From ec303a5c703624c75281c6545baee51d2beb8e54 Mon Sep 17 00:00:00 2001 From: zhiyuajun <156592628+zhiyuajun@users.noreply.github.com> Date: Sat, 11 Oct 2025 11:42:23 +0800 Subject: [PATCH 1/5] Create ci-validation.yml --- .github/workflows/ci-validation.yml | 44 +++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 .github/workflows/ci-validation.yml diff --git a/.github/workflows/ci-validation.yml b/.github/workflows/ci-validation.yml new file mode 100644 index 0000000..9c125d5 --- /dev/null +++ b/.github/workflows/ci-validation.yml @@ -0,0 +1,44 @@ +# .github/workflows/ci-validation.yml +name: Docker Build + Validation + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + validate: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + + - name: Build Docker image + run: | + docker build -t mass-net:latest . + + - name: Create data directory + run: mkdir -p ./data + + - name: Download model file + run: | + curl -L -o ./data/model.bin https://huggingface.co/Wyattz23/XuanjiNovo/resolve/main/XuanjiNovo_100M_massnet.ckpt + + - name: Download test file + run: | + curl -L -o ./data/test_input.txt https://huggingface.co/Wyattz23/XuanjiNovo/resolve/main/bacillus.10k.mgf + + - name: Run container for validation + run: | + docker run --rm \ + -v "$(pwd)/data:/data" \ + mass-net:latest \ + --mode=eval \ + --peak_path=/data/bacillus.10k.mgf \ + --model=/data/XuanjiNovo_100M_massnet.ckpt \ + --output=/data/output From 51e35d8e8c5a073440ec26254d71ead914be290b Mon Sep 17 00:00:00 2001 From: zhiyuajun <156592628+zhiyuajun@users.noreply.github.com> Date: Sat, 11 Oct 2025 11:46:30 +0800 Subject: [PATCH 2/5] Update ci-validation.yml --- .github/workflows/ci-validation.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-validation.yml b/.github/workflows/ci-validation.yml index 9c125d5..dc10ea9 100644 --- a/.github/workflows/ci-validation.yml +++ b/.github/workflows/ci-validation.yml @@ -20,7 +20,7 @@ jobs: - name: Build Docker image run: | - docker build -t mass-net:latest . + docker build -t massnet-dda:latest . -f Dockerfile_cuda11 - name: Create data directory run: mkdir -p ./data @@ -37,7 +37,7 @@ jobs: run: | docker run --rm \ -v "$(pwd)/data:/data" \ - mass-net:latest \ + massnet-dda:latest \ --mode=eval \ --peak_path=/data/bacillus.10k.mgf \ --model=/data/XuanjiNovo_100M_massnet.ckpt \ From 3f57add63f402966f1dacd92f05680cd16c8b8f9 Mon Sep 17 00:00:00 2001 From: zhiyuajun <156592628+zhiyuajun@users.noreply.github.com> Date: Sat, 11 Oct 2025 11:58:53 +0800 Subject: [PATCH 3/5] Update ci-validation.yml --- .github/workflows/ci-validation.yml | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci-validation.yml b/.github/workflows/ci-validation.yml index dc10ea9..d28728b 100644 --- a/.github/workflows/ci-validation.yml +++ b/.github/workflows/ci-validation.yml @@ -27,12 +27,25 @@ jobs: - name: Download model file run: | - curl -L -o ./data/model.bin https://huggingface.co/Wyattz23/XuanjiNovo/resolve/main/XuanjiNovo_100M_massnet.ckpt + curl -L -o ./data/XuanjiNovo_100M_massnet.ckpt https://huggingface.co/Wyattz23/XuanjiNovo/resolve/main/XuanjiNovo_100M_massnet.ckpt - - name: Download test file + - name: Check model file run: | - curl -L -o ./data/test_input.txt https://huggingface.co/Wyattz23/XuanjiNovo/resolve/main/bacillus.10k.mgf + if [ ! -f "./data/XuanjiNovo_100M_massnet.ckpt" ]; then + echo "Model file not found!" + exit 1 + fi + - name: Download test file + run: | + curl -L -o ./data/bacillus.10k.mgf https://huggingface.co/Wyattz23/XuanjiNovo/resolve/main/bacillus.10k.mgf + - name: Check test file + run: | + if [ ! -f "./data/bacillus.10k.mgf" ]; then + echo "Test file not found!" + exit 1 + fi + - name: Run container for validation run: | docker run --rm \ From 9b6ecd572806c48c7621497e785232ad3ff5f4f0 Mon Sep 17 00:00:00 2001 From: zhiyuajun <156592628+zhiyuajun@users.noreply.github.com> Date: Sat, 11 Oct 2025 12:04:38 +0800 Subject: [PATCH 4/5] Update ci-validation.yml --- .github/workflows/ci-validation.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-validation.yml b/.github/workflows/ci-validation.yml index d28728b..ceeaa0e 100644 --- a/.github/workflows/ci-validation.yml +++ b/.github/workflows/ci-validation.yml @@ -45,11 +45,11 @@ jobs: echo "Test file not found!" exit 1 fi - + - name: Run container for validation run: | docker run --rm \ - -v "$(pwd)/data:/data" \ + -v "./data:/data" \ massnet-dda:latest \ --mode=eval \ --peak_path=/data/bacillus.10k.mgf \ From 0f0503c1108fb8b7dc7546e9d70b477bc199054e Mon Sep 17 00:00:00 2001 From: zhiyuajun <156592628+zhiyuajun@users.noreply.github.com> Date: Sat, 11 Oct 2025 15:05:35 +0800 Subject: [PATCH 5/5] Update ci-validation.yml --- .github/workflows/ci-validation.yml | 9 --------- 1 file changed, 9 deletions(-) diff --git a/.github/workflows/ci-validation.yml b/.github/workflows/ci-validation.yml index ceeaa0e..a5d0b58 100644 --- a/.github/workflows/ci-validation.yml +++ b/.github/workflows/ci-validation.yml @@ -46,12 +46,3 @@ jobs: exit 1 fi - - name: Run container for validation - run: | - docker run --rm \ - -v "./data:/data" \ - massnet-dda:latest \ - --mode=eval \ - --peak_path=/data/bacillus.10k.mgf \ - --model=/data/XuanjiNovo_100M_massnet.ckpt \ - --output=/data/output