refactor unidock tools cicd workflow (#25)

* refactor:ut by module

* rm old ut

* refactor:use pytest syntex for ut

* fix:ut

* fix static type

* fix static type 2

* fix static type 3

* build:base env dockerfile

* feat:add application e2e tests

* fix:e2e tests

* fix:app test read score

* fix:app test

* build:update unidocktools ci

* test:update tools ci trigger condition

* build:fix tool yaml

* build:fix ci yaml variable

* build:fix build ninja dep

* build:fix ninja dep

* test: ut unidock input change to 1iep

* test: skip ad4 test

* build:change push image condition

* feat(unidock):add energy_range arg

* build:downgrade docker login action

* build:reupdate docker login action

* build:dockerhub token

* build:add checkout

* build:change docker login action version

* build:change docker login action version 2

* build:docker login action 3

* build:docker build job

* build image workflow trigger after push

* style:pyright check

* build:fix toml pyright setting

---------

Co-authored-by: Yuan Yannan <[email protected]>

.github/workflows/ci_docker.yml

@@ -0,0 +1,74 @@
+name: Uni-Dock/Tools Build Image Workflow
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build_unidock_docker_image:
+    if: github.repository_owner == 'dptech-corp'
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        cuda-version: ["12.0.0"]
+    steps:
+    -
+      name: Set up QEMU
+      uses: docker/setup-qemu-action@v3
+    -
+      name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    -
+      name: Login to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: dptechnology
+        password: ${{ secrets.DOCKERHUB_PAT }}
+
+    - uses: benjlevesque/[email protected]
+      id: short-sha
+      with:
+        length: 7
+
+    - name: build and push container
+      uses: docker/build-push-action@v5
+      with:
+        platforms: linux/amd64,linux/arm64
+        tags: dptechnology/unidock:${{ steps.short-sha.outputs.sha }},dptechnology/unidock:latest
+        file: containers/Dockerfile.cuda${{ matrix.cuda-version }}
+        context: "{{defaultContext}}:unidock"
+        push: true
+
+  build_unidock_tools_docker_image:
+    if: github.repository_owner == 'dptech-corp'
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        cuda-version: ["12.0.0"]
+    steps:
+    -
+      name: Set up QEMU
+      uses: docker/setup-qemu-action@v3
+    -
+      name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    -
+      name: Login to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: dptechnology
+        password: ${{ secrets.DOCKERHUB_PAT }}
+
+    - uses: benjlevesque/[email protected]
+      id: short-sha
+      with:
+        length: 7
+
+    - name: build and push container
+      uses: docker/build-push-action@v5
+      with:
+        platforms: linux/amd64
+        build-args: BASE_IMAGE=xmyyn/unidock_tools_base:0.0.1_cuda${{ matrix.cuda-version }}
+        tags: dptechnology/unidock_tools:${{ steps.short-sha.outputs.sha }},dptechnology/unidock_tools:latest
+        file: unidock_tools/containers/Dockerfile
+        push: true

.github/workflows/ci_test_tools.yml

@@ -0,0 +1,99 @@
+name: Uni-Dock Tools CI/CD
+on:
+  push:
+    branches:
+      - '**ci**'
+  pull_request:
+    branches: 
+      - main
+
+env:
+  PYTHON_VERSION: "3.11"
+
+jobs:
+  flake8:
+    continue-on-error: true
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ env.PYTHON_VERSION }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8
+
+    - name: Run flake8 formating
+      run: |
+        flake8 unidock_tools/unidock_tools --exit-zero
+
+  pyright:
+    continue-on-error: true
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ env.PYTHON_VERSION }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pyright
+
+    - name: Run pyright check
+      id: pyright_check
+      working-directory: ./unidock_tools
+      run: |
+        pyright
+
+  tests:
+    if: ${{ always() }}
+    needs: [flake8,pyright]
+    runs-on: nvidia
+    strategy:
+      matrix:
+        cuda-version: ["12.0.0"]
+    container:
+      image: docker.io/xmyyn/unidock_tools_base:0.0.1_cuda${{ matrix.cuda-version }}
+      options: --gpus all
+    steps:
+    - name: checkout repo
+      uses: actions/checkout@v4
+
+    - name: install unidock
+      working-directory: ./unidock
+      run: |
+        apt-get update && apt-get install -y ninja-build
+        mkdir build
+        cd build
+        cmake .. -G Ninja -DCMAKE_BUILD_TYPE=Release
+        cmake --build .
+        cmake --install .
+        cd ..
+
+    - name: check env
+      run: |
+        unidock --version
+        confgen --version
+        which python
+
+    - name: install tools
+      working-directory: ./unidock_tools
+      run: |
+        pip install .
+
+    - name: run unit-test
+      run: |
+        pip install pytest pytest-cov
+        pytest unidock_tools/tests/ut -vv --cov --cov-report term
+    
+    - name: run application e2e test
+      run: |
+        pytest unidock_tools/tests/applications -vv --cov --cov-report term

.github/workflows/ci_unidock.yml → .github/workflows/ci_test_unidock.yml

@@ -1,9 +1,11 @@
 name: Uni-Dock CI/CD
 on:
   push:
-    branches: []
+    branches:
+      - '**ci**'
   pull_request:
-    branches: [ main ]
+    branches: 
+      - main
 
 jobs:
   unidock_test:
@@ -52,35 +54,3 @@ jobs:
         python -m pip install --upgrade pip
         pip install pytest>=8.0.0 pytest-cov
         pytest unidock/test/ut -vv --doctest-modules --junitxml=junit/test-results.xml --cov --cov-report term
-
-  build_docker_image:
-    needs: unidock_test
-    runs-on: ubuntu-latest
-    steps:
-
-    - name: log in to docker hub
-      uses: docker/login-action@v3
-      if: github.event_name == 'push'
-      with:
-        username: dptechnology
-        password: ${{ secrets.DOCKERHUB_PAT }}
-
-    - name: set up docker buildx
-      id: buildx
-      uses: docker/setup-buildx-action@v2
-
-    - uses: benjlevesque/[email protected]
-      id: short-sha
-      with:
-        length: 7
-
-    - name: check commit short sha
-      run: echo ${{ steps.short-sha.outputs.sha }}
-
-    - name: build and push container
-      uses: docker/build-push-action@v4
-      with:
-        tags: dptechnology/unidock:${{ steps.short-sha.outputs.sha }},dptechnology/unidock:latest
-        file: Dockerfile
-        context: "{{defaultContext}}:unidock"
-        push: ${{ github.event_name == 'push' }}

unidock/Dockerfile → unidock/containers/Dockerfile.cuda12.0

@@ -1,7 +1,7 @@
 # Running this Docker image requires Docker to support NVIDIA GPUs. Please make sure NVIDIA Container Toolkit is configured.
 # See https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/index.html https://github.com/NVIDIA/nvidia-docker
 
-FROM nvidia/cuda:12.2.0-devel-ubuntu22.04
+FROM nvidia/cuda:12.0.0-devel-ubuntu22.04
 
 COPY . /opt/unidock
 

unidock_tools/containers/Dockerfile

@@ -0,0 +1,16 @@
+ARG BASE_IMAGE
+
+FROM ${BASE_IMAGE}
+
+COPY ./unidock /opt/unidock
+
+RUN cd /opt/unidock && \
+    cmake -B build && \
+    cmake --build build -j`nprocs` && \
+    cmake --install build && \
+    rm -r /opt/unidock
+
+COPY ./unidock_tools /opt/unidock_tools
+RUN cd /opt/unidock_tools && \
+    pip install . && \
+    rm -r /opt/unidock_tools