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Ignore docs folder for assembler tests #1275

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merged 1 commit into from
Apr 16, 2024
Merged

Ignore docs folder for assembler tests #1275

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4 changes: 4 additions & 0 deletions .github/workflows/basic.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,11 @@ on:
- next
tags:
- '*'
paths-ignore:
- 'docs/**'
pull_request:
paths-ignore:
- 'docs/**'

env:
BUILD_TYPE: Release
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10 changes: 6 additions & 4 deletions .github/workflows/docs.yml
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Expand Up @@ -3,10 +3,12 @@ name: docs
on:
push:
branches:
- master
- master
- main
- next

paths:
- 'docs/**'

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add mkdocs.yml too?

permissions:
contents: write

Expand All @@ -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
1 change: 0 additions & 1 deletion .github/workflows/full_runs.yml
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Expand Up @@ -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

20 changes: 11 additions & 9 deletions .github/workflows/gcc.yml
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Expand Up @@ -2,6 +2,9 @@ name: SPAdes GCC & Python versions

on:
workflow_dispatch:
pull_request:
paths-ignore:
- 'docs/**'
push:
tags:
- '*'
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -75,7 +78,7 @@ jobs:
set -e &&
shopt -s dotglob &&
rm -rf *

- name: '📦 Download package'
uses: actions/download-artifact@v3
with:
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -148,7 +151,7 @@ jobs:
set -e &&
shopt -s dotglob &&
rm -rf *

- name: '📦 Download package'
uses: actions/download-artifact@v3
with:
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -221,7 +224,7 @@ jobs:
set -e &&
shopt -s dotglob &&
rm -rf *

- name: '📦 Download package'
uses: actions/download-artifact@v3
with:
Expand Down Expand Up @@ -294,7 +297,7 @@ jobs:
set -e &&
shopt -s dotglob &&
rm -rf *

- name: '📦 Download package'
uses: actions/download-artifact@v3
with:
Expand Down Expand Up @@ -367,7 +370,7 @@ jobs:
set -e &&
shopt -s dotglob &&
rm -rf *

- name: '📦 Download package'
uses: actions/download-artifact@v3
with:
Expand All @@ -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

6 changes: 4 additions & 2 deletions .github/workflows/iontorrent.yml
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Expand Up @@ -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
Expand Down Expand Up @@ -123,4 +126,3 @@ jobs:
--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
--no_contig_archive
/data/spades_tests/IT_PB_E.coli.info

2 changes: 2 additions & 0 deletions .github/workflows/isolated.yml
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Expand Up @@ -3,6 +3,8 @@ name: SPAdes isolated datasets tests
on:
workflow_dispatch:
pull_request:
paths-ignore:
- 'docs/**'
push:
tags:
- '*'
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2 changes: 2 additions & 0 deletions .github/workflows/long_reads.yml
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Expand Up @@ -3,6 +3,8 @@ name: SPAdes long-read tests
on:
workflow_dispatch:
pull_request:
paths-ignore:
- 'docs/**'
push:
tags:
- '*'
Expand Down
5 changes: 3 additions & 2 deletions .github/workflows/mate_pairs.yml
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Expand Up @@ -3,6 +3,8 @@ name: SPAdes mate-pairs tests
on:
workflow_dispatch:
pull_request:
paths-ignore:
- 'docs/**'
push:
tags:
- '*'
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -284,4 +286,3 @@ jobs:
--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
--no_contig_archive
/data/spades_tests/MP_S.smaragdinae_quake.info

3 changes: 2 additions & 1 deletion .github/workflows/meta.yml
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Expand Up @@ -3,6 +3,8 @@ name: metaSPAdes tests
on:
workflow_dispatch:
pull_request:
paths-ignore:
- 'docs/**'
push:
tags:
- '*'
Expand Down Expand Up @@ -284,4 +286,3 @@ jobs:
--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
--no_contig_archive
/data/meta_tests/SYNTH_64_SUB_0p2.info

3 changes: 2 additions & 1 deletion .github/workflows/rna.yml
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Expand Up @@ -3,6 +3,8 @@ name: rnaSPAdes tests
on:
workflow_dispatch:
pull_request:
paths-ignore:
- 'docs/**'
push:
tags:
- '*'
Expand Down Expand Up @@ -220,4 +222,3 @@ jobs:
--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
--no_contig_archive
/data/rna_tests/CELEGANS_RNA_FL.info

3 changes: 2 additions & 1 deletion .github/workflows/single_cell.yml
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Expand Up @@ -3,6 +3,8 @@ name: SPAdes single-cell datasets tests
on:
workflow_dispatch:
pull_request:
paths-ignore:
- 'docs/**'
push:
tags:
- '*'
Expand Down Expand Up @@ -348,4 +350,3 @@ jobs:
--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
--no_contig_archive
/data/spades_tests/SC_SE_P.marinus.info

4 changes: 3 additions & 1 deletion .github/workflows/sra.yml
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Expand Up @@ -2,6 +2,9 @@ name: SPAdes SRA input

on:
workflow_dispatch:
pull_request:
paths-ignore:
- 'docs/**'
push:
tags:
- '*'
Expand Down Expand Up @@ -92,4 +95,3 @@ jobs:
--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
--no_contig_archive
/data/pipeline_tests/SRA_C.trachomatis.info

4 changes: 4 additions & 0 deletions .github/workflows/usecases.yml
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Expand Up @@ -9,7 +9,11 @@ on:
- next
tags:
- '*'
paths-ignore:
- 'docs/**'
pull_request:
paths-ignore:
- 'docs/**'

env:
BUILD_TYPE: Release
Expand Down
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