Merge pull request #862 from pangeo-data/pep621-compliance

Adopt PEP621 and src layout, support Python3.12, drop Python3.8
pangeo-data · Jul 5, 2024 · 61b3254 · 61b3254
2 parents 831d109 + ab3b619
commit 61b3254
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diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -10,30 +10,36 @@ jobs:
   benchmark:
     if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
     name: Linux
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     env:
       ASV_DIR: "./asv_bench"
-
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.10"]
     steps:
       # We need the full repo to avoid this issue
       # https://github.com/actions/checkout/issues/23
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up conda (micromamba)
+        uses: mamba-org/setup-micromamba@v1
         with:
-          # installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-          installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+          environment-name: climpred-benchmarks
+          cache-environment: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+            conda
 
-      - name: Setup some dependencies
-        shell: bash -l {0}
+      - name: Set Up Dependencies
         run: |
-          pip install asv
+          python -m pip install asv
           sudo apt-get update -y
       - name: Run benchmarks
-        shell: bash -l {0}
         id: benchmark
         env:
           OPENBLAS_NUM_THREADS: 1

diff --git a/.github/workflows/climpred_installs.yml b/.github/workflows/climpred_installs.yml
@@ -25,42 +25,44 @@ jobs:
           keyword: "[skip-ci]"
 
   install-climpred-complete:  # Installs climpred on various OS.
-    name: Install climpred[complete], ${{ matrix.os }}
+    name: Install climpred[complete], ${{ matrix.os }}, Python${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
     strategy:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.9"]
     steps:
     - uses: actions/checkout@v4
     - name: Setup Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         pip install -e .[complete]
         python -c "import climpred"
 
   install-climpred:  # Installs climpred on various OS.
-    name: Install climpred, ${{ matrix.os }}
+    name: Install climpred, ${{ matrix.os }}, Python${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
     strategy:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.9"]
     steps:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0 # Fetch all history for all branches and tags.
     - name: Setup Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         pip install -e .

diff --git a/.github/workflows/climpred_testing.yml b/.github/workflows/climpred_testing.yml
@@ -27,13 +27,16 @@ jobs:
           keyword: "[skip-ci]"
 
   minimum-test:  # Runs testing suite with minimal dependencies
-    name: Test minimum dependencies, Python3.9
+    name: Test minimum dependencies, Python${{ matrix.python-version }}
     runs-on: ubuntu-latest
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
     defaults:
         run:
           shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.12"]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -45,7 +48,7 @@ jobs:
           environment-name: climpred-minimum-tests
           cache-environment: true
           create-args: >-
-            python=3.9
+            python=${{ matrix.python-version }}
             conda
       - name: Install climpred
         run: |
@@ -75,16 +78,22 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        env: [""]
         include:
           - env: "climpred-maximum-tests"
             python-version: "3.9"
+            extras: "esmpy=*=mpi*"  # Ensures MPI works with version of esmpy.
             os: ubuntu-latest
           - env: "climpred-maximum-tests"
             python-version: "3.10"
+            extras: "esmpy=*=mpi*"  # Ensures MPI works with version of esmpy.
             os: ubuntu-latest
           - env: "climpred-maximum-tests-upstream"
             python-version: "3.11"
+            extras: "esmpy=*=mpi*"  # Ensures MPI works with version of esmpy.
+            os: ubuntu-latest
+          - env: "climpred-maximum-tests"
+            python-version: "3.12"
+            extras: "esmpy"  # MPI is not supported in lastest esmpy conda packages for Python3.12
             os: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -96,10 +105,11 @@ jobs:
           environment-file: ci/requirements/maximum-tests.yml
           environment-name: climpred-maximum-tests
           cache-environment: true
-          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+          cache-environment-key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-${{ env.TODAY }}-${{ hashFiles(env.CONDA_ENV_FILE) }}"
           create-args: >-
-            python=${{matrix.python-version}}
             conda
+            python=${{ matrix.python-version }}
+            ${{ matrix.extras }}
       - name: Install climpred[complete]
         run: |
           python -m pip install -e .[complete]
@@ -128,11 +138,14 @@ jobs:
           fail_ci_if_error: false
 
