Merge branch 'main' into feature/hic-write

paulsengroup · Jan 21, 2024 · 8a1ade6 · 8a1ade6
2 parents 0633542 + 6b087ea
commit 8a1ade6
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Showing 15 changed files with 43 additions and 41 deletions.
diff --git a/.github/workflows/build-dockerfile.yml b/.github/workflows/build-dockerfile.yml
@@ -54,7 +54,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Restore test dataset
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: ${{ needs.cache-test-dataset.outputs.cache-key }}
           path: test/data/hictk_test_data.tar.xz

diff --git a/.github/workflows/cache-test-dataset.yml b/.github/workflows/cache-test-dataset.yml
@@ -39,7 +39,7 @@ jobs:
 
       - name: Restore cache
         id: cache-dset
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: ${{ steps.generate-cache-key.outputs.key }}
           path: ${{ env.TEST_DATASET_PATH }}
@@ -71,7 +71,7 @@ jobs:
           shasum -c checksum.sha256
 
       - name: Save cache
-        uses: actions/cache/save@v3
+        uses: actions/cache/save@v4
         if: steps.cache-dset.outputs.cache-hit != 'true'
         with:
           key: ${{ steps.generate-cache-key.outputs.key }}

diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
@@ -80,7 +80,7 @@ jobs:
 
       - name: Restore Conan cache
         id: cache-conan
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: conan-${{ steps.cache-key.outputs.conan-key }}
           path: ${{ env.CONAN_HOME }}
@@ -112,7 +112,7 @@ jobs:
           conan cache clean "*" --source
 
       - name: Save Conan cache
-        uses: actions/cache/save@v3
+        uses: actions/cache/save@v4
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
           key: conan-${{ steps.cache-key.outputs.conan-key }}
@@ -135,7 +135,7 @@ jobs:
                 -B build
 
       - name: Cache Ccache folder
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: ${{ steps.cache-key.outputs.ccache-key }}
           restore-keys: ${{ steps.cache-key.outputs.ccache-restore-key }}
@@ -148,7 +148,7 @@ jobs:
         run: ccache -s
 
       - name: Restore test dataset
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: ${{ needs.cache-test-dataset.outputs.cache-key }}
           path: test/data/hictk_test_data.tar.xz
@@ -176,7 +176,7 @@ jobs:
 
       - name: Cache hic_tools
         id: cache-hictools
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: hic_tools
           path: hic_tools.jar

diff --git a/.github/workflows/fuzzy-testing.yml b/.github/workflows/fuzzy-testing.yml
@@ -147,7 +147,7 @@ jobs:
 
       - name: Restore Conan cache
         id: cache-conan
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: conan-${{ steps.cache-key.outputs.key }}
           path: ${{ env.CONAN_HOME }}
@@ -200,7 +200,7 @@ jobs:
           pip install . -v
 
       - name: Save Conan cache
-        uses: actions/cache/save@v3
+        uses: actions/cache/save@v4
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
           key: conan-${{ steps.cache-key.outputs.key }}

diff --git a/.github/workflows/macos-ci.yml b/.github/workflows/macos-ci.yml
@@ -131,7 +131,7 @@ jobs:
 
       - name: Restore Conan cache
         id: cache-conan
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: conan-${{ steps.cache-key.outputs.conan-restore-key }}
           path: ${{ env.CONAN_HOME }}
@@ -169,14 +169,14 @@ jobs:
           conan cache clean "*" --source
 
       - name: Save Conan cache
-        uses: actions/cache/save@v3
+        uses: actions/cache/save@v4
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
           key: conan-${{ steps.cache-key.outputs.conan-key }}
           path: ${{ env.CONAN_HOME }}
 
       - name: Cache Ccache folder
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: ${{ steps.cache-key.outputs.ccache-key }}
           restore-keys: ${{ steps.cache-key.outputs.ccache-restore-key }}
@@ -258,7 +258,7 @@ jobs:
           chown -R $(id -u):$(id -g) $PWD
 
       - name: Restore test dataset
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: ${{ needs.cache-test-dataset.outputs.cache-key }}
           path: test/data/hictk_test_data.tar.xz
@@ -329,7 +329,7 @@ jobs:
 
       - name: Cache hic_tools
         id: cache-hictools
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: hic_tools
           path: hic_tools.jar
@@ -341,7 +341,7 @@ jobs:
                -o hic_tools.jar
 
