process_omol25 0.1.11__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- process_omol25-0.1.11/.agents/workflows/publish-github-pages.md +17 -0
- process_omol25-0.1.11/.agents/workflows/publish-pypi.md +20 -0
- process_omol25-0.1.11/.agents/workflows/publish-zenodo.md +16 -0
- process_omol25-0.1.11/.github/workflows/gh-pages.yml +38 -0
- process_omol25-0.1.11/.github/workflows/publish.yml +57 -0
- process_omol25-0.1.11/.github/workflows/test.yml +41 -0
- process_omol25-0.1.11/.gitignore +74 -0
- process_omol25-0.1.11/LICENSE +27 -0
- process_omol25-0.1.11/PKG-INFO +15 -0
- process_omol25-0.1.11/README.md +51 -0
- process_omol25-0.1.11/data/noble_gas_compounds_prefix.json +74 -0
- process_omol25-0.1.11/data/noble_gas_compounds_prefix_full.json +146 -0
- process_omol25-0.1.11/docs/Makefile +20 -0
- process_omol25-0.1.11/docs/api.rst +18 -0
- process_omol25-0.1.11/docs/conf.py +42 -0
- process_omol25-0.1.11/docs/index.rst +18 -0
- process_omol25-0.1.11/docs/make.bat +35 -0
- process_omol25-0.1.11/pyproject.toml +32 -0
- process_omol25-0.1.11/release.sh +14 -0
- process_omol25-0.1.11/src/process_omol25/__init__.py +3 -0
- process_omol25-0.1.11/src/process_omol25/cli.py +148 -0
- process_omol25-0.1.11/src/process_omol25/download_omol25.py +260 -0
- process_omol25-0.1.11/src/process_omol25/process_omol25.py +707 -0
- process_omol25-0.1.11/src/process_omol25/verify_processed_omol25.py +161 -0
- process_omol25-0.1.11/tests/test_process_omol25.py +554 -0
- process_omol25-0.1.11/tests/test_verify_processed_omol25.py +120 -0
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description: Automatically build and verify Sphinx documentation for GitHub Pages
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---
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# Publish Documentation to GitHub Pages
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This workflow allows the AI/User to natively test the Sphinx documentation compilation pipeline locally on the machine before pushing to the `main` branch, ensuring the GitHub Action executes flawlessly.
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1. Install the main package and all necessary documentation rendering engines.
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// turbo
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2. `micromamba run -n janus pip install -e . sphinx sphinx-material`
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4. `cd docs && make html`
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5. **Deployment Warning**: The remote deployment to GitHub Pages is handled 100% autonomously by the `.github/workflows/gh-pages.yml` Action attached to this repository. You do not need to manually push the `gh-pages` branch unless the CI token is broken.
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description: Build and publish the process_omol25 distribution package to PyPI manually
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---
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# Publish to PyPI
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This workflow dictates the native process to manually formulate the distribution tarballs and binary wheels and push them up to the Python Package Index, verifying the steps autonomous CI undertakes.
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1. Ensure the `uv` toolchain is globally installed.
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// turbo
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2. `curl -LsSf https://astral.sh/uv/install.sh | sh`
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3. Compile the Python package from source using `pyproject.toml`.
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// turbo
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4. `uv build`
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5. Once built, the `/dist` directory will contain the `.tar.gz` and `.whl` files. Publish them to PyPI natively utilizing `uv publish`. (Note: This will prompt for your PyPI API token).
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6. `uv publish dist/*`
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**Warning**: The `.github/workflows/publish-pypi.yml` handles this 100% autonomously whenever a new GitHub Release is fully published via UI. Manual uv publish interaction is purely for fallback or TestPyPI staging.
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description: Automatically publish the repository codebase to Zenodo when a new tag is cut
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---
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# Publish to Zenodo
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This workflow maps out how to construct and verify the `Zenodo` Data Object Identifier (DOI) publishing mechanism using the Janus Core architecture.
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1. Ensure your repository root has a `.zenodo.json` file (optional, but highly recommended) storing your specific JSON schema metadata.
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2. Navigate directly to the Zenodo Web UI, link your GitHub account natively, and flick the repository toggle to 'On'.
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3. Trigger the deployment natively via standard git tagging:
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// turbo
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4. `git tag v1.0.0 && git push origin v1.0.0`
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5. The `.github/workflows/publish-zenodo.yml` pipeline will automatically spin up, instantiate `uv`, ensure the `pyproject.toml` version explicitly matches your tag using `uvx toml`, and finally invoke `ncipollo/release-action`.
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6. This officially mints a GitHub Release. Because you flicked the Zenodo toggle in Step 2, Zenodo's native Webhooks will securely intercept the GitHub Release event and automatically mint your DOI! This approach guarantees that GitHub Releases and Zenodo DOIs are perfectly structurally paired.
