Add Chai-1 fork

.pre-commit-config.yaml

@@ -16,7 +16,6 @@ repos:
       - id: detect-private-key
       - id: check-executables-have-shebangs
       - id: check-toml
-      - id: check-case-conflict
       - id: check-added-large-files
         args: ["--maxkb=15000"]
 

README.md

@@ -96,6 +96,9 @@ cd forks/NeuralPLexer/ && pip3 install -e . && cd ../../
 mamba env create -f environments/rfaa_environment.yaml --prefix forks/RoseTTAFold-All-Atom/RFAA/
 conda activate forks/RoseTTAFold-All-Atom/RFAA/  # NOTE: one still needs to use `conda` to (de)activate environments
 cd forks/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/ && pip3 install --no-cache-dir -r requirements.txt && python3 setup.py install && cd ../../../../
+# - Chai-1 environment (~6 GB)
+mamba env create -f environments/chai_lab_environment.yaml --prefix forks/chai-lab/chai-lab/
+conda activate forks/chai-lab/chai-lab/  # NOTE: one still needs to use `conda` to (de)activate environments
 # - AutoDock Vina Tools environment (~1 GB)
 mamba env create -f environments/adfr_environment.yaml --prefix forks/Vina/ADFR/
 conda activate forks/Vina/ADFR/  # NOTE: one still needs to use `conda` to (de)activate environments

