squashing readthedocs commits

.readthedocs.yaml

@@ -0,0 +1,19 @@
+# .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 version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-4.10"
+
+conda:
+  environment: docs/environment.yml
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py

conda-build/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.0.0" %}
+{% set version = "0.1.0" %}
 
 package:
   name:               repic
@@ -40,15 +40,14 @@ about:
   license_family:     BSD
   license_file:       LICENSE
   summary:            REPIC - an ensemble learning approach to cryo-EM particle picking.
-  description:        REPIC is an ensemble learning approach to cryogenic-electron\
-    \ microscopy (cryo-EM) particle picking. It identifies particles common to\
-    \ multiple picked particle sets (i.e., consensus particles) using graph\
-    \ theory and integer linear programming (ILP). Picked particle sets may be\
-    \ found by a human specialist (manual), template matching, mathematical\
-    \ function (e.g., RELION's Laplacian-of-Gaussian auto-picking), or\
-    \ machine-learning method. REPIC expects particle sets to be in BOX file\
-    \ format (*.box) and contain particle coordinates, detection box size (in\
-    \ pixels), and (optional) score [0-1].
+  description:        REPIC is an ensemble learning approach to cryogenic-electron
+  microscopy (cryo-EM) particle picking. It identifies particles common to multiple
+  picked particle sets (i.e., consensus particles) using graph theory and integer
+  linear programming (ILP). Picked particle sets may be found by a human specialist
+  (manual), template matching, mathematical function (e.g., RELION's
+  Laplacian-of-Gaussian auto-picking), or machine-learning method. REPIC expects
+  particle sets to be in BOX file format (*.box) and contain particle coordinates,
+  detection box size (in pixels), and (optional) score [0-1].
   dev_url:            https://github.com/ccameron/REPIC
 
 extra:

docs/conf.py

@@ -0,0 +1,75 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import os
+import subprocess
+import sys
+
+sys.path.insert(0, os.path.abspath('.'))
+
+
+def convert_readme_to_rest():
+    """
+    Converts GitHub README (MarkDown) to Sphinx reST format
+    """
+    #   myst-parser doesn't include titles in toctree nor properly handles images
+    #   steps:
+    #       1) converts from MarkDown to reST
+    #       2) remove redundant REPIC header
+    subprocess.run(["""pandoc ../README.md -f gfm -t rst -s -o readme.rst"""],
+                   shell=True)
+    #   ; perl -i -p0e 's/REPIC\n=====\n\n//se' readme.rst
+    #   update local REPIC schematic image
+    #   steps:
+    #       1) cp imgs/ to sphinx_docs/
+    #       2) update overview img reference in readme.rst
+    #       3) update icon img reference in readme.rst
+    subprocess.run(["""cp -R ../imgs .;
+echo ".. image:: imgs/repic_overview.png
+  :width: 90%
+  :alt: REPIC schematic
+  :align: center
+|" > tmp.txt;
+perl -i -p0e 's/\.\. raw:: html\n\n   <p align=(.|\n)*\.png">\n   <\/p>\n/`cat tmp.txt`/se' readme.rst;
+echo ".. image:: imgs/repic_icon.png
+  :width: 25%
+  :alt: REPIC icon" > tmp.txt;
+ perl -i -p0e 's/\.\. raw:: html\n\n   <img width=.*\.png">\n/`cat tmp.txt`/se' readme.rst;
+rm tmp.txt"""],
+                   shell=True)
+
+
+convert_readme_to_rest()
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'REPIC'
+copyright = '2023, Christopher JF Cameron'
+author = 'Christopher JF Cameron'
+release = '0.0.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'autoapi.extension',
+    'sphinx.ext.napoleon'
+]
+autoapi_dirs = ['../repic']
+autoapi_type = "python"
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_theme_options = {
+    'collapse_navigation': False,
+}
+html_static_path = ['_static']

docs/environment.yml

@@ -0,0 +1,15 @@
+name: repic
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.8
+  - repic
+  - pandoc
+  - sphinx==6.2.1
+  - sphinx_rtd_theme
+  - sphinx-autoapi
+  - pip:
+      - readthedocs-sphinx-search
+prefix: /Users/ccameron/miniconda3/envs/repic

docs/index.rst

@@ -0,0 +1,13 @@
+Welcome to REPIC's documentation!
+=================================
+
+REliable PIcking by Consensus (REPIC) identifies cryogenic electron microscopy
+(cryo-EM) particles common to multiple picked particle sets using graph theory
+and integer linear programming.
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Contents:
+
+   readme.rst
+   autoapi/index.rst

repic/__version__.py

@@ -1,2 +1,2 @@
 #!/usr/bin/env python3
-__version__ = "0.0.0"
+__version__ = "0.1.0"