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name: Publish Docs to GitHub Pages
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on:
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push:
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branches:
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- main
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workflow_dispatch:
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permissions:
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contents: write
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build-and-deploy:
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steps:
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uses: actions/checkout@v4
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uses: actions/setup-python@v5
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python-version: '3.12'
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pip install sphinx sphinx-material
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- name: Build Sphinx Documentation
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run: |
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cd docs
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make html
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./docs/_build/html
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name: Publish Release
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on:
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publish:
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environment: pypi
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# Required for GitHub Releases and PyPI Trusted Publishing OIDC handshakes
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permissions:
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id-token: write
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contents: write
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uses: actions/checkout@v4
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uses: astral-sh/setup-uv@v5
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run: uv build
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run: echo "VERSION=$(uvx --from=toml-cli toml get --toml-path=pyproject.toml project.version)" >> $GITHUB_ENV
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echo "Git tag does not match version in pyproject.toml. Expected v${{ env.VERSION }}"
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exit 1
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- name: Create GitHub Release (Triggers Zenodo Archival)
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uses: ncipollo/release-action@v1
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with:
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artifacts: "dist/*"
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draft: false
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generateReleaseNotes: true
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run: uv publish
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name: Test process_omol25
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sudo apt-get install -y openmpi-bin libopenmpi-dev
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- name: Run tests
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OMPI_MCA_rmaps_base_oversubscribe: 1
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pytest tests/
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# Byte-compiled / optimized / DLL files
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.Python
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# PyInstaller
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*.spec
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# Installer logs
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# Unit test / coverage reports
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# Documentation
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docs/_build/
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# Jupyter Notebook
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# Environments
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env/
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venv/
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ENV/
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# Logs
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*.log
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# Secrets
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psdi-argonne-omol25-ro.json
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*.parquet
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Copyright (c) 2026, Alin M Elena
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Metadata-Version: 2.4
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Name: process_omol25
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Version: 0.1.11
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Summary: A Python package for processing omol-25 data using MPI.
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Author: Alin M Elena
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License-File: LICENSE
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Requires-Python: >=3.10
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Requires-Dist: ase
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Requires-Dist: boto3
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Requires-Dist: mpi4py
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Requires-Dist: pandas
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# process_omol25
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[](https://pypi.org/project/process_omol25/)
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[](https://pypi.org/project/process_omol25/)
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[](LICENSE)
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[](https://github.com/astral-sh/ruff)
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[](https://github.com/ddmms/process_omol25/actions/workflows/gh-pages.yml)
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[](https://github.com/ddmms/process_omol25/actions/workflows/publish.yml)
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[](https://github.com/ddmms/process_omol25/actions/workflows/publish.yml)
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A Python package for processing omol-25 data using MPI.
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## Installation
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You can install this package locally:
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```bash
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pip install -e .
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```
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## Usage
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This package provides three primary command-line interfaces:
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### 1. Processing Data
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Extract, process, and combine molecular data from an S3 bucket (or local directory):
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```bash
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process_omol25 --help
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```
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* **MPI Support**: Add `--mpi` and run via `mpirun` to distribute tasks across multiple workers natively via hybrid RMA.
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* **Smart Restart**: Add `--restart` to automatically sweep the output directory, recover orphaned Parquet/XYZ pairs, and pick up right where you left off.
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* **Logging**: Specify `--log-file my_log.log` to write text streams to disk (existing logs are automatically appended to, not overwritten).
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* **Batch Flushing**: Use `--batch-size N` to control disk writes. If not specified, workers dynamically flush at 1% increments (with a strict minimum of 100 output structures).
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### 2. Downloading Raw Data
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Download original raw `orca.out` datasets from S3 without running processing logic natively on them:
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```bash
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download_omol25 --help
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```
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### 3. Verification Utility
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Cross-reference a generated Parquet dataset with its respective ExtXYZ file to guarantee absolutely zero data corruption or structural mismatching:
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```bash
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verify_processed_omol25 --parquet props_group.parquet --extxyz structs_group.xyz
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```
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* This rigorously structurally aligns both tables via `geom_sha1` and flags any mathematically misassigned properties.
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* Embedded timing metadata such as `process_time_s` are strictly and unconditionally excluded to prevent false-positive errors.
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## License
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This project is licensed under the BSD 3-Clause License - see the [LICENSE](LICENSE) file for details.
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API Reference
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=============
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Main Processor module
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---------------------
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.. automodule:: process_omol25.process_omol25
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:members:
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CLI Module
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----------
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.. automodule:: process_omol25.cli
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# Configuration file for the Sphinx documentation builder.
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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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9
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+
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10
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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12
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+
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project = 'process_omol25'
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copyright = '2026, Alin M Elena'
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author = 'Alin M Elena'
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+
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version = "0.1.11"
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release = "0.1.11"
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+
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20
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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+
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extensions = [
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'sphinx.ext.autodoc',
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25
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'sphinx_material',
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26
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]
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27
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+
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autodoc_mock_imports = [
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"ase", "boto3", "botocore", "zstandard", "pandas",
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"numpy", "tqdm", "mpi4py"
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]
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32
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+
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templates_path = ['_templates']
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34
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
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35
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+
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36
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+
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37
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+
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38
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# -- Options for HTML output -------------------------------------------------
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39
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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40
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+
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41
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html_theme = 'sphinx_material'
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42
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html_static_path = ['_static']
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@@ -0,0 +1,18 @@
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1
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+
.. process_omol25 documentation master file, created by
|
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2
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sphinx-quickstart on Sat Mar 21 08:10:34 2026.
|
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3
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You can adapt this file completely to your liking, but it should at least
|
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4
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contain the root `toctree` directive.
|
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5
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+
|
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6
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+
process_omol25 documentation
|
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============================
|
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+
|
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9
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Add your content using ``reStructuredText`` syntax. See the
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`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
|
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documentation for details.
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+
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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api
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