environments/chai_lab_environment.yaml

@@ -0,0 +1,174 @@
+name: chai-lab
+channels:
+  - conda-forge
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - bzip2=1.0.8=h4bc722e_7
+  - ca-certificates=2024.8.30=hbcca054_0
+  - ld_impl_linux-64=2.43=h712a8e2_0
+  - libexpat=2.6.3=h5888daf_0
+  - libffi=3.4.2=h7f98852_5
+  - libgcc=14.1.0=h77fa898_1
+  - libgcc-ng=14.1.0=h69a702a_1
+  - libgomp=14.1.0=h77fa898_1
+  - libnsl=2.0.1=hd590300_0
+  - libsqlite=3.46.1=hadc24fc_0
+  - libuuid=2.38.1=h0b41bf4_0
+  - libxcrypt=4.4.36=hd590300_1
+  - libzlib=1.3.1=h4ab18f5_1
+  - ncurses=6.5=he02047a_1
+  - openssl=3.3.2=hb9d3cd8_0
+  - pip=24.2=pyh8b19718_1
+  - python=3.11.10=hc5c86c4_1_cpython
+  - readline=8.2=h8228510_1
+  - setuptools=74.1.2=pyhd8ed1ab_0
+  - tk=8.6.13=noxft_h4845f30_101
+  - wheel=0.44.0=pyhd8ed1ab_0
+  - xz=5.2.6=h166bdaf_0
+  - pip:
+      - aiobotocore==2.15.1
+      - aiohappyeyeballs==2.4.0
+      - aiohttp==3.10.5
+      - aioitertools==0.12.0
+      - aiosignal==1.3.1
+      - antipickle==0.2.0
+      - asttokens==2.4.1
+      - attrs==24.2.0
+      - beartype==0.18.5
+      - biopython==1.83
+      - botocore==1.35.23
+      - cachetools==5.5.0
+      - certifi==2024.8.30
+      - cfgv==3.4.0
+      - charset-normalizer==3.3.2
+      - click==8.1.7
+      - comm==0.2.2
+      - contourpy==1.3.0
+      - cycler==0.12.1
+      - db-dtypes==1.3.0
+      - debugpy==1.8.5
+      - decorator==5.1.1
+      - distlib==0.3.8
+      - einops==0.8.0
+      - executing==2.1.0
+      - filelock==3.16.1
+      - fonttools==4.54.1
+      - frozenlist==1.4.1
+      - fsspec==2024.9.0
+      - gcsfs==2024.9.0.post1
+      - gemmi==0.6.7
+      - google-api-core==2.20.0
+      - google-auth==2.35.0
+      - google-auth-oauthlib==1.2.1
+      - google-cloud-bigquery==3.25.0
+      - google-cloud-core==2.4.1
+      - google-cloud-storage==2.18.2
+      - google-crc32c==1.6.0
+      - google-resumable-media==2.7.2
+      - googleapis-common-protos==1.65.0
+      - grpcio==1.66.1
+      - grpcio-status==1.66.1
+      - huggingface-hub==0.25.1
+      - identify==2.6.1
+      - idna==3.10
+      - iniconfig==2.0.0
+      - ipykernel==6.29.5
+      - ipython==8.27.0
+      - jaxtyping==0.2.34
+      - jedi==0.19.1
+      - jinja2==3.1.4
+      - jmespath==1.0.1
+      - jupyter-client==8.6.3
+      - jupyter-core==5.7.2
+      - kiwisolver==1.4.7
+      - markdown-it-py==3.0.0
+      - markupsafe==2.1.5
+      - matplotlib==3.9.2
+      - matplotlib-inline==0.1.7
+      - mdurl==0.1.2
+      - mpmath==1.3.0
+      - msgpack==1.1.0
+      - multidict==6.1.0
+      - mypy==1.11.2
+      - mypy-extensions==1.0.0
+      - nest-asyncio==1.6.0
+      - networkx==3.3
+      - nodeenv==1.9.1
+      - numpy==1.26.4
+      - nvidia-cublas-cu12==12.1.3.1
+      - nvidia-cuda-cupti-cu12==12.1.105
+      - nvidia-cuda-nvrtc-cu12==12.1.105
+      - nvidia-cuda-runtime-cu12==12.1.105
+      - nvidia-cudnn-cu12==8.9.2.26
+      - nvidia-cufft-cu12==11.0.2.54
+      - nvidia-curand-cu12==10.3.2.106
+      - nvidia-cusolver-cu12==11.4.5.107
+      - nvidia-cusparse-cu12==12.1.0.106
+      - nvidia-nccl-cu12==2.20.5
+      - nvidia-nvjitlink-cu12==12.6.68
+      - nvidia-nvtx-cu12==12.1.105
+      - oauthlib==3.2.2
+      - packaging==24.1
+      - pandas==2.2.3
+      - pandas-gbq==0.23.2
+      - pandas-stubs==2.2.2.240909
+      - parso==0.8.4
+      - pexpect==4.9.0
+      - pillow==10.4.0
+      - platformdirs==4.3.6
+      - pluggy==1.5.0
+      - pre-commit==3.8.0
+      - prompt-toolkit==3.0.47
+      - proto-plus==1.24.0
+      - protobuf==5.28.2
+      - psutil==6.0.0
+      - ptyprocess==0.7.0
+      - pure-eval==0.2.3
+      - pyarrow==17.0.0
+      - pyasn1==0.6.1
+      - pyasn1-modules==0.4.1
+      - pydata-google-auth==1.8.2
+      - pygments==2.18.0
+      - pyparsing==3.1.4
+      - pytest==8.3.3
+      - python-dateutil==2.9.0.post0
+      - pytz==2024.2
+      - pyyaml==6.0.2
+      - pyzmq==26.2.0
+      - rdkit==2023.9.5
+      - regex==2024.9.11
+      - requests==2.32.3
+      - requests-oauthlib==2.0.0
+      - rich==13.8.1
+      - rsa==4.9
+      - ruff==0.6.3
+      - s3fs==2024.9.0
+      - safetensors==0.4.5
+      - shellingham==1.5.4
+      - six==1.16.0
+      - stack-data==0.6.3
+      - sympy==1.13.3
+      - tmtools==0.2.0
+      - tokenizers==0.19.1
+      - torch==2.3.1
+      - tornado==6.4.1
+      - tqdm==4.66.5
+      - traitlets==5.14.3
+      - transformers==4.44.2
+      - triton==2.3.1
+      - typeguard==2.13.3
+      - typer==0.12.5
+      - types-pytz==2024.2.0.20240913
+      - types-pyyaml==6.0.12.20240917
+      - types-requests==2.32.0.20240914
+      - types-tqdm==4.66.0.20240417
+      - typing-extensions==4.12.2
+      - tzdata==2024.2
+      - urllib3==2.2.3
+      - virtualenv==20.26.5
+      - wcwidth==0.2.13
+      - wrapt==1.16.0
+      - yarl==1.12.1
+prefix:
+  forks/chai-lab/chai-lab

