Merge branch 'master' of github.com:insilichem/esigen

.gitignore

@@ -58,6 +58,7 @@ docs/_build/
 .directory
 *~
 *.sublime-workspace
+.vscode
 
 # PyCharm
 .idea
@@ -69,4 +70,9 @@ tests/.pytest*
 .pytest*
 
 # Constructor
-esigen*-*-*-*.sh
+esigen*-*-*-*.sh
+
+# self-signed certs
+host.cert
+host.key
+cert.pem

README.rst

@@ -0,0 +1,90 @@
+ESIgen: Supporting information generator
+========================================
+
+|Build Status| |Install with conda| |DOI|
+
+Automatically generate supporting information documents for your
+Chemistry publications online.
+
+.. figure:: docs/img/esigen.gif
+   :alt: Example
+
+
+Documentation and support
+=========================
+
+Latest documentation is always available at `esigen.readthedocs.io`_.
+
+If you have problems using ESIgen, feel free to `create an issue`_!
+Also, make sure to visit our main webpage at `insilichem.com`_.
+
+Citation
+========
+
+|DOI|
+
+ESIgen is scientific software, funded by public research grants: Spanish
+MINECO (project CTQ2017-87889-P), Generalitat de Catalunya (project
+2014SGR989), J.R.G.P.: Generalitat de Catalunya (grant 2017FI_B2_00168),
+P.G.O.: Spanish MINECO (grant FPI BES-2015-074190). If you make use of
+ESIgen in scientific publications, please cite `our article in JCIM`_.
+It will help measure the impact of our research and future funding!
+
+::
+
+    @article{doi:10.1021/acs.jcim.7b00714,
+        author = {Rodríguez-Guerra Pedregal, Jaime and Gómez-Orellana, Pablo and Maréchal, Jean-Didier Pierre},
+        title = {ESIgen: Electronic Supporting Information Generator for Computational Chemistry Publications},
+        journal = {Journal of Chemical Information and Modeling},
+        year = {2018},
+        doi = {10.1021/acs.jcim.7b00714},
+            note ={PMID: 29506387},
+        URL = {
+                https://doi.org/10.1021/acs.jcim.7b00714
+        },
+        eprint = {
+                https://doi.org/10.1021/acs.jcim.7b00714
+        }
+    }
+
+Acknowledgments
+===============
+
+Inspired by `Chauncey Garrett’s collection of scripts`_, this project
+was conceived as a Python-only CLI attempt at solving the same problem.
+Then more features were added (like markdown reports or image
+rendering), and finally was turned into a online service.
+
+ESIgen is possible thanks to great open-source projects:
+
+-  Backend: `CCLib`_, `Jinja`_.
+-  Web UI: `NGL`_, `Flask`_, `requests`_, `HTML5 UP`_, `Dropzone`_,
+   `clipboard.js`_, `FileSaver.js`_, `JSZip`_, `CloudFormatter`_.
+-  CLI: `PyMol`_.
+-  Installer: `Conda Constructor`_.
+
+.. _Conda Constructor: https://github.com/conda/constructor
+.. _esigen.readthedocs.io: https://esigen.readthedocs.io
+.. _create an issue: https://github.com/insilichem/esigen/issues
+.. _insilichem.com: http://www.insilichem.com
+.. _our article in JCIM: https://pubs.acs.org/doi/10.1021/acs.jcim.7b00714
+.. _Chauncey Garrett’s collection of scripts: https://github.com/chauncey-garrett/gaussian-tools
+.. _CCLib: https://github.com/cclib/cclib
+.. _Jinja: http://jinja.pocoo.org/
+.. _NGL: https://github.com/arose/ngl
+.. _Flask: https://github.com/pallets/flask
+.. _requests: http://docs.python-requests.org
+.. _HTML5 UP: https://html5up.net/
+.. _Dropzone: https://github.com/enyo/dropzone
+.. _clipboard.js: https://clipboardjs.com/
+.. _FileSaver.js: https://github.com/eligrey/FileSaver.js/
+.. _JSZip: https://stuk.github.io/jszip/
+.. _CloudFormatter: http://www.cloudformatter.com/CSS2Pdf
+.. _PyMol: https://sourceforge.net/projects/pymol/
+
+.. |Build Status| image:: https://travis-ci.org/insilichem/esigen.svg?branch=master
+   :target: https://travis-ci.org/insilichem/esigen
+.. |Install with conda| image:: https://anaconda.org/insilichem/esigen/badges/downloads.svg
+   :target: https://anaconda.org/InsiliChem/esigen
+.. |DOI| image:: https://img.shields.io/badge/doi-10.1021%2Facs.jcim.7b00714-blue.svg
+   :target: https://pubs.acs.org/doi/10.1021/acs.jcim.7b00714

devtools/conda-recipe/bld.bat

@@ -2,6 +2,6 @@ if not exist "%PREFIX%\Menu" mkdir "%PREFIX%\Menu"
 copy "%RECIPE_DIR%\menu-windows.json" "%PREFIX%\Menu"
 copy "%RECIPE_DIR%\app.ico" "%PREFIX%\Menu"
 
-"%SCRIPTS%\pip" install apscheduler cclib flask flask-sslify markdown gunicorn requests
+"%SCRIPTS%\pip" install apscheduler cclib flask flask-sslify markdown gunicorn requests GitHub-Flask requests_oauthlib
 if %errorlevel% neq 0 exit /b %errorlevel%
 "%PYTHON%" setup.py install

devtools/conda-recipe/build.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
-pip install apscheduler cclib flask flask-sslify markdown gunicorn requests
+pip install apscheduler cclib flask flask-sslify markdown gunicorn requests GitHub-Flask requests_oauthlib
 $PYTHON setup.py install

docs/conf.py

@@ -0,0 +1,179 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# ESIgen documentation build configuration file, created by
+# sphinx-quickstart on Thu Feb 15 17:32:23 2018.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# 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('.'))
+
+
+# -- 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.mathjax',
+    'sphinx.ext.viewcode']
+
+# 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'
+
+# General information about the project.
+project = 'ESIgen'
+copyright = '2018, Jaime RGP, InsiliChem'
+author = 'Jaime RGP, InsiliChem'
+
+import sys
+sys.path.insert(0, '..')
+import versioneer
+import os
+os.chdir('..')
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = versioneer.get_version()
+# The full version, including alpha/beta/rc tags.
+release = version
+os.chdir('docs/')
+# 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 = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'ESIgendoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'ESIgen.tex', 'ESIgen Documentation',
+     'Jaime RGP, InsiliChem', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'esigen', 'ESIgen Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'ESIgen', 'ESIgen Documentation',
+     author, 'ESIgen', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+