dmsroute 0.1.2__tar.gz

dmsroute-0.1.2/.gitignore

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+# Byte-compiled / optimized / DLL files
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+
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+# Marimo
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+# Local repository archives
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+/dms-parser.zip

dmsroute-0.1.2/CHANGELOG.md

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+# Changelog
+
+All notable changes to DMSRoute are recorded here. Versions follow [Semantic Versioning](https://semver.org/).
+
+## 0.1.2
+
+- First release on PyPI (`pip install dmsroute`).
+- `dmsroute.__version__` exposes the package version.
+- Requires Python 3.11 or newer (Python 3.10 reached end of life).

dmsroute-0.1.2/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "DMSRoute"
+abstract: "Utilities for acquiring, parsing, validating, harmonizing, and standardizing DMS datasets from MaveDB and ProteinGym."
+type: software
+license: "MIT"
+url: "https://github.com/kren-ai-lab/dms-route"
+authors:
+  - family-names: "Fernández-Villegas"
+    given-names: "Diego"
+    affiliation: "Universidad de Magallanes"
+  - family-names: "Escobedo"
+    given-names: "Sebastián"
+    affiliation: "Universidad de Magallanes"
+  - family-names: "Alarcón"
+    given-names: "Tomás"
+    affiliation: "Universidad de Magallanes"
+  - family-names: "Medina-Ortiz"
+    given-names: "David"
+    affiliation: "Universidad de Magallanes"
+repository-code: "https://github.com/kren-ai-lab/dms-route"
+keywords:
+  - "deep mutational scanning"
+  - "data harmonization"
+  - "DMS datasets"
+  - "MaveDB"
+  - "ProteinGym"
+  - "bioinformatics"
+  - "protein"
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.21924522
+    description: "Concept DOI (all versions)"

dmsroute-0.1.2/DEVELOPMENT.md

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+# Development Guide
+
+This project is the `DMSRoute` Python package and command-line interface for acquiring, parsing, validating, harmonizing, and standardizing DMS datasets from MaveDB and ProteinGym.
+
+## Requirements
+
+The project currently declares:
+
+- Python `>=3.11`
+- core runtime dependencies in `pyproject.toml`
+- the `dev` extra includes `pytest>=8.0`
+
+## Development installation
+
+Create a virtual environment and install the project in editable mode:
+
+```bash
+python -m venv .venv
+# Linux/macOS
+. .venv/bin/activate
+# Windows PowerShell
+# .\.venv\Scripts\Activate.ps1
+python -m pip install --upgrade pip
+python -m pip install -e ".[dev]"
+```
+
+This uses the repository's actual editable-install workflow and dev extra.
+
+## Repository architecture
+
+The package lives directly at the repository root as `dmsroute/`.
+
+- root-level orchestration modules: `builders.py`, `catalog.py`, `config.py`, `downloads.py`, `pipeline.py`, and `cli.py`
+- `dmsroute/core/`: parsing, validation, transformation, and domain primitives
+- `dmsroute/acquisition/`: cache, fetch, and I/O infrastructure
+- `dmsroute/sources/`: MaveDB and ProteinGym source-specific adapters and catalogs
+- `tests/`: automated regression and behavior tests
+- `examples/`: usage examples and notebooks
+
+## Testing
+
+Run the full suite:
+
+```bash
+pytest -q
+```
+
+Run a focused test file:
+
+```bash
+pytest -q tests/test_parsing.py
+```
+
+Run one focused test:
+
+```bash
+pytest -q tests/test_parsing.py -k hgvs_to_sequence
+```
+
+Run dependency validation:
+
+```bash
+python -m pip check
+```
+
+Run compile checking:
+
+```bash
+python -m compileall -q dmsroute tests examples
+```
+
+## CLI smoke testing
+
+The supported public CLI entry point is `dmsroute`.
+
+Use the following commands:
+
+```bash
+dmsroute --help
+dmsroute download --help
+dmsroute download-many --help
+dmsroute run --help
+dmsroute snapshot --help
+dmsroute cache --help
+```
+
+`python -m dmsroute.cli` is intentionally not a supported public invocation and is not documented as such.
+
+## External access policy
+
+Unit tests should not depend on live MaveDB, ProteinGym, Zenodo, or other external services.
+
+Use offline deterministic tests unless a specific test is designed to exercise an external integration path intentionally.
+
+## Packaging validation
+
+For release-oriented checks, use the repository's current packaging workflow:
+
+```bash
+python -m build --sdist --wheel
+python -m twine check --strict dist/*
+```
+
+Optional clean-install validation:
+
+```bash
+python -m venv /tmp/dmsroute-check
+# activate the temporary environment and install the built wheel
+python -m pip install dist/dmsroute-*-py3-none-any.whl
+python -m pip check
+dmsroute --help
+```
+
+Do not add or require `uv.lock` for normal development.
+
+## Contribution and change principles
+
+- Source adapters should keep source-specific behavior inside `dmsroute/sources/`.
+- Generic acquisition logic belongs in `dmsroute/acquisition/`.
+- Generic parsing, validation, and domain logic belongs in `dmsroute/core/`.
+- Orchestration remains in the root-level facade modules.
+- Changes to standardized data contracts require explicit tests.
+- Avoid unrelated cleanup while implementing a requested change.
+
+## Release checklist
+
+Before tagging or publishing a release candidate, confirm:
+
+- worktree is clean
+- full test suite passes
+- `python -m pip check` passes
+- project builds successfully
+- `twine check --strict` passes
+- clean install succeeds in a temporary environment
+- CLI smoke checks pass
+- `dmsroute/_version.py` and `CHANGELOG.md` are updated
+- tag only after all checks pass; pushing a `v*` tag publishes to PyPI through `.github/workflows/publish-pypi.yml`
+

