From 48ef7844ca68ea02092cb1c1b2cf439fafad45e9 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Tue, 9 Jan 2024 21:52:59 +0100 Subject: [PATCH 1/3] Fix macOS builds --- .../hic/include/hictk/hic/impl/pixel_selector_impl.hpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) 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 index 9231ec3f..b5f87728 100644 --- 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 PixelSelector::transform_pixel(ThinPixel 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(expected.size() - 1)); return float(expected[i]); }(); @@ -693,7 +694,8 @@ inline ThinPixel PixelSelector::iterator::transform_pixel(ThinPixel return float(_reader->avg()); } - const auto i = std::min(bin2 - bin1, expected.size() - 1); + const auto i = + std::min(bin2 - bin1, conditional_static_cast(expected.size() - 1)); return float(expected[i]); }(); From ac5b4e5eb840879429209e59ab873aebdf83457f Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Thu, 11 Jan 2024 23:17:51 +0100 Subject: [PATCH 2/3] Prepare for release --- cmake/Versioning.cmake | 2 +- docs/conf.py | 2 +- docs/installation.rst | 6 +++--- docs/installation_src.rst | 4 ++-- docs/quickstart_api.rst | 4 ++-- docs/quickstart_cli.rst | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/cmake/Versioning.cmake b/cmake/Versioning.cmake index 8f34ef1c..33e9da39 100644 --- 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 index 4729070f..7d98a0cb 100644 --- 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 index 35a6509c..99075a96 100644 --- 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 index b45db523..c4fefd27 100644 --- a/docs/installation_src.rst +++ b/docs/installation_src.rst @@ -61,7 +61,7 @@ Download from the `Release `_ 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 index bc7d1c7f..10898a00 100644 --- 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 Date: Thu, 18 Jan 2024 01:15:33 +0000 Subject: [PATCH 3/3] Bump actions/cache from 3 to 4 Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/build-dockerfile.yml | 2 +- .github/workflows/cache-test-dataset.yml | 4 ++-- .github/workflows/codecov.yml | 10 +++++----- .github/workflows/fuzzy-testing.yml | 4 ++-- .github/workflows/macos-ci.yml | 12 ++++++------ .github/workflows/run-clang-tidy.yml | 6 +++--- .github/workflows/ubuntu-ci.yml | 12 ++++++------ .github/workflows/windows-ci.yml | 8 ++++---- 8 files changed, 29 insertions(+), 29 deletions(-) diff --git a/.github/workflows/build-dockerfile.yml b/.github/workflows/build-dockerfile.yml index 73e16e0d..195a582d 100644 --- 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 index 46d05bae..6f629a48 100644 --- 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: ${{ steps.generate-cache-key.outputs.key }} diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml index 80bcefd2..8f6615d0 100644 --- a/.github/workflows/codecov.yml +++ b/.github/workflows/codecov.yml @@ -80,7 +80,7 @@ jobs: - name: Restore Conan cache id: cache-conan - uses: actions/cache/restore@v3 + uses: actions/cache/restore@v4 with: key: conan-${{ 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: ${{ needs.cache-test-dataset.outputs.cache-key }} path: test/data/hictk_test_data.tar.xz @@ -176,7 +176,7 @@ jobs: - name: Cache hic_tools id: cache-hictools - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: hic_tools path: hic_tools.jar diff --git a/.github/workflows/fuzzy-testing.yml b/.github/workflows/fuzzy-testing.yml index d74956f5..1f084be4 100644 --- a/.github/workflows/fuzzy-testing.yml +++ b/.github/workflows/fuzzy-testing.yml @@ -147,7 +147,7 @@ jobs: - name: Restore Conan cache id: cache-conan - uses: actions/cache/restore@v3 + uses: actions/cache/restore@v4 with: key: conan-${{ 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 index fa6f8bcd..4c88d595 100644 --- 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: ${{ needs.cache-test-dataset.outputs.cache-key }} path: test/data/hictk_test_data.tar.xz diff --git a/.github/workflows/run-clang-tidy.yml b/.github/workflows/run-clang-tidy.yml index 42bde0eb..ffeb5583 100644 --- a/.github/workflows/run-clang-tidy.yml +++ b/.github/workflows/run-clang-tidy.yml @@ -77,7 +77,7 @@ jobs: - name: Restore Conan cache id: cache-conan - uses: actions/cache/restore@v3 + uses: actions/cache/restore@v4 with: key: conan-${{ 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: ${{ steps.cache-key.outputs.ccache-restore-key }} diff --git a/.github/workflows/ubuntu-ci.yml b/.github/workflows/ubuntu-ci.yml index b72cf36d..c4c11ef8 100644 --- a/.github/workflows/ubuntu-ci.yml +++ b/.github/workflows/ubuntu-ci.yml @@ -199,7 +199,7 @@ jobs: - name: Restore Conan cache id: cache-conan - uses: actions/cache/restore@v3 + uses: actions/cache/restore@v4 with: key: conan-${{ 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: ${{ needs.cache-test-dataset.outputs.cache-key }} path: test/data/hictk_test_data.tar.xz diff --git a/.github/workflows/windows-ci.yml b/.github/workflows/windows-ci.yml index 521e8ecf..85032934 100644 --- a/.github/workflows/windows-ci.yml +++ b/.github/workflows/windows-ci.yml @@ -110,7 +110,7 @@ jobs: - name: Restore Conan cache id: cache-conan - uses: actions/cache/restore@v3 + uses: actions/cache/restore@v4 with: key: conan-${{ 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