Refactor docs and fix style (#80)

* Try to use correct theme * Fix source root * A lot of reformatting
sdrobert · Oct 20, 2023 · 1afe745 · 1afe745
1 parent 0cb997f
commit 1afe745
Show file tree

Hide file tree

Showing 31 changed files with 418 additions and 94 deletions.
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -2,7 +2,7 @@ docutils>=0.17
 myst-parser
 param
 pydrobert-param>=0.4.0
-sphinx_rtd_theme>=0.5
+sphinx-rtd-theme>=0.5
 sphinx-autodoc-typehints
 Sphinx>=4.4
 typing_extensions
diff --git a/docs/source/api/pydrobert/torch.rst b/docs/source/api/pydrobert/torch.rst
@@ -0,0 +1,8 @@
+pydrobert.torch
+===============
+
+.. toctree::
+   :glob:
+   :maxdepth: 1
+
+   torch/*
diff --git a/docs/source/api/pydrobert/torch/argcheck.rst b/docs/source/api/pydrobert/torch/argcheck.rst
@@ -0,0 +1,100 @@
+argcheck
+========
+
+.. toctree::
+
+.. automodule:: pydrobert.torch.argcheck
+
+.. autofunction:: as_bool
+.. autofunction:: as_closed01
+.. autofunction:: as_dir
+.. autofunction:: as_file
+.. autofunction:: as_float
+.. autofunction:: as_int
+.. autofunction:: as_nat
+.. autofunction:: as_negf
+.. autofunction:: as_negi
+.. autofunction:: as_nonnegf
+.. autofunction:: as_nonnegi
+.. autofunction:: as_nonposf
+.. autofunction:: as_nonposi
+.. autofunction:: as_open01
+.. autofunction:: as_path_dir
+.. autofunction:: as_path_file
+.. autofunction:: as_path
+.. autofunction:: as_posf
+.. autofunction:: as_posi
+.. autofunction:: as_str
+.. autofunction:: as_tensor
+.. autofunction:: has_ndim
+.. autofunction:: is_a
+.. autofunction:: is_bool
+.. autofunction:: is_btw_closed
+.. autofunction:: is_btw_closedf
+.. autofunction:: is_btw_closedi
+.. autofunction:: is_btw_closedt
+.. autofunction:: is_btw_open
+.. autofunction:: is_btw_openf
+.. autofunction:: is_btw_openi
+.. autofunction:: is_btw_opent
+.. autofunction:: is_btw
+.. autofunction:: is_btwf
+.. autofunction:: is_btwi
+.. autofunction:: is_btwt
+.. autofunction:: is_closed01
+.. autofunction:: is_closed01f
+.. autofunction:: is_closed01i
+.. autofunction:: is_closed01t
+.. autofunction:: is_dir
+.. autofunction:: is_equal
+.. autofunction:: is_equalf
+.. autofunction:: is_equali
+.. autofunction:: is_equalt
+.. autofunction:: is_exactly
+.. autofunction:: is_file
+.. autofunction:: is_float
+.. autofunction:: is_gt
+.. autofunction:: is_gte
+.. autofunction:: is_gtef
+.. autofunction:: is_gtei
+.. autofunction:: is_gtet
+.. autofunction:: is_gtf
+.. autofunction:: is_gti
+.. autofunction:: is_gtt
+.. autofunction:: is_in
+.. autofunction:: is_int
+.. autofunction:: is_lt
+.. autofunction:: is_lte
+.. autofunction:: is_ltef
+.. autofunction:: is_ltei
+.. autofunction:: is_ltet
+.. autofunction:: is_ltf
+.. autofunction:: is_lti
+.. autofunction:: is_ltt
+.. autofunction:: is_nat
+.. autofunction:: is_neg
+.. autofunction:: is_negf
+.. autofunction:: is_negi
+.. autofunction:: is_negt
+.. autofunction:: is_nonempty
+.. autofunction:: is_nonneg
+.. autofunction:: is_nonnegf
+.. autofunction:: is_nonnegi
+.. autofunction:: is_nonnegt
+.. autofunction:: is_nonpos
+.. autofunction:: is_nonposf
+.. autofunction:: is_nonposi
+.. autofunction:: is_nonpost
+.. autofunction:: is_numlike
+.. autofunction:: is_open01
+.. autofunction:: is_open01f
+.. autofunction:: is_open01i
+.. autofunction:: is_open01t
+.. autofunction:: is_path
+.. autofunction:: is_pos
+.. autofunction:: is_posf
+.. autofunction:: is_posi
+.. autofunction:: is_post
+.. autofunction:: is_str
+.. autofunction:: is_tensor
+.. autofunction:: is_token
diff --git a/docs/source/api/pydrobert/torch/config.rst b/docs/source/api/pydrobert/torch/config.rst
@@ -0,0 +1,8 @@
+config
+======
+
+.. toctree::
+
+.. automodule:: pydrobert.torch.config
+  :members:
+
diff --git a/docs/source/api/pydrobert/torch/data.rst b/docs/source/api/pydrobert/torch/data.rst
@@ -0,0 +1,7 @@
+data
+====
+
+.. toctree::
+
+.. automodule:: pydrobert.torch.data
+   :members:
diff --git a/docs/source/api/pydrobert/torch/distributions.rst b/docs/source/api/pydrobert/torch/distributions.rst
@@ -0,0 +1,7 @@
+distributions
+=============
+
+.. toctree::
+
+.. automodule:: pydrobert.torch.distributions
+   :members:
diff --git a/docs/source/api/pydrobert/torch/estimators.rst b/docs/source/api/pydrobert/torch/estimators.rst
@@ -0,0 +1,7 @@
+estimators
+==========
+
+.. toctree::
+
+.. automodule:: pydrobert.torch.estimators
+   :members:
