Add xarray dependencies for doctest

Author: thodson-usgs

.github/workflows/ci-osx.yaml

@@ -0,0 +1,75 @@
+name: OSX CI
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Conda
+        uses: conda-incubator/[email protected]
+        with:
+            channels: conda-forge
+            miniforge-version: latest
+            python-version: ${{ matrix.python-version }}
+
+      - name: Show info about `base` environment
+        shell: "bash -l {0}"
+        run: |
+          conda info
+          conda config --show-sources
+          conda list --show-channel-urls
+
+      - name: Set up `env`
+        shell: "bash -l {0}"
+        run: >
+          conda create -n env
+          c-compiler cxx-compiler 'clang>=12.0.1'
+          python=${{matrix.python-version}} wheel pip
+
+      - name: Show info about `env` environment
+        shell: "bash -l {0}"
+        run: |
+          conda list --show-channel-urls -n env
+
+      - name: Install numcodecs
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          export DISABLE_NUMCODECS_AVX2=""
+          python -m pip install -v -e .[test,test_extras,doctest,msgpack,zfpy,pcodec]
+
+      - name: List installed packages
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          python -m pip list
+
+      - name: Run tests
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          pytest -v
+
+      - uses: codecov/codecov-action@v3
+        with:
+          #token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+            #files: ./coverage1.xml,./coverage2.xml # optional
+            #flags: unittests # optional
+            #name: codecov-umbrella # optional
+            #fail_ci_if_error: true # optional (default = false)
+          verbose: true # optional (default = false)

.github/workflows/ci-windows.yaml

@@ -0,0 +1,67 @@
+name: Windows CI
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Conda
+        uses: conda-incubator/[email protected]
+        with:
+            channels: conda-forge
+            miniforge-version: latest
+            python-version: ${{ matrix.python-version }}
+
+      - name: Set up `env`
+        shell: "bash -l {0}"
+        run: >
+          conda create -n env
+          c-compiler cxx-compiler
+          python=${{matrix.python-version}} wheel pip
+
+      - name: Show info about `env` environment
+        shell: "bash -l {0}"
+        run: |
+          conda list --show-channel-urls -n env
+
+      - name: Install numcodecs
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          python -m pip install -v -e .[test,test_extras,doctest,msgpack,zfpy,pcodec]
+
+      - name: List installed packages
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          python -m pip list
+
+      - name: Run tests
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          pytest -v
+
+      - uses: codecov/codecov-action@v3
+        with:
+          #token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+            #files: ./coverage1.xml,./coverage2.xml # optional
+            #flags: unittests # optional
+            #name: codecov-umbrella # optional
+            #fail_ci_if_error: true # optional (default = false)
+          verbose: true # optional (default = false)

numcodecs/bitinfo.py

@@ -33,16 +33,20 @@ class BitInfo(BitRound):
 
     Examples
     --------
+    This example applies the BitInfo codec to an xarray dataset and
+    writes the data out using xarray's `to_zarr` method. Using this pattern, the
+    information content is computed chunkwise, which is recommended for
+    datasets with variable information content. Note that these data have
+    been quantized creating erroneous results, which is apparent in
+    the output. Do not use with quantized data in practice.
+
     >>> import xarray as xr
     >>> ds = xr.tutorial.open_dataset("air_temperature")
-    >>> # Note these data have already undergone lossy compression,
-    >>> # which should not be combined with bitinformation in practice
-
     >>> from numcodecs import Blosc, BitInfo
     >>> compressor = Blosc(cname="zstd", clevel=3)
     >>> filters = [BitInfo(info_level=0.99)]
     >>> encoding = {"air": {"compressor": compressor, "filters": filters}}
-    >>> ds.to_zarr('xbit.zarr', mode="w", encoding=encoding)
+    >>> _ = ds.to_zarr('xbit.zarr', mode="w", encoding=encoding)
     """
 
     codec_id = 'bitinfo'

pyproject.toml

@@ -59,7 +59,12 @@ test = [
 ]
 test_extras = [
     "importlib_metadata",
+]
+doctest = [
     "xarray",
+    "pooch",
+    "netCDF4",
+    "zarr",
 ]
 msgpack = [
     "msgpack",