UV-first benchmark workflow, CLI entrypoints, and HPC docs polish

.editorconfig

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+root = true
+
+[*.py]
+charset = utf-8
+end_of_line = lf
+indent_style = space
+indent_size = 4
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.md]
+trim_trailing_whitespace = false
+
+[*.{yml,yaml,toml}]
+indent_style = space
+indent_size = 2

.env.example

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+# Bento runtime paths
+BENTO_WORKDIR=/path/to/Bento
+BENTO_DATABASES_DIR=/path/to/datasets
+BENTO_GLOSA_DIR=/path/to/glosa_v2.2
+
+# Optional CLI override
+# BENTO_REPO_ROOT=/path/to/Bento

.github/CONTRIBUTING.md

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+# How to contribute
+
+We welcome contributions from external contributors, and this document
+describes how to merge code changes into this openadmet_models.
+
+## Getting Started
+
+* Make sure you have a [GitHub account](https://github.com/signup/free).
+* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub.
+* On your local machine,
+  [clone](https://help.github.com/articles/cloning-a-repository/) your fork of
+  the repository.
+
+## Making Changes
+
+* Add some really awesome code to your local fork.  It's usually a [good
+  idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/)
+  to make changes on a
+  [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
+  with the branch name relating to the feature you are going to add.
+* When you are ready for others to examine and comment on your new feature,
+  navigate to your fork of openadmet_models on GitHub and open a [pull
+  request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
+  after you launch a PR from one of your fork's branches, all
+  subsequent commits to that branch will be added to the open pull request
+  automatically.  Each commit added to the PR will be validated for
+  mergability, compilation and test suite compliance; the results of these tests
+  will be visible on the PR page.
+* If you're providing a new feature, you must add test cases and documentation.
+* When the code is ready to go, make sure you run the test suite using pytest.
+* When you're ready to be considered for merging, check the "Ready to go"
+  box on the PR page to let the openadmet_models devs know that the changes are complete.
+  The code will not be merged until this box is checked, the continuous
+  integration returns checkmarks,
+  and multiple core developers give "Approved" reviews.
+
+# Additional Resources
+
+* [General GitHub documentation](https://help.github.com/)
+* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/)
+* [A guide to contributing to software packages](http://www.contribution-guide.org)
+* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR)

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    name: Ruff
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: latest
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Sync lint environment
+        run: uv sync --frozen --no-editable --extra lint
+
+      - name: Ruff format check
+        run: uv run ruff format --check .
+
+      - name: Ruff lint check
+        run: uv run ruff check .
+
+  tests:
+    name: Pytest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: latest
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Sync test environment
+        run: uv sync --frozen --no-editable --extra test
+
+      - name: Run tests
+        run: uv run pytest

.gitignore

@@ -1,3 +1,25 @@
 # Large files (exceeding GitHub 100MB limit)
 similarity_scores/pocket_scores.tsv
 similarity_scores/tanimoto_distances.csv
+
+# Python
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.coverage
+htmlcov/
+.mypy_cache/
+
+# UV / virtual environments
+.venv/
+uv.lock.bak
+
+# Notebook checkpoints
+.ipynb_checkpoints/
+
+# Runtime outputs
+outputs/
+bs/
+
+# Local research notes
+.thoughts/

CONTRIBUTING.md

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+# Contributing
+
+## Development Workflow
+
+1. Create a feature branch from `main`.
+2. Install dependencies with uv:
+   - `uv sync --no-editable --extra lint --extra test`
+3. Run checks locally:
+   - `uv run ruff check .`
+   - `uv run ruff format --check .`
+   - `uv run pytest`
+4. Open a pull request with a clear description of the change and validation steps.
+
+## Coding Standards
+
+- Use Python 3.10+ compatible syntax.
+- Keep scripts and docs in English.
+- Prefer small, reviewable commits.
+- Include tests for behavior changes.
+
+## Data and Large Files
+
+- Do not commit generated artifacts or local runtime caches.
+- Keep large benchmark artifacts outside the repository when possible and document retrieval steps in PRs.

LICENSE

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+MIT License
+
+Copyright (c) 2026 LigandPro Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.