tacular-omics 0.1.0__tar.gz

tacular_omics-0.1.0/.github/copilot-instructions.md

@@ -0,0 +1,13 @@
+# Copilot instructions
+
+The canonical guide for AI agents in this repo is [`CLAUDE.md`](../CLAUDE.md). Read it
+first. The rules that matter most:
+
+1. This is a meta-package: no functionality beyond `versions()`. Do not add features;
+   they belong in a member package.
+2. Every member dependency has a floor and a cap (`peptacular>=4.2,<5`,
+   `mzmlpy>=0.9.3,<0.10`). Keep `PACKAGES` in `src/tacular_omics/__init__.py` in step
+   with `[project] dependencies`.
+3. Before pushing, run what CI runs:
+   `uv run ruff check src tests scripts/smoke.py && uv run ruff format --check src tests scripts/smoke.py && uv run ty check src && uv run pytest tests`.
+4. Never bump the version, tag or publish: only the tacular-omics overseer releases.

tacular_omics-0.1.0/.github/dependabot.yml

@@ -0,0 +1,16 @@
+version: 2
+updates:
+  - package-ecosystem: uv
+    directory: /
+    schedule:
+      interval: weekly
+    groups:
+      python-dependencies:
+        patterns: ["*"]
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    groups:
+      github-actions:
+        patterns: ["*"]

tacular_omics-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,85 @@
+# Standard tacular-omics CI (canonical copy: tacular-omics workspace templates/),
+# adapted for the meta-package: the tests are install smoke tests, and the extra
+# jobs install the built wheel into a fresh environment from PyPI, like a user would.
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # Weekly: catches a member release inside the caps that breaks the set.
+    - cron: "0 6 * * 1"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+      - run: uv sync --locked --all-extras --all-groups
+      - run: uv run ruff check src tests scripts/smoke.py
+      - run: uv run ruff format --check src tests scripts/smoke.py
+      - run: uv run ty check src
+      - run: python scripts/release_version.py check
+
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python: ["3.12", "3.13", "3.14"]
+        include:
+          - { os: macos-latest, python: "3.13" }
+          - { os: windows-latest, python: "3.13" }
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+        with:
+          python-version: ${{ matrix.python }}
+      - run: uv sync --locked --all-extras --all-groups
+      - run: uv run pytest tests
+
+  # The floors are the tested releases: install exactly those.
+  lowest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+        with:
+          python-version: "3.12"
+      - run: uv sync --resolution lowest-direct --all-groups
+      - run: uv run pytest tests
+
+  # Build the wheel, install it into a fresh environment from PyPI (no lock file,
+  # newest versions inside the caps) and import every member.
+  wheel:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        extra: ["", "[all]"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+        with:
+          python-version: "3.13"
+      - run: uv build
+      - run: python scripts/release_version.py check --dist dist
+      - name: Smoke test the built wheel outside the checkout
+        shell: bash
+        working-directory: ${{ runner.temp }}
+        run: |
+          whl=$(ls "${{ github.workspace }}"/dist/*.whl)
+          uv run --isolated --no-project --with "${whl}${{ matrix.extra }}" python "${{ github.workspace }}/scripts/smoke.py"
+          uv run --isolated --no-project --with "${whl}${{ matrix.extra }}" python -m tacular_omics

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

@@ -0,0 +1,46 @@
+# Standard tacular-omics release. Canonical copy: tacular-omics workspace templates/.
+# Runs when a GitHub release is published. Publishes with PyPI trusted publishing:
+# the PyPI project must list this repo, workflow "publish.yml", environment "pypi".
+name: Publish
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+      - name: Release tag, version and changelog agree
+        run: python scripts/release_version.py check --tag "${{ github.event.release.tag_name }}"
+      - run: uv sync --locked --all-extras --all-groups
+      - run: uv run ruff check src tests
+      - run: uv run ty check src
+      - run: uv run pytest tests
+      - run: uv build
+      - name: Smoke test the built wheel outside the checkout
+        working-directory: ${{ runner.temp }}
+        run: uv run --isolated --no-project --with "$(ls ${{ github.workspace }}/dist/*.whl)" python "${{ github.workspace }}/scripts/smoke.py"
+      - run: python scripts/release_version.py check --tag "${{ github.event.release.tag_name }}" --dist dist
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2

