orthodb 0.1.3__tar.gz

orthodb-0.1.3/LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2026 Gustavo Madeira Santana
+
+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.
+

orthodb-0.1.3/PKG-INFO

@@ -0,0 +1,186 @@
+Metadata-Version: 2.4
+Name: orthodb
+Version: 0.1.3
+Summary: Agent-friendly CLI for cached OrthoDB downloads and live API queries.
+Author: Gustavo Madeira Santana
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/gumadeiras/orthodb-cli
+Project-URL: Repository, https://github.com/gumadeiras/orthodb-cli
+Project-URL: Issues, https://github.com/gumadeiras/orthodb-cli/issues
+Keywords: orthodb,orthologs,bioinformatics,cli
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: release
+Requires-Dist: build>=1.2.2; extra == "release"
+Requires-Dist: twine>=6.1.0; extra == "release"
+Dynamic: license-file
+
+# orthodb
+
+Agent-friendly CLI for OrthoDB v12.
+
+Repo:
+
+```text
+https://github.com/gumadeiras/orthodb-cli
+```
+
+Goals:
+
+- cache official OrthoDB flat files locally with checksums
+- answer common lookups from cached data when available
+- fall back to the live OrthoDB URL API when local data is missing or too large
+- emit machine-readable JSON by default for API responses and cache metadata
+- stay easy to package for Homebrew
+
+## Install
+
+Homebrew:
+
+```bash
+brew tap gumadeiras/tap
+brew install orthodb
+```
+
+PyPI with `pipx`:
+
+```bash
+pipx install orthodb
+```
+
+PyPI with plain `pip`:
+
+```bash
+python3 -m pip install orthodb
+```
+
+From source:
+
+```bash
+python3 -m venv .venv
+. .venv/bin/activate
+python -m pip install -e .
+```
+
+## Examples
+
+```bash
+orthodb version
+orthodb search p450 --level 33208 --singlecopy 0.8 --take 2
+orthodb group 4977at9604
+orthodb orthologs 4977at9604 --species 9606_0,10090_0
+orthodb fasta 4977at9604 --species 9606_0 --output group.fa
+orthodb cache manifest
+orthodb cache download species
+orthodb cache plan orthologs
+orthodb cache index species
+orthodb cache sync minimal --index
+orthodb resolve 4977at9604
+orthodb local species "Homo sapiens"
+orthodb local og "olfactory"
+orthodb export ogs --query "olfactory receptor" --limit 10
+```
+
+`/blast`, `/fasta`, and `/tab` calls are rate-limited to one request per
+second, matching OrthoDB's published API guidance.
+
+## Cache
+
+Default cache root:
+
+```text
+$XDG_CACHE_HOME/orthodb-cli
+```
+
+or:
+
+```text
+~/.cache/orthodb-cli
+```
+
+Override with:
+
+```bash
+orthodb --cache-dir /path/to/cache cache status
+```
+
+The flat-file manifest is read from:
+
+```text
+https://data.orthodb.org/current/download/odb_data_dump
+```
+
+Large data files are intentionally not auto-downloaded. Use
+`orthodb cache manifest` first, then download a named dataset.
+
+Curated sync profiles:
+
+- `minimal`: species, levels, level-to-species
+- `annotations`: minimal metadata plus OG annotations
+- `orthologs`: OG tables, skipping multi-GB files unless `--include-large`
+
+Build a local SQLite index from downloaded files:
+
+```bash
+orthodb cache index all
+orthodb cache db
+```
+
+Indexed local queries:
+
+```bash
+orthodb local species "Homo sapiens"
+orthodb local og "Cytochrome P450"
+orthodb local gene P12345
+orthodb local orthologs 4977at9604
+orthodb export species --query "Homo sapiens" --limit 2
+```
+
+`export` emits newline-delimited JSON from the local SQLite index, capped by
+`--limit`.
+
+Resolve IDs before choosing a query path:
+
+```bash
+orthodb resolve 4977at9604
+orthodb resolve 9606_0:0017fc
+orthodb resolve P12345
+```
+
+## Release
+
+Current release: `v0.1.1`.
+
+Tag pushes like `vX.Y.Z` run the release workflow: build artifacts, create a
+GitHub release, publish to PyPI, and update `gumadeiras/homebrew-tap`.
+
+Release prerequisites:
+
+- PyPI trusted publishing configured for this repo.
+- `HOMEBREW_TAP_TOKEN` repository secret can write to
+  `gumadeiras/homebrew-tap`.
+
+Release artifacts are attached to GitHub releases for Homebrew packaging:
+
+```text
+https://github.com/gumadeiras/orthodb-cli/releases
+```
+
+## Source Notes
+
+Primary references:
+
+- OrthoDB v12 user guide and URL API: <https://www.ezlab.org/orthodb_v12_userguide.html#api>
+- OrthoDB current flat files: <https://data.orthodb.org/current/download/odb_data_dump>
+- OrthoDB-py: <https://gitlab.com/ezlab/orthodb_py>
+
+The official Python package is useful reference material, but this CLI uses
+direct HTTP calls and local flat files for a smaller runtime surface and simpler
+Homebrew packaging.

