Merge branch 'main' into test_numpy_complex2

Author: MichaelTiemannOSC

.github/workflows/code-checks.yml

@@ -33,7 +33,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -109,7 +109,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -143,7 +143,7 @@ jobs:
         run: docker image prune -f
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -164,7 +164,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/codeql.yml

@@ -27,7 +27,7 @@ jobs:
           - python
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: github/codeql-action/init@v2
         with:
           languages: ${{ matrix.language }}

.github/workflows/comment-commands.yml

@@ -51,7 +51,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/docbuild-and-upload.yml

@@ -36,7 +36,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 

.github/workflows/package-checks.yml

@@ -34,7 +34,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -62,7 +62,7 @@ jobs:
       cancel-in-progress: true
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/unit-tests.yml

@@ -136,7 +136,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -194,7 +194,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -230,11 +230,13 @@ jobs:
               git -c user.email="you@example.com" merge --no-commit my_ref_name
           fi
       - name: Build environment and Run Tests
+        # https://github.com/numpy/numpy/issues/24703#issuecomment-1722379388
         run: |
           /opt/python/cp311-cp311/bin/python -m venv ~/virtualenvs/pandas-dev
           . ~/virtualenvs/pandas-dev/bin/activate
-          python -m pip install --no-cache-dir -U pip wheel setuptools meson[ninja]==1.0.1 meson-python==0.13.1
-          python -m pip install --no-cache-dir versioneer[toml] "cython<3.0.1" numpy python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
+          python -m pip install --no-cache-dir -U pip wheel setuptools meson[ninja]==1.2.1 meson-python==0.13.1
+          python -m pip install numpy --config-settings=setup-args="-Dallow-noblas=true"
+          python -m pip install --no-cache-dir versioneer[toml] cython python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
           python -m pip install --no-cache-dir --no-build-isolation -e .
           python -m pip list --no-cache-dir
           export PANDAS_CI=1
@@ -271,8 +273,8 @@ jobs:
         run: |
           /opt/python/cp311-cp311/bin/python -m venv ~/virtualenvs/pandas-dev
           . ~/virtualenvs/pandas-dev/bin/activate
-          python -m pip install --no-cache-dir -U pip wheel setuptools meson-python==0.13.1 meson[ninja]==1.0.1
-          python -m pip install --no-cache-dir versioneer[toml] "cython<3.0.1" numpy python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
+          python -m pip install --no-cache-dir -U pip wheel setuptools meson-python==0.13.1 meson[ninja]==1.2.1
+          python -m pip install --no-cache-dir versioneer[toml] cython numpy python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
           python -m pip install --no-cache-dir --no-build-isolation -e .
           python -m pip list --no-cache-dir
 
@@ -330,7 +332,7 @@ jobs:
       PYTEST_TARGET: pandas
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -342,10 +344,10 @@ jobs:
       - name: Build Environment
         run: |
           python --version
-          python -m pip install --upgrade pip setuptools wheel meson[ninja]==1.0.1 meson-python==0.13.1
+          python -m pip install --upgrade pip setuptools wheel meson[ninja]==1.2.1 meson-python==0.13.1
           python -m pip install --pre --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
           python -m pip install versioneer[toml]
-          python -m pip install python-dateutil pytz tzdata "cython<3.0.1" hypothesis>=6.46.1 pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-cov pytest-asyncio>=0.17
+          python -m pip install python-dateutil pytz tzdata cython hypothesis>=6.46.1 pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-cov pytest-asyncio>=0.17
           python -m pip install -ve . --no-build-isolation --no-index
           python -m pip list
 

.github/workflows/wheels.yml

@@ -48,7 +48,7 @@ jobs:
       sdist_file: ${{ steps.save-path.outputs.sdist_name }}
     steps:
       - name: Checkout pandas
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -103,7 +103,7 @@ jobs:
       IS_SCHEDULE_DISPATCH: ${{ github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' }}
     steps:
       - name: Checkout pandas
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

ci/deps/actions-310.yaml

@@ -6,8 +6,8 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33, <3.0.1
-  - meson[ninja]=1.0.1
+  - cython>=0.29.33
+  - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
   # test dependencies
@@ -34,7 +34,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   - numba>=0.55.2
   - numexpr>=2.8.0
   - odfpy>=1.4.1
@@ -46,6 +46,7 @@ dependencies:
   - pymysql>=1.0.2
   - pyreadstat>=1.1.5
   - pytables>=3.7.0
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

ci/deps/actions-311-downstream_compat.yaml

@@ -7,8 +7,8 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33, <3.0.1
-  - meson[ninja]=1.0.1
+  - cython>=0.29.33
+  - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
   # test dependencies
@@ -35,7 +35,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   - numba>=0.55.2
   - numexpr>=2.8.0
   - odfpy>=1.4.1
@@ -47,6 +47,7 @@ dependencies:
   - pymysql>=1.0.2
   - pyreadstat>=1.1.5
   - pytables>=3.7.0
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

ci/deps/actions-311-numpydev.yaml

@@ -6,8 +6,9 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.2.1
   - meson-python=0.13.1
+  - cython>=0.29.33
 