diff --git a/docs/source/api/pydrobert/torch/functional.rst b/docs/source/api/pydrobert/torch/functional.rst
@@ -0,0 +1,55 @@
+functional
+==========
+
+.. toctree::
+
+.. automodule:: pydrobert.torch.functional
+
+Combinatorics
+-------------
+.. autofunction:: binomial_coefficient
+.. autofunction:: enumerate_vocab_sequences
+.. autofunction:: enumerate_binary_sequences
+.. autofunction:: enumerate_binary_sequences_with_cardinality
+.. autofunction:: simple_random_sampling_without_replacement
+
+Decoding
+--------
+.. autofunction:: beam_search_advance
+.. autofunction:: ctc_greedy_search
+.. autofunction:: ctc_prefix_search_advance
+.. autofunction:: random_walk_advance
+.. autofunction:: sequence_log_probs
+
+Features
+--------
+.. autofunction:: chunk_by_slices
+.. autofunction:: chunk_token_sequences_by_slices
+.. autofunction:: dense_image_warp
+.. autofunction:: feat_deltas
+.. autofunction:: mean_var_norm
+.. autofunction:: pad_masked_sequence
+.. autofunction:: pad_variable
+.. autofunction:: polyharmonic_spline
+.. autofunction:: random_shift
+.. autofunction:: slice_spect_data
+.. autofunction:: sparse_image_warp
+.. autofunction:: spec_augment
+.. autofunction:: spec_augment_apply_parameters
+.. autofunction:: spec_augment_draw_parameters
+.. autofunction:: warp_1d_grid
+
+Reinforcement Learning
+----------------------
+.. autofunction:: time_distributed_return
+
+String Matching
+---------------
+.. autofunction:: edit_distance
+.. autofunction:: error_rate
+.. autofunction:: fill_after_eos
+.. autofunction:: hard_optimal_completion_distillation_loss
+.. autofunction:: minimum_error_rate_loss
+.. autofunction:: optimal_completion
+.. autofunction:: prefix_edit_distances
+.. autofunction:: prefix_error_rates
diff --git a/docs/source/api/pydrobert/torch/lightning.rst b/docs/source/api/pydrobert/torch/lightning.rst
@@ -0,0 +1,7 @@
+lightning
+=========
+
+.. toctree::
+
+.. automodule:: pydrobert.torch.lightning
+   :members:
diff --git a/docs/source/api/pydrobert/torch/modules.rst b/docs/source/api/pydrobert/torch/modules.rst
@@ -0,0 +1,65 @@
+modules
+=======
+
+.. toctree::
+
+.. automodule:: pydrobert.torch.modules
+
+Attention
+---------
+.. autoclass:: GlobalSoftAttention
+.. autoclass:: ConcatSoftAttention
+.. autoclass:: DotProductSoftAttention
+.. autoclass:: GeneralizedDotProductSoftAttention
+.. autoclass:: MultiHeadedAttention
+
+Decoding
+--------
+.. autoclass:: BeamSearch
+.. autoclass:: CTCGreedySearch
+.. autoclass:: CTCPrefixSearch
+.. autoclass:: RandomWalk
+.. autoclass:: SequenceLogProbabilities
+
+Features
+--------
+.. autoclass:: ChunkBySlices
+.. autoclass:: ChunkTokenSequencesBySlices
+.. autoclass:: DenseImageWarp
+.. autoclass:: FeatureDeltas
+.. autoclass:: MeanVarianceNormalization
+.. autoclass:: PadMaskedSequence
+.. autoclass:: PadVariable
+.. autoclass:: PolyharmonicSpline
+.. autoclass:: RandomShift
+.. autoclass:: SliceSpectData
+.. autoclass:: SparseImageWarp
+.. autoclass:: SpecAugment
+.. autoclass:: Warp1DGrid
+
+Language Models
+---------------
+.. autoclass:: ExtractableSequentialLanguageModel
+.. autoclass:: MixableSequentialLanguageModel
+.. autoclass:: SequentialLanguageModel
+.. autoclass:: ExtractableShallowFusionLanguageModel
+.. autoclass:: LookupLanguageModel
+.. autoclass:: MixableShallowFusionLanguageModel
+.. autoclass:: ShallowFusionLanguageModel
+
+Reinforcement Learning
+----------------------
+.. autoclass:: GumbelOneHotCategoricalRebarControlVariate
+.. autoclass:: LogisticBernoulliRebarControlVariate
+.. autoclass:: TimeDistributedReturn
+
+String Matching
+---------------
+.. autoclass:: EditDistance
+.. autoclass:: ErrorRate
+.. autoclass:: FillAfterEndOfSequence
+.. autoclass:: HardOptimalCompletionDistillationLoss
+.. autoclass:: MinimumErrorRateLoss
+.. autoclass:: OptimalCompletion
+.. autoclass:: PrefixEditDistances
+.. autoclass:: PrefixErrorRates
diff --git a/docs/source/api/pydrobert/torch/training.rst b/docs/source/api/pydrobert/torch/training.rst
@@ -0,0 +1,7 @@
+training
+========
+
+.. toctree::
+
+.. automodule:: pydrobert.torch.training
+   :members:
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -36,11 +36,11 @@
 extensions = [
     "myst_parser",
     "sphinx.ext.autodoc",
-    "sphinx.ext.autosectionlabel",
     "sphinx.ext.intersphinx",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
     "sphinx_autodoc_typehints",
+    "sphinx_rtd_theme",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -81,11 +81,11 @@
 
