Uni-Dock v1.1 (#77)

* get template parameter * add small size template mode * add small config template * success run template docking * add large medium extra_large template * fix missing template parameter * fix template parameter error * adjust ExtraLarge template parameter * update Version number to 1.1.0 * success run template mode docking * Add GPU model support policy * feat: remove template code * create issue templates (#18) * create issue templates * Create CONTRIBUTING.md * refactor of unidock_tools (#19) * unidock tools 2 * unidock and mcdock runner * fix unidock pipeline runner * fix mcdock * main entry * fix savedir name * feat:pdb2pdbqt and ligprep module * build:use toml * fix toml * fix: package data * fix: toml package data * (feat):Update time measurement in vina.h * 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]> * rename dockerfile name * Update unidock/CMakeLists.txt * Feature:Refactor docking process and remove unnecessary code * Found a situation where the program hang without printf * Create dependabot.yml * Add instructions to build a docker image for unidock * format cdpkit dockerfile * use CDPKit from release * set default cuda version * Bump actions/setup-python from 3 to 5 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v3...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump docker/build-push-action from 2 to 5 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 2 to 5. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v2...v5) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump docker/login-action from 1 to 3 Bumps [docker/login-action](https://github.com/docker/login-action) from 1 to 3. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@v1...v3) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump actions/checkout from 2 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * build:unidock_tools image base on unidock image * flatten folder structure * Update CUDA device synchronization and CUDA architectures * Remove cudaMalloc output * Delete test data files * Update MAX_NUM_OF_RIGID and MAX_NUM_OF_ATOMS constants * Update MAX_NUM_OF_ATOMS_ constant values * Update CI workflows and add benchmark (#32) * Refactor Docker image building workflow * remove outdated actions * add benchmark workflow * download test dataset * fix requirements * upload test result in benchmark * build:fix bm test vs result * fix missing path for python scripts --------- Co-authored-by: Yuan Yannan <[email protected]> * update issue template for bug report (#34) * fix:tool dockerfile * Set `wget --quiet` in Dockerfile * Update MAX_NUM_OF_LIG_TORSION and MAX_NUM_OF_ATOMS constants * Update MAX_NUM_OF_ATOMS_ constant values * Update kernel.h * doc: update unidock_tools README (#42) * doc:tool readme 1 * update unidocktools readme * update readme --------- Co-authored-by: Yuan Yannan <[email protected]> * Update Readme Files (#41) * Update readme files * Update README.md * Unify the spelling * Prompt source code access * Update deepmodeling badge * re-organize paragraphs * Remove unidock-tools subtitles --------- Co-authored-by: Yuan Yannan <[email protected]> * doc:update unidock new bm test result images (#43) * Add unit test case (#40) * Add Catch2 unit test * Fix unit test * Add git support in Dockerfile * Add git in CI basic packages * Fix file path in parse_pdqt_test.cpp * Update CMakeLists.txt to link unit_tests with lib and cuda --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: ysy <[email protected]> Co-authored-by: dp-yuanyn <[email protected]> Co-authored-by: Yuan Yannan <[email protected]> Co-authored-by: YANG SHAOYI <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
dptech-corp · Feb 29, 2024 · 5895952 · 5895952
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -0,0 +1,63 @@
+# Contribution Guidelines
+
+Thank you for your interest in contributing to Uni-Dock! We value your time and effort, and aim to make the contribution process enjoyable and efficient. To ensure consistency and maintainability, please follow these guidelines when submitting your contributions.
+
+## Troubleshooting
+
+If you encountered problems using Uni-Dock, please refer to our GitHub [issue tracker](https://github.com/dptech-corp/Uni-Dock/issues), and check if it is a known problem.
+If you found a bug, you can help us improve by [submitting a new issue](https://github.com/dptech-corp/Uni-Dock/issues/new) to our GitHub Repository. Provide a clear and concise title and description, including steps to reproduce the issue (if applicable) and any relevant context.
+Even better, you can submit a Pull Request with a patch.
+
+## Feature requests
+
+We highly appreciate your contributions, and would like to help you crafting the changes and making contributions to the community.
+If you would like to implement a new feature, please **submit a feature requesting issue with a proposal for your work first**.
+This help fitting your ideas and work with the development road map well, coordinating our efforts, and avoiding duplication of work.
+
+## Submitting a Pull Request
+
+**Please fork your own copy of the Uni-Dock repository, and draft your changes there.** Once the modified codes work as expected, please submit a pull request to merge your contributions.
+
+1. [Fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) the [Uni-Dock repository](https://github.com/dptech-corp/Uni-Dock). If you already had an existing fork, [sync](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork) the fork to keep your modification up-to-date.
+
+2. Pull your forked repository, create a new git branch, and make your changes in it:
+
+     ```shell
+     git checkout -b bug-fix
+     ```
+
+3. Coding your patch and commit the changes.
+
+4. Push your branch to GitHub:
+
+    ```shell
+    git push origin my-fix-branch
+    ```
+
+5. On GitHub, create a pull request (PR) from your bug-fix branch targeting `dptech-corp/Uni-Dock`.
+
+6. After your pull request is merged, you can safely delete your branch and sync the changes from the main (upstream) repository:
+
+- Delete the remote branch on GitHub either [through the GitHub web UI](https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/managing-branches-in-your-repository/deleting-and-restoring-branches-in-a-pull-request#deleting-a-branch-used-for-a-pull-request) or your local shell as follows:
+
+    ```shell
+    git push origin --delete my-fix-branch
+    ```
+
+- Check out the master branch:
+
+    ```shell
+    git checkout develop -f
+    ```
+
+- Delete the local branch:
+
+    ```shell
+    git branch -D my-fix-branch
+    ```
+
+- Update your master with the latest upstream version:
+
+    ```shell
+    git pull --ff upstream develop
+    ```
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,56 @@
+name: Bug Report
+description: Create a report to help us improve
+labels: [bug]
+assignees: ["ysyecust"]
+body:
+  - type: textarea
+    attributes:
+      label: Describe the bug
+      description: |
+        A clear and concise description of what the bug is. The bug may results in:
+        - abnormal interruption of the program,
+        - systematic or randomized numerical error, or
+        - relatively low efficiency.
+      placeholder: |
+        Example: Uni-Dock crashed with the following error message ...
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Expected behavior
+      description: |
+        A clear and concise description of what you expected to happen.
+      placeholder: |
+        Example: Uni-Dock should output the result as ...
+
+  - type: textarea
+    attributes:
+      label: To Reproduce
+      description: |
+        Steps to reproduce the behavior.
+        Please provide necessary information including input file, running commands, error log, etc.
+        It is strongly recommended to attach your input files here for the developers to reproduce the bug.
+      placeholder: |
+        Example:
+        1. Build Uni-Dock
+        2. Run the following command ...
+
+  - type: textarea
+    attributes:
+      label: Environment
+      description: |
+        - CUDA version
+        - GPU model
+        - Uni-Dock version
+      placeholder: |
+        Example:
+        - CUDA 12.2.0
+        - GPU: NVIDIA A100
+        - Uni-Dock on commit: 9ad06c4
+
+  - type: textarea
+    attributes:
+      label: Additional Context
+      description: |
+        Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/custom.md b/.github/ISSUE_TEMPLATE/custom.md
@@ -0,0 +1,10 @@
+---
+name: Custom issue template
+about: Describe this issue template's purpose here.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: 'Feature Request: '
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is.
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -0,0 +1,49 @@
+name: Uni-Dock Benchmark
+on:
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: "Docker image used"
+        required: false
+        default: "latest"
+jobs:
+  unidock_benchmark:
+    runs-on: nvidia
+    container:
+      image: dptechnology/unidock:${{ github.event.inputs.tag }}
+      options: --gpus all
+    steps:
+      - name: Checkout test suites
+        uses: actions/checkout@v4
+        with:
+          repository: dptech-corp/Uni-Dock-Benchmarks
+      - name: Setup Python
+        uses: actions/setup-python@v5
+      - name: Install requirements
+        run: |
+          apt update && apt install -y wget unzip
+          pip install -r scripts/requirements.txt
+
+      - name: Run molecular docking benchmarks
+        run: |
+          python3 scripts/test_molecular_docking.py
+      - name: Upload docking results
+        uses: actions/upload-artifact@v4
+        with:
+          name: molecular_docking_results.csv
+          path: results/results.csv
+      - name: Upload docking metrics
+        uses: actions/upload-artifact@v4
+        with:
+          name: molecular_docking_metrics.csv
+          path: results/metrics.csv
+
+      - name: Run virtual screening benchmarks
+        run: |
+          rm -rf results
+          python3 scripts/test_virtual_screening.py
+      - name: Upload virtual screening results
+        uses: actions/upload-artifact@v4
+        with:
+          name: virtual_screening_results.csv
+          path: results/results.csv
diff --git a/.github/workflows/ci_test_tools.yml b/.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
diff --git a/.github/workflows/ci_unidock.yml → .github/workflows/ci_test_unidock.yml b/.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:
@@ -13,12 +15,12 @@ jobs:
       options: --gpus all
     steps:
     - name: checkout repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: install basic packages
       run: |
         apt-get update
-        apt-get install -y build-essential cmake libboost-all-dev ninja-build
+        apt-get install -y build-essential cmake libboost-all-dev ninja-build git
 
     - if: ${{ env.ACT }}
       name: Hack container for local development
@@ -43,7 +45,7 @@ jobs:
         unidock --version
 
     - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
 
@@ -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' }}