Fix windows builds (#3)

.github/workflows/pip.yml

@@ -49,8 +49,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # platform: [windows-latest, macos-latest, ubuntu-latest]
-        platform: [macos-latest, ubuntu-latest]
+        platform: [windows-latest, macos-latest, ubuntu-latest]
         python-version: ["3.7", "3.11"]
 
     runs-on: ${{ matrix.platform }}
@@ -90,7 +89,8 @@ jobs:
         path: ${{ env.CONAN_HOME }}
 
     - name: Test
-      run: python -m pytest test
+      if: matrix.platform != 'windows-latest'
+      run: python -m pytest test -v
 
 
   pip-status-check:

.github/workflows/wheels.yml

@@ -50,7 +50,7 @@ env:
   CCACHE_DIR: "${{ github.workspace }}/ccache/"
 
 jobs:
-  build_sdist:
+  build-sdist:
     name: Build SDist
     runs-on: ubuntu-latest
     steps:
@@ -138,3 +138,65 @@ jobs:
         with:
           name: wheels-macos-py${{ matrix.python-version }}
           path: ./*.whl
+
+  build-wheels-windows:
+    name: Wheels on Windows
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11' ]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Generate cache key
+        id: cache-key
+        run: |
+          hash="${{ hashFiles('conanfile.txt') }}" #, '.github/workflows/wheels.yml') }}"
+
+          echo "conan-key=conan-windows-$hash" >> $GITHUB_OUTPUT
+
+      - name: Restore Conan cache
+        id: cache-conan
+        uses: actions/cache/restore@v3
+        with:
+          key: ${{ steps.cache-key.outputs.conan-key }}
+          path: ${{ env.CONAN_HOME }}
+
+      - name: Build wheels
+        run: pip wheel . -vv --no-deps
+
+      - name: Save Conan cache
+        uses: actions/cache/save@v3
+        if: steps.cache-conan.outputs.cache-hit != 'true'
+        with:
+          key: ${{ steps.cache-key.outputs.conan-key }}
+          path: ${{ env.CONAN_HOME }}
+
+      - name: Fix wheels
+        run: |
+          pip install delvewheel
+
+          mkdir dlls/
+          find "$CONAN_HOME/p/" -type f -name deflate.dll -exec cp '{}' dlls/ \;
+          find "$CONAN_HOME/p/" -type f -name hdf5.dll -exec cp '{}' dlls/ \;
+          find "$CONAN_HOME/p/" -type f -name zlib.dll -exec cp '{}' dlls/ \;
+
+          delvewheel repair --add-path ./dlls/ hictkpy*.whl
+
+      - name: Test wheels
+        run: |
+          wheel=(wheelhouse/hictkpy*.whl)
+          pip install "${wheel[@]}[test]"
+          pytest test -v
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels-windows-py${{ matrix.python-version }}
+          path: wheelhouse/*.whl

README.md

@@ -48,11 +48,11 @@ m2 = sel.to_coo()    # Get interactions as a scipy.sparse.coo_matrix
 
 # Loop over interactions
 for bin1_id, bin2_id, count in clr.fetch("chr1"):
-  print(bin1_id ...)
+  print(bin1_id, ...)
 
 # Loop over interactions
 for chrom1, start1, end1, chrom2, start2, end2, count in clr.fetch("chr1", join=True):
-  print(chrom1 ...)
+  print(chrom1, ...)
 
 # Fetch interactions using UCSC queries
 clr.fetch("chr1:0-10,000,000").to_df()

setup.cfg

@@ -9,6 +9,7 @@ author = Roberto Rossini
 author_email = [email protected]
 description = Blazing fast toolkit to work with .hic and .cool files
 long_description = file: README.md, LICENSE
+long_description_content_type = text/markdown
 license = MIT
 classifiers =
     Programming Language :: Python :: 3
@@ -17,6 +18,7 @@ classifiers =
 zip_safe = False
 python_requires = >=3.6
 install_requires =
+    msvc-runtime; os_name=="nt"
     numpy
     pandas
     scipy

setup.py

@@ -35,7 +35,11 @@ class CMakeBuild(build_ext):
     def build_extension(self, ext: CMakeExtension) -> None:
         # Must be in this form due to bug in .resolve() only fixed in Python 3.10+
         ext_fullpath = Path.cwd() / self.get_ext_fullpath(ext.name)
-        extdir = ext_fullpath.parent.resolve()
+        extdir = ext_fullpath.parent.resolve() / ext.name
+        extdir.mkdir(exist_ok=True, parents=True)
+        with open(extdir / "__init__.py", "w") as f:
+            symbols = ["File", "is_cooler", "is_hic_file", "__version__"]
+            f.write("from .hictkpy import " + ", ".join(symbols) + "\n")
 
         # Using this requires trailing slash for auto-detection & inclusion of
         # auxiliary "native" libs

src/hictkpy_pixel_selector.cpp

@@ -158,7 +158,7 @@ py::object PixelSelector::to_coo() const {
   const auto num_rows = span1 == 0 ? bins().size() : (span1 + bin_size - 1) / bin_size;
   const auto num_cols = span2 == 0 ? bins().size() : (span2 + bin_size - 1) / bin_size;
   return std::visit(
-      [&](const auto& s) {
+      [&, num_rows, num_cols](const auto& s) {
         if (int_pixels()) {
           using T = std::int32_t;
           return pixel_iterators_to_coo(s->template begin<T>(), s->template end<T>(), num_rows,
@@ -183,7 +183,7 @@ py::object PixelSelector::to_numpy() const {
   const auto mirror_matrix = coord1().bin1.chrom() == coord2().bin1.chrom();
 
   return std::visit(
-      [&](const auto& s) {
+      [&, num_rows, num_cols, mirror_matrix](const auto& s) {
         if (int_pixels()) {
           using T = std::int32_t;
           return pixel_iterators_to_numpy(s->template begin<T>(), s->template end<T>(), num_rows,