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* Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`). * Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels. * Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL. * jfjoch_viewer: Opens the same XFEL file formats. * Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL. * Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded. * jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start. Reviewed-on: #88 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
93 lines
3.1 KiB
Python
93 lines
3.1 KiB
Python
# Configuration file for the Sphinx documentation builder.
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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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project = 'Jungfraujoch'
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copyright = '2024, Paul Scherrer Institute'
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author = 'Filip Leonarski'
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release = '1.0.0-rc.178'
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = [
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'myst_parser',
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'sphinx.ext.mathjax',
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]
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templates_path = ['_templates']
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# docs/review/ is gitignored working material (review reports, work plans); Sphinx renders
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# whatever is on disk, so without this a local review file would become a published page.
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exclude_patterns = ['review']
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myst_enable_extensions = [
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'linkify',
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'smartquotes',
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'dollarmath',
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'amsmath',
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]
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myst_heading_anchors = 3
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# The OpenAPI Python-client pages under docs/python_client/ are generated by the
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# openapi-generator and contain header-level jumps and intra-page anchors that MyST
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# cannot resolve. We do not hand-edit generated files, so silence that noise here;
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# the hand-written docs are anchor-clean once myst_heading_anchors is set above.
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# 'config.cache' fires only because the sphinx_material theme stores a function in
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# html_context, which is harmless for our single-shot builds.
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suppress_warnings = ['myst.header', 'myst.xref_missing', 'config.cache']
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# Render LaTeX-style math nicely in HTML and support AMS-style equation numbering.
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mathjax3_config = {
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"tex": {
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"tags": "ams",
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"inlineMath": [['\\(', '\\)'], ['$', '$']],
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"displayMath": [['\\[', '\\]'], ['$$', '$$']],
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"processEscapes": True,
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}
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}
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_theme = 'sphinx_material'
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html_static_path = ['../broker/redoc-static.html']
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#html_theme_options = {
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# 'sidebar_width': '300px',
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# 'page_width': 'auto'
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#}
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html_theme_options = {
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'repo_url': 'https://gitea.psi.ch/mx/jungfraujoch',
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'repo_name': 'Jungfraujoch',
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'nav_title': 'PSI Jungfraujoch',
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'html_minify': True,
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'css_minify': True,
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'globaltoc_depth': 2,
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# The generated python-client pages live in a hidden toctree on PYTHON_CLIENT.md: built and
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# linked, but out of the sidebar - with the default includehidden=True they were 195 of the
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# sidebar's 256 entries.
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'globaltoc_includehidden': False,
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# sphinx_material only knows github/gitlab/bitbucket; the repository is Gitea, so 'gitlab' is
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# picked purely for the icon it renders next to repo_url above.
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'repo_type': 'gitlab',
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'color_primary': 'indigo',
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'color_accent': 'lime',
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'logo_icon': ''
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}
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html_logo = 'jfjoch.png'
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html_favicon = 'jfjoch.png'
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html_sidebars = {
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"**": ["logo-text.html", "globaltoc.html", "searchbox.html"]
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}
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html_show_sourcelink = False
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