From 9ac07290193ddf58c3b4b0717a2a109e78fbe0f7 Mon Sep 17 00:00:00 2001 From: "seqan-actions[bot]" Date: Sat, 31 Jan 2026 13:21:35 +0100 Subject: [PATCH 1/7] [INFRA] Update CPM Packages --- cmake/package-lock.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake index f2e1f3e..ae3425a 100644 --- a/cmake/package-lock.cmake +++ b/cmake/package-lock.cmake @@ -8,7 +8,7 @@ # cmake-format: off # hibf -set (NEEDLE_HIBF_VERSION fc4e40d8672f496a32df73c608915d45e715f6a8 CACHE STRING "") +set (NEEDLE_HIBF_VERSION bbca76409f5445f1404c206021fcfa37f1fd7054 CACHE STRING "") CPMDeclarePackage (hibf NAME hibf GIT_TAG ${NEEDLE_HIBF_VERSION} # main From c592a095652f62da1afe57276ee7e915f8757bdd Mon Sep 17 00:00:00 2001 From: "seqan-actions[bot]" Date: Sun, 1 Mar 2026 13:17:44 +0100 Subject: [PATCH 2/7] [INFRA] Update CPM Packages --- cmake/package-lock.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake index ae3425a..31fce44 100644 --- a/cmake/package-lock.cmake +++ b/cmake/package-lock.cmake @@ -19,7 +19,7 @@ CPMDeclarePackage (hibf ) # seqan3 -set (NEEDLE_SEQAN3_VERSION 3.4.0 CACHE STRING "") +set (NEEDLE_SEQAN3_VERSION 3.4.1 CACHE STRING "") CPMDeclarePackage (seqan3 NAME seqan3 VERSION ${NEEDLE_SEQAN3_VERSION} @@ -31,7 +31,7 @@ CPMDeclarePackage (seqan3 ) # sharg -set (NEEDLE_SHARG_VERSION 1.2.1 CACHE STRING "") +set (NEEDLE_SHARG_VERSION 1.2.2 CACHE STRING "") CPMDeclarePackage (sharg NAME sharg VERSION ${NEEDLE_SHARG_VERSION} From f2a1d90112a73d0a21cd74ec6e97420d7b736297 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 2 Mar 2026 04:22:39 +0000 Subject: [PATCH 3/7] Bump actions/upload-artifact from 6 to 7 Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 6 to 7. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v6...v7) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ci_install.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_install.yml b/.github/workflows/ci_install.yml index 5514bda..e1111ff 100644 --- a/.github/workflows/ci_install.yml +++ b/.github/workflows/ci_install.yml @@ -95,7 +95,7 @@ jobs: - name: Upload source package if: contains(matrix.compiler, 'gcc') - uses: actions/upload-artifact@v6 + uses: actions/upload-artifact@v7 with: name: needle-source-package path: create_source_package/needle-*.tar.xz* From 4da18431b06f2aed46816b7f30a14729fe6d6be3 Mon Sep 17 00:00:00 2001 From: "seqan-actions[bot]" Date: Thu, 19 Mar 2026 09:13:19 +0100 Subject: [PATCH 4/7] chore(deps): update CPM packages --- cmake/package-lock.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake index 31fce44..6a7e6e7 100644 --- a/cmake/package-lock.cmake +++ b/cmake/package-lock.cmake @@ -19,7 +19,7 @@ CPMDeclarePackage (hibf ) # seqan3 -set (NEEDLE_SEQAN3_VERSION 3.4.1 CACHE STRING "") +set (NEEDLE_SEQAN3_VERSION 3.4.2 CACHE STRING "") CPMDeclarePackage (seqan3 NAME seqan3 VERSION ${NEEDLE_SEQAN3_VERSION} From c7784a3b789e572be49e60b6081289bac74fc1df Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 23 Mar 2026 04:19:52 +0000 Subject: [PATCH 5/7] Bump codecov/codecov-action from 5.5.2 to 5.5.3 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5.5.2 to 5.5.3. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v5.5.2...v5.5.3) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-version: 5.5.3 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/ci_coverage.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml index 18ebd5a..e10b23a 100644 --- a/.github/workflows/ci_coverage.yml +++ b/.github/workflows/ci_coverage.yml @@ -79,7 +79,7 @@ jobs: --output ${GITHUB_WORKSPACE}/build/coverage_report.xml - name: Submit coverage build - uses: codecov/codecov-action@v5.5.2 + uses: codecov/codecov-action@v5.5.3 with: disable_search: true fail_ci_if_error: false From 6832383b449afda0a6ada5c6e55feeb4c7510db6 Mon Sep 17 00:00:00 2001 From: "seqan-actions[bot]" Date: Sat, 28 Mar 2026 13:28:59 +0100 Subject: [PATCH 6/7] chore(deps): update CPM packages --- cmake/package-lock.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake index 6a7e6e7..ccf13ea 100644 --- a/cmake/package-lock.cmake +++ b/cmake/package-lock.cmake @@ -8,7 +8,7 @@ # cmake-format: off # hibf -set (NEEDLE_HIBF_VERSION bbca76409f5445f1404c206021fcfa37f1fd7054 CACHE STRING "") +set (NEEDLE_HIBF_VERSION eca65729de77a5d411160c487adcafe8f972342b CACHE STRING "") CPMDeclarePackage (hibf NAME hibf GIT_TAG ${NEEDLE_HIBF_VERSION} # main From 536f19c51320946ef45d21f02c4e3ce0712768e1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 30 Mar 2026 04:37:59 +0000 Subject: [PATCH 7/7] Bump codecov/codecov-action from 5.5.3 to 6.0.0 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5.5.3 to 6.0.0. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v5.5.3...v6.0.0) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-version: 6.0.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ci_coverage.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml index e10b23a..7a0eb2a 100644 --- a/.github/workflows/ci_coverage.yml +++ b/.github/workflows/ci_coverage.yml @@ -79,7 +79,7 @@ jobs: --output ${GITHUB_WORKSPACE}/build/coverage_report.xml - name: Submit coverage build - uses: codecov/codecov-action@v5.5.3 + uses: codecov/codecov-action@v6.0.0 with: disable_search: true fail_ci_if_error: false