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James K. Glasbrenner
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Documentation refactoring to use RTD theme
 * Adopt RTD theme for docs HTML rendering. * Refactored the settings related to generating the table of contents as this is rendered somewhat differently in the RTD theme. * Update RTD configuration settings, just install requirements in setup.py file instead of using environment.yaml. * Generate individual rst files for all individual functions. * Add CSS file to fix wrapping issues as discussed here, readthedocs/sphinx_rtd_theme#432 (comment). * Revise content on index.rst file.
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‎.readthedocs.yml

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python:
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version: 3.6
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conda:
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file: environment.yaml
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setup_py_install: true
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extra_requirements:
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- docs
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formats: []
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...

‎docs/_static/theme_overrides.css

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/* override table width restrictions */
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@media screen and (min-width: 767px) {
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.wy-table-responsive table td {
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/* !important prevents the common CSS stylesheets from overriding
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this as on RTD they are loaded after this stylesheet */
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white-space: normal !important;
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}
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.wy-table-responsive {
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overflow: visible !important;
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}
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}

‎docs/conf.py

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# The full version, including alpha/beta/rc tags
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release = '0.0.1'
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# -- Autodoc configuration ---------------------------------------------------
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autodoc_member_order = "bysource"
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autosummary_generate = True
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# -- General configuration ---------------------------------------------------
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# If your documentation needs a minimal Sphinx version, state it here.
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#
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# This is also used if you do content translation via gettext catalogs.
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# Usually you set "language" from the command line for these cases.
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language = None
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language = "en"
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path .
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'sphinx'
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# pygments_style = 'sphinx'
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# If true, the current module name will be prepended to all description
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# unit titles (such as .. function::).
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add_module_names = False
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'nature'
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on_rtd = os.environ.get('READTHEDOCS') == 'True'
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if on_rtd:
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html_theme = 'default'
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else:
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html_theme = 'sphinx_rtd_theme'
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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# documentation.
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#
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# html_theme_options = {}
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html_use_index = False
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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html_context = {
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'css_files': [
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'_static/theme_overrides.css', # override wide tables in RTD theme
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],
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}
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# Custom sidebar templates, must be a dictionary that maps document names
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# to template names.
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#
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# -- Extension configuration -------------------------------------------------
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# -- Options for autodoc extension -------------------------------------------
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autodoc_member_order = "bysource"
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autosummary_generate = True
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# -- Options for todo extension ----------------------------------------------
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# If true, `todo` and `todoList` produce output, else they produce nothing.

‎docs/index.rst

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API
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===
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Modules
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-------
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.. toctree::
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:maxdepth: 2
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modules
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``interactions``
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^^^^^^^^^^^^^^^^
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.. automodule:: neighbormodels.interactions
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.. rubric:: Primary method
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.. autosummary::
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build_model
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.. rubric:: Functions
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.. autosummary::
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aggregate_interaction_coefficients
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build_magnetic_patterns_data_frame
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compute_interaction_signs
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compute_model_coefficients
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group_subspecie_pairs_and_rank_by_distance
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label_interaction_parameters
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multiply_interaction_signs_and_neighbor_count
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spread_parameter_name_column
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``neighbors``
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^^^^^^^^^^^^^
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.. automodule:: neighbormodels.neighbors
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.. rubric:: Primary method
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.. autosummary::
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count_neighbors
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.. rubric:: Functions
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.. autosummary::
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add_subspecie_labels_if_missing
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append_site_i_neighbor_distance_data
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count_neighbors_within_distance_groups
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define_bin_intervals
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define_bins_to_group_and_sort_by_distance
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extract_neighbor_distance_data
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find_unique_distances
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get_neighbor_distances_data_frame
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group_site_index_pairs_by_distance
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.. rubric:: Classes
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.. autosummary::
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NeighborData
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``structure``
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^^^^^^^^^^^^^
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.. automodule:: neighbormodels.structure
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.. rubric:: Primary methods
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.. autosummary::
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from_file
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from_parameters
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.. autosummary::
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.. rubric:: Functions
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.. autosummary::
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get_subspecies_labels
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label_subspecies
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.. rubric:: Classes
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.. autosummary::
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StructureParameters
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

‎docs/modules.rst

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neighbormodels
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==============
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Modules
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=======
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.. toctree::
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neighbormodels
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neighbormodels.interactions
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neighbormodels.neighbors
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neighbormodels.structure

‎docs/modules/neighbormodels.interactions.aggregate_interaction_coefficients.rst

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neighbormodels.interactions.aggregate\_interaction\_coefficients
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================================================================
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.. currentmodule:: neighbormodels.interactions
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.. autofunction:: aggregate_interaction_coefficients

