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Add release snapshots workflow #1287

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merged 21 commits into from
May 7, 2024
+584 −280
Merged

Add release snapshots workflow #1287

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e89d9c4
Fix the name
asl Apr 29, 2024
b87eda4
Try to fix paths inside container
asl Apr 29, 2024
85f529b
Install deps
asl Apr 29, 2024
94021ff
Fixes
asl Apr 29, 2024
83a538d
Use new versions of actions
asl Apr 29, 2024
0150c3f
Build mode for release
asl Apr 29, 2024
9faa6cb
Try to infer libdir / includedir
asl Apr 30, 2024
6bbf361
Version bump
asl Apr 30, 2024
935ea64
Make this explicitly linux
asl Apr 30, 2024
c861910
Try to build mac as well
asl Apr 30, 2024
f0e6681
Fix openmp builds
asl Apr 30, 2024
a61e405
Typo
asl Apr 30, 2024
b627048
Install & use clang + libomp
asl Apr 30, 2024
d440c7a
Try to unbreak macos build
asl Apr 30, 2024
e5dc7b1
Be explicit with OS settings. Also try to workaround https://github.c…
asl Apr 30, 2024
01d6e56
Install deps for tests (temporary)
asl Apr 30, 2024
88953d8
Modernize basic checks
asl Apr 30, 2024
d829412
Add mac builds
asl Apr 30, 2024
6d3cb2f
Another try with mac builds
asl Apr 30, 2024
fed0342
Add release upload
asl May 6, 2024
f8d6833
Release only tested stuff
asl May 6, 2024
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241 changes: 207 additions & 34 deletions .github/workflows/basic.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,15 +17,16 @@ on:

env:
BUILD_TYPE: Release
BUILD_DIR: ${{github.workspace}}/build
BUILD_DIR: './build'
SRC_DIR: './src'
INSTALL_DIR: ${{github.workspace}}/spades
SRC_DIR: ${{github.workspace}}/src
PKG: SPAdes-*-Linux
PKG_LINUX: SPAdes-*-Linux
PKG_MAC: SPAdes-*-Darwin

jobs:
build:
build-linux:
runs-on: self-hosted
name: '🚧 Build SPAdes'
name: '🐧 Build SPAdes for Linux'

steps:
- name: '🧹 Cleanup'
Expand All @@ -35,23 +36,23 @@ jobs:
rm -rf *

- name: '🧰 Checkout'
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 1

- name: '⚙️ Install ccache'
uses: hendrikmuhs/[email protected]
with:
variant: sccache
key: sccache-${{env.BUILD_TYPE}}
key: sccache-${{env.BUILD_TYPE}}-linux

- name: '⚙️ Configure CMake'
run: >
cmake
-B ${{env.BUILD_DIR}}
-S ${{env.SRC_DIR}}
-B $BUILD_DIR
-S $SRC_DIR
-DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all
-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
-DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}

- name: '🚧 Build'
run: >
Expand All @@ -61,18 +62,18 @@ jobs:
-t package include_test debruijn_test

- name: '📦 Package'
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: build-artifacts
name: build-artifacts-linux
path: |
${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz
${{env.BUILD_DIR}}/${{env.PKG_LINUX}}.tar.gz
${{env.BUILD_DIR}}/bin/debruijn_test
${{env.BUILD_DIR}}/bin/include_test

spades-1k-checks:
name: 'E. coli 1k smoke checks'
spades-1k-checks-linux:
name: '🚬 E. coli 1k smoke checks'
runs-on: self-hosted
needs: build
needs: build-linux

steps:
- name: '🧹 Cleanup'
Expand All @@ -82,42 +83,44 @@ jobs:
rm -rf *

- name: '📦 Download package'
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: build-artifacts
name: build-artifacts-linux
path: ${{env.INSTALL_DIR}}

- name: '📦 Unpack package'
working-directory: ${{env.INSTALL_DIR}}
run: >
tar -zxf ${{env.PKG}}.tar.gz
tar -zxf $PKG_LINUX.tar.gz

- name: '1k multi-cell'
run: >
${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test
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$INSTALL_DIR/$PKG_LINUX/bin/spades.py --test

- name: '1k single-cell'
run: >
${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --sc --test
$INSTALL_DIR/$PKG_LINUX/bin/spades.py --sc --test

- name: '1k meta'
run: >
${{env.INSTALL_DIR}}/${{env.PKG}}/bin/metaspades.py --test
$INSTALL_DIR/$PKG_LINUX/bin/metaspades.py --test

- name: '1k plasmid'
run: >
${{env.INSTALL_DIR}}/${{env.PKG}}/bin/plasmidspades.py --test
$INSTALL_DIR/$PKG_LINUX/bin/plasmidspades.py --test

- name: '1k rna'
run: >
${{env.INSTALL_DIR}}/${{env.PKG}}/bin/rnaspades.py --test
$INSTALL_DIR/$PKG_LINUX/bin/rnaspades.py --test

- name: '1k corona'
run: >
${{env.INSTALL_DIR}}/${{env.PKG}}/bin/coronaspades.py --test
$INSTALL_DIR/$PKG_LINUX/bin/coronaspades.py --test

spades-unittests:
spades-unittests-linux:
name: 'SPAdes unittests'
runs-on: self-hosted
needs: build
needs: build-linux

steps:
- name: '🧹 Cleanup'
Expand All @@ -127,25 +130,195 @@ jobs:
rm -rf *

- name: '🧰 Checkout'
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 1

- name: '📦 Download package'
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: build-artifacts
name: build-artifacts-linux
path: ${{env.BUILD_DIR}}

