Create documentation page

jvsguerra · jvsguerra · commit 860a387bd57b · 2022-08-22T16:29:24.000-03:00
diff --git a/README.rst b/README.rst
diff --git a/docs/INSTRUCTIONS.rst b/docs/INSTRUCTIONS.rst
@@ -0,0 +1,10 @@
+Instructions
+============
+
+Source files are in **source** directory.
+
+To create pyKVFinder documentation as a GitHub page, run:
+
+.. code-block:: bash
+
+    make html
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,28 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+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 $(SPHINXOPTS).
+%: Makefile
+	@mv source/ Makefile INSTRUCTIONS.rst ..
+	@if [ -f ".nojekyll" ]; then rm .nojekyll; fi
+	@if [ -f ".buildinfo" ]; then rm .buildinfo; fi
+	@if [ -d ".doctrees" ]; then rm -r .doctrees; fi
+	@if [ -f "index.html" ]; then rm -r *; fi
+	@mv ../source/ ../Makefile ../INSTRUCTIONS.rst .
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@mv $(BUILDDIR)/$@/* $(BUILDDIR)/$@/.nojekyll $(BUILDDIR)/$@/.buildinfo .
+	@mv $(BUILDDIR)/doctrees .doctrees
+	@rm -r $(BUILDDIR)
diff --git a/docs/source/_about/index.rst b/docs/source/_about/index.rst
@@ -0,0 +1,39 @@
+.. raw:: html
+
+    <h1>About</h1>
+
+Issues
+======
+
+SERD package uses of GitHub for project management. Please help us by reporting any problems or requests.
+
+On `Issues <https://github.com/jvsguerra/SERD/issues>`_ page, you can file a:
+
+.. toctree::
+    
+    Bug Report <https://github.com/jvsguerra/SERD/issues/new?assignees=&labels=&template=bug_report.md&title=>
+    Request for a new feature <https://github.com/jvsguerra/SERD/issues/new?assignees=&labels=&template=feature_request.md&title=>
+
+Only make sure the bug or request has not already been reported. Click on “Search” and enter some keywords to search.
+
+Thank you for helping us improve SERD!
+
+Scientific team
+===============
+
+SERD was developed by:
+
+- João Victor da Silva Guerra
+- Gabriel Ernesto Jara
+- José Geraldo de Carvalho Pereira
+- Paulo Sergio Lopes de Oliveira
+
+
+Computational Biology Laboratory (`LBC <https://github.com/LBC-LNBio>`_), Brazilian Biosciences National Laboratory (`LNBio <https://lnbio.cnpem.br/>`_), Brazilian Center for Research in Energy and Materials (`CNPEM <https://cnpem.br>`_)
+
+If you have any further questions, inquires or if you wish to contribute to SERD, please contact us at jvsguerra@gmail.com.
+
+License
+=======
+
+The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
diff --git a/docs/source/_api_reference/index.rst b/docs/source/_api_reference/index.rst
@@ -0,0 +1,49 @@
+SERD.detect
+***********
+
+.. autofunction:: SERD.detect
+
+SERD.g2pdb
+**********
+
+.. autofunction:: SERD.g2pdb
+
+SERD.get_vertices
+*****************
+
+.. autofunction:: SERD.get_vertices
+
+SERD.interface
+**************
+
+.. autofunction:: SERD.interface
+
+SERD.r2g
+********
+
+.. autofunction:: SERD.r2g
+
+SERD.read_vdw
+*************
+
+.. autofunction:: SERD.read_vdw
+
+SERD.read_pdb
+*************
+
+.. autofunction:: SERD.read_pdb
+
+SERD.save
+*********
+
+.. autofunction:: SERD.save
+
+SERD.save_session
+*****************
+
+.. autofunction:: SERD.save_session
+
+SERD.surface
+************
+
+.. autofunction:: SERD.surface
diff --git a/docs/source/_installation/index.rst b/docs/source/_installation/index.rst
@@ -0,0 +1,57 @@
+Requirements
+============
+
+If you don’t have Python v3 and/or SWIG yet, the installation procedure differs depending on the operating system.
+
+Python and SWIG can be installed with conda, or with a package manager on Linux and macOS.
+
+Package managers
+----------------
+
+On Linux:
+
+.. code-block:: bash
+    
+  sudo apt install python3 swig
+
+On macOS:
+
+.. code-block:: bash
+    
+  brew install python3 swig
+
+.. note:: 
+
+  Users can use their preferred package manager to install SWIG and Python v3.
+
+Conda
+-----
+
+If you use conda, you can install Python v3 and SWIG from the defaults channel:
+
+.. code-block:: bash
+    
+  # Use an environment rather than install in base environement (recommended)
+  conda create -n myenv python=3
+  conda activate myenv
+  # The SWIG install command
+  conda install swig
+
+Installation
+============
+
+The prerequisites for installing SERD is SWIG, Python v3 and PyMOL v2.
+
+To install the latest release on `PyPI <https://pypi.org/project/SERD>`_, 
+run:
+
+::
+
+  pip install SERD
+
+Or to install the latest developmental version, run:
+
+::
+
+  git clone https://github.com/jvsguerra/SERD.git
+  pip install SERD
diff --git a/docs/source/_static/icon.ico b/docs/source/_static/icon.ico
diff --git a/docs/source/_tutorial/index.rst b/docs/source/_tutorial/index.rst
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -0,0 +1,122 @@
+# -*- coding: utf-8 -*-
+# 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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "SERD"
+copyright = "2022, João Victor da Silva Guerra"
+author = "João Victor da Silva Guerra"
+
+# The short X.Y version
+from SERD import __version__
+
+version = ".".join(__version__.split(".")[0:2])
+# The full version, including alpha/beta/rc tags
+release = __version__
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# 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,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# HTML favicon
+html_favicon = "_static/icon.ico"
+
+# HTML logo
+# html_logo = "_static/icon.ico"
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ["search.html"]
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {"https://docs.python.org/": None}
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -0,0 +1,29 @@
+.. SERD documentation master file, created by
+   sphinx-quickstart on Mon Aug 22 15:05:54 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to SERD's documentation!
+================================
+
+Welcome to the **Solvent-Exposed Residues Detection (SERD)**, this page was built to help you get started with our package.
+
+.. toctree::
+   :caption: Installation
+
+   _installation/index
+
+.. toctree::
+   :caption: Tutorial
+   
+   _tutorial/index
+
+.. toctree::
+   :caption: API Reference
+
+   _api_reference/index
+
+.. toctree::
+   :caption: About
+
+   _about/index
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-networkx>=2.6.3
-numpy>=1.20.3
-pyKVFinder>=0.2.5
-scipy>=1.7.1
+networkx>=2.8.6
+numpy>=1.23.2
+pyKVFinder>=0.4.2
+scipy>=1.9.0
