Merge branch 'main' into chunksize-empty-arrays

.circleci/config.yml

@@ -0,0 +1,42 @@
+# This builds a preview of the docs which can be seen on pull requests. It
+# also uses the .github/workflows/docs-preview.yml GitHub Actions workflow.
+
+# This is separate from the GitHub Actions build that builds the docs, which
+# also deploys the docs
+version: 2
+
+# Aliases to reuse
+_defaults: &defaults
+  docker:
+    # CircleCI maintains a library of pre-built images
+    # documented at https://circleci.com/docs/2.0/circleci-images/
+    - image: cimg/python:3.10.2
+  working_directory: ~/repo
+
+jobs:
+  Build Docs Preview:
+    <<: *defaults
+    steps:
+      - checkout
+      - attach_workspace:
+          at: ~/
+      - run:
+          name: Install dependencies
+          no_output_timeout: 25m
+          command: |
+            cd docs
+            pip install -r requirements.txt
+      - run:
+          name: Build docs
+          no_output_timeout: 25m
+          command: |
+            cd docs
+            make html
+      - store_artifacts:
+          path: docs/_build/html
+
+workflows:
+  version: 2
+  default:
+    jobs:
+      - Build Docs Preview

.github/workflows/docs-preview.yml

@@ -0,0 +1,21 @@
+name: Docs Preview
+on: [status]
+jobs:
+  circleci_artifacts_redirector_job:
+    if: "${{ github.event.context == 'ci/circleci: Build Docs Preview' }}"
+    runs-on: ubuntu-latest
+    name: Run CircleCI artifacts redirector
+    steps:
+      - name: GitHub Action step
+        id: step1
+        uses: larsoner/circleci-artifacts-redirector-action@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          artifact-path: 0/docs/_build/html/index.html
+          circleci-jobs: Build Docs Preview
+          job-title: Click here to see a preview of the documentation.
+          api-token: ${{ secrets.CIRCLECI_TOKEN }}
+      - name: Check the URL
+        if: github.event.status != 'pending'
+        run: |
+          curl --fail ${{ steps.step1.outputs.url }} | grep $GITHUB_SHA

.github/workflows/docs.yml

@@ -22,7 +22,7 @@ jobs:
           conda config --add channels conda-forge
           conda update -q conda
           conda info -a
-          conda create -n test-environment python=${{ matrix.python-version }} pyflakes pytest pytest-doctestplus numpy hypothesis doctr sphinx myst-parser sphinx_rtd_theme pytest-cov pytest-flakes
+          conda create -n test-environment python=${{ matrix.python-version }} --file docs/requirements.txt
           conda init
 
       - name: Build Docs
@@ -51,3 +51,14 @@ jobs:
           conda activate test-environment
           cd docs
           make html
+
+      # Note, the gh-pages deployment requires setting up a SSH deploy key.
+      # See
+      # https://github.com/JamesIves/github-pages-deploy-action/tree/dev#using-an-ssh-deploy-key-
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@v4
+        if: ${{ github.ref == 'refs/heads/main' }}
+        with:
+          folder: docs/_build/html
+          ssh-key: ${{ secrets.DEPLOY_KEY }}
+          clean-exclude: benchmarks/

.github/workflows/tests.yml

@@ -5,7 +5,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12-dev']
+        # https://numpy.org/neps/nep-0029-deprecation_policy.html
+        numpy-version: ['1.22', 'latest', 'dev']
+        exclude:
+          - python-version: '3.12-dev'
+            numpy-version: '1.22'
       fail-fast: false
     steps:
       - uses: actions/checkout@v2
@@ -16,39 +21,19 @@ jobs:
         run: |
           set -x
           set -e
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          echo $CONDA/bin >> $GITHUB_PATH
-          conda config --set always_yes yes --set changeps1 no
-          conda config --add channels conda-forge
-          conda update -q conda
-          conda info -a
-          conda create -n test-environment python=${{ matrix.python-version }} pyflakes pytest pytest-doctestplus numpy hypothesis doctr sphinx myst-parser sphinx_rtd_theme pytest-cov pytest-flakes packaging
-          conda init
-
-      - name: Run Tests
-        run: |
-          # Copied from .bashrc. We can't just source .bashrc because it exits
-          # when the shell isn't interactive.
-
-          # >>> conda initialize >>>
-          # !! Contents within this block are managed by 'conda init' !!
-          __conda_setup="$('/usr/share/miniconda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
-          if [ $? -eq 0 ]; then
-              eval "$__conda_setup"
+          python -m pip install pyflakes pytest pytest-doctestplus hypothesis pytest-cov pytest-flakes packaging
+          if [[ ${{ matrix.numpy-version }} == 'latest' ]]; then
+              python -m pip install --pre --upgrade numpy
+          elif [[ ${{ matrix.numpy-version }} == 'dev' ]]; then
+              python -m pip install --pre --upgrade --extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
           else
-              if [ -f "/usr/share/miniconda/etc/profile.d/conda.sh" ]; then
-                  . "/usr/share/miniconda/etc/profile.d/conda.sh"
-              else
-                  export PATH="/usr/share/miniconda/bin:$PATH"
-              fi
+              python -m pip install --upgrade numpy==${{ matrix.numpy-version }}.*
           fi
-          unset __conda_setup
-          # <<< conda initialize <<<
-
+      - name: Run Tests
+        run: |
           set -x
           set -e
 