       - name: Restore test dataset
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: ${{ needs.cache-test-dataset.outputs.cache-key }}
           path: test/data/hictk_test_data.tar.xz

diff --git a/.github/workflows/run-clang-tidy.yml b/.github/workflows/run-clang-tidy.yml
@@ -77,7 +77,7 @@ jobs:
 
       - name: Restore Conan cache
         id: cache-conan
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: conan-${{ steps.cache-key.outputs.conan-key }}
           path: ${{ env.CONAN_HOME }}
@@ -109,7 +109,7 @@ jobs:
           conan cache clean "*" --source
 
       - name: Save Conan cache
-        uses: actions/cache/save@v3
+        uses: actions/cache/save@v4
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
           key: conan-${{ steps.cache-key.outputs.conan-key }}
@@ -131,7 +131,7 @@ jobs:
                 -B build
 
       - name: Cache Ccache folder
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: ${{ steps.cache-key.outputs.ccache-key }}
           restore-keys: ${{ steps.cache-key.outputs.ccache-restore-key }}

diff --git a/.github/workflows/ubuntu-ci.yml b/.github/workflows/ubuntu-ci.yml
@@ -199,7 +199,7 @@ jobs:
 
       - name: Restore Conan cache
         id: cache-conan
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: conan-${{ steps.cache-key.outputs.conan-restore-key }}
           path: ${{ env.CONAN_HOME }}
@@ -231,14 +231,14 @@ jobs:
           conan cache clean "*" --source
 
       - name: Save Conan cache
-        uses: actions/cache/save@v3
+        uses: actions/cache/save@v4
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
           key: conan-${{ steps.cache-key.outputs.conan-key }}
           path: ${{ env.CONAN_HOME }}
 
       - name: Cache Ccache folder
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: ${{ steps.cache-key.outputs.ccache-key }}
           restore-keys: ${{ steps.cache-key.outputs.ccache-restore-key }}
@@ -324,7 +324,7 @@ jobs:
           chown -R $(id -u):$(id -g) $PWD
 
       - name: Restore test dataset
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: ${{ needs.cache-test-dataset.outputs.cache-key }}
           path: test/data/hictk_test_data.tar.xz
@@ -385,7 +385,7 @@ jobs:
 
       - name: Cache hic_tools
         id: cache-hictools
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: hic_tools
           path: hic_tools.jar
@@ -398,7 +398,7 @@ jobs:
                -o hic_tools.jar
 
       - name: Restore test dataset
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: ${{ needs.cache-test-dataset.outputs.cache-key }}
           path: test/data/hictk_test_data.tar.xz

diff --git a/.github/workflows/windows-ci.yml b/.github/workflows/windows-ci.yml
@@ -110,7 +110,7 @@ jobs:
 
       - name: Restore Conan cache
         id: cache-conan
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: conan-${{ steps.cache-key.outputs.conan-restore-key }}
           path: ${{ env.CONAN_HOME }}
@@ -148,14 +148,14 @@ jobs:
           conan cache clean "*" --source
 
       - name: Save Conan cache
-        uses: actions/cache/save@v3
+        uses: actions/cache/save@v4
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
           key: conan-${{ steps.cache-key.outputs.conan-key }}
           path: ${{ env.CONAN_HOME }}
 
       - name: Cache Ccache folder
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: ${{ steps.cache-key.outputs.ccache-key }}
           restore-keys: ${{ steps.cache-key.outputs.ccache-restore-key }}
@@ -182,7 +182,7 @@ jobs:
         run: ccache -s
 
       - name: Restore test dataset
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           key: ${{ needs.cache-test-dataset.outputs.cache-key }}
           path: test/data/hictk_test_data.tar.xz

diff --git a/cmake/Versioning.cmake b/cmake/Versioning.cmake
@@ -4,7 +4,7 @@
 
 set(HICTK_PROJECT_VERSION_MAJOR 0)
 set(HICTK_PROJECT_VERSION_MINOR 0)
-set(HICTK_PROJECT_VERSION_PATCH 5)
+set(HICTK_PROJECT_VERSION_PATCH 6)
 set(HICTK_PROJECT_VERSION_SUFFIX "")
 
 option(HICTK_ENABLE_GIT_VERSION_TRACKING "Retrieve project version and metadata from git" ON)

diff --git a/docs/conf.py b/docs/conf.py
@@ -49,7 +49,7 @@
 # built documents.
 
