Nightly build for Windows

.github/workflows/nightly.yml

@@ -105,11 +105,64 @@ jobs:
             -r TileDB-VCF/ci/nightly/requirements-test.txt
       - name: Build (and test) tiledbvcf-py
         run: bash TileDB-VCF/ci/nightly/build-tiledbvcf-py.sh
+  windows:
+    runs-on: windows-latest
+    name: win-libtiledb-${{ matrix.libtiledb_version }}
+    strategy:
+      fail-fast: false
+      matrix:
+        libtiledb_version: [release-2.18, dev]
+    defaults:
+      run:
+        shell: cmd
+    steps:
+      - name: Clone TileDB
+        uses: actions/checkout@v3
+        with:
+          repository: TileDB-Inc/TileDB
+          ref: ${{ matrix.libtiledb_version }}
+          path: TileDB
+      - name: Clone TileDB-VCF
+        uses: actions/checkout@v3
+        with:
+          path: TileDB-VCF
+          fetch-depth: 0 # fetch everything for python setuptools_scm
+      - name: Build libtiledb
+        run: cmd /C CALL TileDB-VCF/ci/nightly/build-libtiledb.bat
+      - name: Build libtiledbvcf
+        run: cmd /C CALL TileDB-VCF\ci\nightly\build-libtiledbvcf.bat
+      - name: Upload installation directory as artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: win-nightly-libtiledbvcf-libtiledb-${{ matrix.libtiledb_version }}
+          path: |
+            install/*
+          retention-days: 14
+      - uses: ilammy/msvc-dev-cmd@v1
+      - name: Confirm linking
+        run: |
+          echo %GITHUB_WORKSPACE%
+          dumpbin /dependents %GITHUB_WORKSPACE%\install\bin\tiledbvcf.dll
+          dumpbin /dependents %GITHUB_WORKSPACE%\install\bin\tiledbvcf.exe
+          dumpbin /imports %GITHUB_WORKSPACE%\install\bin\tiledbvcf.dll | findstr /i dll
+          dumpbin /imports %GITHUB_WORKSPACE%\install\bin\tiledbvcf.dll
+      # - name: Test libtiledbvcf
+      #   run: cmd /C CALL TileDB-VCF\ci\nightly\test-libtiledbvcf.bat
+      - name: Setup conda env
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: TileDB-VCF/ci/nightly/environment.yaml
+          cache-environment: true
+          init-shell: cmd.exe
+      - name: Build (and test) tiledbvcf-py
+        # need custom shell directive to activate conda env
+        shell: cmd /C CALL {0}
+        run: cmd /C CALL TileDB-VCF\ci\nightly\build-tiledbvcf-py.bat
   issue:
     permissions:
       issues: write
     runs-on: ubuntu-latest
-    needs: [linux, osx]
+    needs: [linux, osx, windows]
     if: ( failure() || cancelled() ) && github.repository_owner == 'TileDB-Inc' && github.event_name == 'schedule'
     steps:
       - uses: actions/checkout@v3

ci/nightly/build-libtiledb.bat

@@ -0,0 +1,18 @@
+@echo on
+
+rem Build libtiledb assuming source code directory is .\TileDB
+
+cmake -S TileDB -B build-libtiledb ^
+  -D CMAKE_BUILD_TYPE=Release ^
+  -D CMAKE_INSTALL_PREFIX:PATH=%GITHUB_WORKSPACE%\install\ ^
+  -D TILEDB_WERROR=ON ^
+  -D TILEDB_SERIALIZATION=ON ^
+  -D TILEDB_VCPKG=OFF ^
+  -D TILEDB_S3=ON
+if %ERRORLEVEL% neq 0 exit 1
+
+cmake --build build-libtiledb -j2 --config Release
+if %ERRORLEVEL% neq 0 exit 1
+
+cmake --build build-libtiledb --config Release --target install-tiledb
+if %ERRORLEVEL% neq 0 exit 1

ci/nightly/build-libtiledbvcf.bat

@@ -0,0 +1,22 @@
+@echo on
+
+rem Build libtiledbvcf assuming source code directory is .\TileDB-VCF\libtiledbvcf
+
+cmake -S TileDB-VCF\libtiledbvcf -B build-libtiledbvcf ^
+  -D CMAKE_BUILD_TYPE=Release ^
+  -D CMAKE_INSTALL_PREFIX:PATH=%GITHUB_WORKSPACE%\install\ ^
+  -D OVERRIDE_INSTALL_PREFIX=OFF ^
+  -D TILEDB_WERROR=OFF ^
+  -D CMAKE_INSTALL_LIBDIR=bin
+if %ERRORLEVEL% neq 0 exit 1
+
+cmake --build build-libtiledbvcf -j2 --config Release
+if %ERRORLEVEL% neq 0 exit 1
+
+cmake --build build-libtiledbvcf --config Release --target install-libtiledbvcf
+if %ERRORLEVEL% neq 0 exit 1
+
+dir /s %GITHUB_WORKSPACE%\install\
+
+rem %GITHUB_WORKSPACE%\install\bin\tiledbvcf version
+rem if %ERRORLEVEL% neq 0 exit 1

ci/nightly/build-tiledbvcf-py.bat

@@ -0,0 +1,17 @@
+@echo on
+
+rem Build (and test) tiledbvcf-py assuming source code directory is
+rem .\TileDB-VCF\apis\python
+
+set PATH=%GITHUB_WORKSPACE%\install\bin;%PATH%
+echo "PATH: %PATH%"
+
+cd TileDB-VCF\apis\python
+python setup.py develop --libtiledbvcf=%GITHUB_WORKSPACE%\install\
+if %ERRORLEVEL% neq 0 exit 1
+
+python -c "import tiledbvcf; print(tiledbvcf.version)"
+if %ERRORLEVEL% neq 0 exit 1
+
+pytest
+if %ERRORLEVEL% neq 0 exit 1

ci/nightly/test-libtiledbvcf.bat

@@ -0,0 +1,11 @@
+@echo on
+
+rem Test libtiledbvcf assuming source code directory is .\TileDB-VCF\libtiledbvcf
+rem and build directory is build-libtiledbvcf
+
+make -j2 -C build-libtiledbvcf\libtiledbvcf tiledb_vcf_unit
+$GITHUB_WORKSPACE\build-libtiledbvcf\libtiledbvcf\test\tiledb_vcf_unit
+
+rem cli tests (require bcftools)
+rem USAGE: run-cli-tests.sh <build-dir> <inputs-dir>
+bash $GITHUB_WORKSPACE\TileDB-VCF\libtiledbvcf\test\run-cli-tests.sh build-libtiledbvcf TileDB-VCF\libtiledbvcf\test\inputs