From 16231cce9502a16cd82454d0c01af7eaef5d9090 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 12 Mar 2026 08:04:35 +0100 Subject: [PATCH 1/5] update CI --- .github/workflows/ci.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 001c52b4a..8533db92b 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -8,10 +8,10 @@ jobs: strategy: fail-fast: true matrix: - python-version: [3.9] + python-version: [3.12] steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 + - uses: actions/checkout@v6 + - uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} - name: Install python dependencies From 7aca938f39b8bef96b26d9c0b26595c1796e9c01 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 12 Mar 2026 17:06:04 +0100 Subject: [PATCH 2/5] Update ci.yaml --- .github/workflows/ci.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 8533db92b..7e5b730ea 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -18,7 +18,8 @@ jobs: run: | #python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/util #python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/tool_util - python -m pip install galaxy-tool-util + python -m pip install git+https://git@github.com/bgruening/galaxy.git@mulled_quay_enhancements#subdirectory=packages/tool_util + #python -m pip install galaxy-tool-util - run: docker --version - run: docker info - name: Build images From 86c577d3ba9f0350fd488034008086016ac1e68e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 12 Mar 2026 17:14:28 +0100 Subject: [PATCH 3/5] Update ci.yaml --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 7e5b730ea..561e189cd 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -18,7 +18,7 @@ jobs: run: | #python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/util #python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/tool_util - python -m pip install git+https://git@github.com/bgruening/galaxy.git@mulled_quay_enhancements#subdirectory=packages/tool_util + python -m pip install "git+https://github.com/bgruening/galaxy.git@mulled_quay_enhancements#subdirectory=packages/tool_util" #python -m pip install galaxy-tool-util - run: docker --version - run: docker info From e1341898dcc6d4ee4a8a7fb40866241f8056597d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 12 Mar 2026 17:24:56 +0100 Subject: [PATCH 4/5] Update ci.yaml --- .github/workflows/ci.yaml | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 561e189cd..7efee6008 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -2,6 +2,7 @@ name: Build image on: [push, pull_request] env: MULLED_NAMESPACE: biocontainers + MULLED_TOOL_UTIL_SOURCE: git+https://github.com/bgruening/galaxy.git@mulled_quay_enhancements#subdirectory=packages/tool_util jobs: build-and-test: runs-on: ubuntu-latest @@ -10,21 +11,16 @@ jobs: matrix: python-version: [3.12] steps: - - uses: actions/checkout@v6 - - uses: actions/setup-python@v6 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - name: Install python dependencies - run: | - #python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/util - #python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/tool_util - python -m pip install "git+https://github.com/bgruening/galaxy.git@mulled_quay_enhancements#subdirectory=packages/tool_util" - #python -m pip install galaxy-tool-util + - uses: astral-sh/setup-uv@v7 - run: docker --version - run: docker info - name: Build images run: | - mulled-build-files --check-published --singularity --namespace $MULLED_NAMESPACE build-and-test ./combinations --verbose + uvx --from "$MULLED_TOOL_UTIL_SOURCE" mulled-build-files --check-published --singularity --namespace $MULLED_NAMESPACE build-and-test ./combinations --verbose - name: Upload images (if pushed to master branch) if: github.ref == 'refs/heads/master' && github.repository_owner == 'BioContainers' env: @@ -35,6 +31,6 @@ jobs: ssh-keyscan -t rsa depot.galaxyproject.org >> ~/.ssh/known_hosts ssh-agent -a $SSH_AUTH_SOCK > /dev/null ssh-add - <<< "${{ secrets.ORVAL_KEY }}" - mulled-build-files --check-published --namespace $MULLED_NAMESPACE --oauth-token ${{ secrets.QUAY_OAUTH_TOKEN }} push ./combinations + uvx --from "$MULLED_TOOL_UTIL_SOURCE" mulled-build-files --check-published --namespace $MULLED_NAMESPACE --oauth-token ${{ secrets.QUAY_OAUTH_TOKEN }} push ./combinations ls -l singularity_import [ "$(ls -A singularity_import)" ] && echo 'uploading Singularity images' && scp singularity_import/*:* singularity@depot.galaxyproject.org:/srv/nginx/depot.galaxyproject.org/root/singularity/ From 83004d412966226c161da56fcb66379bb99618d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 12 Mar 2026 19:32:49 +0100 Subject: [PATCH 5/5] Update ci.yaml --- .github/workflows/ci.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 7efee6008..1edaa9f68 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -9,7 +9,7 @@ jobs: strategy: fail-fast: true matrix: - python-version: [3.12] + python-version: [3.9] steps: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 @@ -20,7 +20,7 @@ jobs: - run: docker info - name: Build images run: | - uvx --from "$MULLED_TOOL_UTIL_SOURCE" mulled-build-files --check-published --singularity --namespace $MULLED_NAMESPACE build-and-test ./combinations --verbose + uv run --with "$MULLED_TOOL_UTIL_SOURCE" python -m galaxy.tool_util.deps.mulled.mulled_build_files --check-published --singularity --namespace $MULLED_NAMESPACE build-and-test ./combinations --verbose - name: Upload images (if pushed to master branch) if: github.ref == 'refs/heads/master' && github.repository_owner == 'BioContainers' env: @@ -31,6 +31,6 @@ jobs: ssh-keyscan -t rsa depot.galaxyproject.org >> ~/.ssh/known_hosts ssh-agent -a $SSH_AUTH_SOCK > /dev/null ssh-add - <<< "${{ secrets.ORVAL_KEY }}" - uvx --from "$MULLED_TOOL_UTIL_SOURCE" mulled-build-files --check-published --namespace $MULLED_NAMESPACE --oauth-token ${{ secrets.QUAY_OAUTH_TOKEN }} push ./combinations + uv run --with "$MULLED_TOOL_UTIL_SOURCE" python -m galaxy.tool_util.deps.mulled.mulled_build_files --check-published --namespace $MULLED_NAMESPACE --oauth-token ${{ secrets.QUAY_OAUTH_TOKEN }} push ./combinations ls -l singularity_import [ "$(ls -A singularity_import)" ] && echo 'uploading Singularity images' && scp singularity_import/*:* singularity@depot.galaxyproject.org:/srv/nginx/depot.galaxyproject.org/root/singularity/