- name: '🔎 Include tests'
working-directory: ${{github.workspace}}
run: >
chmod +x $BUILD_DIR/bin/include_test &&
$BUILD_DIR/bin/include_test

- name: '🔎 De-Bruijn tests'
working-directory: ${{github.workspace}}
run: >
chmod +x $BUILD_DIR/bin/debruijn_test &&
$BUILD_DIR/bin/debruijn_test

build-mac:
strategy:
matrix:
include:
- os: macos-13
arch: x86_64
- os: macos-14
arch: arm64

name: '🍎 Build SPAdes for macOS'
runs-on: ${{ matrix.os }}

steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *

- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1

- name: '⚙️ Install dependencies'
run: >
brew install llvm libomp bzip2

- name: '⚙️ Install ccache'
uses: hendrikmuhs/[email protected]
with:
variant: sccache
key: sccache-${{env.BUILD_TYPE}}-${{ matrix.os }}

- name: '⚙️ Configure CMake'
run: >
cmake
-B $BUILD_DIR
-S $SRC_DIR
-DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all
-DCMAKE_C_COMPILER=$(brew --prefix llvm)/bin/clang
-DCMAKE_CXX_COMPILER=$(brew --prefix llvm)/bin/clang++
-DCMAKE_EXE_LINKER_FLAGS=-L$(brew --prefix llvm)/lib/c++
-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache

- name: '🚧 Build'
run: >
cmake
--build $BUILD_DIR
-j16
-t package include_test debruijn_test

- name: '📦 Package'
uses: actions/upload-artifact@v4
with:
name: build-artifacts-mac-${{ matrix.arch }}
path: |
${{env.BUILD_DIR}}/${{env.PKG_MAC}}.tar.gz
${{env.BUILD_DIR}}/bin/debruijn_test
${{env.BUILD_DIR}}/bin/include_test

spades-1k-checks-mac:
name: '🚬 E. coli 1k smoke checks'
strategy:
matrix:
include:
- os: macos-13
arch: x86_64
- os: macos-14
arch: arm64

runs-on: ${{ matrix.os }}

needs: build-mac

steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *

- name: '⚙️ Install dependencies'
run: >
brew install llvm libomp bzip2

- name: '📦 Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-mac-${{ matrix.arch }}
path: ${{env.INSTALL_DIR}}

- name: '📦 Unpack package'
working-directory: ${{env.INSTALL_DIR}}
run: >
tar -zxf ${{env.PKG_MAC}}.tar.gz

- name: '1k multi-cell'
run: >
$INSTALL_DIR/$PKG_MAC/bin/spades.py --test

- name: '1k single-cell'
run: >
$INSTALL_DIR/$PKG_MAC/bin/spades.py --sc --test

- name: '1k meta'
run: >
$INSTALL_DIR/$PKG_MAC/bin/metaspades.py --test

- name: '1k plasmid'
run: >
$INSTALL_DIR/$PKG_MAC/bin/plasmidspades.py --test

- name: '1k rna'
run: >
$INSTALL_DIR/$PKG_MAC/bin/rnaspades.py --test

- name: '1k corona'
run: >
$INSTALL_DIR/$PKG_MAC/bin/coronaspades.py --test


spades-unittests-mac:
name: 'SPAdes unittests'

strategy:
matrix:
include:
- os: macos-13
arch: x86_64
- os: macos-14
arch: arm64

runs-on: ${{ matrix.os }}

needs: build-mac

steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *

- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1

- name: '📦 Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-mac-${{ matrix.arch }}
path: ${{env.BUILD_DIR}}

- name: '⚙️ Install dependencies'
run: >
brew install llvm libomp bzip2

- name: '🔎 Include tests'
working-directory: ${{github.workspace}}
run: >
chmod +x ${{env.BUILD_DIR}}/bin/include_test &&
${{env.BUILD_DIR}}/bin/include_test
chmod +x $BUILD_DIR/bin/include_test &&
$BUILD_DIR/bin/include_test

- name: '🔎 De-Bruijn tests'
working-directory: ${{github.workspace}}
run: >
chmod +x ${{env.BUILD_DIR}}/bin/debruijn_test &&
${{env.BUILD_DIR}}/bin/debruijn_test
chmod +x $BUILD_DIR/bin/debruijn_test &&
$BUILD_DIR/bin/debruijn_test
12 changes: 6 additions & 6 deletions .github/workflows/full_runs.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:
rm -rf *

- name: '🧰 Checkout'
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 1

Expand All @@ -54,7 +54,7 @@ jobs:
-t package

- name: '📦 Package'
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: build-artifacts
path: |
Expand All @@ -73,11 +73,11 @@ jobs:
rm -rf *

- name: '🧰 Checkout'
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: build-artifacts
path: ${{env.INSTALL_DIR}}
Expand Down Expand Up @@ -105,11 +105,11 @@ jobs:
rm -rf *

- name: '🧰 Checkout'
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: build-artifacts
path: ${{env.INSTALL_DIR}}
Expand Down
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