From 6282fc38c2fc76ad8e734a6f412d1859367c9e7d Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Sat, 10 Aug 2024 08:19:15 -0400
Subject: [PATCH] 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

https://github.com/jdblischak/centralized-tiledb-nightlies/commit/81849b95e56dbac94ca2b04e91595482644c51cb

* Bump nightly build release branch to 2.25

* Pin pyarrow==12
---
 .github/workflows/nightly.yml    | 14 ++------------
 ci/nightly/build-tiledb-py.sh    | 29 +++++++++++++++++++++++++++++
 ci/nightly/build-tiledbvcf-py.sh |  2 +-
 ci/nightly/requirements.txt      |  9 ---------
 4 files changed, 32 insertions(+), 22 deletions(-)
 create mode 100644 ci/nightly/build-tiledb-py.sh
 delete mode 100644 ci/nightly/requirements.txt

diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
index 283556419..9e5b8decb 100644
--- a/.github/workflows/nightly.yml
+++ b/.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:
diff --git a/ci/nightly/build-tiledb-py.sh b/ci/nightly/build-tiledb-py.sh
new file mode 100644
index 000000000..bbc988ace
--- /dev/null
+++ b/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())"
diff --git a/ci/nightly/build-tiledbvcf-py.sh b/ci/nightly/build-tiledbvcf-py.sh
index 54fc1af45..ef50f77ce 100644
--- a/ci/nightly/build-tiledbvcf-py.sh
+++ b/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
diff --git a/ci/nightly/requirements.txt b/ci/nightly/requirements.txt
deleted file mode 100644
index aca17f814..000000000
--- a/ci/nightly/requirements.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-numpy<2
-pandas
-pyarrow==11
-pyarrow-hotfix
-pybind11
-setuptools
-setuptools_scm
-setuptools_scm_git_archive
-wheel