
+          auto-update-conda: false
+      - name: Install sharrow
+        run: |
+          python -m pip install --no-deps -e .
       - name: Conda checkup
         run: |
-          conda info
+          conda info -a
           conda list
       - name: Lint with flake8
         run: |
@@ -39,4 +49,4 @@ jobs:
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-          pytest
+          python -m pytest

.gitignore

@@ -130,3 +130,6 @@ dmypy.json
 _version.py
 .idea
 .vscode
+
+# Sharrow
+!sharrow/example_data/skims.zarr/**

docs/walkthrough/encoding.ipynb

@@ -55,7 +55,6 @@
    "source": [
     "# check versions\n",
     "import packaging\n",
-    "assert packaging.version.parse(sh.__version__) >= packaging.version.parse(\"1.0.0\")\n",
     "assert packaging.version.parse(xr.__version__) >= packaging.version.parse(\"0.20.2\")"
    ]
   },

docs/walkthrough/one-dim.ipynb

@@ -39,7 +39,6 @@
    "source": [
     "# check versions\n",
     "import packaging\n",
-    "assert packaging.version.parse(sh.__version__) >= packaging.version.parse(\"1.0.0\")\n",
     "assert packaging.version.parse(xr.__version__) >= packaging.version.parse(\"0.20.2\")"
    ]
   },

docs/walkthrough/two-dim.ipynb

@@ -39,7 +39,6 @@
    "source": [
     "# TEST check versions\n",
     "import packaging\n",
-    "assert packaging.version.parse(sh.__version__) >= packaging.version.parse(\"1.0.0\")\n",
     "assert packaging.version.parse(xr.__version__) >= packaging.version.parse(\"0.20.2\")"
    ]
   },

envs/testing.yml

@@ -8,8 +8,17 @@ dependencies:
   - pandas>=1.2
   - pyarrow
   - xarray
+  - dask
+  - networkx
   - numba>=0.53
   - numexpr
   - filelock
   - flake8
+  # required for testing
   - pytest
+  - pytest-cov
+  - pytest-regressions
+  - pytest-xdist
+  - nbmake
+  - openmatrix
+  - zarr

setup.cfg

@@ -18,6 +18,8 @@ install_requires =
     numba >= 0.53
     numexpr
     filelock
+    dask
+    networkx
 
 [flake8]
 exclude =

sharrow/example_data/skims.zarr/DIST/.zarray

@@ -0,0 +1,22 @@
+{
+    "chunks": [
+        25,
+        25
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<f4",
+    "fill_value": "NaN",
+    "filters": null,
+    "order": "C",
+    "shape": [
+        25,
+        25
+    ],
+    "zarr_format": 2
+}

sharrow/example_data/skims.zarr/DIST/.zattrs

@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "otaz",
+        "dtaz"
+    ]
+}