Merge branch 'main' into fix-windows

.clang-format

@@ -0,0 +1,159 @@
+# Copyright (C) 2022 Roberto Rossini <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+---
+Language:        Cpp
+# BasedOnStyle:  Google
+AccessModifierOffset: -1
+AlignAfterOpenBracket: Align
+AlignConsecutiveMacros: AcrossEmptyLinesAndComments
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Left
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortLambdasOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: WithoutElse
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterCaseLabel:  false
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     100
+CommentPragmas:  '^ IWYU pragma:| NOLINT'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: true
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Regroup
+IncludeCategories:
+  - Regex:           '^<ext/.*\.h>'
+    Priority:        2
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentPPDirectives: None
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Never
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+RawStringFormats:
+  - Language:        Cpp
+    Delimiters:
+      - cc
+      - CC
+      - cpp
+      - Cpp
+      - CPP
+      - 'c++'
+      - 'C++'
+    CanonicalDelimiter: ''
+    BasedOnStyle:    google
+  - Language:        TextProto
+    Delimiters:
+      - pb
+      - PB
+      - proto
+      - PROTO
+    EnclosingFunctions:
+      - EqualsProto
+      - EquivToProto
+      - PARSE_PARTIAL_TEXT_PROTO
+      - PARSE_TEST_PROTO
+      - PARSE_TEXT_PROTO
+      - ParseTextOrDie
+      - ParseTextProtoOrDie
+    CanonicalDelimiter: ''
+    BasedOnStyle:    google
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Auto
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        8
+UseTab:          Never
+...

.github/workflows/pip.yml

@@ -118,10 +118,10 @@ jobs:
     - name: Build and install
       env:
         CMAKE_ARGS: "-DCMAKE_PREFIX_PATH=${{ github.workspace}}/conan_build"
-      run: pip install --verbose .
+      run: pip install --verbose .[test]
 
     - name: Test
-      run: python -v -c 'import hictkpy; print(hictkpy.__version__)'
+      run: python -m pytest test
 
 
   pip-status-check:

.github/workflows/wheels.yml

@@ -0,0 +1,131 @@
+# Copyright (C) 2023 Roberto Rossini ([email protected])
+# SPDX-License-Identifier: MIT
+
+name: Wheels
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+    paths:
+      - ".github/workflows/wheels.yml"
+      - "cmake/**"
+      - "src/**"
+      - "test/**"
+      - "CMakeLists.txt"
+      - "conanfile.txt"
+      - "pyproject.toml"
+      - "setup.cfg"
+      - "setup.py"
+    tags:
+      - 'v*.*.*'
+
+  pull_request:
+    paths:
+      - ".github/workflows/wheels.yml"
+      - "cmake/**"
+      - "src/**"
+      - "test/**"
+      - "CMakeLists.txt"
+      - "conanfile.txt"
+      - "pyproject.toml"
+      - "setup.cfg"
+      - "setup.py"
+
+  release:
+    types:
+      - published
+
+# https://stackoverflow.com/a/72408109
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash
+
+env:
+  CONAN_HOME: "${{ github.workspace }}/conan/"
+  CCACHE_DIR: "${{ github.workspace }}/ccache/"
+
+jobs:
+  build_sdist:
+    name: Build SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - name: Check metadata
+        run: pipx run twine check dist/*
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+
+  build_wheels:
+    name: Wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v2
+        with:
+          platforms: all
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          CIBW_ARCHS_LINUX: x86_64
+          CIBW_ARCHS_MACOS: x86_64 arm64
+          CIBW_ARCHS_WINDOWS: AMD64
+
+      - name: Build wheels (PR)
+        uses: pypa/[email protected]
+        if: ${{ github.event_name == 'pull_request' }}
+        env:
+          CIBW_ARCHS_LINUX: x86_64
+          CIBW_ARCHS_MACOS: x86_64 arm64
+          CIBW_ARCHS_WINDOWS: AMD64
+          CIBW_BUILD: "cp311-*"
+
+      - name: Verify clean directory
+        run: git diff --exit-code
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          path: wheelhouse/*.whl
+
+
+  upload_all:
+    name: Upload if release
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.pypi_password }}

CMakeLists.txt

@@ -27,7 +27,7 @@ include(FetchContent)
 FetchContent_Declare(
   hictk
   GIT_REPOSITORY "https://github.com/paulsengroup/hictk.git"
-  GIT_TAG        "6e9d46efc3cd3a4efa06db9d05b9af9fe91df4fe"
+  GIT_TAG        "5a27e5c4a071c3384bfc521747c0fe5c329b221f"
   SYSTEM)
 
 set(BUILD_SHARED_LIBS ON)
@@ -37,6 +37,7 @@ set(HICTK_BUILD_BENCHMARKS OFF)
 set(HICTK_BUILD_PYTHON_BINDINGS OFF)
 set(HICTK_WITH_EIGEN OFF)
 set(HICTK_BUILD_TOOLS OFF)
+set(HICTK_INSTALL OFF)
 FetchContent_MakeAvailable(hictk)
 
 add_library(hictkpy_project_options INTERFACE)

MANIFEST.in

@@ -0,0 +1,7 @@
+# Copyright (C) 2023 Roberto Rossini ([email protected])
+#
+# SPDX-License-Identifier: MIT
+
+include conanfile.txt README.md LICENSE
+graft cmake/ src/
+global-include CMakeLists.txt

conanfile.txt

@@ -16,7 +16,13 @@ spdlog/1.12.0
 CMakeDeps
 
 [options]
+fmt*:header_only=True
+hdf5*:enable_cxx=False
+hdf5*:hl=False
+hdf5*:threadsafe=False
+hdf5*:parallel=False
 highfive*:with_boost=False
 highfive*:with_eigen=False
 highfive*:with_opencv=False
 highfive*:with_xtensor=False
+spdlog*:header_only=True

devel/cibw/linux/cibw_setup_deps.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+# Copyright (C) 2023 Roberto Rossini ([email protected])
+# SPDX-License-Identifier: MIT
+
+set -e
+set -u
+
+# readlink -f is not available on macos...
+function readlink_py {
+  set -eu
+  python3 -c 'import os, sys; print(os.path.realpath(sys.argv[1]))' "$1"
+}
+
+install_prefix="$(readlink_py "${1-/usr/local}")"
+
+conan install conanfile.txt \
+  -s build_type=Release \
+  -s compiler.cppstd=17 \
+  --output-folder "$install_prefix/share/cmake/" \
+  -o '*/*:shared=True' \
+  --build="missing"

devel/cibw/linux/conanfile.txt

@@ -0,0 +1,28 @@
+# Copyright (C) 2023 Roberto Rossini <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+
+[requires]
+fast_float/5.2.0
+fmt/10.0.0
+hdf5/1.14.0
+highfive/2.7.1
+libdeflate/1.18
+parallel-hashmap/1.3.11
+pybind11/2.10.4
+spdlog/1.12.0
+
+[generators]
+CMakeDeps
+
+[options]
+fmt*:header_only=True
+hdf5*:enable_cxx=False
+hdf5*:hl=False
+hdf5*:threadsafe=False
+hdf5*:parallel=False
+highfive*:with_boost=False
+highfive*:with_eigen=False
+highfive*:with_opencv=False
+highfive*:with_xtensor=False
+spdlog*:header_only=True