tacular_omics-0.1.0/.gitignore

@@ -0,0 +1,83 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+junit.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# uv
+.venv
+
+# ruff
+.ruff_cache/
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# editors
+.vscode/
+.idea/

tacular_omics-0.1.0/.zenodo.json

@@ -0,0 +1,43 @@
+{
+  "title": "tacular-omics: Install the tacular-omics proteomics packages together",
+  "description": "tacular-omics is a meta-package that installs the tacular-omics core Python packages for mass-spectrometry proteomics (tacular, psimodpy, unimodpy, uniprotptmpy, fastatacular, pefftacular, mzmlpy, tdfpy, peptacular, paftacular and spxtacular) at a set of released versions tested together, each pinned with a floor and a major-version cap. It has no functionality of its own beyond reporting the installed member versions. It requires Python 3.12 or later.",
+  "creators": [
+    {
+      "name": "Garrett, Patrick T.",
+      "orcid": "0000-0002-8434-9693",
+      "affiliation": "Scripps Research Institute"
+    },
+    {
+      "name": "Yates, John R. III",
+      "orcid": "0000-0001-5267-1672",
+      "affiliation": "Scripps Research Institute"
+    }
+  ],
+  "upload_type": "software",
+  "access_right": "open",
+  "license": "mit",
+  "language": "eng",
+  "keywords": [
+    "Python",
+    "Proteomics",
+    "Mass spectrometry",
+    "Bioinformatics"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "https://github.com/tacular-omics/tacular-omics",
+      "relation": "isSupplementTo",
+      "scheme": "url"
+    },
+    {
+      "identifier": "https://pypi.org/project/tacular-omics/",
+      "relation": "isAlternateIdentifier",
+      "scheme": "url"
+    }
+  ],
+  "communities": [
+    {
+      "identifier": "proteomics"
+    }
+  ]
+}

tacular_omics-0.1.0/AGENTS.md

@@ -0,0 +1,6 @@
+# AGENTS.md
+
+See [`CLAUDE.md`](CLAUDE.md) for the guide for AI coding agents working in this repo
+(commands, layout, pins, releasing). That file is
+canonical; this one exists because some tools look for `AGENTS.md` specifically.
+Users of the library: see [`llms.txt`](llms.txt) and [`llms-full.txt`](llms-full.txt).

tacular_omics-0.1.0/CHANGELOG.md

@@ -0,0 +1,16 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [Unreleased]
+
+## [0.1.0] (2026-09-24)
+
+### Added
+
+- First release. Installs the tacular-omics core packages at their current released
+  versions: tacular 1.2, psimodpy 1.0, unimodpy 1.0, uniprotptmpy 1.0, fastatacular
+  1.0, pefftacular 1.0, mzmlpy 0.9.3, tdfpy 4.1.1, peptacular 4.2, paftacular 1.4,
+  spxtacular 0.8. Extras `mcp` and `all`.
+- `tacular_omics.versions()` and `python -m tacular_omics` report the installed
+  version of each member package.

tacular_omics-0.1.0/CITATION.cff

@@ -0,0 +1,31 @@
+cff-version: 1.2.0
+message: "Please cite the member packages you use; each has its own CITATION.cff and Zenodo DOI (see README)."
+type: software
+title: "tacular-omics: Install the tacular-omics proteomics packages together"
+abstract: >-
+  tacular-omics is a meta-package that installs the tacular-omics core Python
+  packages for mass-spectrometry proteomics (tacular, psimodpy, unimodpy,
+  uniprotptmpy, fastatacular, pefftacular, mzmlpy, tdfpy, peptacular,
+  paftacular and spxtacular) at a set of released versions tested together,
+  each pinned with a floor and a major-version cap. It has no functionality of
+  its own beyond reporting the installed member versions. It requires Python
+  3.12 or later.
+version: "0.1.0"
+date-released: "2026-09-24"
+authors:
+  - family-names: Garrett
+    given-names: Patrick T.
+    orcid: https://orcid.org/0000-0002-8434-9693
+    affiliation: Scripps Research Institute
+  - family-names: Yates
+    given-names: John R.
+    name-suffix: III
+    orcid: https://orcid.org/0000-0001-5267-1672
+    affiliation: Scripps Research Institute
+repository-code: https://github.com/tacular-omics/tacular-omics
+license: MIT
+keywords:
+  - Python
+  - Proteomics
+  - Mass spectrometry
+  - Bioinformatics