dmsroute-0.1.2/LICENSE

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+MIT License
+
+Copyright (c) 2026 DMSRoute contributors
+
+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.

dmsroute-0.1.2/PKG-INFO

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+Metadata-Version: 2.5
+Name: dmsroute
+Version: 0.1.2
+Summary: Utilities for acquiring, parsing, validating, harmonizing, and standardizing DMS datasets from MaveDB and ProteinGym.
+Project-URL: Homepage, https://github.com/kren-ai-lab/dms-route
+Project-URL: Repository, https://github.com/kren-ai-lab/dms-route
+Project-URL: Issues, https://github.com/kren-ai-lab/dms-route/issues
+Project-URL: Documentation, https://github.com/kren-ai-lab/dms-route#readme
+Author: Diego Fernández-Villegas, Sebastián Escobedo, Tomás Alarcón, David Medina-Ortiz
+Maintainer: Diego Fernández-Villegas, Sebastián Escobedo, Tomás Alarcón, David Medina-Ortiz
+License-Expression: MIT
+License-File: LICENSE
+Keywords: bioinformatics,data-harmonization,deep-mutational-scanning,dms,mavedb,protein,proteingym
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Requires-Dist: pyarrow>=15.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: requests>=2.31
+Requires-Dist: typer<0.28,>=0.27.1
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# DMSRoute
+
+[![PyPI](https://img.shields.io/pypi/v/dmsroute?style=flat-square)](https://pypi.org/project/dmsroute/)
+[![PyVersions](https://img.shields.io/pypi/pyversions/dmsroute?style=flat-square)](https://github.com/kren-ai-lab/dms-route)
+[![Tests](https://img.shields.io/github/actions/workflow/status/kren-ai-lab/dms-route/ci.yml?style=flat-square)](https://github.com/kren-ai-lab/dms-route/actions/workflows/ci.yml)
+![License](https://img.shields.io/github/license/kren-ai-lab/dms-route?style=flat-square)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.21924522-blue?style=flat-square)](https://doi.org/10.5281/zenodo.21924522)
+
+DMSRoute obtains and standardizes Deep Mutational Scanning (DMS) datasets
+from ProteinGym and MaveDB. It provides a command-line interface, a Python API,
+and a YAML pipeline for producing consistent datasets from source-specific
+tables and metadata.
+
+The project name is DMSRoute. The distribution, Python package, and console
+command are named `dmsroute`.
+
+Supported sources:
+
+- ProteinGym substitution and indel datasets, identified by canonical
+  `DMS_id` values.
+- MaveDB score sets, identified by permanent score-set URNs and acquired from
+  the public API or a fixed bulk snapshot.
+
+## Installation
+
+DMSRoute requires Python 3.11 or newer.
+
+```bash
+pip install dmsroute
+# or with uv:
+uv add dmsroute
+```
+
+Check the installation with:
+
+```bash
+dmsroute --help
+```
+
+Development setup and validation commands are documented in
+[`DEVELOPMENT.md`](https://github.com/kren-ai-lab/dms-route/blob/main/DEVELOPMENT.md).
+
+## Quick start
