diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..0726389 --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +.venv/ +.github/ +docs/_build/ +specification/annotation-schema.md diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst new file mode 100644 index 0000000..fb9e4f5 --- /dev/null +++ b/CONTRIBUTING.rst @@ -0,0 +1,55 @@ +############ +Contributing +############ + +This document briefly describes how to contribute to +`mzPAF `_. + + + +Before you begin +################ + +If you have an idea for a feature, use case to add or an approach for a bugfix, +you are welcome to communicate it with the community by opening a +thread in `GitHub Issues `_. + + + +Documentation local setup +######################### + +To work on the documentation and get a live preview, install the requirements +and run ``sphinx-autobuild``: + +.. code-block:: sh + + pip install -r ./docs/requirements.txt + sphinx-autobuild ./docs/ ./docs/_build/ + +Then browse to http://localhost:8000 to watch the live preview. + + + +How to contribute +################# + +- Fork `mzPAF `_ on GitHub to + make your changes. +- Commit and push your changes to your + `fork `_. +- Ensure that the tests and documentation (both Python docstrings and files in + ``/docs/``) have been updated according to your changes. Python + docstrings are formatted in the + `numpydoc style `_. +- Open a + `pull request `_ + with these changes. You pull request message ideally should include: + + - A description of why the changes should be made. + - A description of the implementation of the changes. + - A description of how to test the changes. + +- The pull request should pass all the continuous integration tests which are + automatically run by + `GitHub Actions `_. diff --git a/README.md b/README.md index f504428..16bf026 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,86 @@ # mzPAF Peak Annotation Format -The mzPAF proposed standard is a specification for a fragment ion peak annotation format for mass spectra, focused on peptides. This provides for a standardized format for describing the origin of fragment ions to be used in spectral libraries, other formats that aim to describe fragment ions, and software tools that annotate fragment ions. +## About -The main home page for mzPAF is at the PSI web site: https://psidev.info/mzPAF +The mzPAF proposed standard is a specification for a fragment ion peak annotation format for mass spectra, focused on +peptides. This provides for a standardized format for describing the origin of fragment ions to be used in spectral +libraries, other formats that aim to describe fragment ions, and software tools that annotate fragment ions. -# Status +- Official mzPAF homepage: [psidev.info/mzPAF](https://psidev.info/mzPAF) +- mzPAF documentation: [mzpaf.readthedocs.io](https://mzpaf.readthedocs.io) -Updated: 2023-02-25 -The specification has been submitted to the PSI Document Process and is undergoing review. It will take several months starting January 2023 to undergo rigorous review before potentially becoming a PSI standard. +## Specification status -# Available Materials -- The current DRAFT specification: https://github.com/HUPO-PSI/mzPAF/blob/main/specification/mzPAF_specification_v1.0-draft10.docx?raw=true +Updated: 2023-09-01 + +The specification has been resubmitted to the PSI Document Process and is undergoing final community review. Ratification to formally become a PSI standard is anticipated near the end of 2023. + +Your comments and suggestions are still very much welcome. Please submit an issue at the repo to +provide your feedback and send an e-mail to the HUPO-PSI editor Sylvie Ricard-Blum +(sylvie.ricard-blum@univ-lyon1.fr). + + +## In short + +- mzPAF is a single string of characters, case sensitive, without length limit +- Multiple possible explanations are separated with a comma +- Deltas of observed – theoretical *m/z* values are prefixed with a slash (`/`) +- Confidences can be provided for different annotations prefixed with an asterisk (`*`) + +The basic format of each annotation is: + +``` +annotation1/delta,annotation2/delta,... +``` + +or: + +``` +annotation1/delta*confidence,annotation2/delta*confidence,... +``` + +For example: + +``` +b2-H2O/3.2ppm,b4-H2O^2/3.2ppm +``` + +or: + +``` +b2-H2O/3.2ppm*0.75,b4-H2O^2/3.2ppm*0.25 +``` + +mzPAF supports: + +- Annotations of multiple analytes: `1@y12/0.13,2@b9-NH3/0.23` +- Mass deltas in ppm instead of *m/z* unit: `y1/-1.4ppm` +- Confidence levels per annotation: `y1/-1.4ppm*0.75` +- Advanced ion notation: `[ion type](neutral loss)(isotope)(adduct type)(charge)`, e.g.: `y4-H2O+2i[M+H+Na]^2`: + - Ion types: + - Peptide ion series (a, b, c, x, y, z): `y4` + - Unknown ions: `?