Merge branch 'main' into groupby-refactor-init

* main: pass kwargs through from save_mfdataset to to_netcdf (pydata#6686) Docs: indexing.rst finetuning (pydata#6685) use micromamba instead of mamba (pydata#6674) install the development version of `matplotlib` into the upstream-dev CI (pydata#6675) Add whatsnew section for v2022.06.0 release notes for 2022.06.0rc0 release notes for the pre-release (pydata#6676) more testpypi workflow fixes (pydata#6673) thin: add examples (pydata#6663) Update multidimensional-coords.ipynb (pydata#6672) try to finally fix the TestPyPI workflow (pydata#6671) pin setuptools in the modify script (pydata#6669) fix the python version for the TestPyPI workflow (pydata#6668) upload wheels from `main` to TestPyPI (pydata#6660) Set keep_attrs for flox (pydata#6667)
dcherian · Jun 12, 2022 · 6bd276c · 6bd276c
2 parents cac2249 + 89b1fac
commit 6bd276c
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diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -39,22 +39,29 @@ jobs:
       run:
         shell: bash -l {0}
 
+    env:
+      CONDA_ENV_FILE: ci/requirements/environment.yml
+      PYTHON_VERSION: "3.10"
+
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          channels: conda-forge
-          channel-priority: strict
-          mamba-version: "*"
-          activate-environment: xarray-tests
-          auto-update-conda: false
-          python-version: "3.9"
 
-      - name: Install conda dependencies
+      - name: set environment variables
         run: |
-          mamba env update -f ci/requirements/environment.yml
+          echo "TODAY=$(date  +'%Y-%m-%d')" >> $GITHUB_ENV
+
+      - name: Setup micromamba
+        uses: mamba-org/provision-with-micromamba@de032af7fb3675649f3d4bbdda85178ba412ee41
+        with:
+          environment-file: ${{env.CONDA_ENV_FILE}}
+          environment-name: xarray-tests
+          extra-specs: |
+            python=${{env.PYTHON_VERSION}}
+          cache-env: true
+          cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+
       - name: Install xarray
         run: |
           python -m pip install --no-deps -e .
@@ -76,23 +83,27 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
+    env:
+      CONDA_ENV_FILE: ci/requirements/environment.yml
+      PYTHON_VERSION: "3.10"
 
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          channels: conda-forge
-          channel-priority: strict
-          mamba-version: "*"
-          activate-environment: xarray-tests
-          auto-update-conda: false
-          python-version: "3.9"
 
-      - name: Install conda dependencies
+      - name: set environment variables
         run: |
-          mamba env update -f ci/requirements/environment.yml
+          echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+      - name: Setup micromamba
+        uses: mamba-org/provision-with-micromamba@de032af7fb3675649f3d4bbdda85178ba412ee41
+        with:
+          environment-file: ${{env.CONDA_ENV_FILE}}
+          environment-name: xarray-tests
+          extra-specs: |
+            python=${{env.PYTHON_VERSION}}
+          cache-env: true
+          cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
       - name: Install xarray
         run: |
           python -m pip install --no-deps -e .
@@ -118,20 +129,28 @@ jobs:
       run:
         shell: bash -l {0}
 
+    strategy:
+      matrix:
+        environment-file: ["bare-minimum", "min-all-deps"]
+      fail-fast: false
+
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
-      - uses: conda-incubator/setup-miniconda@v2
+
+      - name: Setup micromamba
+        uses: mamba-org/provision-with-micromamba@de032af7fb3675649f3d4bbdda85178ba412ee41
         with:
+          environment-name: xarray-tests
+          environment-file: false
+          extra-specs: |
+            python=3.10
+            pyyaml
+            conda
+            python-dateutil
           channels: conda-forge
-          channel-priority: strict
-          mamba-version: "*"
-          auto-update-conda: false
-          python-version: "3.9"
 
       - name: minimum versions policy
         run: |
-          mamba install -y pyyaml conda python-dateutil
-          python ci/min_deps_check.py ci/requirements/bare-minimum.yml
-          python ci/min_deps_check.py ci/requirements/min-all-deps.yml
+          python ci/min_deps_check.py ci/requirements/${{ matrix.environment-file }}.yml
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -65,6 +65,8 @@ jobs:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set environment variables
         run: |
+          echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+
           if [[ ${{ matrix.os }} == windows* ]] ;
           then
             echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
@@ -83,25 +85,13 @@ jobs:
 
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
 
-      - name: Cache conda
-        uses: actions/cache@v3
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-py${{ matrix.python-version }}-${{ hashFiles('ci/requirements/**.yml') }}-${{ matrix.env }}
-
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: Setup micromamba
+        uses: mamba-org/provision-with-micromamba@de032af7fb3675649f3d4bbdda85178ba412ee41
         with:
-          channels: conda-forge
-          channel-priority: strict
-          mamba-version: "*"
-          activate-environment: xarray-tests
-          auto-update-conda: false
-          python-version: ${{ matrix.python-version }}
-          use-only-tar-bz2: true
-
-      - name: Install conda dependencies
-        run: |
-          mamba env update -f $CONDA_ENV_FILE
+          environment-file: ${{ env.CONDA_ENV_FILE }}
+          environment-name: xarray-tests
+          cache-env: true
+          cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
 
       # We only want to install this on one run, because otherwise we'll have
       # duplicate annotations.

diff --git a/.github/workflows/configure-testpypi-version.py b/.github/workflows/configure-testpypi-version.py
@@ -0,0 +1,50 @@
+import argparse
+import copy
+import pathlib
+
+import tomli
+import tomli_w
+
+
+def split_path(path, sep="/"):
+    if isinstance(path, str):
+        return [part for part in path.split(sep) if part]
+    else:
+        return path
+
+
+def extract(mapping, path, sep="/"):
+    parts = split_path(path, sep=sep)
+    cur = mapping
+    for part in parts:
+        cur = cur[part]
+
+    return cur
+
+
+def update(mapping, path, value, sep="/"):
+    new = copy.deepcopy(mapping)
+
+    parts = split_path(path, sep=sep)
+    parent = extract(new, parts[:-1])
+    parent[parts[-1]] = value
+
+    return new
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("path", type=pathlib.Path)
+args = parser.parse_args()
+
+content = args.path.read_text()
+decoded = tomli.loads(content)
+with_local_scheme = update(
+    decoded, "tool.setuptools_scm.local_scheme", "no-local-version", sep="."
+)
+# work around a bug in setuptools / setuptools-scm
+with_setuptools_pin = copy.deepcopy(with_local_scheme)
+requires = extract(with_setuptools_pin, "build-system.requires", sep=".")
+requires[0] = "setuptools>=42,<60"
+
+new_content = tomli_w.dumps(with_setuptools_pin)
+args.path.write_text(new_content)
diff --git a/.github/workflows/testpypi-release.yaml b/.github/workflows/testpypi-release.yaml
@@ -0,0 +1,87 @@
+name: Build and Upload xarray to PyPI
+on:
+  push:
+    branches:
+      - 'main'
+
+# no need for concurrency limits
+
+jobs:
+  build-artifacts:
+    runs-on: ubuntu-latest
+    if: github.repository == 'pydata/xarray'
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v3
+        name: Install Python
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build setuptools setuptools-scm wheel twine check-manifest
+          python -m pip install tomli tomli_w
+
+      - name: Disable local versions
+        run: |
+          python .github/workflows/configure-testpypi-version.py pyproject.toml
+          git update-index --assume-unchanged pyproject.toml
+          cat pyproject.toml
+
+      - name: Build tarball and wheels
+        run: |
+          git clean -xdf
+          python -m build --sdist --wheel .
+
+      - name: Check built artifacts
+        run: |
+          python -m twine check dist/*
+          pwd
+          if [ -f dist/xarray-0.0.0.tar.gz ]; then
+            echo "❌ INVALID VERSION NUMBER"
+            exit 1
+          else
+            echo "✅ Looks good"
+          fi
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: releases
+          path: dist
+
+  test-built-dist:
+    needs: build-artifacts
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/setup-python@v3
+        name: Install Python
+        with:
+          python-version: "3.10"
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - name: List contents of built dist
+        run: |
+          ls -ltrh
+          ls -ltrh dist
+
+      - name: Verify the built dist/wheel is valid
+        if: github.event_name == 'push'
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install dist/xarray*.whl
+          python -m xarray.util.print_versions
+
+      - name: Publish package to TestPyPI
+        if: github.event_name == 'push'
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.TESTPYPI_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+          verbose: true
diff --git a/.github/workflows/upstream-dev-ci.yaml b/.github/workflows/upstream-dev-ci.yaml
@@ -55,17 +55,15 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          channels: conda-forge
-          channel-priority: strict
-          mamba-version: "*"
-          activate-environment: xarray-tests
-          auto-update-conda: false
-          python-version: ${{ matrix.python-version }}
       - name: Set up conda environment
+        uses: mamba-org/provision-with-micromamba@de032af7fb3675649f3d4bbdda85178ba412ee41
+        with:
+          environment-file: ci/requirements/environment.yml
+          environment-name: xarray-tests
+          extra-specs: |
+            python=${{ matrix.python-version }}
+      - name: Install upstream versions
         run: |
-          mamba env update -f ci/requirements/environment.yml
           bash ci/install-upstream-wheels.sh
       - name: Install xarray
         run: |

diff --git a/ci/install-upstream-wheels.sh b/ci/install-upstream-wheels.sh
@@ -18,22 +18,18 @@ conda uninstall -y --force \
     flox \
     h5netcdf \
     xarray
+# new matplotlib dependency
+python -m pip install --upgrade contourpy
 # to limit the runtime of Upstream CI
-python -m pip install pytest-timeout
 python -m pip install \
     -i https://pypi.anaconda.org/scipy-wheels-nightly/simple \
     --no-deps \
     --pre \
     --upgrade \
     numpy \
     scipy \
+    matplotlib \
     pandas
-python -m pip install \
-    -f https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com \
-    --no-deps \
-    --pre \
-    --upgrade \
-    matplotlib
 python -m pip install \
     --no-deps \
     --upgrade \
@@ -50,3 +46,4 @@ python -m pip install \
     git+https://github.com/SciTools/nc-time-axis \
     git+https://github.com/dcherian/flox \
     git+https://github.com/h5netcdf/h5netcdf
+python -m pip install pytest-timeout
diff --git a/ci/requirements/bare-minimum.yml b/ci/requirements/bare-minimum.yml
@@ -10,6 +10,6 @@ dependencies:
   - pytest-cov
   - pytest-env
   - pytest-xdist
-  - numpy=1.18
+  - numpy=1.19
   - packaging=20.0
-  - pandas=1.1
+  - pandas=1.2
diff --git a/doc/examples/multidimensional-coords.ipynb b/doc/examples/multidimensional-coords.ipynb
@@ -175,7 +175,7 @@
     "# define a label for each bin corresponding to the central latitude\n",
     "lat_center = np.arange(1, 90, 2)\n",
     "# group according to those bins and take the mean\n",
-    "Tair_lat_mean = ds.Tair.groupby_bins(\"xc\", lat_bins, labels=lat_center).mean(\n",
+    "Tair_lat_mean = ds.Tair.groupby_bins(\"yc\", lat_bins, labels=lat_center).mean(\n",
     "    dim=xr.ALL_DIMS\n",
     ")\n",
     "# plot the result\n",
@@ -186,7 +186,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The resulting coordinate for the `groupby_bins` operation got the `_bins` suffix appended: `xc_bins`. This help us distinguish it from the original multidimensional variable `xc`.\n",
+    "The resulting coordinate for the `groupby_bins` operation got the `_bins` suffix appended: `yc_bins`. This help us distinguish it from the original multidimensional variable `yc`.\n",
     "\n",
     "**Note**: This group-by-latitude approach does not take into account the finite-size geometry of grid cells. It simply bins each value according to the coordinates at the cell center. Xarray has no understanding of grid cells and their geometry. More precise geographic regridding for xarray data is available via the [xesmf](https://xesmf.readthedocs.io) package."
    ]

diff --git a/doc/getting-started-guide/installing.rst b/doc/getting-started-guide/installing.rst
@@ -147,6 +147,15 @@ installed, take a look at the ``[options.extras_require]`` section in
    :start-at: [options.extras_require]
    :end-before: [options.package_data]
 
+Development versions
+--------------------
+To install the most recent development version, install from github::
+
+     $ python -m pip install git+https://github.com/pydata/xarray.git
+
+or from TestPyPI::
+
+     $ python -m pip install --index-url https://test.pypi.org/simple --extra-index-url https://pypi.org/simple --pre xarray
 
 Testing
 -------