diff --git a/.github/workflows/basic.yml b/.github/workflows/basic.yml index cfa61a167..5f68857d0 100644 --- a/.github/workflows/basic.yml +++ b/.github/workflows/basic.yml @@ -9,7 +9,11 @@ on: - next tags: - '*' + paths-ignore: + - 'docs/**' pull_request: + paths-ignore: + - 'docs/**' env: BUILD_TYPE: Release diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index f074672b2..9647a3a86 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -3,10 +3,12 @@ name: docs on: push: branches: - - master + - master - main - next - + paths: + - 'docs/**' + permissions: contents: write @@ -22,12 +24,12 @@ jobs: - uses: actions/setup-python@v5 with: python-version: 3.x - - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV + - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV - uses: actions/cache@v4 with: key: mkdocs-material-${{ env.cache_id }} path: .cache restore-keys: | mkdocs-material- - - run: pip install mkdocs-material + - run: pip install mkdocs-material - run: mkdocs gh-deploy --force diff --git a/.github/workflows/full_runs.yml b/.github/workflows/full_runs.yml index 4bbb05f4e..caea71d4a 100644 --- a/.github/workflows/full_runs.yml +++ b/.github/workflows/full_runs.yml @@ -123,4 +123,3 @@ jobs: --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin --no_contig_archive /data/spades_tests/FR_E.coli_UCSD_lane1.info - diff --git a/.github/workflows/gcc.yml b/.github/workflows/gcc.yml index 27eea8264..4319ec8f1 100644 --- a/.github/workflows/gcc.yml +++ b/.github/workflows/gcc.yml @@ -2,6 +2,9 @@ name: SPAdes GCC & Python versions on: workflow_dispatch: + pull_request: + paths-ignore: + - 'docs/**' push: tags: - '*' @@ -44,7 +47,7 @@ jobs: cmake -B ${{env.BUILD_DIR}} -S ${{env.SRC_DIR}} - -DCMAKE_C_COMPILER=gcc-9 -DCMAKE_CXX_COMPILER=g++-9 + -DCMAKE_C_COMPILER=gcc-9 -DCMAKE_CXX_COMPILER=g++-9 -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}} -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC9-Linux @@ -75,7 +78,7 @@ jobs: set -e && shopt -s dotglob && rm -rf * - + - name: '📦 Download package' uses: actions/download-artifact@v3 with: @@ -117,7 +120,7 @@ jobs: cmake -B ${{env.BUILD_DIR}} -S ${{env.SRC_DIR}} - -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10 + -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10 -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}} -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC10-Linux @@ -148,7 +151,7 @@ jobs: set -e && shopt -s dotglob && rm -rf * - + - name: '📦 Download package' uses: actions/download-artifact@v3 with: @@ -190,7 +193,7 @@ jobs: cmake -B ${{env.BUILD_DIR}} -S ${{env.SRC_DIR}} - -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ + -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}} -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC11-Linux @@ -221,7 +224,7 @@ jobs: set -e && shopt -s dotglob && rm -rf * - + - name: '📦 Download package' uses: actions/download-artifact@v3 with: @@ -294,7 +297,7 @@ jobs: set -e && shopt -s dotglob && rm -rf * - + - name: '📦 Download package' uses: actions/download-artifact@v3 with: @@ -367,7 +370,7 @@ jobs: set -e && shopt -s dotglob && rm -rf * - + - name: '📦 Download package' uses: actions/download-artifact@v3 with: @@ -380,4 +383,3 @@ jobs: - name: 'E.coli 1K Isolate with Python 3.13' run: > python3.12 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --isolate - diff --git a/.github/workflows/iontorrent.yml b/.github/workflows/iontorrent.yml index 81cde6b58..912659995 100644 --- a/.github/workflows/iontorrent.yml +++ b/.github/workflows/iontorrent.yml @@ -2,12 +2,15 @@ name: SPAdes IonTorrent datasets tests on: workflow_dispatch: + pull_request: + paths-ignore: + - 'docs/**' push: tags: - '*' schedule: - cron: '0 3 14,28 * *' - + env: BUILD_TYPE: Release BUILD_DIR: ${{github.workspace}}/build @@ -123,4 +126,3 @@ jobs: --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin --no_contig_archive /data/spades_tests/IT_PB_E.coli.info - diff --git a/.github/workflows/isolated.yml b/.github/workflows/isolated.yml index 3ca0d6e7c..b5cb029b4 100644 --- a/.github/workflows/isolated.yml +++ b/.github/workflows/isolated.yml @@ -3,6 +3,8 @@ name: SPAdes isolated datasets tests on: workflow_dispatch: pull_request: + paths-ignore: + - 'docs/**' push: tags: - '*' diff --git a/.github/workflows/long_reads.yml b/.github/workflows/long_reads.yml index 2a6758a30..2a7613f6b 100644 --- a/.github/workflows/long_reads.yml +++ b/.github/workflows/long_reads.yml @@ -3,6 +3,8 @@ name: SPAdes long-read tests on: workflow_dispatch: pull_request: + paths-ignore: + - 'docs/**' push: tags: - '*' diff --git a/.github/workflows/mate_pairs.yml b/.github/workflows/mate_pairs.yml index 1d4ce5fc1..6c4864378 100644 --- a/.github/workflows/mate_pairs.yml +++ b/.github/workflows/mate_pairs.yml @@ -3,6 +3,8 @@ name: SPAdes mate-pairs tests on: workflow_dispatch: pull_request: + paths-ignore: + - 'docs/**' push: tags: - '*' @@ -252,7 +254,7 @@ jobs: --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin --no_contig_archive /data/spades_tests/NX_R.sphaeroides.info - + mp-ssmaragdinae: name: 'Mate-pairs S.smaragdinae quaked' runs-on: self-hosted @@ -284,4 +286,3 @@ jobs: --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin --no_contig_archive /data/spades_tests/MP_S.smaragdinae_quake.info - diff --git a/.github/workflows/meta.yml b/.github/workflows/meta.yml index 9c41b659c..0248168b2 100644 --- a/.github/workflows/meta.yml +++ b/.github/workflows/meta.yml @@ -3,6 +3,8 @@ name: metaSPAdes tests on: workflow_dispatch: pull_request: + paths-ignore: + - 'docs/**' push: tags: - '*' @@ -284,4 +286,3 @@ jobs: --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin --no_contig_archive /data/meta_tests/SYNTH_64_SUB_0p2.info - diff --git a/.github/workflows/rna.yml b/.github/workflows/rna.yml index fbbd3bf14..ee9ad0598 100644 --- a/.github/workflows/rna.yml +++ b/.github/workflows/rna.yml @@ -3,6 +3,8 @@ name: rnaSPAdes tests on: workflow_dispatch: pull_request: + paths-ignore: + - 'docs/**' push: tags: - '*' @@ -220,4 +222,3 @@ jobs: --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin --no_contig_archive /data/rna_tests/CELEGANS_RNA_FL.info - diff --git a/.github/workflows/single_cell.yml b/.github/workflows/single_cell.yml index 5c4e80d3f..03f5d42cf 100644 --- a/.github/workflows/single_cell.yml +++ b/.github/workflows/single_cell.yml @@ -3,6 +3,8 @@ name: SPAdes single-cell datasets tests on: workflow_dispatch: pull_request: + paths-ignore: + - 'docs/**' push: tags: - '*' @@ -348,4 +350,3 @@ jobs: --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin --no_contig_archive /data/spades_tests/SC_SE_P.marinus.info - diff --git a/.github/workflows/sra.yml b/.github/workflows/sra.yml index 9636eeef9..2ce87d5d4 100644 --- a/.github/workflows/sra.yml +++ b/.github/workflows/sra.yml @@ -2,6 +2,9 @@ name: SPAdes SRA input on: workflow_dispatch: + pull_request: + paths-ignore: + - 'docs/**' push: tags: - '*' @@ -92,4 +95,3 @@ jobs: --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin --no_contig_archive /data/pipeline_tests/SRA_C.trachomatis.info - diff --git a/.github/workflows/usecases.yml b/.github/workflows/usecases.yml index 95d0b10a5..85ad40d0e 100644 --- a/.github/workflows/usecases.yml +++ b/.github/workflows/usecases.yml @@ -9,7 +9,11 @@ on: - next tags: - '*' + paths-ignore: + - 'docs/**' pull_request: + paths-ignore: + - 'docs/**' env: BUILD_TYPE: Release