+
+Inspect a MaveDB score set:
+
+```bash
+dmsroute metadata \
+  --source mavedb \
+  --dataset-id urn:mavedb:00000001-a-4
+```
+
+Download and standardize it:
+
+```bash
+dmsroute download \
+  --source mavedb \
+  --dataset-id urn:mavedb:00000001-a-4 \
+  --output-dir datasets/ube2i
+```
+
+ProteinGym uses canonical `DMS_id` values:
+
+```bash
+dmsroute list --source proteingym --query BRCA1 --limit 10
+
+dmsroute download \
+  --source proteingym \
+  --dataset-id BRCA1_HUMAN_Findlay_2018 \
+  --output-dir datasets/brca1
+```
+
+ProteinGym substitutions are selected by default. Use `--variant-type indels`
+for the indel resource.
+
+## CLI
+
+The main commands are:
+
+| Command | Purpose |
+| --- | --- |
+| `dmsroute list` | Search a ProteinGym or MaveDB catalog |
+| `dmsroute metadata` | Retrieve metadata for one dataset |
+| `dmsroute download` | Download and standardize one dataset |
+| `dmsroute download-many` | Process several datasets from one source |
+| `dmsroute run` | Run a YAML pipeline |
+| `dmsroute discover` | Search a fixed local MaveDB snapshot |
+| `dmsroute snapshot` | Fetch snapshots or extract archival tables |
+| `dmsroute cache` | Inspect the local cache without modifying it |
+
+Each command provides its complete options through `--help`.
+
+For example, a batch can be specified with repeated identifiers:
+
+```bash
+dmsroute download-many \
+  --source proteingym \
+  --dataset-id BRCA1_HUMAN_Findlay_2018 \
+  --dataset-id PTEN_HUMAN_Mighell_2018 \
+  --output-dir datasets
+```
+
+Source artifacts are cached under `~/.cache/dmsroute` by default. Use
+`--cache-dir` to select another location.
+
+## MaveDB acquisition
+
+### API
+
+API acquisition is the default for MaveDB catalog, metadata, and download
+commands. It retrieves the current score-set metadata and scores for a
+permanent URN.
+
+```bash
+dmsroute download \
+  --source mavedb \
+  --dataset-id urn:mavedb:00000001-a-4 \
+  --output-dir datasets/ube2i
+```
+
+### Snapshot
+
+Bulk snapshots are versioned Zenodo records. Snapshot acquisition is explicit
+and requires the selected record to be present in the local cache.
+
+```bash
+dmsroute snapshot fetch --record 20840937
+
+dmsroute discover \
+  --snapshot 20840937 \
+  --query BRCA1
+
+dmsroute download \
+  --source mavedb \
+  --dataset-id urn:mavedb:00000001-a-4 \
+  --acquisition snapshot \
+  --snapshot-record 20840937 \
+  --output-dir datasets/ube2i-snapshot
+```
+
+`dmsroute snapshot extract` extracts raw score and count tables. Snapshot
+standardization is available through `download` and `download-many`; the YAML
+pipeline uses the MaveDB API.
+
+## Configuration
+
+Run a configured pipeline with:
+
+```bash
+dmsroute run --config examples/pipeline.yml
+```
+
+A configuration may contain ProteinGym, MaveDB, or both:
+
+```yaml
+proteingym:
+  resource: dms_substitutions
+  dir_base: datasets/proteingym
+  datasets:
