[DOC] update doc (#16)

* ignore version

* update doc

* reformat changelog

.github/workflows/black.yml

@@ -1,5 +1,5 @@
 ---
-name: Black
+name: black
 
 on:
     push:

.github/workflows/codespell.yml

@@ -1,5 +1,5 @@
 ---
-name: Codespell
+name: codespell
 
 on:
     push:

.github/workflows/update_precommit_hooks.yml

@@ -1,5 +1,5 @@
 ---
-name: Update precommit hooks
+name: update precommit hooks
 
 
 on:
@@ -50,4 +50,4 @@ jobs:
                 token: ${{ secrets.GITHUB_TOKEN }}
                 delete-branch: true
                 title: '[BOT] update pre-commit hooks'
-                body: done via this [GitHub Action](https://github.com/${{ github.repository_owner }}/neuropower/blob/master/.github/workflows/update_precommit_hooks.yml)
+                body: done via this [GitHub Action](https://github.com/${{ github.repository_owner }}/neurodesign/blob/master/.github/workflows/update_precommit_hooks.yml)

.gitignore

@@ -3,7 +3,8 @@ examples/test.pdf
 output
 design_*
 
-test_db/
+# hatch handles this one
+neurodesign/_version.py
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

CHANGES.md

@@ -1,130 +1,203 @@
-0.2.02 - 08/24/2018
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+<!--
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+-->
+
+## [Unreleased]
+
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+
+## [0.2.02] - 2018-08-24
+
 * bug with timepoints fix
 
-0.2.01 - 02/09/2018
+## [0.2.01] - 2018-02-09
+
 * bug in report.py
 
-0.2.00 - 02/09/2018
+## [0.2.00] - 2018-02-09
+
 * change names to reflect new options
 * update examples
 * reflects JSS submission
 
-0.1.13 - 02/06/2018
+## [0.1.13] - 2018-02-06
+
 * fix on not doing FdMax and FeMax if not necessary
 
-0.1.12 - 02/06/2018
+## [0.1.12] - 2018-02-06
+
 * fix on matplotlib bug
 
-0.1.08-11 - 02/06/2018
+## [0.1.08]-11 - 2018-02-06
+
 * fix on duration bug
 
-0.1.07 - 02/05/2018
+## [0.1.07] - 2018-02-05
+
 * added option for random design generation
 
-0.1.06 - 01/22/2018
+## [0.1.06] - 2018-11-22
+
 * debug conda matplotlib
 * remove shift in onsets
 * ensure ITI is nominal value
 * improve handling of resolution
 * improve handling of hrf (resolution)
 
-0.1.05 - 11/22/2017
+## [0.1.05] - 2017-11-22
+
 * report: remove bug ndarray check in report
 
-0.1.04 - 08/30/2017
+## [0.1.04] - 2017-08-30
+
 * add hrf_precision as parameter: not same as resolution
 
-0.1.03 - 08/09/2017
+## [0.1.03] - 2017-08-09
+
 * remove indentation bugs
 * replace often reoccuring warnings with internal warning
 
-0.1.02 - 07/31/2017
+## [0.1.02] - 2017-07-31
+
 * debug first ITI (should be 0)
 * debug Hardprob
 * debug maximum ITI with resolution
 * round ITI to resolution before computing onsets
 * added exceptions for longer designs
 
-0.1.01 - 07/03/2017
+## [0.1.01] - 2017-07-03
+
 * debug numpy exception
 
-0.1.00 - 04/26/2017
+## [0.1.00] - 2017-04-26
+
 * package underwent extensive testing through the online application
 * examples are added complementary to the manuscript under revision
 
-0.0.28 - 02/20/2017
+## [0.0.28] - 2017-02-20
+
 * debug correlation check
 
-0.0.27 - 02/20/2017
+## [0.0.27] - 2017-02-20
+
 * debug rest durations
 * debug repeated msequences
 
-0.0.26 - 02/14/2017
+## [0.0.26] - 2017-02-14
+
 * patch reoccurring (but rare) problem with too long a design
 
-0.0.25 - 02/06/2017
+## [0.0.25] - 2017-02-06
+
 * avoid getting stuck while trying to find blocked designs
 
-0.0.24 - 02/02/2017
+## [0.0.24] - 2017-02-02
+
 * add some extra space for max duration (0.5s) to avoid trials exceeding the experiment duration
 
-0.0.23 - 02/01/2017
+## [0.0.23] - 2017-02-01
+
 * remove requirements for now
 
-0.0.22 - 02/01/2017
+## [0.0.22] - 2017-02-01
+
 * update requirements
 
-0.0.21 - 02/01/2017
+## [0.0.21] - 2017-02-01
+
 * remove itertools from requirements
 
