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* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 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.175'
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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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