More docs

README.markdown

@@ -19,22 +19,26 @@ HOLLy is split into *train.py* and *run.py* with the actual net stored in in *ne
 (The diagram below is animated and may take a little time to appear).
 ![Overview diagram](https://shutr.benjamin.computer/static/shutr_files/original/diagram.gif)
 
+## Documentation
+
+This readme covers most of the details of HOLLy, but we also have more documentation available at [Read The Docs](https://holly.readthedocs.io/en/latest/).
+
 ## Publication
 
 [3D Structure from 2D Microscopy images using Deep Learning - Frontiers in Bioinformatics](https://www.frontiersin.org/articles/10.3389/fbinf.2021.740342/abstract)
 
- @article{blundell3DStructure2D01,
-   title = {{{3D Structure}} from {{2D Microscopy}} Images Using {{Deep Learning}}},
-   author = {Blundell, Benjamin James and Rosten, Ed and Ch'ng, QueeLim and Cox, Susan and Manley, Suliana and Sieben, Christian},
-   year = {2021},
-   journal = {Frontiers in Bioinformatics},
-   volume = {0},
-   publisher = {{Frontiers}},
-   issn = {2673-7647},
-   doi = {10.3389/fbinf.2021.740342},
-   copyright = {All rights reserved},
-   langid = {english},
- }
+    @article{blundell3DStructure2D01,
+        title = {{{3D Structure}} from {{2D Microscopy}} Images Using {{Deep Learning}}},
+        author = {Blundell, Benjamin James and Rosten, Ed and Ch'ng, QueeLim and Cox, Susan and Manley, Suliana and Sieben, Christian},
+        year = {2021},
+        journal = {Frontiers in Bioinformatics},
+        volume = {0},
+        publisher = {{Frontiers}},
+        issn = {2673-7647},
+        doi = {10.3389/fbinf.2021.740342},
+        copyright = {All rights reserved},
+        langid = {english},
+    }
 
 ### Citing with Bibtex
 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,35 @@
+# Configuration file for the Sphinx documentation builder.
+
+# -- Project information
+
+project = 'Lumache'
+copyright = '2021, Graziella'
+author = 'Graziella'
+
+release = '0.1'
+version = '0.1.0'
+
+# -- General configuration
+
+extensions = [
+    'sphinx.ext.duration',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+]
+
+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'

docs/source/index.rst

@@ -1,7 +1,7 @@
 Welcome to HOLLy's documentation!
 ===================================
 
-** HOLLy ** is a PyTorch based program that attempts to recreate 3D structure from a series of 2D 'Single Molecule Localisation Microscopy' images.
+**HOLLy** is a `PyTorch <https://pytorch.org>` based program that attempts to recreate 3D structure from a series of 2D *Single Molecule Localisation Microscopy* images.
 
 .. note::
 
@@ -12,5 +12,6 @@ Contents
 
 .. toctree::
 
+   install
    usage