 # Read the listed version
-version = "0.0.5"
+version = "0.0.6"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -20,7 +20,7 @@ hictk package for Linux and MacOS is available on bioconda and can be installed
   hictk: /home/user/.miniconda3/envs/hictk/bin/hictk
 
   (hictk) user@dev:/tmp$ hictk --version
-  hictk-v0.0.5-bioconda
+  hictk-v0.0.6-bioconda
 
 
 Containers (Docker or Singularity/Apptainer)
@@ -66,10 +66,10 @@ Downloading and running the latest stable release can be done as follows:
 .. code-block:: console
 
   # Using Docker, may require sudo
-  user@dev:/tmp$ docker run ghcr.io/paulsengroup/hictk:0.0.5 --help
+  user@dev:/tmp$ docker run ghcr.io/paulsengroup/hictk:0.0.6 --help
 
   # Using Singularity/Apptainer
-  user@dev:/tmp$ singularity run ghcr.io/paulsengroup/hictk:0.0.5 --help
+  user@dev:/tmp$ singularity run ghcr.io/paulsengroup/hictk:0.0.6 --help
 
   Blazing fast tools to work with .hic and .cool files.
   Usage: /usr/local/bin/hictk [OPTIONS] SUBCOMMAND

diff --git a/docs/installation_src.rst b/docs/installation_src.rst
@@ -61,7 +61,7 @@ Download from the `Release <https://github.com/paulsengroup/hictk/releases>`_ pa
 .. code-block:: bash
 
   mkdir /tmp/hictk
-  curl -L 'https://github.com/paulsengroup/hictk/archive/refs/tags/v0.0.5.tar.gz' | tar --strip-components=1 -C /tmp/hictk -xzf -
+  curl -L 'https://github.com/paulsengroup/hictk/archive/refs/tags/v0.0.6.tar.gz' | tar --strip-components=1 -C /tmp/hictk -xzf -
 
 
 Using git.
@@ -71,7 +71,7 @@ Using git.
   git clone https://github.com/paulsengroup/hictk.git /tmp/hictk
 
   cd /tmp/hictk
-  git checkout v0.0.5  # Skip this step if you want to build the latest commit from main
+  git checkout v0.0.6  # Skip this step if you want to build the latest commit from main
 
 Compiling hictk
 ---------------

diff --git a/docs/quickstart_api.rst b/docs/quickstart_api.rst
@@ -18,7 +18,7 @@ To install libhictk using Conan, first create a conanfile.txt like the following
 .. code-block::
 
   [requires]
-  hictk/0.0.5
+  hictk/0.0.6
 
   [generators]
   CMakeDeps
@@ -62,7 +62,7 @@ To install and configure hictk using `FetchContent <https://cmake.org/cmake/help
   FetchContent_Declare(
     hictk
     GIT_REPOSITORY  "https://github.com/paulsengroup/hictk.git"
-    GIT_TAG         v0.0.5
+    GIT_TAG         v0.0.6
     SYSTEM)
 
   # Customize hictk build flags

diff --git a/docs/quickstart_cli.rst b/docs/quickstart_cli.rst
@@ -12,7 +12,7 @@ Next, verify that hictk was installed correctly with:
 .. code-block:: console
 
   user@dev:/tmp$ hictk --version
-  hictk-v0.0.5
+  hictk-v0.0.6
 
 Command line interface
 ======================

diff --git a/src/libhictk/hic/include/hictk/hic/impl/pixel_selector_impl.hpp b/src/libhictk/hic/include/hictk/hic/impl/pixel_selector_impl.hpp
@@ -124,7 +124,8 @@ inline ThinPixel<N> PixelSelector::transform_pixel(ThinPixel<float> pixel) const
       return float(_reader->avg());
     }
 
-    const auto i = std::min(bin2 - bin1, expected.size() - 1);
+    const auto i =
+        std::min(bin2 - bin1, conditional_static_cast<std::uint64_t>(expected.size() - 1));
     return float(expected[i]);
   }();
 
@@ -693,7 +694,8 @@ inline ThinPixel<N> PixelSelector::iterator<N>::transform_pixel(ThinPixel<float>
       return float(_reader->avg());
     }
 
-    const auto i = std::min(bin2 - bin1, expected.size() - 1);
+    const auto i =
+        std::min(bin2 - bin1, conditional_static_cast<std::uint64_t>(expected.size() - 1));
     return float(expected[i]);
   }();