   doctest:  # tests all docstrings
-    name: Doctests, Python3.9
-    runs-on: "ubuntu-latest"
+    name: Doctests, Python${{ matrix.python-version }}
+    runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.9"]
     steps:
       - uses: actions/checkout@v4
       - name: Setup conda (micromamba)
@@ -142,7 +155,7 @@ jobs:
           environment-name: climpred-maximum-tests
           cache-environment: true
           create-args: >-
-            python=3.9
+            python=${{ matrix.python-version }}
             conda
       - name: Install climpred[complete]
         run: |
@@ -156,14 +169,17 @@ jobs:
           conda list
       - name: Run doctests
         run: |
-          python -m pytest --doctest-modules climpred --ignore climpred/tests
+          python -m pytest --doctest-modules src/climpred --ignore src/climpred/tests
 
   notebooks:  # Checks that pre-compiled notebooks in docs still work.
-    name: Notebooks, Python3.9
+    name: Notebooks, Python${{ matrix.python-version }}
     runs-on: ubuntu-latest
     defaults:
         run:
           shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.9"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up conda (micromamba)
@@ -173,7 +189,7 @@ jobs:
           environment-name: climpred-docs
           cache-environment: true
           create-args: >-
-            python=3.9
+            python=${{ matrix.python-version }}
             conda
       - name: Install climpred
         run: |

diff --git a/.github/workflows/publish-production-pypi.yml b/.github/workflows/publish-production-pypi.yml
@@ -17,7 +17,7 @@ jobs:
       - name: Set up Python3
         uses: actions/setup-python@v5
         with:
-          python-version: '3.x'
+          python-version: "3.x"
       - name: Install packaging libraries
         run: |
           python -m pip install --upgrade pip

diff --git a/.github/workflows/publish-staging-testpypi.yml b/.github/workflows/publish-staging-testpypi.yml
@@ -34,7 +34,7 @@ jobs:
     - name: Set up Python3
       uses: actions/setup-python@v5
       with:
-        python-version: '3.x'
+        python-version: "3.x"
     - name: Install packaging libraries
       run: |
         python -m pip install --upgrade pip

diff --git a/.github/workflows/upstream-dev-ci.yml b/.github/workflows/upstream-dev-ci.yml
@@ -28,7 +28,7 @@ jobs:
           keyword: "[test-upstream]"
 
   upstream-dev:
-    name: upstream-dev
+    name: upstream-dev, Python${{ matrix.python-version }}
     runs-on: ubuntu-latest
     needs: detect-ci-trigger
     if: |

diff --git a/.gitignore b/.gitignore
@@ -114,6 +114,10 @@ asv_bench/.asv/
 # VS Code
 .vscode/
 
+# PyCharm
+.idea/
+
+# dask
 dask-worker-space
 
 # End of https://www.gitignore.io/api/python
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -21,6 +21,11 @@ repos:
         exclude: '.ipynb|asv.conf.json'
       - id: trailing-whitespace
 
+  -   repo: https://github.com/pappasam/toml-sort
+      rev: v0.23.1
+      hooks:
+      - id: toml-sort-fix
+
   -   repo: https://github.com/psf/black-pre-commit-mirror
       rev: 24.4.2
       hooks:
@@ -30,6 +35,7 @@ repos:
       rev: 7.1.0
       hooks:
       - id: flake8
+        args: [ '--max-line-length=93', '--extend-ignore=W503' ]
 
   -   repo: https://github.com/PyCQA/isort
       rev: 5.13.2

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -22,6 +22,9 @@ Internals/Minor Fixes
 - Fixed some issues with the documentation build to address rendering errors and reduce the number of warnings on ReadTheDocs. (pr:`843`) `Trevor James Smith`_
 - Fixed some issues with the typing hints of classes functions. (pr:`850`) `Trevor James Smith`_
 - Fixed several issues with incompatible dependency configurations in the CI and addressed a few deprecations. (pr:`861`) `Trevor James Smith`_
+- `climpred` has adopted `PEP 621 <https://peps.python.org/pep-0621/>`_ for specifying project metadata. (pr:`862`) `Trevor James Smith`_
+- `climpred` now uses the `src layout <https://packaging.python.org/en/latest/discussions/src-layout-vs-flat-layout/>`_  for the package file structure. (pr:`862`) `Trevor James Smith`_
+- Drop ``python<=3.8`` support. (:pr:`862`) `Trevor James Smith`_.
 
