diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..545961b --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,42 @@ +name: Build documentation + +on: + push: + branches: + - main + workflow_dispatch: + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: 3.11 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r docs/requirements.txt + - name: Build docs + run: | + sphinx-build -b html docs docs/_build/html + - name: Upload artifact + uses: actions/upload-pages-artifact@v3 + with: + path: "docs/_build/html/" + + deploy: + needs: build + permissions: + pages: write + id-token: write + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/README.md b/README.md index 65c8200..11312e4 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ ![Watchers](https://flat.badgen.net/github/watchers/HUPO-PSI/mzSpecLib) ![Stars](https://flat.badgen.net/github/stars/HUPO-PSI/mzSpecLib) -**HUPO-PSI standardized spectral library format** +**HUPO-PSI standardized spectral library format** mzSpecLib is a formal standard and file format in development at [HUPO-PSI](http://www.psidev.info/) to store and distribute spectral libraries/archives. The target main target audience for this format are @@ -61,16 +61,17 @@ is used as a central point of information regarding the format's development: - [mzSpecLib general data model schematic](https://drive.google.com/file/d/1OVh5ATfKXA77pM4CYzRfdupeRGu3vt5c/view?usp=sharing) -Currently, the project's progress can be split up into the development of the -[main specification](https://github.com/HUPO-PSI/mzSpecLib/tree/master/specification) -and into a [Python implementation](https://github.com/HUPO-PSI/mzSpecLib/tree/master/implementations/python) -of this specification. +## Reference implementation + +A reference implementation of the mzSpecLib format is available in the form of a Python package. +Check out the [mzspeclib-py](https://github.com/HUPO-PSI/mzspeclib-py) repository or the +[Python package documentation](https://mzspeclib.readthedocs.io/) for more information. ## Contributing All community input is welcome! Feel free to join the discussions in the [Issue tracker](https://github.com/HUPO-PSI/SpectralLibraryFormat/issues) or to open a -new issue if you have questions, recommendations or requests. Additionally, +new issue if you have questions, recommendations or requests. Additionally, everyone is allowed to post comments in the Google documents or to request full write access to fully contribute to the specification. diff --git a/docs/.readthedocs.yaml b/docs/.readthedocs.yaml deleted file mode 100644 index 31c93e2..0000000 --- a/docs/.readthedocs.yaml +++ /dev/null @@ -1,21 +0,0 @@ -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/conf.py b/docs/conf.py index 943e443..e8229aa 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -7,15 +7,7 @@ github_doc_root = "https://github.com/HUPO-PSI/mzSpecLib/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", -] +extensions = ["myst_parser"] source_suffix = [".rst"] master_doc = "index" exclude_patterns = ["_build"] @@ -35,19 +27,6 @@ ] } -# 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/implementations/index.rst b/docs/implementations/index.rst deleted file mode 100644 index ebb51a9..0000000 --- a/docs/implementations/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -############### -Implementations -############### - -.. toctree:: - :caption: Contents - :maxdepth: 2 - :glob: - - */index - diff --git a/docs/implementations/python/api.rst b/docs/implementations/python/api.rst deleted file mode 100644 index a2874c7..0000000 --- a/docs/implementations/python/api.rst +++ /dev/null @@ -1,7 +0,0 @@ -********** -Python API -********** - -.. automodule:: mzlib - :members: - :imported-members: diff --git a/docs/implementations/python/cli.rst b/docs/implementations/python/cli.rst deleted file mode 100644 index f57470e..0000000 --- a/docs/implementations/python/cli.rst +++ /dev/null @@ -1,7 +0,0 @@ -********************** -Command line interface -********************** - -.. click:: mzlib.tools.cli:main - :prog: mzspeclib - :nested: full diff --git a/docs/implementations/python/index.rst b/docs/implementations/python/index.rst deleted file mode 100644 index 7d589cf..0000000 --- a/docs/implementations/python/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -##################### -Python implementation -##################### - -.. toctree:: - :caption: Contents - :maxdepth: 2 - :glob: - - * - diff --git a/docs/index.rst b/docs/index.rst index b9b2c5a..2f481c6 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -9,5 +9,4 @@ Home specification/index - implementations/index contributing diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..ec7ce83 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,3 @@ +sphinx +pydata_sphinx_theme +myst-parser