   # test dependencies
   - pytest>=7.3.2
@@ -25,7 +26,6 @@ dependencies:
   - pip
 
   - pip:
-    - "cython<3.0.1"
     - "--extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
     - "--pre"
     - "numpy"

ci/deps/actions-311-pyarrownightly.yaml

@@ -6,8 +6,8 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - meson[ninja]=1.0.1
-  - cython>=0.29.33, <3.0.1
+  - meson[ninja]=1.2.1
+  - cython>=0.29.33
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/actions-311.yaml

@@ -6,8 +6,8 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33, <3.0.1
-  - meson[ninja]=1.0.1
+  - cython>=0.29.33
+  - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
   # test dependencies
@@ -34,7 +34,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   - numba>=0.55.2
   - numexpr>=2.8.0
   - odfpy>=1.4.1
@@ -46,6 +46,7 @@ dependencies:
   - pymysql>=1.0.2
   - pyreadstat>=1.1.5
   # - pytables>=3.7.0, 3.8.0 is first version that supports 3.11
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

ci/deps/actions-39-minimum_versions.yaml

@@ -8,8 +8,8 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33, <3.0.1
-  - meson[ninja]=1.0.1
+  - cython>=0.29.33
+  - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
   # test dependencies
@@ -48,6 +48,7 @@ dependencies:
   - pymysql=1.0.2
   - pyreadstat=1.1.5
   - pytables=3.7.0
+  - python-calamine=0.1.6
   - pyxlsb=1.0.9
   - s3fs=2022.05.0
   - scipy=1.8.1

ci/deps/actions-39.yaml

@@ -6,8 +6,8 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33, <3.0.1
-  - meson[ninja]=1.0.1
+  - cython>=0.29.33
+  - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
   # test dependencies
@@ -34,7 +34,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   - numba>=0.55.2
   - numexpr>=2.8.0
   - odfpy>=1.4.1
@@ -46,6 +46,7 @@ dependencies:
   - pymysql>=1.0.2
   - pyreadstat>=1.1.5
   - pytables>=3.7.0
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

ci/deps/actions-pypy-39.yaml

@@ -9,8 +9,8 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33, <3.0.1
-  - meson[ninja]=1.0.1
+  - cython>=0.29.33
+  - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/circle-310-arm64.yaml

@@ -6,8 +6,8 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33, <3.0.1
-  - meson[ninja]=1.0.1
+  - cython>=0.29.33
+  - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
   # test dependencies
@@ -34,7 +34,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   # test_numba_vs_cython segfaults with numba 0.57
   - numba>=0.55.2, <0.57.0
   - numexpr>=2.8.0
@@ -47,6 +47,7 @@ dependencies:
   - pymysql>=1.0.2
   # - pyreadstat>=1.1.5 not available on ARM
   - pytables>=3.7.0
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

doc/make.py

@@ -123,14 +123,14 @@ def _sphinx_build(self, kind: str):
 
         Parameters
         ----------
-        kind : {'html', 'latex'}
+        kind : {'html', 'latex', 'linkcheck'}
 
         Examples
         --------
         >>> DocBuilder(num_jobs=4)._sphinx_build('html')
         """
-        if kind not in ("html", "latex"):
-            raise ValueError(f"kind must be html or latex, not {kind}")
+        if kind not in ("html", "latex", "linkcheck"):
+            raise ValueError(f"kind must be html, latex or linkcheck, not {kind}")
 
         cmd = ["sphinx-build", "-b", kind]
         if self.num_jobs:
@@ -288,6 +288,12 @@ def zip_html(self):
         os.chdir(dirname)
         self._run_os("zip", zip_fname, "-r", "-q", *fnames)
 
+    def linkcheck(self):
+        """
+        Check for broken links in the documentation.
+        """
+        return self._sphinx_build("linkcheck")
+
 
 def main():
     cmds = [method for method in dir(DocBuilder) if not method.startswith("_")]