-          conda activate test-environment
           python -We:invalid -We::SyntaxWarning -m compileall -f -q ndindex/
           # The coverage requirement check is done by the coverage report line below
           PYTEST_FLAGS="$PYTEST_FLAGS -v --cov-fail-under=0";

MANIFEST.in

@@ -1,3 +1,6 @@
 include versioneer.py
 include ndindex/_version.py
 include LICENSE
+include pytest.ini
+include conftest.py
+include run_doctests.py

conftest.py

@@ -13,6 +13,10 @@
 if LooseVersion(numpy.__version__) < LooseVersion('1.20'):
     raise RuntimeError("NumPy 1.20 (development version) or greater is required to run the ndindex tests")
 
+# Show the NumPy version in the pytest header
+def pytest_report_header(config):
+    return f"project deps: numpy-{numpy.__version__}"
+
 # Add a --hypothesis-max-examples flag to pytest. See
 # https://github.com/HypothesisWorks/hypothesis/issues/2434#issuecomment-630309150
 

docs/_pygments/styles.py

@@ -0,0 +1,102 @@
+"""
+Pygments styles used for syntax highlighting.
+
+These are based on the Sphinx style (see
+https://github.com/sphinx-doc/sphinx/blob/master/sphinx/pygments_styles.py)
+for light mode and the Friendly style for dark mode.
+
+The styles here have been adjusted so that they are WCAG AA compatible. The
+tool at https://github.com/mpchadwick/pygments-high-contrast-stylesheets was
+used to identify colors that should be adjusted.
+
+"""
+from pygments.style import Style
+from pygments.styles.friendly import FriendlyStyle
+from pygments.styles.native import NativeStyle
+from pygments.token import Comment, Generic, Literal, Name, Number, Text
+
+class SphinxHighContrastStyle(Style):
+    """
+    Like Sphinx (which is like friendly, but a bit darker to enhance contrast
+    on the green background) but with higher contrast colors.
+
+    """
+
+    @property
+    def _pre_style(self):
+        # This is used instead of the default 125% so that multiline Unicode
+        # pprint output looks good
+        return 'line-height: 120%;'
+
+    background_color = '#eeffcc'
+    default_style = ''
+
+    styles = FriendlyStyle.styles
+    styles.update({
+        # These are part of the Sphinx modification to "friendly"
+        Generic.Output: '#333',
+        Number: '#208050',
+
+        # These are adjusted from "friendly" (Comment is adjusted from
+        # "sphinx") to have better color contrast against the background.
+        Comment: 'italic #3c7a88',
+        Comment.Hashbang: 'italic #3c7a88',
+        Comment.Multiline: 'italic #3c7a88',
+        Comment.PreprocFile: 'italic #3c7a88',
+        Comment.Single: 'italic #3c7a88',
+        Comment.Special: '#3a7784 bg:#fff0f0',
+        Generic.Error: '#e60000',
+        Generic.Inserted: '#008200',
+        Generic.Prompt: 'bold #b75709',
+        Name.Class: 'bold #0e7ba6',
+        Name.Constant: '#2b79a1',
+        Name.Entity: 'bold #c54629',
+        Name.Namespace: 'bold #0e7ba6',
+        Name.Variable: '#ab40cd',
+        Text.Whitespace: '#707070',
+        Literal.String.Interpol: 'italic #3973b7',
+        Literal.String.Other: '#b75709',
+        Name.Variable.Class: '#ab40cd',
+        Name.Variable.Global: '#ab40cd',
+        Name.Variable.Instance: '#ab40cd',
+        Name.Variable.Magic: '#ab40cd',
+    })
+
+
+
+class NativeHighContrastStyle(NativeStyle):
+    """
+    Like native, but with higher contrast colors.
+    """
+    @property
+    def _pre_style(self):
+        # This is used instead of the default 125% so that multiline Unicode
+        # pprint output looks good
+        return 'line-height: 120%;'
+
+    styles = NativeStyle.styles
+
+    # These are adjusted to have better color contrast against the background
+    styles.update({
+        Comment.Preproc: 'bold #e15a5a',
+        Comment.Special: 'bold #f75050 bg:#520000',
+        Generic.Deleted: '#e75959',
+        Generic.Error: '#e75959',
+        Generic.Traceback: '#e75959',
+        Literal.Number: '#438dc4',
+        Name.Builtin: '#2594a1',
+        # We also remove the underline here from the original style
+        Name.Class: '#548bd3',
+        Name.Function: '#548bd3',
+        # We also remove the underline here from the original style
+        Name.Namespace: '#548bd3',
+        Text.Whitespace: '#878787',
+        Literal.Number.Bin: '#438dc4',
+        Literal.Number.Float: '#438dc4',
+        Literal.Number.Hex: '#438dc4',
+        Literal.Number.Integer: '#438dc4',
+        Literal.Number.Oct: '#438dc4',
+        Name.Builtin.Pseudo: '#2594a1',
+        Name.Function.Magic: '#548bd3',
+        Literal.Number.Integer.Long: '#438dc4',
+    })