initial release of chai-1

show one more parameter

exclude folders from pypi package build

add workflow to auto-deploy to pypi on tag creation

improve docstring

merge changes from chai-internal

.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"
+            ]
+        }
+    }
+}

.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

.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. -->

.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 .

.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"

.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

.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

.gitignore

@@ -0,0 +1,162 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm/JetBrains
+.idea/
+
+# outputs from the model
+outputs/
+

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+---
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.6.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+      # Run the formatter.
+      - id: ruff-format

.vscode/extensions.json

@@ -0,0 +1,15 @@
+// We use Dev Containers to run the code in a container. As a result,
+// VS Code runs extensions in one of two places: locally on the UI /
+// client side, or in the container. When adding extensions, take care
+// to ensure you add them to the right list: container extensions should
+// be added to the list in ../.devcontainer/devcontainer.json, and UI
+// extensions should be added to the list below. See
+// https://code.visualstudio.com/docs/devcontainers/containers#_managing-extensions
+{
+    "recommendations": [
+        "ms-vscode-remote.remote-containers",
+        "ms-vscode-remote.remote-ssh",
+        "ms-vscode-remote.remote-ssh-edit",
+        "ms-vscode.remote-explorer"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,16 @@
+{
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+        "source.fixAll": "explicit",
+        "source.organizeImports": "explicit"
+    },
+    "python.analysis.autoImportCompletions": true,
+    "terminal.integrated.scrollback": 30000,
+    "mypy-type-checker.cwd": "${workspaceFolder}",
+    // pytest setup
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+}