Fix nightly build by updating source build of TileDB-Py (#756)

* Migrate TileDB-Py to scikit-build-core and don't check for deprecations

* Run TileDB-Py import test outside of Git repo

jdblischak/centralized-tiledb-nightlies@81849b9

* Bump nightly build release branch to 2.25

* Pin pyarrow==12

.github/workflows/nightly.yml

@@ -24,7 +24,7 @@ jobs:
       matrix:
         os: [macos-12, ubuntu-latest]
         branches:
-          - {libtiledb: release-2.24, tiledb-py: 0.30.1}
+          - {libtiledb: release-2.25, tiledb-py: 0.31.1}
           - {libtiledb: dev, tiledb-py: dev}
     env:
       MACOSX_DEPLOYMENT_TARGET: 10.15
@@ -75,18 +75,8 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.10"
-      - name: Install dependencies for tiledb-py build
-        run: |
-          python -m pip install --prefer-binary \
-            -r TileDB-VCF/ci/nightly/requirements.txt
-          pip list
       - name: Build tiledb-py from source
-        run: |
-          cd TileDB-Py/
-          python setup.py develop --tiledb=../install/
-          python -c "import tiledb; print('successful import')"
-          python -c "import tiledb; print(tiledb.libtiledb.version())"
-          python -c "import tiledb; print(tiledb.version())"
+        run: bash TileDB-VCF/ci/nightly/build-tiledb-py.sh
       - name: Build (and test) tiledbvcf-py
         run: bash TileDB-VCF/ci/nightly/build-tiledbvcf-py.sh
   issue:

ci/nightly/build-tiledb-py.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+set -ex
+
+# Build tiledb-py assuming source code directory is ./TileDB-Py/ and libtiledb
+# shared library installed in $GITHUB_WORKSPACE/install/
+
+OS=$(uname)
+echo "OS: $OS"
+if [[ $OS == Linux ]]
+then
+  export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/install/lib:${LD_LIBRARY_PATH-}
+  echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
+elif [[ $OS == Darwin ]]
+then
+  export DYLD_LIBRARY_PATH=$GITHUB_WORKSPACE/install/lib:${DYLD_LIBRARY_PATH-}
+  echo "DYLD_LIBRARY_PATH: $DYLD_LIBRARY_PATH"
+fi
+
+export TILEDB_PATH=$GITHUB_WORKSPACE/install/
+
+cd TileDB-Py/
+python -m pip install -Cskbuild.cmake.define.TILEDB_REMOVE_DEPRECATIONS=OFF -v . pyarrow==12
+
+# Can't run the import inside of the Git repo because Python automatically looks
+# for `./module/__init.py__`
+cd ..
+python -c "import tiledb; print('successful import')"
+python -c "import tiledb; print(tiledb.libtiledb.version())"
+python -c "import tiledb; print(tiledb.version())"

ci/nightly/build-tiledbvcf-py.sh

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