` + - Immonium ions: `IY` + - Internal fragment ions: `m3:6` + - Intact precursor ions: `p^2` + - A set of reference ions: `r[TMT127N]` + - Named compounds: `_{Urocanic Acid}` + - Chemical formulas: `f{C16H22O}` + - Smiles: `s{CN=C=O}[M+H]` + - Embedded ProForma annotations: `0@b2{LC[Carbamidomethyl]}` + - Neutral gains and losses: `y2+CO-H2O` + - Isotopes: `y2+2i` + - Adduct types: `y2[M+H]` + - Charge states: `^2` +- Multiple peaks per annotation: `&y7/-0.001` and `y7/0.000*0.95` + +Read the [full specificiation](https://mzpaf.readthedocs.io/specification) for more details and +examples. + + +### Available Materials +- The current DRAFT specification: https://github.com/HUPO-PSI/mzPAF/blob/main/specification/mzPAF_specification_v1.0-draft14.docx?raw=true - The GitHub repo associated with mzPAF: https://github.com/HUPO-PSI/mzPAF -- The GitHub repo assocated with the related mzSpecLib standard: https://github.com/HUPO-PSI/mzSpecLib +- The GitHub repo associated with the related mzSpecLib standard: https://github.com/HUPO-PSI/mzSpecLib diff --git a/docs/.readthedocs.yaml b/docs/.readthedocs.yaml new file mode 100644 index 0000000..31c93e2 --- /dev/null +++ b/docs/.readthedocs.yaml @@ -0,0 +1,21 @@ +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.11" + +sphinx: + configuration: docs/conf.py + builder: dirhtml + +formats: + - pdf + - epub + +python: + install: + - method: pip + path: implementations/python + extra_requirements: + - docs diff --git a/docs/LICENSE.txt b/docs/LICENSE.txt new file mode 100644 index 0000000..1eaa3b0 --- /dev/null +++ b/docs/LICENSE.txt @@ -0,0 +1,435 @@ +Attribution-NonCommercial-ShareAlike 4.0 International + +======================================================================= + +Creative Commons Corporation ("Creative Commons") is not a law firm and +does not provide legal services or legal advice. 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For +the avoidance of doubt, this paragraph does not form part of the public +licenses. + +Creative Commons may be contacted at creativecommons.org. diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css new file mode 100644 index 0000000..01f2deb --- /dev/null +++ b/docs/_static/css/custom.css @@ -0,0 +1,20 @@ +@import url('https://fonts.googleapis.com/css2?family=Open+Sans&family=Roboto+Slab:wght@500&display=swap'); + +html { + --pst-font-family-base: 'Open Sans', sans-serif; + --pst-font-family-heading: 'Roboto Slab', serif; + --pst-font-weight-heading: 500; +} + +html[data-theme="light"] { + --pst-color-primary: #3b5880; +} + +html[data-theme="dark"] { + --pst-color-primary: #5c87c2; + +} + +a:visited { + color: var(--pst-color-link); +} diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..78c58bf --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,74 @@ +"""Configuration file for the Sphinx documentation builder.""" + +# Scripts +import json +import jsonschema2md + +def get_jsonschema_docs(input_json, output_markdown): + """Generate markdown documentation from a JSON schema.""" + parser = jsonschema2md.Parser() + with open(input_json, encoding="utf-8") as f_in: + output_md = parser.parse_schema(json.load(f_in)) + + with open(output_markdown, "w", encoding="utf-8") as f_out: + f_out.writelines(output_md) + +get_jsonschema_docs( + "../specification/annotation-schema.json", + "../specification/annotation-schema.md" +) + + +# Project information +project = "mzPAF" +author = "HUPO-PSI" +github_project_url = "https://github.com/HUPO-PSI/mzPAF" +github_doc_root = "https://github.com/HUPO-PSI/mzPAF/tree/master/docs" + +# General configuration +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.autosectionlabel", + "sphinx.ext.autosummary", + "sphinx.ext.napoleon", + "sphinx.ext.intersphinx", + "sphinx_click.ext", + "myst_parser", +] +source_suffix = [".rst", ".md"] +master_doc = "index" +exclude_patterns = ["_build"] + +# Options for HTML output +html_theme = "pydata_sphinx_theme" +html_static_path = ["_static"] +html_css_files = ["css/custom.css"] +html_theme_options = { + "icon_links": [ + { + "name": "GitHub", + "url": "https://github.com/HUPO-PSI/mzPAF", + "icon": "fa-brands fa-github", + "type": "fontawesome", + } + ] +} + +# Autodoc options +autodoc_default_options = {"members": True, "show-inheritance": True} +autodoc_member_order = "bysource" +autodoc_typehints = "description" +autoclass_content = "init" + +# Intersphinx options +intersphinx_mapping = { + "python": ("https://docs.python.org/3", None), + "psims": ("https://mobiusklein.github.io/psims/docs/build/html/", None), + "pyteomics": ("https://pyteomics.readthedocs.io/en/stable/", None), +} + + +def setup(app): + config = {"enable_eval_rst": True} # noqa: F841 + + diff --git a/docs/contributing.rst b/docs/contributing.rst new file mode 100644 index 0000000..a021d3e --- /dev/null +++ b/docs/contributing.rst @@ -0,0 +1 @@ +.. include:: ../CONTRIBUTING.rst diff --git a/docs/implementations/index.rst b/docs/implementations/index.rst new file mode 100644 index 0000000..ebb51a9 --- /dev/null +++ b/docs/implementations/index.rst @@ -0,0 +1,11 @@ +############### +Implementations +############### + +.. toctree:: + :caption: Contents + :maxdepth: 2 + :glob: + + */index + diff --git a/docs/implementations/json/index.rst b/docs/implementations/json/index.rst new file mode 100644 index 0000000..c4ec07d --- /dev/null +++ b/docs/implementations/json/index.rst @@ -0,0 +1,36 @@ +########### +JSON Schema +########### + +About +===== + +Instead of representing mzPAF as a single string, it can alternatively be expressed as a JSON +object. This format is more compatible for inter-program communication, especially through web +APIs. You can find the JSON schema for mzPAF on GitHub via the following link: + +https://raw.githubusercontent.com/HUPO-PSI/mzPAF/main/specification/annotation-schema.json + +Replace ``main`` in the URL with the desired version tag to access the schema for a particular +version. + +Examples +======== + +.. literalinclude:: ../../../specification/annotation-example-1.json + :language: json + +.. literalinclude:: ../../../specification/annotation-example-2.json + :language: json + +.. literalinclude:: ../../../specification/annotation-example-3.json + :language: json + + + +Full schema documentation +========================= + +.. include:: ../../../specification/annotation-schema.md + :parser: myst_parser.sphinx_ + :start-line: 4 diff --git a/docs/implementations/python/api.rst b/docs/implementations/python/api.rst new file mode 100644 index 0000000..f88fe3c --- /dev/null +++ b/docs/implementations/python/api.rst @@ -0,0 +1,7 @@ +********** +Python API +********** + +.. automodule:: mzpaf + :members: + :imported-members: diff --git a/docs/implementations/python/index.rst b/docs/implementations/python/index.rst new file mode 100644 index 0000000..fb7e568 --- /dev/null +++ b/docs/implementations/python/index.rst @@ -0,0 +1,20 @@ +##################### +Python implementation +##################### + +About +===== + +.. include:: ../../../implementations/python/README.md + :parser: myst_parser.sphinx_ + + +Full API documentation +====================== + +.. toctree:: + :caption: Contents + :maxdepth: 2 + :glob: + + * diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..b9b2c5a --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,13 @@ +.. include:: ../README.md + :parser: myst_parser.sphinx_ + +.. toctree:: + :caption: About + :hidden: + :includehidden: + :glob: + + Home + specification/index + implementations/index + contributing diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..62e5ab6 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,7 @@ +sphinx +pydata-sphinx-theme +numpydoc +sphinx_click +myst-parser +sphinx-autobuild +jsonschema2md diff --git a/docs/specification/index.rst b/docs/specification/index.rst new file mode 100644 index 0000000..18f0806 --- /dev/null +++ b/docs/specification/index.rst @@ -0,0 +1,5 @@ +#################### +Format specification +#################### + +[TODO: Add when released]