tacular_omics-0.1.0/CLAUDE.md

@@ -0,0 +1,84 @@
+# tacular-omics — Claude Code Guide
+
+## Project overview
+
+`tacular-omics` is a meta-package: `pip install tacular-omics` installs every core
+tacular-omics package at a set of released versions tested together. It has no
+functionality of its own beyond `versions()` and `python -m tacular_omics`, which report
+the installed member versions.
+
+Place in the tacular-omics graph: the top. It depends on all eleven core packages
+(tacular, psimodpy, unimodpy, uniprotptmpy, fastatacular, pefftacular, mzmlpy, tdfpy,
+peptacular, paftacular, spxtacular) and nothing depends on it. It is always released
+**last** in a batch, after every member it pins is on PyPI.
+
+## Commands
+
+```bash
+just install        # uv sync --all-extras
+just lint           # ruff check src tests scripts/smoke.py
+just format         # ruff isort fix + ruff format -- WRITES FILES
+just ty             # ty check src
+just test           # pytest tests (imports every member, checks pins)
+just check          # lint + ty + test
+just smoke          # build the wheel, install it fresh from PyPI, import every member
+just check-version  # python scripts/release_version.py check
+```
+
+CI (`.github/workflows/ci.yml`): lint, pytest on 3.12-3.14 + macOS/Windows from the
+lock, a lowest-direct run (the floors), and a `wheel` job that installs the built wheel
+(plain and `[all]`) into a fresh env from PyPI on Linux/macOS/Windows and runs
+`scripts/smoke.py`. CI also runs weekly, to catch a member release inside the caps that
+breaks the set.
+
+## Architecture
+
+```
+src/tacular_omics/
+  __init__.py   # __version__ (version source), PACKAGES (member names, dependency order), versions()
+  __main__.py   # main(): prints the versions; exit 1 if a member is missing. Also the `tacular-omics` script
+tests/test_members.py   # PACKAGES == dependencies, every member imports, installed versions satisfy the pins
+scripts/smoke.py        # import every member from an installed wheel (CI wheel job, publish.yml)
+scripts/release_version.py  # version sync/check, byte-identical copy of the workspace template
+```
+
+## Public API
+
+- `tacular_omics.versions() -> dict[str, str | None]`: installed version of each member
+  (`None` if missing), from `importlib.metadata`; imports nothing.
+- `tacular_omics.PACKAGES`: member distribution names in dependency order.
+- `tacular_omics.__version__`.
+
+## Conventions
+
+- **Pins**: every member in `[project] dependencies` has a floor (the released version
+  of the tested set) and a cap (next major, or next minor for 0.x), per the workspace
+  sibling pin policy. The `mcp` and `all` extras repeat the same specifiers.
+- `PACKAGES` must list exactly the `dependencies` names in the same order (a test
+  enforces it). Distribution name == import name for every member.
+- Ruff rules E, W, F, I, B, UP; line length 120; `ty check src` clean.
+
+## Gotchas
+
+- Inside the workspace, the members resolve to the local checkouts, so
+  `test_installed_versions_satisfy_pins` fails as soon as a local member is bumped past
+  a cap. That is the signal to raise the pins in the next tacular-omics release.
+- Extras names differ per member: the MCP server extra is `server` for psimodpy,
+  unimodpy and uniprotptmpy, and `mcp` elsewhere. tacular, fastatacular, pefftacular and
+  spxtacular have no MCP server.
+
+## Releasing
+
+Only the tacular-omics overseer bumps versions or publishes. See `just --list`
+(`set-version`, `sync-version`, `check-version`) and the workspace CLAUDE.md release
+checklist. Version source: `__version__` in `src/tacular_omics/__init__.py`
+(`[tool.hatch.version]`), mirrored in `CITATION.cff` by `scripts/release_version.py`.
+A release raises the pins to the member versions just released, then refreshes
+`uv.lock` (`just lock tacular-omics` from the workspace root). Publishing is
+`publish.yml` on a GitHub release (PyPI trusted publishing, environment `pypi`).
+
+## Workspace note
+
+This repo is also developed inside the tacular-omics uv workspace
+(`~/Repos/tacular-omics/packages/tacular-omics`); there `uv run` uses the shared
+`.venv` and root `uv.lock`, not this repo's `uv.lock`. See the workspace CLAUDE.md.

