Adding documentation in RTD

README.md

@@ -1,4 +1,4 @@
-<img alt="Phys2BIDS" src="https://github.com/physiopy/phys2bids/blob/master/docs/phys2bids_logo1280×640.png" height="150">
+<img alt="Phys2BIDS" src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/phys2bids_logo1280×640.png" height="150">
 
 phys2bids
 =========
@@ -40,9 +40,6 @@ if your output is: ``phys2bids 1.2.0-beta`` or similar, phys2bids is ready to be
 **The project is currently under development**.
 Any suggestion/bug report is welcome! Feel free to open an issue.
 
-At the very moment, it assumes all the extracted channels from a file
-have the same sampling freq.
-
 This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
 
 ## Contributors ✨

docs/api.rst

@@ -0,0 +1,7 @@
+.. _api:
+
+===
+API
+===
+
+Coming soon.

docs/bestpractice.rst

@@ -0,0 +1,7 @@
+.. _bestpractice:
+
+================================================
+Best Practices for Collecting Physiological Data
+================================================
+
+Coming soon.

docs/cli.rst

@@ -1,15 +1,15 @@
 .. _cli:
 
-------------------
+==================
 Command-line usage
-------------------
+==================
 
 You can invoke the primary workflow of ``phys2bids`` from the command line.
 
 .. _cli_phys2bids:
 
 The ``phys2bids`` command
-=========================
+-------------------------
 
 .. argparse::
    :ref: phys2bids.cli.run._get_parser

docs/conf.py

@@ -31,6 +31,8 @@
 
 # -- General configuration ---------------------------------------------------
 
+master_doc = 'index'
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
@@ -75,6 +77,14 @@
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
+# Integrate GitHub
+html_context = {
+    "display_github": True,  # Integrate GitHub
+    "github_user": "physiopy",  # Username
+    "github_repo": "phys2bids",  # Repo name
+    "github_version": "master",  # Version
+    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
+}
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -87,7 +97,7 @@
 # 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 = {}
+# 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,
@@ -97,7 +107,11 @@
 # https://github.com/rtfd/sphinx_rtd_theme/issues/117
 def setup(app):  # noqa
     app.add_stylesheet('theme_overrides.css')
+    app.add_javascript("https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js")
+
 
+html_favicon = '_static/phys2bids_logo2000x400.png'
+html_logo = '_static/phys2bids_logo2000x400.png'
 
 # -- Options for HTMLHelp output ---------------------------------------------
 
@@ -110,5 +124,4 @@ def setup(app):  # noqa
     'python': ('https://docs.python.org/3.6', None),
     'matplotlib': ('https://matplotlib.org', None),
     'numpy': ('https://docs.scipy.org/doc/numpy', None),
-    'pandas': ('https://pandas-docs.github.io/pandas-docs-travis/', None),
 }

docs/contributing.rst

@@ -0,0 +1,34 @@
+.. _contributing:
+
+=============================
+Contributing to ``phys2bids``
+=============================
+
+First of all: thank you!
+
+Contributions can be made in different ways, not only code!
+As we follow the `all-contributors`_ specification, any contribution will be recognised accordingly.
+
+The first thing you might want to do, is having a look at the ``contributors.md`` file as well as the ``conduct.md`` guidelines.
+
+The second thing is to install ``phys2bids`` as a developer.
+This will let you run the program with the latest modification, without requiring to re-install it every time.
+
+.. _`all-contributors`: https://github.com/all-contributors/all-contributors
+
+
+Linux and mac developer installation
+------------------------------------
+
+Be sure to have git installed, then open a terminal and use the command::
+``git clone https://github.com/smoia/phys2bids.git``
+
+Move in the ``phy2bids`` folder and execute the command::
+``pip3 install -e .``
+
+
+User testing
+------------
+
+Coming soon.
+

docs/heuristic.rst

@@ -0,0 +1,7 @@
+.. _heuristic:
+
+==============================
+How to set up a heuristic file
+==============================
+
+Tutorial coming soon.

docs/howto.rst

@@ -0,0 +1,7 @@
+.. _howto:
+
+====================
+How to use phys2bids
+====================
+
+Tutorial coming soon.

docs/index.rst

@@ -2,10 +2,36 @@
 phys2bids
 =========
 
+.. image:: _static/phys2bids_logo1280×640.png
+   :alt: phys2bids logo
+   :align: center
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3586045.svg
+   :target: https://doi.org/10.5281/zenodo.3586045
+
+.. image:: https://badges.gitter.im/phys2bids/community.svg
+   :target: https://badges.gitter.im/phys2bids/community.svg)](https://gitter.im/phys2bids/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+
+Phys2bids is a python3 library meant to format physiological files in BIDS.
+It was born for AcqKnowledge files (BIOPAC), and at the moment it supports
+``.acq`` files as well as ``.txt`` files obtained by labchart
+(ADInstruments).
+It doesn't support physiological files recorded with the MRI, as you can find a software for it [here](https://github.com/tarrlab/physio2bids).
+
+**The project is currently under development**.
+Any suggestion/bug report is welcome! Feel free to open an issue.
+
 Contents
 --------
 
 .. toctree::
    :maxdepth: 1
 
+   installation
+   howto
+   heuristic
+   bestpractice
    cli
+   contributing
+   license
+   api

docs/installation.rst

@@ -0,0 +1,54 @@
+.. _installation:
+
+============
+Installation
+============
+
+Requirements
+------------
+
+``phys2bids`` requires python 3.6 or above, as well as the modules:
+- ``numpy >= 1.9.3``
+- ``matplotlib >= 3.1.1``
+
+Depending on the processed files, it might require the **manual installation** of other modules.
+At the moment, those modules are:
+- `bioread`_, for AcqKnowledge (``.acq``) files.
+
+.. _`bioread`: https://github.com/uwmadison-chm/bioread
+
+Linux and mac installation
+--------------------------
+
+Download the package from github and uncompress it.
+Alternatively, if you have ``git``, use the command::
+``git clone https://github.com/smoia/phys2bids.git``
+
+Install with ``pip``
+^^^^^^^^^^^^^^^^^^^^
+
+Open a terminal in the ``phy2bids`` folder and execute the command::
+``pip3 install .``
+
+If python 3 is already your default, you might use instead::
+``pip install .``
+
+If you need to install other libraries, you can call again ``pip``::
+``pip3 install bioread``
+
+Install without ``pip``
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Open a terminal in the phy2bids folder and execute the command::
+``python3 setup.py``
+
+If python 3 is already your default, you might use instead::
+``python setup.py``
+
+Check your installation!
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+Type the command::
+``phys2bids -v``
+
+If your output is: ``phys2bids 1.2.0-beta`` or similar, ``phys2bids`` is ready to be used.

docs/license.rst

@@ -0,0 +1,19 @@
+.. _license:
+
+=======
+License
+=======
+
+Copyright 2019, The Phys2BIDS community.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.