forks/chai-lab/.devcontainer/devcontainer.json

@@ -0,0 +1,42 @@
+{
+    "name": "ChaiLab",
+    "build": {
+        "context": "..",
+        "dockerfile": "../Dockerfile.chailab",
+        "target": "chailab-baseimage"
+    },
+    "runArgs": [
+        // by default use all GPUs, can be overriden by envvar
+        "--gpus=${localEnv:DEVBOX_GPU_SPEC:all}",
+        "--ipc=host",
+        "-v=/data/instance:/data/instance",
+        // default container name is chai-lab-container
+        "--name=chai-lab-${localEnv:DEVBOX_USER:container}",
+        // set restrictions on CPU and RAM memory usage
+        "--cpus=60.0",
+        "--memory=1000g"
+    ],
+    "shutdownAction": "none",
+    "postCreateCommand": "uv pip install -e . && pre-commit install -f",
+    "customizations": {
+        "vscode": {
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/venv/bin/python"
+            },
+            "extensions": [
+                "ms-azuretools.vscode-docker",
+                "ms-python.python",
+                "ms-python.vscode-pylance",
+                "ms-python.mypy-type-checker",
+                "charliermarsh.ruff",
+                "ms-toolsai.jupyter",
+                "arianjamasb.protein-viewer",
+                "redhat.vscode-yaml",
+                // very optional git-specific stuff
+                "arturock.gitstash",
+                "mhutchie.git-graph",
+                "GitHub.vscode-pull-request-github"
+            ]
+        }
+    }
+}

forks/chai-lab/.github/dependabot.yml

@@ -0,0 +1,12 @@
+# 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 more information:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+# https://containers.dev/guide/dependabot
+
+version: 2
+updates:
+  - package-ecosystem: "devcontainers"
+    directory: "/"
+    schedule:
+      interval: weekly

forks/chai-lab/.github/pull_request_template.md

@@ -0,0 +1,9 @@
+## Description
+<!--- Describe your changes in detail -->
+
+## Motivation
+<!--- Why is this change required? What problem does it solve? -->
+<!--- If it fixes an open issue, please link to the issue here. -->
+
+## Test plan
+<!--- Please describe in detail how you tested your changes. -->

forks/chai-lab/.github/workflows/mypy.yml

@@ -0,0 +1,27 @@
+name: Mypy
+on:
+  # Triggered whenever a commit is added to the main branch
+  push:
+    branches:
+      - main
+  # Triggered whenever a PR is opened or updated
+  pull_request:
+jobs:
+  mypy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          # install uv and cpu-only torch
+          pip install --no-deps uv -r <( cat requirements.in | grep torch) --extra-index-url https://download.pytorch.org/whl/cpu
+          # install requirements, except torch and potentially nvidia-related stuff
+          uv pip install --system -r <( cat requirements.in | grep -v nvidia | grep -v torch )
+          uv pip install --system --no-deps -e .
+      - name: Run mypy
+        run: mypy .

forks/chai-lab/.github/workflows/prettier_yaml.yml

@@ -0,0 +1,27 @@
+name: Prettier
+
+on:
+  # Triggered whenever a commit is added to the main branch
+  push:
+    branches:
+      - main
+  # Triggered whenever a PR is opened or updated
+  pull_request:
+jobs:
+  yaml:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install dependencies
+        run: npm install --save-dev --save-exact prettier
+
+      - name: Run Prettier to check YAML format
+        run: npx prettier --check "**/*.yml" "**/*.yaml"

forks/chai-lab/.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,27 @@
+name: Deploy to pypi
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          pip install . && pip install hatch
+      - name: Publish to PyPi
+        env:
+          HATCH_INDEX_USER: "__token__"
+          HATCH_INDEX_AUTH: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          hatch build --clean && hatch publish

forks/chai-lab/.github/workflows/pytest.yml

@@ -0,0 +1,27 @@
+name: Pytest
+on:
+  # Triggered whenever a commit is added to the main branch
+  push:
+    branches:
+      - main
+  # Triggered whenever a PR is opened or updated
+  pull_request:
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10" # ensure we support 3.10
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          # install uv and cpu-only torch
+          pip install --no-deps uv -r <( cat requirements.in | grep torch) --extra-index-url https://download.pytorch.org/whl/cpu
+          # install requirements, except torch and potentially nvidia-related stuff
+          uv pip install --system -r <( cat requirements.in | grep -v nvidia | grep -v torch )
+          uv pip install --system --no-deps -e .
+      - name: Run pytest
+        run: pytest ./tests/

forks/chai-lab/.github/workflows/ruff.yml

@@ -0,0 +1,27 @@
+name: Ruff
+on:
+  # Triggered whenever a commit is added to the main branch
+  push:
+    branches:
+      - main
+  # Triggered whenever a PR is opened or updated
+  pull_request:
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install
+        run: pip install pre-commit
+      - name: Run pre-commit checks on all files
+        # run specific ruff pre-commit hooks on all files
+        run: >
+          pip install pre-commit
+          && pre-commit install -f
+          && pre-commit run ruff --all-files
+          && pre-commit run ruff-format --all-files