orthodb-0.1.3/README.md

@@ -0,0 +1,162 @@
+# orthodb
+
+Agent-friendly CLI for OrthoDB v12.
+
+Repo:
+
+```text
+https://github.com/gumadeiras/orthodb-cli
+```
+
+Goals:
+
+- cache official OrthoDB flat files locally with checksums
+- answer common lookups from cached data when available
+- fall back to the live OrthoDB URL API when local data is missing or too large
+- emit machine-readable JSON by default for API responses and cache metadata
+- stay easy to package for Homebrew
+
+## Install
+
+Homebrew:
+
+```bash
+brew tap gumadeiras/tap
+brew install orthodb
+```
+
+PyPI with `pipx`:
+
+```bash
+pipx install orthodb
+```
+
+PyPI with plain `pip`:
+
+```bash
+python3 -m pip install orthodb
+```
+
+From source:
+
+```bash
+python3 -m venv .venv
+. .venv/bin/activate
+python -m pip install -e .
+```
+
+## Examples
+
+```bash
+orthodb version
+orthodb search p450 --level 33208 --singlecopy 0.8 --take 2
+orthodb group 4977at9604
+orthodb orthologs 4977at9604 --species 9606_0,10090_0
+orthodb fasta 4977at9604 --species 9606_0 --output group.fa
+orthodb cache manifest
+orthodb cache download species
+orthodb cache plan orthologs
+orthodb cache index species
+orthodb cache sync minimal --index
+orthodb resolve 4977at9604
+orthodb local species "Homo sapiens"
+orthodb local og "olfactory"
+orthodb export ogs --query "olfactory receptor" --limit 10
+```
+
+`/blast`, `/fasta`, and `/tab` calls are rate-limited to one request per
+second, matching OrthoDB's published API guidance.
+
+## Cache
+
+Default cache root:
+
+```text
+$XDG_CACHE_HOME/orthodb-cli
+```
+
+or:
+
+```text
+~/.cache/orthodb-cli
+```
+
+Override with:
+
+```bash
+orthodb --cache-dir /path/to/cache cache status
+```
+
+The flat-file manifest is read from:
+
+```text
+https://data.orthodb.org/current/download/odb_data_dump
+```
+
+Large data files are intentionally not auto-downloaded. Use
+`orthodb cache manifest` first, then download a named dataset.
+
+Curated sync profiles:
+
+- `minimal`: species, levels, level-to-species
+- `annotations`: minimal metadata plus OG annotations
+- `orthologs`: OG tables, skipping multi-GB files unless `--include-large`
+
+Build a local SQLite index from downloaded files:
+
+```bash
+orthodb cache index all
+orthodb cache db
+```
+
+Indexed local queries:
+
+```bash
+orthodb local species "Homo sapiens"
+orthodb local og "Cytochrome P450"
+orthodb local gene P12345
+orthodb local orthologs 4977at9604
+orthodb export species --query "Homo sapiens" --limit 2
+```
+
+`export` emits newline-delimited JSON from the local SQLite index, capped by
+`--limit`.
+
+Resolve IDs before choosing a query path:
+
+```bash
+orthodb resolve 4977at9604
+orthodb resolve 9606_0:0017fc
+orthodb resolve P12345
+```
+
+## Release
+
+Current release: `v0.1.1`.
+
+Tag pushes like `vX.Y.Z` run the release workflow: build artifacts, create a
+GitHub release, publish to PyPI, and update `gumadeiras/homebrew-tap`.
+
+Release prerequisites:
+
+- PyPI trusted publishing configured for this repo.
+- `HOMEBREW_TAP_TOKEN` repository secret can write to
+  `gumadeiras/homebrew-tap`.
+
+Release artifacts are attached to GitHub releases for Homebrew packaging:
+
+```text
+https://github.com/gumadeiras/orthodb-cli/releases
+```
+
+## Source Notes
+
+Primary references:
+
+- OrthoDB v12 user guide and URL API: <https://www.ezlab.org/orthodb_v12_userguide.html#api>
+- OrthoDB current flat files: <https://data.orthodb.org/current/download/odb_data_dump>
+- OrthoDB-py: <https://gitlab.com/ezlab/orthodb_py>
+
+The official Python package is useful reference material, but this CLI uses
+direct HTTP calls and local flat files for a smaller runtime surface and simpler
+Homebrew packaging.

