Merge pull request #342 from Noble-Lab/man-pages

CLI documentation page generation

casanovo/casanovo.py

@@ -93,22 +93,27 @@ def __init__(self, *args, **kwargs) -> None:
 
 @click.group(context_settings=dict(help_option_names=["-h", "--help"]))
 def main() -> None:
-    """# Casanovo
+    """
+    Casanovo
+    ========
 
     Casanovo de novo sequences peptides from tandem mass spectra using a
     Transformer model. Casanovo currently supports mzML, mzXML, and MGF files
     for de novo sequencing and annotated MGF files, such as those from
     MassIVE-KB, for training new models.
 
     Links:
-    - Documentation: [https://casanovo.readthedocs.io]()
-    - Official code repository: [https://github.com/Noble-Lab/casanovo]()
+
+    - Documentation: https://casanovo.readthedocs.io
+    - Official code repository: https://github.com/Noble-Lab/casanovo
 
     If you use Casanovo in your work, please cite:
+
     - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo
-    mass spectrometry peptide sequencing with a transformer model. Proceedings
-    of the 39th International Conference on Machine Learning - ICML '22 (2022)
-    doi:10.1101/2022.02.07.479481.
+      mass spectrometry peptide sequencing with a transformer model. Proceedings
+      of the 39th International Conference on Machine Learning - ICML '22 (2022)
+      doi:10.1101/2022.02.07.479481.
+
 
     """
     return

docs/cli.rst

@@ -0,0 +1,10 @@
+Casanovo CLI
+============
+
+After installing the Casanovo package and all of its dependencies, the Casanovo CLI can be used to access Casanovo functionality from the command line. 
+For Casanovo installation instructions, see the :doc:`Getting Started <getting_started>`.
+
+.. click:: casanovo.casanovo:main
+   :prog: casanovo
+   :nested: full
+   :commands: configure, evaluate, sequence, train, version

docs/conf.py

@@ -12,9 +12,11 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath("."))
+import os
+import sys
+
+
+sys.path.insert(0, os.path.abspath("."))
 
 
 # -- Project information -----------------------------------------------------
@@ -30,7 +32,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named "sphinx.ext.*") or your custom
 # ones.
-extensions = ["myst_parser"]
+extensions = ["myst_parser", "sphinx_click", "sphinx_click_handlers"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]