tacular_omics-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Patrick Garrett
+
+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.

tacular_omics-0.1.0/PKG-INFO

@@ -0,0 +1,143 @@
+Metadata-Version: 2.5
+Name: tacular-omics
+Version: 0.1.0
+Summary: Install the tacular-omics proteomics packages together.
+Project-URL: Homepage, https://github.com/tacular-omics/tacular-omics
+Project-URL: Documentation, https://github.com/tacular-omics/tacular-omics#readme
+Project-URL: Repository, https://github.com/tacular-omics/tacular-omics
+Project-URL: Issues, https://github.com/tacular-omics/tacular-omics/issues
+Project-URL: Changelog, https://github.com/tacular-omics/tacular-omics/blob/main/CHANGELOG.md
+Author-email: Patrick Garrett <pgarrett@scripps.edu>
+Maintainer-email: Patrick Garrett <pgarrett@scripps.edu>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: bioinformatics,fasta,mass spectrometry,mzml,mzpaf,proforma,proteomics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.12
+Requires-Dist: fastatacular<2,>=1.0
+Requires-Dist: mzmlpy<0.10,>=0.9.3
+Requires-Dist: paftacular<2,>=1.4
+Requires-Dist: pefftacular<2,>=1.0
+Requires-Dist: peptacular<5,>=4.2
+Requires-Dist: psimodpy<2,>=1.0
+Requires-Dist: spxtacular<0.9,>=0.8
+Requires-Dist: tacular<2,>=1.2
+Requires-Dist: tdfpy<5,>=4.1.1
+Requires-Dist: unimodpy<2,>=1.0
+Requires-Dist: uniprotptmpy<2,>=1.0
+Provides-Extra: all
+Requires-Dist: mzmlpy[mcp]<0.10,>=0.9.3; extra == 'all'
+Requires-Dist: mzmlpy[numpress,rapidgzip,zstd]<0.10,>=0.9.3; extra == 'all'
+Requires-Dist: paftacular[all]<2,>=1.4; extra == 'all'
+Requires-Dist: paftacular[mcp]<2,>=1.4; extra == 'all'
+Requires-Dist: peptacular[interop]<5,>=4.2; extra == 'all'
+Requires-Dist: peptacular[mcp]<5,>=4.2; extra == 'all'
+Requires-Dist: psimodpy[server]<2,>=1.0; extra == 'all'
+Requires-Dist: spxtacular[all]<0.9,>=0.8; extra == 'all'
+Requires-Dist: tdfpy[mcp]<5,>=4.1.1; extra == 'all'
+Requires-Dist: tdfpy[viz]<5,>=4.1.1; extra == 'all'
+Requires-Dist: unimodpy[server]<2,>=1.0; extra == 'all'
+Requires-Dist: uniprotptmpy[server]<2,>=1.0; extra == 'all'
+Provides-Extra: mcp
+Requires-Dist: mzmlpy[mcp]<0.10,>=0.9.3; extra == 'mcp'
+Requires-Dist: paftacular[mcp]<2,>=1.4; extra == 'mcp'
+Requires-Dist: peptacular[mcp]<5,>=4.2; extra == 'mcp'
+Requires-Dist: psimodpy[server]<2,>=1.0; extra == 'mcp'
+Requires-Dist: tdfpy[mcp]<5,>=4.1.1; extra == 'mcp'
+Requires-Dist: unimodpy[server]<2,>=1.0; extra == 'mcp'
+Requires-Dist: uniprotptmpy[server]<2,>=1.0; extra == 'mcp'
+Description-Content-Type: text/markdown
+
+# tacular-omics
+
+[![PyPI](https://img.shields.io/pypi/v/tacular-omics)](https://pypi.org/project/tacular-omics/)
+[![CI](https://github.com/tacular-omics/tacular-omics/actions/workflows/ci.yml/badge.svg)](https://github.com/tacular-omics/tacular-omics/actions/workflows/ci.yml)
+[![License](https://img.shields.io/github/license/tacular-omics/tacular-omics)](https://github.com/tacular-omics/tacular-omics/blob/main/LICENSE)
+[![Python](https://img.shields.io/pypi/pyversions/tacular-omics)](https://pypi.org/project/tacular-omics/)
+
+One install for the [tacular-omics](https://github.com/tacular-omics) proteomics packages.
+`tacular-omics` has no code of its own: it depends on every core package at a set of
+released versions that were tested together. Import the member packages directly.
+
+## Install
+
+```bash
+pip install tacular-omics
+```
+
+Optional extras:
+
+```bash
+pip install "tacular-omics[mcp]"   # the MCP servers of every package that ships one