orthodb-0.1.3/pyproject.toml

@@ -0,0 +1,45 @@
+[build-system]
+requires = ["setuptools>=69"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "orthodb"
+dynamic = ["version"]
+description = "Agent-friendly CLI for cached OrthoDB downloads and live API queries."
+readme = "README.md"
+requires-python = ">=3.11"
+license = "MIT"
+authors = [{ name = "Gustavo Madeira Santana" }]
+keywords = ["orthodb", "orthologs", "bioinformatics", "cli"]
+dependencies = []
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Environment :: Console",
+  "Intended Audience :: Science/Research",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.optional-dependencies]
+release = [
+  "build>=1.2.2",
+  "twine>=6.1.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/gumadeiras/orthodb-cli"
+Repository = "https://github.com/gumadeiras/orthodb-cli"
+Issues = "https://github.com/gumadeiras/orthodb-cli/issues"
+
+[project.scripts]
+orthodb = "orthodb_cli.cli:main"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.dynamic]
+version = {attr = "orthodb_cli.__version__"}
+
+[tool.setuptools.packages.find]
+where = ["src"]

orthodb-0.1.3/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

orthodb-0.1.3/src/orthodb.egg-info/PKG-INFO

@@ -0,0 +1,186 @@
+Metadata-Version: 2.4
+Name: orthodb
+Version: 0.1.3
+Summary: Agent-friendly CLI for cached OrthoDB downloads and live API queries.
+Author: Gustavo Madeira Santana
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/gumadeiras/orthodb-cli
+Project-URL: Repository, https://github.com/gumadeiras/orthodb-cli
+Project-URL: Issues, https://github.com/gumadeiras/orthodb-cli/issues
+Keywords: orthodb,orthologs,bioinformatics,cli
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: release
+Requires-Dist: build>=1.2.2; extra == "release"
+Requires-Dist: twine>=6.1.0; extra == "release"
+Dynamic: license-file
+
+# orthodb
+
+Agent-friendly CLI for OrthoDB v12.
+
+Repo:
+
+```text
+https://github.com/gumadeiras/orthodb-cli
+```
+
+Goals:
+
+- cache official OrthoDB flat files locally with checksums
+- answer common lookups from cached data when available
+- fall back to the live OrthoDB URL API when local data is missing or too large
+- emit machine-readable JSON by default for API responses and cache metadata
+- stay easy to package for Homebrew
+
+## Install
+
+Homebrew:
+
+```bash
+brew tap gumadeiras/tap
+brew install orthodb
+```
+
+PyPI with `pipx`:
+
+```bash
+pipx install orthodb
+```
+
+PyPI with plain `pip`:
+
+```bash
+python3 -m pip install orthodb
+```
+
+From source:
+
+```bash
+python3 -m venv .venv
+. .venv/bin/activate
+python -m pip install -e .
+```
+
+## Examples
+
+```bash
+orthodb version
+orthodb search p450 --level 33208 --singlecopy 0.8 --take 2
+orthodb group 4977at9604
+orthodb orthologs 4977at9604 --species 9606_0,10090_0
+orthodb fasta 4977at9604 --species 9606_0 --output group.fa
+orthodb cache manifest
+orthodb cache download species
+orthodb cache plan orthologs
+orthodb cache index species
+orthodb cache sync minimal --index
+orthodb resolve 4977at9604
+orthodb local species "Homo sapiens"
+orthodb local og "olfactory"
+orthodb export ogs --query "olfactory receptor" --limit 10
+```
+
+`/blast`, `/fasta`, and `/tab` calls are rate-limited to one request per
+second, matching OrthoDB's published API guidance.