 # -- Options for HTML output -------------------------------------------------
 
-on_rtd = os.environ.get("READTHEDOCS") == "True"
-if on_rtd:
-    html_theme = "default"
-else:
-    html_theme = "sphinx_rtd_theme"
+# on_rtd = os.environ.get("READTHEDOCS") == "True"
+# if on_rtd:
+#     html_theme = "default"
+# else:
+html_theme = "sphinx_rtd_theme"
 
 # 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,
@@ -105,6 +105,14 @@
     (param.ipython.cyan % " ").split()[1],
 }
 
+html_context = {
+    "display_github": True,  # Integrate GitHub
+    "github_user": "sdrobert",  # Username
+    "github_repo": "pydrobert-pytorch",  # Repo name
+    "github_version": "master",  # Version
+    "conf_py_path": "/docs/source/",  # Path in the checkout to the docs root
+}
+
 
 def docstring_handler(app, what, name, obj, options, lines):
     if "Params" in name.split(".")[-1]:

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -2,13 +2,21 @@
    :parser: myst_parser.sphinx_
 
 .. toctree::
+   :glob:
+   :caption: Tutorials
+
+   tutorials/*
+
+.. toctree::
+   :caption: API
    :maxdepth: 2
-   :caption: Contents:
 
-   advanced_attention
+   api/pydrobert/torch
+
+.. toctree::
+   :caption: Other
+
    cli
-   lm
-   modules
    references
 
 Indices and tables

diff --git a/docs/source/modules.rst b/docs/source/modules.rst
diff --git a/docs/source/pydrobert.torch.config.rst b/docs/source/pydrobert.torch.config.rst
diff --git a/docs/source/pydrobert.torch.data.rst b/docs/source/pydrobert.torch.data.rst