Build with NumPy 2 (#762)

Author: gspowley

.azure-pipelines.yml

@@ -53,10 +53,6 @@ stages:
               repository: tiledb/tiledbvcf-py
               context: .
               test_cmd: -c "import tiledbvcf; print(tiledbvcf.version)"
-            # dask:
-            #   dockerfile: docker/Dockerfile-dask-py
-            #   repository: tiledb/tiledbvcf-dask
-            #   context: .
         steps:
         - template: ci/build-images.yml
 

.github/workflows/macos.yml

@@ -86,8 +86,6 @@ jobs:
         with:
           environment-name: ci
           create-args: tiledb
-      - name: Install dependencies
-        run: python -m pip install --prefer-binary pyarrow==10.0.1
       - name: Build tiledbvcf-py
         env:
           LIBTILEDBVCF_PATH: "${{ github.workspace }}/dist"
@@ -163,8 +161,6 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-      - name: Install dependencies
-        run: python -m pip install --prefer-binary pyarrow==10.0.1
       - name: Build tiledbvcf-py
         run: cd apis/python && python -m pip install -v .[test]
       - name: Confirm linking

apis/python/conda-env.yml

@@ -29,18 +29,18 @@ dynamic = ["version"]
 description = "TileDB-VCF Python client"
 license = { text = "MIT" }
 authors = []
-requires-python = "~=3.8"
+requires-python = "~=3.9"
 classifiers = [
     "Development Status :: 4 - Beta",
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 
-dependencies = ["pandas", "pyarrow", "pyarrow-hotfix", "numpy<2"]
+dependencies = ["pandas", "pyarrow>=14.0.1", "numpy"]
 
 [project.optional-dependencies]
 test = ["dask[distributed]", "pytest", "tiledb"]

apis/python/pyproject.toml

@@ -1,6 +1,5 @@
 # Initialize pyarrow first.
 import pyarrow
-import pyarrow_hotfix
 
 import ctypes
 import os

apis/python/src/tiledbvcf/__init__.py

@@ -8,13 +8,12 @@ dependencies:
   - cmake
   - git
   - m2w64-htslib
-  - tiledb=2.15
+  - tiledb=2.25
   - vs2019_win-64
   # build tiledbvcf-py
-  - numpy<2
-  - pandas<2.0
-  - pyarrow=9.0
-  - pyarrow-hotfix
+  - numpy
+  - pandas
+  - pyarrow>=14.0.1
   - pybind11
   - python
   - rpdb

ci/gha-win-env.yml

@@ -19,7 +19,7 @@ fi
 export TILEDB_PATH=$GITHUB_WORKSPACE/install/
 
 cd TileDB-Py/
-python -m pip install -Cskbuild.cmake.define.TILEDB_REMOVE_DEPRECATIONS=OFF -v . pyarrow==12
+python -m pip install -Cskbuild.cmake.define.TILEDB_REMOVE_DEPRECATIONS=OFF -v .
 
 # Can't run the import inside of the Git repo because Python automatically looks
 # for `./module/__init.py__`

ci/nightly/build-tiledb-py.sh

@@ -20,7 +20,7 @@ fi
 export LIBTILEDBVCF_PATH=$GITHUB_WORKSPACE/install/
 
 cd TileDB-VCF/apis/python
-python -m pip install .[test] pyarrow==12
+python -m pip install .[test]
 python -c "import tiledbvcf; print(tiledbvcf.version)"
 
 pytest