+
+## Cache
+
+Default cache root:
+
+```text
+$XDG_CACHE_HOME/orthodb-cli
+```
+
+or:
+
+```text
+~/.cache/orthodb-cli
+```
+
+Override with:
+
+```bash
+orthodb --cache-dir /path/to/cache cache status
+```
+
+The flat-file manifest is read from:
+
+```text
+https://data.orthodb.org/current/download/odb_data_dump
+```
+
+Large data files are intentionally not auto-downloaded. Use
+`orthodb cache manifest` first, then download a named dataset.
+
+Curated sync profiles:
+
+- `minimal`: species, levels, level-to-species
+- `annotations`: minimal metadata plus OG annotations
+- `orthologs`: OG tables, skipping multi-GB files unless `--include-large`
+
+Build a local SQLite index from downloaded files:
+
+```bash
+orthodb cache index all
+orthodb cache db
+```
+
+Indexed local queries:
+
+```bash
+orthodb local species "Homo sapiens"
+orthodb local og "Cytochrome P450"
+orthodb local gene P12345
+orthodb local orthologs 4977at9604
+orthodb export species --query "Homo sapiens" --limit 2
+```
+
+`export` emits newline-delimited JSON from the local SQLite index, capped by
+`--limit`.
+
+Resolve IDs before choosing a query path:
+
+```bash
+orthodb resolve 4977at9604
+orthodb resolve 9606_0:0017fc
+orthodb resolve P12345
+```
+
+## Release
+
+Current release: `v0.1.1`.
+
+Tag pushes like `vX.Y.Z` run the release workflow: build artifacts, create a
+GitHub release, publish to PyPI, and update `gumadeiras/homebrew-tap`.
+
+Release prerequisites:
+
+- PyPI trusted publishing configured for this repo.
+- `HOMEBREW_TAP_TOKEN` repository secret can write to
+  `gumadeiras/homebrew-tap`.
+
+Release artifacts are attached to GitHub releases for Homebrew packaging:
+
+```text
+https://github.com/gumadeiras/orthodb-cli/releases
+```
+
+## Source Notes
+
+Primary references:
+
+- OrthoDB v12 user guide and URL API: <https://www.ezlab.org/orthodb_v12_userguide.html#api>
+- OrthoDB current flat files: <https://data.orthodb.org/current/download/odb_data_dump>
+- OrthoDB-py: <https://gitlab.com/ezlab/orthodb_py>
+
+The official Python package is useful reference material, but this CLI uses
+direct HTTP calls and local flat files for a smaller runtime surface and simpler
+Homebrew packaging.

orthodb-0.1.3/src/orthodb.egg-info/SOURCES.txt

@@ -0,0 +1,21 @@
+LICENSE
+README.md
+pyproject.toml
+src/orthodb.egg-info/PKG-INFO
+src/orthodb.egg-info/SOURCES.txt
+src/orthodb.egg-info/dependency_links.txt
+src/orthodb.egg-info/entry_points.txt
+src/orthodb.egg-info/requires.txt
+src/orthodb.egg-info/top_level.txt
+src/orthodb_cli/__init__.py
+src/orthodb_cli/cache.py
+src/orthodb_cli/cli.py
+src/orthodb_cli/client.py
+src/orthodb_cli/db.py
+src/orthodb_cli/errors.py
+src/orthodb_cli/identify.py
+src/orthodb_cli/local.py
+tests/test_cache.py
+tests/test_client.py
+tests/test_db.py
+tests/test_identify.py

orthodb-0.1.3/src/orthodb.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

orthodb-0.1.3/src/orthodb.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+orthodb = orthodb_cli.cli:main

orthodb-0.1.3/src/orthodb.egg-info/requires.txt

@@ -0,0 +1,4 @@
+
+[release]
+build>=1.2.2
+twine>=6.1.0

orthodb-0.1.3/src/orthodb.egg-info/top_level.txt

@@ -0,0 +1 @@
+orthodb_cli

orthodb-0.1.3/src/orthodb_cli/__init__.py

@@ -0,0 +1,3 @@
+"""Command-line tools for OrthoDB."""
+
+__version__ = "0.1.3"