‎docs/modules/neighbormodels.interactions.build_magnetic_patterns_data_frame.rst

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neighbormodels.interactions.build\_magnetic\_patterns\_data\_frame
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==================================================================
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.. currentmodule:: neighbormodels.interactions
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.. autofunction:: build_magnetic_patterns_data_frame

‎docs/modules/neighbormodels.interactions.build_model.rst

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neighbormodels.interactions.build\_model
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========================================
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.. currentmodule:: neighbormodels.interactions
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.. autofunction:: build_model

‎docs/modules/neighbormodels.interactions.compute_interaction_signs.rst

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neighbormodels.interactions.compute\_interaction\_signs
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=======================================================
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.. currentmodule:: neighbormodels.interactions
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.. autofunction:: compute_interaction_signs

‎docs/modules/neighbormodels.interactions.compute_model_coefficients.rst

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neighbormodels.interactions.compute\_model\_coefficients
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========================================================
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.. currentmodule:: neighbormodels.interactions
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.. autofunction:: compute_model_coefficients

‎docs/modules/neighbormodels.interactions.group_subspecie_pairs_and_rank_by_distance.rst

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neighbormodels.interactions.group\_subspecie\_pairs\_and\_rank\_by\_distance
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============================================================================
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.. currentmodule:: neighbormodels.interactions
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.. autofunction:: group_subspecie_pairs_and_rank_by_distance

‎docs/modules/neighbormodels.interactions.label_interaction_parameters.rst

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neighbormodels.interactions.label\_interaction\_parameters
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==========================================================
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.. currentmodule:: neighbormodels.interactions
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.. autofunction:: label_interaction_parameters

‎docs/modules/neighbormodels.interactions.multiply_interaction_signs_and_neighbor_count.rst

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neighbormodels.interactions.multiply\_interaction\_signs\_and\_neighbor\_count
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==============================================================================
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.. currentmodule:: neighbormodels.interactions
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.. autofunction:: multiply_interaction_signs_and_neighbor_count

‎docs/modules/neighbormodels.interactions.spread_parameter_name_column.rst

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neighbormodels.interactions.spread\_parameter\_name\_column
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===========================================================
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.. autofunction:: spread_parameter_name_column

‎docs/modules/neighbormodels.neighbors.NeighborData.rst

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neighbormodels.neighbors.NeighborData
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=====================================
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.. currentmodule:: neighbormodels.neighbors
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.. autoclass:: NeighborData
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.. automethod:: __init__
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.. rubric:: Methods
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.. autosummary::
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~NeighborData.count
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~NeighborData.index
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.. rubric:: Attributes
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.. autosummary::
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~NeighborData.bins_data_frame
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~NeighborData.data_frame
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~NeighborData.structure
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‎docs/modules/neighbormodels.neighbors.add_subspecie_labels_if_missing.rst

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neighbormodels.neighbors.add\_subspecie\_labels\_if\_missing
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============================================================
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.. autofunction:: add_subspecie_labels_if_missing

‎docs/modules/neighbormodels.neighbors.append_site_i_neighbor_distance_data.rst

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neighbormodels.neighbors.append\_site\_i\_neighbor\_distance\_data
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==================================================================
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.. autofunction:: append_site_i_neighbor_distance_data

‎docs/modules/neighbormodels.neighbors.count_neighbors.rst

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neighbormodels.neighbors.count\_neighbors
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=========================================
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.. autofunction:: count_neighbors

‎docs/modules/neighbormodels.neighbors.count_neighbors_within_distance_groups.rst

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neighbormodels.neighbors.count\_neighbors\_within\_distance\_groups
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===================================================================
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.. autofunction:: count_neighbors_within_distance_groups

‎docs/modules/neighbormodels.neighbors.define_bin_intervals.rst

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neighbormodels.neighbors.define\_bin\_intervals
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===============================================
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.. autofunction:: define_bin_intervals

‎docs/modules/neighbormodels.neighbors.define_bins_to_group_and_sort_by_distance.rst

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neighbormodels.neighbors.define\_bins\_to\_group\_and\_sort\_by\_distance
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.. autofunction:: define_bins_to_group_and_sort_by_distance

‎docs/modules/neighbormodels.neighbors.extract_neighbor_distance_data.rst

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neighbormodels.neighbors.extract\_neighbor\_distance\_data
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==========================================================
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.. autofunction:: extract_neighbor_distance_data

‎docs/modules/neighbormodels.neighbors.find_unique_distances.rst

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neighbormodels.neighbors.find\_unique\_distances
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.. autofunction:: find_unique_distances

‎docs/modules/neighbormodels.neighbors.get_neighbor_distances_data_frame.rst

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neighbormodels.neighbors.get\_neighbor\_distances\_data\_frame
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==============================================================
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.. autofunction:: get_neighbor_distances_data_frame

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