Merge pull request #24 from PennLINC/csvdoc

[DOC] Add documentation on key/param group csv's
PennLINC · Nov 4, 2020 · cc7842c · cc7842c
2 parents fe68c84 + 370814f
commit cc7842c
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,8 @@
+version: 2
+
+python:
+ install:
+ - method: pip
+ path: .
+ extra_requirements:
+ - doc
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,16 @@
+# vim ft=yaml
+language: python
+sudo: false
+cache:
+ directories:
+ - $HOME/.cache/pip
+
+python:
+ - 3.6
+
+before_install:
+ - python -m pip install --upgrade pip
+ - pip install "flake8<3.0" flake8-putty
+
+script:
+ - flake8 bond
diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -5,7 +5,7 @@ Credits
 Development Lead
 ----------------
 
-* Matt Cieslak <[email protected]>
+* Matt Cieslak <matthew.cieslak at pennmedicine dot upenn .edu>
 
 Contributors
 ------------

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/mattcieslak/bond/issues.
+Report bugs at https://github.com/PennLINC/bond/issues.
 
 If you are reporting a bug, please include:
 
@@ -45,7 +45,7 @@ articles, and such.
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/mattcieslak/bond/issues.
+The best way to send feedback is to file an issue at https://github.com/PennLINC/bond/issues.
 
 If you are proposing a feature:
 
@@ -103,7 +103,7 @@ Before you submit a pull request, check that it meets these guidelines:
  your new functionality into a function with a docstring, and add the
  feature to the list in README.rst.
 3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
- https://travis-ci.com/mattcieslak/bond/pull_requests
+ https://travis-ci.com/PennLINC/bond/pull_requests
  and make sure that the tests pass for all supported Python versions.
 
 Tips

diff --git a/README.rst b/README.rst
@@ -6,8 +6,8 @@ BOnD: BIDS On Disk
 .. image:: https://img.shields.io/pypi/v/bond.svg
  :target: https://pypi.python.org/pypi/bond
 
-.. image:: https://img.shields.io/travis/mattcieslak/bond.svg
- :target: https://travis-ci.com/mattcieslak/bond
+.. image:: https://img.shields.io/travis/PennLINC/bond.svg
+ :target: https://travis-ci.com/PennLINC/bond
 
 .. image:: https://readthedocs.org/projects/bond/badge/?version=latest
  :target: https://bond.readthedocs.io/en/latest/?badge=latest

diff --git a/bond/__init__.py b/bond/__init__.py
@@ -1,7 +1,7 @@
 """Top-level package for BOnD."""
 
-__author__ = """Matt Cieslak"""
-__email__ = 'mattcieslak@gmail.com'
+__author__ = """PennLINC"""
+__email__ = 'PennLINC@gmail.com'
 __version__ = '0.1.0'
 
