Address DeprecationWarnings and suppress warnings for numpy 1.25+ (#426)

Author: Zeitsperre

.github/workflows/python-publish.yml

@@ -11,36 +11,36 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@master
+        uses: actions/checkout@v4
       - name: Create Release
         id: create_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
+        uses: softprops/action-gh-release@v2
         with:
-          tag_name: ${{ github.ref }}
-          release_name: Release ${{ github.ref }}
           body: |
             Changes in this Release
           draft: false
+          name: Release ${{ github.ref }}
           prerelease: false
+          tag_name: ${{ github.ref }}
+          token: ${{ secrets.GITHUB_TOKEN }}
   deploy:
     needs: release
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install build
+          python -m pip install build
       - name: Build and publish
-        run: python -m build
+        run: |
+          python -m build
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        uses: pypa/gh-action-pypi-publish@v1.12.4
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/upstream-dev-ci.yml

@@ -24,8 +24,9 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
+          persist-credentials: false
           fetch-depth: 2
-      - uses: xarray-contrib/ci-trigger@v1.1
+      - uses: xarray-contrib/ci-trigger@v1.1.1
         id: detect-trigger
         with:
           keyword: "[test-upstream]"
@@ -57,9 +58,10 @@ jobs:
       - name: setup conda (micromamba)
         uses: mamba-org/setup-micromamba@v1
         with:
+          cache-downloads: true
+          cache-environment: true
           environment-file: ci/dev.yml
           environment-name: xskillscore-dev
-          cache-environment: true
           create-args: >-
             python=${{ matrix.python-version }}
             pytest-reportlog
@@ -110,8 +112,10 @@ jobs:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - uses: actions/download-artifact@v2
@@ -127,7 +131,7 @@ jobs:
           wget https://raw.githubusercontent.com/pydata/xarray/master/.github/workflows/parse_logs.py
           python parse_logs.py logs/**/*-log
       - name: Report failures
-        uses: actions/github-script@v3
+        uses: actions/github-script@v6
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |

.github/workflows/xskillscore_installs.yml

@@ -34,13 +34,13 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -e .
+        python -m pip install -e .
         python -c "import xskillscore"

.github/workflows/xskillscore_testing.yml

@@ -15,16 +15,17 @@ jobs:
     outputs:
       triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
+          persist-credentials: false
           fetch-depth: 2
-      - uses: xarray-contrib/ci-trigger@v1.1
+      - uses: xarray-contrib/ci-trigger@v1.1.1
         id: detect-trigger
         with:
           keyword: "[skip-ci]"
 
   test:  # Runs testing suite on various python versions.
-    name: Test xskillscore, python ${{ matrix.python-version }}
+    name: Test xskillscore (Python ${{ matrix.python-version }})
     runs-on: ubuntu-latest
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
@@ -34,24 +35,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up conda
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
         with:
-          auto-update-conda: true
-          channels: conda-forge
-          mamba-version: '*'
-          activate-environment: xskillscore-minimum-tests
-          python-version: ${{ matrix.python-version }}
-      - name: Set up conda environment
-        run: |
-          mamba env update -f ci/minimum-tests.yml
-      - name: Conda info
-        run: conda info
-      - name: Conda list
-        run: conda list
+          persist-credentials: false
+      - name: Set up conda (micromamba)
+        uses: mamba-org/setup-micromamba@v2.0.4
+        with:
+          cache-downloads: true
+          cache-environment: true
+          environment-file: ci/minimum-tests.yml
+          create-args: >
+            python=${{ matrix.python-version }}
       - name: Run tests
         run: |
           pytest -n 4 --cov=xskillscore --cov-report=xml --verbose
@@ -70,25 +66,25 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.9", "3.13" ]
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
         with:
-          auto-update-conda: true
-          channels: conda-forge
-          mamba-version: "*"
-          activate-environment: xskillscore-minimum-tests
-          python-version: 3.9
-      - name: Set up conda environment
-        run: |
-          mamba env update -f ci/minimum-tests.yml
+          persist-credentials: false
+      - name: Set up conda (micromamba)
+        uses: mamba-org/setup-micromamba@v2.0.4
+        with:
+          cache-downloads: true
+          cache-environment: true
+          environment-file: ci/minimum-tests.yml
+          create-args: >
+            python=${{ matrix.python-version }}
       - name: Install xskillscore
         run: |
           python -m pip install --no-deps -e .
-      - name: Conda info
-        run: conda info
-      - name: Conda list
-        run: conda list
       - name: Run doctests
         run: |
           python -m pytest --doctest-modules xskillscore --ignore xskillscore/tests
@@ -100,23 +96,24 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: [ "3.9" ]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up conda
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
         with:
-          auto-update-conda: true
-          channels: conda-forge
-          mamba-version: "*"
-          activate-environment: xskillscore-docs-notebooks
-          python-version: 3.9
-      - name: Set up conda environment
+          persist-credentials: false
+      - name: Set up conda (micromamba)
+        uses: mamba-org/setup-micromamba@v2.0.4
+        with:
+          cache-downloads: true
+          cache-environment: true
+          environment-file: ci/docs_notebooks.yml
+          create-args: >
+            python=${{ matrix.python-version }}
+      - name: Install xskillscore
         run: |
-          mamba env update -f ci/docs_notebooks.yml
-      - name: Conda info
-        run: conda info
-      - name: Conda list
-        run: conda list
+          python -m pip install --no-deps -e .
       - name: Test notebooks in docs
         run: |
           pushd docs

.gitignore

@@ -8,10 +8,17 @@ build
 .ipynb_checkpoints/
 .eggs/
 
+# Visual Studio Code
 .vscode
 
 # asv environments
 .asv
 
 # Mac stuff
 .DS_Store
+
+# JetBrains
+.idea
+
+# Documentation
+docs/build/

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-docstring-first
@@ -34,7 +34,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.3.5"
+    rev: "v0.11.8"
     hooks:
       - id: ruff
         args: ["--select", "E,F,I001"]
@@ -49,7 +49,7 @@ repos:
         additional_dependencies: ["black==23.10.1"]
 
   - repo: https://github.com/PyCQA/doc8
-    rev: v1.1.1
+    rev: v1.1.2
     hooks:
       - id: doc8
         args:
@@ -62,14 +62,14 @@ repos:
           ]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.9.0"
+    rev: "v1.15.0"
     hooks:
       - id: mypy
         exclude: "asv_bench"
         additional_dependencies: [
             # Type stubs
             types-python-dateutil,
-            types-pkg_resources,
+            types-setuptools,
             types-PyYAML,
             types-pytz,
             typing-extensions,
@@ -78,7 +78,7 @@ repos:
           ]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.28.1
+    rev: 0.33.0
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs

readthedocs.yml renamed to .readthedocs.yml

@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: "ubuntu-22.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "mambaforge-22.9"
+    python: "mambaforge-23.11"
   jobs:
     post_checkout:
       - (git --no-pager log --pretty="tformat:%s" -1 | grep -vqF "[skip-rtd]") || exit 183
@@ -15,6 +15,12 @@ conda:
   environment: ci/doc.yml
 
 sphinx:
+  configuration: docs/source/conf.py
   fail_on_warning: false
 
 formats: []
+
+python:
+  install:
+    - method: pip
+      path: .