 climpred v2.4.0 (2023-11-09)
 ============================
@@ -224,7 +227,6 @@ Data variables:
   using :py:func:`~climpred.reference.compute_persistence_from_first_lead`.
   (:issue:`637`, :pr:`706`) `Aaron Spring`_.
 
-
 Internals/Minor Fixes
 ---------------------
 - Reduce dependencies. (:pr:`686`) `Aaron Spring`_.
@@ -1038,6 +1040,7 @@ Documentation
 - Add page for `publications <publications.html>`_ and
   `helpful links <helpful-links.html>`_. (:pr:`270`) `Riley X. Brady`_.
 
+
 climpred v1.1.0 (2019-09-23)
 ============================
 
@@ -1072,6 +1075,7 @@ Documentation
 - Add scope of package to docs for clarity for users and developers. (:pr:`235`)
   `Riley X. Brady`_.
 
+
 climpred v1.0.1 (2019-07-04)
 ============================
 

diff --git a/README.rst b/README.rst
@@ -1,6 +1,6 @@
 .. image:: https://i.imgur.com/HPOdOsR.png
 
-Verification of weather and climate forecasts.
+Verification of weather and climate forecasts
 
 ..
     Table version of badges inspired by pySTEPS.
@@ -128,7 +128,7 @@ You can install the latest release of ``climpred`` using ``pip`` or ``conda``:
 
 .. code-block:: bash
 
-    pip install climpred[complete]
+    python -m pip install climpred[complete]
 
 .. code-block:: bash
 
@@ -141,7 +141,7 @@ repository or installing directly from GitHub:
 
     git clone https://github.com/pangeo-data/climpred.git
     cd climpred
-    pip install . --upgrade
+    python -m pip install . --upgrade
 
 .. code-block:: bash
 

diff --git a/ci/requirements/docs.yml b/ci/requirements/docs.yml
@@ -29,7 +29,7 @@ dependencies:
   - importlib-metadata <8.0.0 # Pin needed for esmpy compatibility. See: https://github.com/pangeo-data/xESMF/issues/374
   - nc-time-axis >=1.4.0
   - numba >=0.52
-  - numpy >=1.25.0
+  - numpy >=1.25.0,<2.0.0  # Pin below v2.0.0 until xclim supports it.
   - xclim
   - xesmf
   - xrft
diff --git a/ci/requirements/maximum-tests.yml b/ci/requirements/maximum-tests.yml
@@ -3,18 +3,18 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python >=3.9
+  - python >=3.9,<3.13
   - bias_correction
   - cftime >=1.5.0
   - coveralls
   - dask-core
   - eofs
-  - esmpy =*=mpi*  # Ensures MPI works with version of esmpy.
+  # - esmpy =*=mpi*  # Ensures MPI works with version of esmpy. # Commented out for CI testing.
   - h5netcdf
-  - importlib-metadata <8.0.0 # Pin needed for esmpy compatibility. See: https://github.com/pangeo-data/xESMF/issues/374
+  - importlib-metadata <8.0.0  # Pin needed for esmpy compatibility. See: https://github.com/pangeo-data/xESMF/issues/374
   - matplotlib-base
   - nc-time-axis >=1.4.0
-  - numpy >=1.25.0
+  - numpy >=1.25.0,<2.0.0  # Pin below v2.0.0 until xclim supports it.
   - pip
   - pooch
   - pytest <8.0.0

diff --git a/ci/requirements/minimum-tests.yml b/ci/requirements/minimum-tests.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python >=3.9,<3.10
+  - python >=3.9,<3.13
   - cftime >=1.5.0
   - coveralls
   - dask-core