+pip install "tacular-omics[all]"   # every optional feature of every package
+```
+
+Check what you got:
+
+```bash
+python -m tacular_omics            # or: tacular-omics
+```
+
+```python
+import tacular_omics
+tacular_omics.versions()   # {"tacular": "1.2.0", "psimodpy": "1.0.0", ...}
+```
+
+## Member packages
+
+| Package | What it does |
+|---|---|
+| [tacular](https://github.com/tacular-omics/tacular) | Proteomics ontology and reference-data lookups (UNIMOD, PSI-MOD, elements, amino acids, proteases, ...). |
+| [psimodpy](https://github.com/tacular-omics/psimodpy) | The PSI-MOD protein modification ontology. |
+| [unimodpy](https://github.com/tacular-omics/unimodpy) | Parse and query the UNIMOD modifications database. |
+| [uniprotptmpy](https://github.com/tacular-omics/uniprotptmpy) | Parse and query the UniProt PTM controlled vocabulary. |
+| [fastatacular](https://github.com/tacular-omics/fastatacular) | Read and write FASTA sequence files. |
+| [pefftacular](https://github.com/tacular-omics/pefftacular) | Read and write PEFF (PSI Extended FASTA Format) files. |
+| [mzmlpy](https://github.com/tacular-omics/mzmlpy) | Lightweight mzML mass spectrometry file parser. |
+| [tdfpy](https://github.com/tacular-omics/tdfpy) | Bruker timsTOF (`.d` / TDF) data with centroiding and noise filtering. |
+| [peptacular](https://github.com/tacular-omics/peptacular) | Parse, annotate and analyze ProForma 2.1 peptide and protein sequences. |
+| [paftacular](https://github.com/tacular-omics/paftacular) | Parse, serialize and analyze HUPO-PSI mzPAF peak annotations. |
+| [spxtacular](https://github.com/tacular-omics/spxtacular) | Mass spectrometry spectrum processing. |
+
+## How versions are chosen
+
+Each `tacular-omics` release pins the member packages to the set that was released
+and tested together: every requirement has a floor (the tested release) and a cap (the
+next major version, or the next minor for 0.x packages such as `mzmlpy>=0.9.3,<0.10`).
+You get bug-fix and feature releases of each member automatically, but never a breaking
+release that has not been tested with the others. When the members release a new
+batch, a new `tacular-omics` version raises the pins. The exact pins are in
+[`pyproject.toml`](pyproject.toml).
+
+To use a newer member than the cap allows, install that package without
+`tacular-omics`.
+
+## Citation
+
+Please cite the packages you use, not this installer. Each member repository has a
+`CITATION.cff` (GitHub's "Cite this repository" button) and a Zenodo DOI:
+
+| Package | DOI |
+|---|---|
+| tacular | [10.5281/zenodo.18475556](https://doi.org/10.5281/zenodo.18475556) |
+| psimodpy | [10.5281/zenodo.22926360](https://doi.org/10.5281/zenodo.22926360) |
+| unimodpy | [10.5281/zenodo.22926362](https://doi.org/10.5281/zenodo.22926362) |
+| uniprotptmpy | [10.5281/zenodo.22926364](https://doi.org/10.5281/zenodo.22926364) |
+| fastatacular | [10.5281/zenodo.22926358](https://doi.org/10.5281/zenodo.22926358) |
+| pefftacular | [10.5281/zenodo.22925639](https://doi.org/10.5281/zenodo.22925639) |
+| mzmlpy | [10.5281/zenodo.21960079](https://doi.org/10.5281/zenodo.21960079) |
+| tdfpy | [10.5281/zenodo.19100532](https://doi.org/10.5281/zenodo.19100532) |
+| peptacular | [10.5281/zenodo.15054278](https://doi.org/10.5281/zenodo.15054278) |
+| paftacular | [10.5281/zenodo.19076277](https://doi.org/10.5281/zenodo.19076277) |
+| spxtacular | [10.5281/zenodo.19342437](https://doi.org/10.5281/zenodo.19342437) |
+
+## License
+
+MIT. Each member package has its own license; see its repository.