Backport PR pandas-dev#61519: BUILD: Bump Cython to 3.1

Author: rhshadrach

asv_bench/asv.conf.json

@@ -41,7 +41,8 @@
     // pip (with all the conda available packages installed first,
     // followed by the pip installed packages).
     "matrix": {
-        "Cython": ["3.0.5"],
+        "pip+build": [],
+        "Cython": [],
         "matplotlib": [],
         "sqlalchemy": [],
         "scipy": [],

ci/deps/actions-310-minimum_versions.yaml

@@ -8,7 +8,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 

ci/deps/actions-310.yaml

@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 

ci/deps/actions-311-downstream_compat.yaml

@@ -7,7 +7,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 

ci/deps/actions-311-numpydev.yaml

@@ -8,7 +8,7 @@ dependencies:
   - versioneer
   - meson=1.2.1
   - meson-python=0.13.1
-  - cython>=0.29.33
+  - cython<4.0.0a0
 
   # test dependencies
   - pytest>=7.3.2

ci/deps/actions-311-pyarrownightly.yaml

@@ -7,7 +7,7 @@ dependencies:
   # build dependencies
   - versioneer
   - meson=1.2.1
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/actions-311.yaml

@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 

ci/deps/actions-312.yaml

@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 

ci/deps/actions-313-freethreading.yaml

@@ -0,0 +1,29 @@
+name: pandas-dev-313-freethreading
+channels:
+  - conda-forge
+dependencies:
+  - python-freethreading
+
+  # build dependencies
+  - setuptools
+  - versioneer
+  - cython<4.0.0a0
+  - meson=1.8.0
+  - meson-python=0.18.0
+
+  # test dependencies
+  - pytest>=7.3.2
+  - pytest-xdist>=2.2.0
+
+  # required dependencies
+  - python-dateutil
+  - numpy
+
+  # optional dependencies
+  - hypothesis>=6.46.1
+
+  - pip:
+    # No free-threaded coveragepy (with the C-extension) on conda-forge yet
+    - pytest-cov
+    - "tzdata>=2022.7"
+    - "--extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"

ci/deps/actions-313.yaml

@@ -0,0 +1,63 @@
+name: pandas-dev-313
+channels:
+  - conda-forge
+dependencies:
+  - python=3.13
+
+  # build dependencies
+  - versioneer
+  - cython<4.0.0a0
+  - meson=1.2.1
+  - meson-python=0.13.1
+
+  # test dependencies
+  - pytest>=7.3.2
+  - pytest-cov
+  - pytest-xdist>=2.2.0
+  - pytest-localserver>=0.8.1
+  - pytest-qt>=4.4.0
+  - boto3
+
+  # required dependencies
+  - python-dateutil
+  - numpy
+
+  # optional dependencies
+  - beautifulsoup4>=4.11.2
+  - blosc>=1.21.3
+  - bottleneck>=1.3.6
+  - fastparquet>=2022.12.0
+  - fsspec>=2022.11.0
+  - html5lib>=1.1
+  - hypothesis>=6.46.1
+  - gcsfs>=2022.11.0
+  - jinja2>=3.1.2
+  - lxml>=4.9.2
+  - matplotlib>=3.6.3
+  - numba>=0.56.4
+  - numexpr>=2.8.4
+  - odfpy>=1.4.1
+  - qtpy>=2.3.0
+  - pyqt>=5.15.9
+  - openpyxl>=3.1.0
+  - psycopg2>=2.9.6
+  - pyarrow>=10.0.1
+  - pymysql>=1.0.2
+  - pyreadstat>=1.2.0
+  - pytables>=3.8.0
+  - python-calamine>=0.1.7
+  - pytz>=2023.4
+  - pyxlsb>=1.0.10
+  - s3fs>=2022.11.0
+  - scipy>=1.10.0
+  - sqlalchemy>=2.0.0
+  - tabulate>=0.9.0
+  - xarray>=2022.12.0
+  - xlrd>=2.0.1
+  - xlsxwriter>=3.0.5
+  - zstandard>=0.19.0
+
+  - pip:
+    - adbc-driver-postgresql>=0.10.0
+    - adbc-driver-sqlite>=0.8.0
+    - tzdata>=2022.7

ci/deps/actions-pypy-39.yaml

@@ -9,7 +9,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 

environment.yml

@@ -8,7 +8,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython=3.0.5
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 

pyproject.toml

@@ -5,8 +5,8 @@ requires = [
     "meson-python>=0.13.1",
     "meson>=1.2.1,<2",
     "wheel",
-    "Cython~=3.0.5",  # Note: sync with setup.py, environment.yml and asv.conf.json
-    # Force numpy higher than 2.0, so that built wheels are compatible
+    "Cython<4.0.0a0",  # Note: sync with setup.py, environment.yml and asv.conf.json
+    # Force numpy higher than 2.0rc1, so that built wheels are compatible
     # with both numpy 1 and 2
     "numpy>=2.0",
     "versioneer[toml]"

requirements-dev.txt

@@ -3,7 +3,7 @@
 
 pip
 versioneer[toml]
-cython==3.0.5
+cython<4.0.0a0
 meson[ninja]==1.2.1
 meson-python==0.13.1
 pytest>=7.3.2