Merge pull request #38 from ccpem/development

Analysis scripts for bioarxiv

.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+python:
+  install:
+    # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html (optional)
+    - requirements: docs/requirements.txt
+    # Install our python package before building the docs
+    # - method: pip
+    #   path: .
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: false
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+   - pdf
+   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#    install:
+#    - requirements: docs/requirements.txt

docs/requirements.txt

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+sphinx
+sphinx-rtd-theme

docs/source/api.rst

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+.. autosummary::
+   :toctree: generated
+
+   roodmus

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+
+# -- Project information
+
+project = "Roodmus"
+copyright = "2023, Joel Greer(UKRI), Tom Burnley (UKRI),\
+    Maarten Joosten (TU Delft), Arjen Jakobi (TU Delft)"
+author = "Joel Greer, Maarten Joosten, Tom Burnley, Arjen Jakobi"
+
+release = "0.2"
+version = "0.0.28"
+
+# -- General configuration
+
+extensions = [
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+]
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
+}
+intersphinx_disabled_domains = ["std"]
+
+templates_path = ["_templates"]
+
+# -- Options for HTML output
+
+html_theme = "sphinx_rtd_theme"
+
+# -- Options for EPUB output
+epub_show_urls = "footnote"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]

docs/source/explanation.rst

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+How Roodmus Works
+=================
+
+Information allowing you to be confident in how Roodmus works "behind-the-scenes".

docs/source/how-to-guides.rst

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+How To Guides
+=============
+
+How to use/extend Roodmus to do various tasks.

docs/source/index.rst

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+Roodmus Docs
+============
+
+Roodmus is software for doing stuff...
+
+.. note::
+
+   This project is under active development.
+
+Contents
+--------
+
+.. toctree::
+
+   tutorials
+   how-to-guides
+   explanation
+   reference
+   api

docs/source/reference.rst

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+Reference
+=========
+
+Useful reference information germane to Roodmus

docs/source/tutorials.rst

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+Tutorials
+=========
+
+How to use Roodmus utilities