 from .bond import BOnD
diff --git a/docs/_static/PNC_example_edited.csv b/docs/_static/PNC_example_edited.csv
@@ -0,0 +1,9 @@
+RenameKeyGroup,MergeInto,KeyGroup,ParamGroup,Counts,FieldmapKey00,NSliceTimes,RepetitionTime
+,,datatype-dwi_run-1_suffix-dwi,1,1361,datatype-fmap_fmap-phase1_suffix-phase1,70,8.1
+acquisition-VariantTr_datatype-dwi_run-1_suffix-dwi,,datatype-dwi_run-1_suffix-dwi,2,1,datatype-fmap_fmap-phase1_suffix-phase1,70,8.4
+,,datatype-dwi_run-1_suffix-dwi,3,15,datatype-fmap_fmap-phasediff_suffix-phasediff,70,8.1
+acquisition-VariantTr_datatype-dwi_run-1_suffix-dwi,,datatype-dwi_run-1_suffix-dwi,4,1,datatype-fmap_fmap-phase1_suffix-phase1,70,9
+,3,datatype-dwi_run-1_suffix-dwi,5,2,datatype-fmap_fmap-phasediff_suffix-phasediff,70,8.1
+acquisition-NoSDC_datatype-dwi_run-1_suffix-dwi,,datatype-dwi_run-1_suffix-dwi,6,16,,70,8.1
+,0,datatype-dwi_run-1_suffix-dwi,7,2,datatype-fmap_fmap-phase1_suffix-phase1,46,8.1
+acquisition-VariantTr_datatype-dwi_run-1_suffix-dwi,,datatype-dwi_run-1_suffix-dwi,8,1,datatype-fmap_fmap-phase1_suffix-phase1,70,12.3
diff --git a/docs/_static/PNC_example_unedited.csv b/docs/_static/PNC_example_unedited.csv
@@ -0,0 +1,9 @@
+RenameKeyGroup,MergeInto,KeyGroup,ParamGroup,Counts,FieldmapKey00,NSliceTimes,RepetitionTime
+,,datatype-dwi_run-1_suffix-dwi,1,1361,datatype-fmap_fmap-phase1_suffix-phase1,70,8.1
+,,datatype-dwi_run-1_suffix-dwi,2,1,datatype-fmap_fmap-phase1_suffix-phase1,70,8.4
+,,datatype-dwi_run-1_suffix-dwi,3,15,datatype-fmap_fmap-phasediff_suffix-phasediff,70,8.1
+,,datatype-dwi_run-1_suffix-dwi,4,1,datatype-fmap_fmap-phase1_suffix-phase1,70,9
+,,datatype-dwi_run-1_suffix-dwi,5,2,datatype-fmap_fmap-phasediff_suffix-phasediff,70,8.1
+,,datatype-dwi_run-1_suffix-dwi,6,16,,70,8.1
+,,datatype-dwi_run-1_suffix-dwi,7,2,datatype-fmap_fmap-phase1_suffix-phase1,46,8.1
+,,datatype-dwi_run-1_suffix-dwi,8,1,datatype-fmap_fmap-phase1_suffix-phase1,70,12.3
diff --git a/docs/conf.py b/docs/conf.py
@@ -47,8 +47,8 @@
 
 # General information about the project.
 project = 'BOnD'
-copyright = "2020, Matt Cieslak"
-author = "Matt Cieslak"
+copyright = "2020, PennLINC"
+author = "PennLINC"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -129,7 +129,7 @@
 latex_documents = [
  (master_doc, 'bond.tex',
  'BOnD Documentation',
- 'Matt Cieslak', 'manual'),
+ 'PennLINC', 'manual'),
 ]
 
 

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -5,24 +5,6 @@ Installation
 ============
 
 
-Stable release
---------------
-
-To install BOnD, run this command in your terminal:
-
-.. code-block:: console
-
- $ pip install bond
-
-This is the preferred method to install BOnD, as it will always install the most recent stable release.
-
-If you don't have `pip`_ installed, this `Python installation guide`_ can guide
-you through the process.
-
-.. _pip: https://pip.pypa.io
-.. _Python installation guide: https://docs.python-guide.org/en/latest/starting/installation/
-
-
 From sources
 ------------
 
@@ -32,13 +14,13 @@ You can either clone the public repository:
 
 .. code-block:: console
 
- $ git clone git:https://github.com/mattcieslak/bond
+ $ git clone git:https://github.com/PennLINC/BOnD
 
 Or download the `tarball`_:
 
 .. code-block:: console
 
- $ curl -OJL https://github.com/mattcieslak/bond/tarball/master
+ $ curl -OJL https://github.com/PennLINC/BOnD/tarball/master
 
 Once you have a copy of the source, you can install it with:
 
@@ -47,5 +29,5 @@ Once you have a copy of the source, you can install it with:
  $ python setup.py install
 
 
-.. _Github repo: https://github.com/mattcieslak/bond
-.. _tarball: https://github.com/mattcieslak/bond/tarball/master
+.. _Github repo: https://github.com/PennLINC/BOnD
+.. _tarball: https://github.com/PennLINC/BOnD/tarball/master