uniprotlib 0.1.0__tar.gz

uniprotlib-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12", "3.13", "3.14"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v4
+      - run: uv python install ${{ matrix.python-version }}
+      - run: uv sync --python ${{ matrix.python-version }}
+      - run: uv run python -m pytest tests/ -v
+
+  publish:
+    needs: test
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    environment: pypi
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v4
+      - run: uv build
+      - uses: pypa/gh-action-pypi-publish@release/v1

uniprotlib-0.1.0/.github/workflows/tests.yml

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+name: Tests
+
+on: push
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12", "3.13", "3.14"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v4
+      - run: uv python install ${{ matrix.python-version }}
+      - run: uv sync --python ${{ matrix.python-version }}
+      - run: uv run pytest tests/ -v

uniprotlib-0.1.0/.gitignore

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+# End of https://www.toptal.com/developers/gitignore/api/python,macos,linux,visualstudiocode,jetbrains+all
+
+# Claude Code
+CLAUDE.md

uniprotlib-0.1.0/.python-version

@@ -0,0 +1 @@
+3.14

uniprotlib-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Martin Preusse
+
+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.

uniprotlib-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: uniprotlib
+Version: 0.1.0
+Summary: Python library for parsing UniProt XML data
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: lxml>=6.0.2
+Description-Content-Type: text/markdown
+
+# uniprotlib
+
+> **Note:** This library was vibe coded with Claude. It works, it's tested, but review accordingly.
+
+Python library for parsing UniProt XML files. Handles both single-entry downloads and multi-GB gzip-compressed database dumps with bounded memory usage.
+
+## Installation
+
+```bash
+pip install uniprotlib
+```
+
+Or with [uv](https://docs.astral.sh/uv/):
+
+```bash
+uv add uniprotlib
+```
+
+## Usage
+
+```python
+from uniprotlib import parse_xml
+
+# single file
+for entry in parse_xml("Q9Y261.xml"):
+    print(entry.primary_accession, entry.protein_name)
+
+# gzipped bulk download
+for entry in parse_xml("uniprot_sprot.xml.gz"):
+    print(entry.gene.primary, entry.organism.scientific_name)
+
+# multiple files
+for entry in parse_xml("human.xml.gz", "mouse.xml.gz"):
+    print(entry.primary_accession)
+```
+
+`parse_xml()` returns an iterator that yields `UniProtEntry` objects. Gzip detection is automatic based on the `.gz` extension. Memory stays bounded regardless of file size.
+
+## Parsed fields
+
+| Model | Fields |
+|---|---|
+| `UniProtEntry` | primary_accession, accessions, entry_name, dataset, protein_name, gene, organism, sequence, keywords, db_references |
+| `Gene` | primary, synonyms, ordered_locus_names, orf_names |
+| `Organism` | scientific_name, common_name, tax_id, lineage |
+| `Sequence` | value, length, mass, checksum |
+| `DbReference` | type, id, molecule, properties |
+
+All model classes are dataclasses with full type annotations and `py.typed` support.
+
+## Development
+
+Requires Python >= 3.12 and [uv](https://docs.astral.sh/uv/).
+
+```bash
+uv sync
+uv run pytest tests/ -v
+```
+
+## License
+
+MIT

uniprotlib-0.1.0/README.md

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+# uniprotlib
+
+> **Note:** This library was vibe coded with Claude. It works, it's tested, but review accordingly.
+
+Python library for parsing UniProt XML files. Handles both single-entry downloads and multi-GB gzip-compressed database dumps with bounded memory usage.
+
+## Installation
+
+```bash
+pip install uniprotlib
+```
+
+Or with [uv](https://docs.astral.sh/uv/):
+
+```bash
+uv add uniprotlib
+```
+
+## Usage
+
+```python
+from uniprotlib import parse_xml
+
+# single file
+for entry in parse_xml("Q9Y261.xml"):
+    print(entry.primary_accession, entry.protein_name)
+
+# gzipped bulk download
+for entry in parse_xml("uniprot_sprot.xml.gz"):
+    print(entry.gene.primary, entry.organism.scientific_name)
+
+# multiple files
+for entry in parse_xml("human.xml.gz", "mouse.xml.gz"):
+    print(entry.primary_accession)
+```
+
+`parse_xml()` returns an iterator that yields `UniProtEntry` objects. Gzip detection is automatic based on the `.gz` extension. Memory stays bounded regardless of file size.
+
+## Parsed fields
+
+| Model | Fields |
+|---|---|
+| `UniProtEntry` | primary_accession, accessions, entry_name, dataset, protein_name, gene, organism, sequence, keywords, db_references |
+| `Gene` | primary, synonyms, ordered_locus_names, orf_names |
+| `Organism` | scientific_name, common_name, tax_id, lineage |
+| `Sequence` | value, length, mass, checksum |
+| `DbReference` | type, id, molecule, properties |
+
+All model classes are dataclasses with full type annotations and `py.typed` support.
+
+## Development
+
+Requires Python >= 3.12 and [uv](https://docs.astral.sh/uv/).
+
+```bash
+uv sync
+uv run pytest tests/ -v
+```
+
+## License
+
+MIT