+    - dataset_id: BLAT_ECOLX_Jacquier_2013
+
+mavedb:
+  dir_base: datasets/mavedb
+  datasets:
+    - dataset_id: "urn:mavedb:00000001-a-4"
+
+output:
+  summary_dir: datasets/summaries
+```
+
+Use `--only proteingym` or `--only mavedb` to select one configured source.
+`--dry-run` resolves configuration and source metadata without writing
+processed datasets. The full configuration contract is documented in
+[`examples/config.reference.yml`](https://github.com/kren-ai-lab/dms-route/blob/main/examples/config.reference.yml).
+
+## Output
+
+A successful `download` writes one dataset bundle:
+
+```text
+output-directory/
+|-- standardized.csv
+|-- summary.csv
+`-- summary.json
+```
+
+The standardized table preserves source columns and adds common dataset,
+variant, sequence, score, and row-status fields. Source scores are copied to
+`score_raw`; score transformations are opt-in.
+
+`download-many` also writes `download-summary.csv` and
+`download-summary.json` at the batch root. YAML pipelines write processed CSV
+files under each source directory and combined summaries under
+`output.summary_dir`.
+
+## Python API
+
+The same download workflow is available from Python:
+
+```python
+from pathlib import Path
+
+from dmsroute import FilesystemCache, download_and_standardize_dataset
+
+cache = FilesystemCache(Path.home() / ".cache" / "dmsroute")
+result = download_and_standardize_dataset(
+    "mavedb",
+    "urn:mavedb:00000001-a-4",
+    output_dir="datasets/ube2i",
+    cache=cache,
+)
+
+print(result.dataset_path)
+```
+
+Local tables can be standardized with `build_proteingym_dataset`,
+`build_proteingym_indel_dataset`, and `build_mavedb_dataset`.
+
+## Documentation
+
+- [`examples/`](https://github.com/kren-ai-lab/dms-route/tree/main/examples) contains notebooks for acquisition, parsing, and
+  score transformations.
+- [`examples/config.reference.yml`](https://github.com/kren-ai-lab/dms-route/blob/main/examples/config.reference.yml) documents
+  every YAML option.
+- [`DEVELOPMENT.md`](https://github.com/kren-ai-lab/dms-route/blob/main/DEVELOPMENT.md) covers development setup, architecture,
+  tests, and packaging checks.
+- `dmsroute <command> --help` is the reference for CLI options.
+
+## Citation
+
+If you use DMSRoute in your research, please cite:
+
+> Fernández-Villegas, D.; Escobedo, S.; Alarcón, T.; Medina-Ortiz, D.
+> *DMSRoute*.
+> Version 0.1.2, 2026. Zenodo.
+> https://doi.org/10.5281/zenodo.21924522
+
+```bibtex
+@software{dmsroute2026,
+  author    = {Fernández-Villegas, Diego and Escobedo, Sebastián and Alarcón, Tomás and Medina-Ortiz, David},
+  title     = {DMSRoute},
+  year      = {2026},
+  version   = {0.1.2},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.21924522},
+  url       = {https://doi.org/10.5281/zenodo.21924522}
+}
+```
+
+## License
+
+MIT. See [`LICENSE`](https://github.com/kren-ai-lab/dms-route/blob/main/LICENSE).