feat: e2e test, build: update tools cicd

.github/workflows/ci_tools.yml

@@ -1,22 +1,24 @@
 name: Uni-Dock Tools CI/CD
 on:
   push:
+    branches: []
   pull_request:
+    branches: [ main ]
+
+env:
+  PYTHON_VERSION: "3.11"
 
 jobs:
   flake8:
     continue-on-error: true
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.9"]
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: ${{ env.PYTHON_VERSION }}
 
     - name: Install dependencies
       run: |
@@ -25,89 +27,109 @@ jobs:
 
     - name: Run flake8 formating
       run: |
-        flake8 unidock_tools/unidock_tools --exit-zero
+        flake8 unidock_tools/unidock_tools
 
-  pylint:
+  pyright:
     continue-on-error: true
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.9"]
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: ${{ env.PYTHON_VERSION }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pylint
-
-    - name: Run pylint formating
-      run: |
-        pylint unidock_tools/unidock_tools --exit-zero
-
-  mypy:
-    continue-on-error: true
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.9"]
+        pip install pyright
 
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install mypy
-
-    - name: Run mypy check
-      id: mypy_check
+    - name: Run pyright check
+      id: pyright_check
+      working-directory: ./unidock_tools
       run: |
-        mypy unidock_tools/unidock_tools --ignore-missing-imports
+        pyright
 
-  ut:
+  tests:
     if: ${{ always() }}
-    needs: [flake8, pylint]
+    needs: [flake8,pyright]
     runs-on: nvidia
     strategy:
       matrix:
-        python-version: ["3.9"]
+        cuda-version: ["12.0.0"]
     container:
-      image: docker.io/dptechnology/unidock:latest
+      image: docker.io/xmyyn/unidock_tools_base:0.0.1_cuda${{ matrix.cuda-version }}
       options: --gpus all
     steps:
     - name: checkout repo
       uses: actions/checkout@v4
 
-    - name: Setup conda
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        miniconda-version: "latest"
-        python-version: ${{ matrix.python-version }}
-
-    - name: install dependency
+    - 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: |
-        conda create -n mgltools mgltools -c bioconda -y
-        conda install -n test -c conda-forge -y openbabel
-        conda run -n test pip install --upgrade pip
-        conda run -n test pip install pytest
+        unidock --version
+        confgen --version
+        which python
 
-    - name: install package
+    - name: install tools
       working-directory: ./unidock_tools
       run: |
-        export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH
-        conda run -n test python setup.py install
+        pip install .
 
-    - name: perform unit-test
+    - name: run unit-test
       run: |
-        export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH
-        conda run -n test pytest unidock_tools/tests/ut -v
+        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
+
+  build_docker_image:
+    needs: tests
+    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
+      if: github.event_name == 'pull_request'
+      with:
+        username: dptechnology
+        password: ${{ secrets.DOCKERHUB_PAT }}
+
+    - uses: benjlevesque/[email protected]
+      id: short-sha
+      with:
+        length: 7
+
+    - name: check commit short sha
+      run: echo ${{ steps.short-sha.outputs.sha }}
+
+    - name: build and push container
+      uses: docker/build-push-action@v5
+      with:
+        platforms: linux/amd64
+        build-args: BASE_IMAGE=xmyyn/unidock_tools_base:0.0.1_cuda${{ matrix.cuda-version }}
+        tags: dptechnology/unidock_tools:${{ steps.short-sha.outputs.sha }},dptechnology/unidock_tools:latest
+        file: unidock_tools/containers/Dockerfile
+        push: ${{ github.event_name == 'pull_request' }}

.github/workflows/ci_unidock.yml

@@ -57,18 +57,20 @@ jobs:
     needs: unidock_test
     runs-on: ubuntu-latest
     steps:
-
-    - name: log in to docker hub
+    -
+      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
-      if: github.event_name == 'push'
+      if: github.event_name == 'pull_request'
       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:

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

unidock_tools/containers/Dockerfile_base

@@ -0,0 +1,37 @@
+ARG CUDA_VERSION
+FROM nvidia/cuda:${CUDA_VERSION}-devel-ubuntu22.04
+
+SHELL ["/bin/bash", "-c"]
+
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt-get clean && apt-get update \
+    && apt-get install -y build-essential zip unzip vim git wget \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN wget -O /tmp/conda.sh \
+    https://mirrors.tuna.tsinghua.edu.cn/github-release/conda-forge/miniforge/LatestRelease/Miniforge3-23.11.0-0-Linux-$(uname -m).sh \
+    && bash /tmp/conda.sh -b -p /opt/conda \
+    && rm /tmp/conda.sh
+ENV PATH /opt/conda/bin:$PATH
+
+RUN mamba install -y cmake boost -c conda-forge
+
+RUN mkdir /root/.ssh
+RUN --mount=type=secret,id=rsa,target=/root/.ssh/id_rsa \
+  ssh-keyscan github.com >> /root/.ssh/known_hosts \
+  && git clone [email protected]:molinfo-vienna/CDPKit.git /tmp/CDPKit
+
+WORKDIR /tmp
+RUN cd /tmp/CDPKit && mkdir build && cd build \
+  && cmake .. -DCMAKE_INSTALL_PREFIX=/opt/CDPKit \
+  && make -j4 && make install
+RUN rm -rf /tmp/CDPKit
+ENV PATH=/opt/CDPKit/Bin:$PATH
+WORKDIR /opt
+
+RUN mamba install -y ipython rdkit openbabel networkx numpy pandas -c conda-forge
+RUN mamba create -y -n mgltools mgltools autogrid -c bioconda
+ENV PATH $PATH:/opt/conda/envs/mgltools/bin
+RUN pip install tqdm
+RUN rm -rf /opt/conda/pkgs/*

unidock_tools/pyproject.toml

@@ -25,6 +25,9 @@ classifiers = [
 #    "networkx",
 #]
 
+[tool.setuptools.packages.find]
+exclude = ["containers"]
+
 [tool.setuptools.package-data]
 "*" = ["*.dat"]
 
@@ -36,4 +39,16 @@ Repository = "https://github.com/dptech-corp/Uni-Dock.git"
 unidocktools = "unidock_tools.main:main_cli"
 
 #[project.entry-points."unidocktools"]
-#unidocktools = "unidock_tools.main:main_cli"
+#unidocktools = "unidock_tools.main:main_cli"
+
+[tool.pyright]
+include = ["unidock_tools"]
+exclude = ["**/node_modules",
+    "**/__pycache__",
+    "unidock_tools/data"
+]
+reportMissingImports = true
+reportMissingTypeStubs = false
+pythonVersion = "3.11"
+pythonPlatform = "Linux"
+reportAttributeAccessIssue = false

unidock_tools/tests/applications/test_ligprep.py

@@ -0,0 +1,34 @@
+from pathlib import Path
+import os
+import shutil
+import subprocess
+import pytest
+
+
+@pytest.fixture
+def input_ligand():
+    return os.path.join(os.path.dirname(os.path.dirname(__file__)), "inputs", "Imatinib.sdf")
+
+
+def test_ligprep_app_ligand_file(input_ligand):
+    results_dir = "prepared_ligands"
+    cmd = f"unidocktools ligprep -l {input_ligand} -sd {results_dir}"
+    print(cmd)
+    resp = subprocess.run(cmd, shell=True, capture_output=True, encoding="utf-8")
+    print(resp.stdout)
+    assert resp.returncode==0, f"run ligprep app err:\n{resp.stderr}"
+    shutil.rmtree(results_dir, ignore_errors=True)
+
+
+def test_ligprep_app_ligand_index(input_ligand):
+    index_file = "ligand_index.txt"
+    with open(index_file, "w") as f:
+        f.write(input_ligand)
+    results_dir = "prepared_ligands"
+    cmd = f"unidocktools ligprep -i {index_file} -sd {results_dir}"
+    print(cmd)
+    resp = subprocess.run(cmd, shell=True, capture_output=True, encoding="utf-8")
+    print(resp.stdout)
+    assert resp.returncode==0, f"run ligprep app err:\n{resp.stderr}"
+    Path(index_file).unlink(missing_ok=True)
+    shutil.rmtree(results_dir, ignore_errors=True)