Function port, compound- and pose set (issue 2264)

.dockerignore

@@ -0,0 +1,44 @@
+# =========================================================
+# .dockerignore
+# =========================================================
+
+# Environment and secrets
+.env
+.env.*
+*.env
+
+# Logs
+*.log
+*.log.*
+
+# Git
+.git/
+.gitignore
+
+# IDE and OS
+.vscode/
+.idea/
+.DS_Store
+Thumbs.db
+._*
+*~
+\#*#
+\#*
+
+
+# Temporary files
+*.tmp
+*.temp
+*.bak
+*.backup
+
+# Virtual environment
+.venv
+venv
+
+#Python cache files
+__pycache__
+*.pyc
+
+dist
+build

.github/workflows/lint.yaml

@@ -0,0 +1,25 @@
+---
+name: Lint
+
+on:
+  push:
+    branches:
+    - '*'
+    tags-ignore:
+    - '*'
+  pull_request:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v6
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        enable-cache: true
+    - name: Install dependencies
+      run: uv sync --frozen
+    - name: Repeat pre-commit
+      run: uv run pre-commit run --all-files

.github/workflows/release.yaml

@@ -0,0 +1,58 @@
+---
+# The standard xchem Python package release process.
+# Run on 'Release' and published to PyPI as a 'trusted' publisher.
+#
+# See https://docs.pypi.org/trusted-publishers/creating-a-project-through-oidc/
+# See https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Release
+
+on:
+  release:
+    types:
+    - published
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v6
+      with:
+        persist-credentials: false
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.x'
+    - name: Install build package
+      run: |
+        python3 -m pip install --upgrade pip
+        python3 -m pip install uv==0.10.6 --user
+    - name: Build
+      run: |
+        uv version ${{ github.ref_name }}
+        uv build
+    - name: Store the distribution
+      uses: actions/upload-artifact@v5
+      with:
+        name: python-package-distribution
+        path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/xchem-hippo
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distribution
+      uses: actions/download-artifact@v6
+      with:
+        name: python-package-distribution
+        path: dist/
+    - name: Publish
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yaml

@@ -0,0 +1,36 @@
+---
+name: Test
+
+on:
+  push:
+    branches:
+    - '*'
+    tags-ignore:
+    - '*'
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    # Test is broken - fix and remove this condition
+    if: false
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install rdkit==2023.9.1 molparse>=0.0.13 tqdm jupyterlab pycule chardet pandas
+        conda install -c conda-forge -y chemicalite
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Test
+      run: |
+        #pytest
+        cd tests
+        python test_A71EV2A.py

.gitignore

@@ -138,6 +138,10 @@ celerybeat.pid
 .venv
 env/
 venv/
+
+# Local docker-compose overrides (per-developer, not shared)
+docker-compose.override.yaml
+docker-compose.override.yml
 ENV/
 env.bak/
 venv.bak/

.pre-commit-config.yaml

@@ -1,11 +1,44 @@
+---
+
 repos:
-  # Using this mirror lets us use mypyc-compiled black, which is about 2x faster
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.1.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
     hooks:
-      - id: black
-        # It is recommended to specify the latest version of Python
-        # supported by your project here, or alternatively use
-        # pre-commit's default_language_version, see
-        # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3
+      - id: check-yaml
+      - id: check-case-conflict
+      - id: check-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        args:
+        - --markdown-linebreak-ext=md
+
+
+  # project tools using uv local environment
+  - repo: local
+    hooks:
+
+      - id: ruff
+        name: ruff lint
+        entry: uv run ruff check --fix
+        language: system
+        types: [python]
+
+      - id: ruff-format
+        name: ruff format
+        entry: uv run ruff format
+        language: system
+        types: [python]
+
+      # - id: mypy
+      #   name: mypy
+      #   entry: uv run mypy
+      #   language: system
+      #   pass_filenames: false
+
+      # - id: ty-check
+      #   name: ty check
+      #   entry: uv run ty check
+      #   language: system
+      #   pass_filenames: false

Dockerfile

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+FROM quay.io/jupyter/minimal-notebook:2025-04-14
+LABEL authors="Max Winokan"
+
+
+# Ported from Max's Dockerfile to support local development
+
+# combines conda and pip environments. There's a conflict somewhere
+# which I haven't resolved (TODO) between something in conda and pip
+# envs, so cannot use a single env
+
+# this is what I'm stuck on. Project depends on numpy v1.23 (why?) and
+# I can't go over 3.12
+ARG PYTHON_VERSION=3.12
+
+
+WORKDIR "/home/code/HIPPO"
+# WORKDIR "/home/code/HIPPO/data"
+# WORKDIR "/home/code/HIPPO/hippo"
+
+USER 0
+
+
+# install package dependencies into different virtual env
+COPY uv.lock pyproject.toml ./
+RUN pip install --upgrade pip && python -m pip install uv
+
+# install all dependencies into active environment without updating lockfile
+# RUN uv sync --frozen --active
+RUN uv venv /home/code/HIPPO/.venv
+RUN uv sync --frozen --python /home/code/HIPPO/.venv/bin/python
+
+# now add venv python to path so conda python can find it
+ENV PATH="/home/code/HIPPO/.venv/bin:$PATH"
+ENV PYTHONPATH="/home/code/HIPPO/.venv/lib/python${PYTHON_VERSION}/site-packages:$PYTHONPATH"
+
+
+# patch rich
+RUN python -c "import mrich; mrich.patch_rich_jupyter_margins()"
+
+
+# notebooks
+RUN chown ${NB_USER} "/home/code" && sudo apt update && sudo apt install screen -y
+
+# force numpy update. since there's now a new venv, make sure conda is
+# used (othewise numpy will be invisible)
+RUN uv pip install --upgrade numpy==2.4.4
+USER ${NB_USER}
+
+
+# WORKDIR "/home/code/HIPPO"