-0.0.20 - 02/01/2017
+## [0.0.20] - 2017-02-01
+
 * remove collections from requirements
 
-0.0.19 - 02/01/2017
+## [0.0.19] - 2017-02-01
+
 * pypi problems
 
-0.0.18 - 02/01/2017
+## [0.0.18] - 2017-02-01
+
 * remove typo in install_requires
 
-0.0.17 - 02/01/2017
+## [0.0.17] - 2017-02-01
+
 * remove requirements.txt
 
-0.0.16 - 02/01/2017
+## [0.0.16] - 2017-02-01
+
 * debug memory problem induced in 0.0.15
 
-0.0.15 - 01/31/2017
+## [0.0.15] - 2017-01-31
+
 * debug LinAlgError
 * debug necessity for calculating both Fe and Fd --> speed up
 * debug initial population weights
 
-0.0.14 - 01/19/2017
+## [0.0.14] - 2017-01-19
+
 * improve which designs are outputted
 * improve report
 
-0.0.13 - 01/18/2017
+## [0.0.13] - 2017-01-18
+
 * debug max number of repeats
 
-0.0.12 - 01/18/2017
+## [0.0.12] - 2017-01-18
+
 * debug generation of ITI's from truncated distribution
 
-0.0.11 - 01/17/2017
+## [0.0.11] - 2017-01-17
+
 * debug generation of ITI's from truncated distribution
 
-0.0.10 - 01/10/2017
+## [0.0.10] - 2017-01-10
+
 * remove direct support for GUI
 
-0.0.9 - 12/19/2016
+## [0.0.9] - 2016-12-19
+
 * change matplotlib backend for report
 
-0.0.8 - 12/19/2016
+## [0.0.8] - 2016-12-19
+
 * debug script
 
-0.0.7 - 12/09/2016
+## [0.0.7] - 2016-12-09
+
 * debug seeds
 * restructure a few parameters in other classes
 
-0.0.6 - 11/18/2016
+## [0.0.6] - 2016-11-18
+
 * add report to download
 
-0.0.2 - 11/18/2016
+## [0.0.2] - 2016-11-18
+
 * remove bug in report when numpy array is given.

docs/_templates/layout.html

@@ -2,8 +2,8 @@
 
 
 {% block rootrellink %}
-        <li><a href="{{ pathto('index') }}">home</a>|&nbsp;</li>
-        <li><a href="{{ pathto('search') }}">search</a>|&nbsp;</li>
+        <li><a href="{{ pathto('index') }}">home</a>&nbsp;|&nbsp;</li>
+        <li><a href="{{ pathto('search') }}">search</a>&nbsp;|&nbsp;</li>
 {% endblock %}
 
 

docs/conf.py

@@ -1,23 +1,25 @@
-#
-# neurodesign documentation build configuration file, created by
-# sphinx-quickstart on Mon Jan 23 16:58:27 2017.
-#
-# 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.
+"""Neurodesign documentation build configuration file.
+
+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.
+"""
+
 import os
 import sys
 from unittest import mock
 
+from neurodesign._version import __version__
+
 # 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.
-sys.path.insert(0, os.path.abspath("../source/"))
+sys.path.insert(0, os.path.abspath("../neurodesign"))
 
 # -- General configuration ------------------------------------------------
 
@@ -46,16 +48,16 @@
 
 # General information about the project.
 project = "neurodesign"
-copyright = "2017, Joke Durnez"
+copyright = "Joke Durnez"
 
 # 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 = "0.0.13"
+version = __version__
 # The full version, including alpha/beta/rc tags.
-release = "0.0.13"
+release = __version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/genalg.rst

@@ -6,24 +6,24 @@ Neurodesign documentation
 
 Neurodesign: design optimisation
 --------------------------------
-.. automodule:: src.neurodesign
+.. automodule:: neurodesign
    :members:
    :noindex:
 
 Generate: generating stimulus order and ITI's
 ---------------------------------------------
-.. automodule:: src.generate
+.. automodule:: neurodesign.generate
    :members:
    :noindex:
 
 Msequence: generating msequences
 --------------------------------
-.. automodule:: src.msequence
+.. automodule:: neurodesign.msequence
    :members:
    :noindex:
 
 Report: summarise results from optimisation
 -------------------------------------------
-.. automodule:: src.report
+.. automodule:: neurodesign.report
    :members:
    :noindex: