Add ASL fields to config (#282)

* Add ASL fields.

* Update constants.py

* Keep working on docstrings.

* Update config.py

* Use PathExists and IsFile for param types.

* Remove type from boolean parameter.

* More work.

* Update some docs.

* Add support for m0scan, aslcontext, asllabeling.

* Update cubids.py

* Update cubids.py

* Try fixing PyPi deployment job.

* Run black.

* Minor changes.

* Update cubids.py

* Update cubids.py

* Address review.

AUTHORS.rst

@@ -4,14 +4,18 @@ Credits
 
 Development Lead
 ----------------
-* Sydney Covitz <sydney.covitz at pennmedicine dot upenn .edu>
+* Taylor Salo <taylor dot salo at pennmedicine dot upenn dot edu>
 
 Contributors
 ------------
-* Matt Cieslak <matthew.cieslak at pennmedicine dot upenn .edu>
-
-* Tinashe Tapera <tinashe.tapera at pennmedicine dot upenn .edu>
+* Matt Cieslak <matthew dot cieslak at pennmedicine dot upenn dot edu>
 
 Principal Investigator
 ----------------------
-* Theodore Satterthwaite <theodore.satterthwaite at pennmedicine dot upenn .edu>
+* Theodore Satterthwaite <theodore dot satterthwaite at pennmedicine dot upenn dot edu>
+
+Previous Contributors
+---------------------
+* Sydney Covitz <sydney dot covitz at pennmedicine dot upenn dot edu> (previous development lead)
+
+* Tinashe Tapera <tinashe dot tapera at pennmedicine dot upenn dot edu>

CONTRIBUTING.rst

@@ -4,8 +4,8 @@
 Contributing
 ============
 
-Contributions are welcome, and they are greatly appreciated! Every little bit
-helps, and credit will always be given.
+Contributions are welcome, and they are greatly appreciated!
+Every little bit helps, and credit will always be given.
 
 You can contribute in many ways:
 
@@ -26,21 +26,20 @@ If you are reporting a bug, please include:
 Fix Bugs
 ~~~~~~~~
 
-Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
-wanted" is open to whoever wants to implement it.
+Look through the GitHub issues for bugs.
+Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.
 
 Implement Features
 ~~~~~~~~~~~~~~~~~~
 
-Look through the GitHub issues for features. Anything tagged with "enhancement"
-and "help wanted" is open to whoever wants to implement it.
+Look through the GitHub issues for features.
+Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.
 
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-CuBIDS could always use more documentation, whether as part of the
-official CuBIDS docs, in docstrings, or even on the web in blog posts,
-articles, and such.
+CuBIDS could always use more documentation, whether as part of the official CuBIDS docs,
+in docstrings, or even on the web in blog posts, articles, and such.
 
 Submit Feedback
 ~~~~~~~~~~~~~~~
@@ -59,60 +58,62 @@ Get Started!
 
 Ready to contribute? Here's how to set up `cubids` for local development.
 
-1. Fork the `cubids` repo on GitHub.
-2. Clone your fork locally::
+1.  Fork the `cubids` repo on GitHub.
+2.  Clone your fork locally::
 
     $ git clone [email protected]:your_name_here/cubids.git
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+3.  Install your local copy into a virtualenv.
+    Assuming you have virtualenvwrapper installed,
+    this is how you set up your fork for local development::
 
     $ mkvirtualenv cubids
     $ cd cubids/
     $ python setup.py develop
 
-4. Create a branch for local development::
+4.  Create a branch for local development::
 
     $ git checkout -b name-of-your-bugfix-or-feature
 
    Now you can make your changes locally.
 
-5. When you're done making changes, check that your changes pass flake8 and the
-   tests, including testing other Python versions with tox::
+5.  When you're done making changes, check that your changes pass flake8 and the
+    tests, including testing other Python versions with tox::
 
     $ flake8 cubids tests
     $ python setup.py test or pytest
     $ tox
 
-   To get flake8 and tox, just pip install them into your virtualenv.
+    To get flake8 and tox, just pip install them into your virtualenv.
 
-6. Commit your changes and push your branch to GitHub::
+6.  Commit your changes and push your branch to GitHub::
 
     $ git add .
     $ git commit -m "Your detailed description of your changes."
     $ git push origin name-of-your-bugfix-or-feature
 
-7. Submit a pull request through the GitHub website.
+7.  Submit a pull request through the GitHub website.
 
 Pull Request Guidelines
 -----------------------
 
 Before you submit a pull request, check that it meets these guidelines:
 
-1. The pull request should include tests.
-2. If the pull request adds functionality, the docs should be updated. Put
-   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://circleci.com/gh/PennLINC/CuBIDS
-   and make sure that the tests pass for all supported Python versions.
+1.  The pull request should include tests.
+2.  If the pull request adds functionality, the docs should be updated. Put
+    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://circleci.com/gh/PennLINC/CuBIDS
+    and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----
 
 To run a subset of tests::
 
-$ cd PATH/TO/LOCAL/CuBIDS/CLONE
-$ py.test -sv --pdb tests
+    $ cd PATH/TO/LOCAL/CuBIDS/CLONE
+    $ py.test -sv --pdb tests
 
 
 Deploying
@@ -122,8 +123,8 @@ A reminder for the maintainers on how to deploy.
 Make sure all your changes are committed (including an entry in HISTORY.rst).
 Then run::
 
-$ bump2version patch # possible: major / minor / patch
-$ git push
-$ git push --tags
+    $ bump2version patch # possible: major / minor / patch
+    $ git push
+    $ git push --tags
 
 CircleCI will then deploy to PyPI if tests pass.

HISTORY.rst

@@ -2,6 +2,29 @@
 History
 =======
 
+1.0.2 (2023-09-07)
+------------------
+
+* Add image orientation by @scovitz in https://github.com/PennLINC/CuBIDS/pull/205
+* review feedback milestone: adding code/CuBIDS option and converting CSVs to TSVs by @scovitz in https://github.com/PennLINC/CuBIDS/pull/217
+* Reviewer feedback incorporated  into docs and pybids layout update by @scovitz in https://github.com/PennLINC/CuBIDS/pull/227
+* Data dictionaries by @scovitz in https://github.com/PennLINC/CuBIDS/pull/230
+* No index metadata by @scovitz in https://github.com/PennLINC/CuBIDS/pull/231
+* updated _update_json to no longer use pybids by @scovitz in https://github.com/PennLINC/CuBIDS/pull/232
+* Minor tune ups: codespell'ing (fixes + tox + CI (github actions)), remove of unintended to be committed 2 files by @yarikoptic in https://github.com/PennLINC/CuBIDS/pull/239
+* ENH: Make "NumVolumes" an integer for 3D images by @cookpa in https://github.com/PennLINC/CuBIDS/pull/211
+* adding note about fmap renamekeygroups by @megardn in https://github.com/PennLINC/CuBIDS/pull/140
+* Update usage.rst by @megardn in https://github.com/PennLINC/CuBIDS/pull/138
+* printing erroneous jsons and only rounding float parameters by @scovitz in https://github.com/PennLINC/CuBIDS/pull/257
+
+New Contributors
+`````````````````
+* @yarikoptic made their first contribution in https://github.com/PennLINC/CuBIDS/pull/239
+* @cookpa made their first contribution in https://github.com/PennLINC/CuBIDS/pull/211
+* @megardn made their first contribution in https://github.com/PennLINC/CuBIDS/pull/140
+
+**Full Changelog**: https://github.com/PennLINC/CuBIDS/compare/v1.0.1...1.0.2
+
 0.1.0 (2020-10-07)
 ------------------
 

README.rst

@@ -18,16 +18,18 @@ About
 
 Curation of BIDS, or ``CuBIDS``, is a workflow and software package designed to facilitate
 reproducible curation of neuroimaging `BIDS <https://bids-specification.readthedocs.io/>`_ datasets.
-CuBIDS breaks down BIDS dataset curation into four main components and addresses each one using 
-various command line programs complete with version control capabilities. These components are not necessarily linear but all are critical 
-in the process of preparing BIDS data for successful preprocessing and analysis pipeline runs. 
+CuBIDS breaks down BIDS dataset curation into four main components and addresses each one using
+various command line programs complete with version control capabilities.
+These components are not necessarily linear but all are critical
+in the process of preparing BIDS data for successful preprocessing and analysis pipeline runs.
 
   1. CuBIDS facilitates the validation of BIDS data.
-  2. CuBIDS visualizes and summarizes the heterogeneity in a BIDS dataset. 
+  2. CuBIDS visualizes and summarizes the heterogeneity in a BIDS dataset.
   3. CuBIDS helps users test pipelines on the entire parameter space of a BIDS dataset.
   4. CuBIDS allows users to perform metadata-based quality control on their BIDS data.
 
 .. image:: https://github.com/PennLINC/CuBIDS/raw/main/docs/_static/cubids_workflow.png
    :width: 600
 
-For full documentation, please visit our `ReadTheDocs <https://cubids.readthedocs.io/en/latest/?badge=latest>`_ 
+For full documentation, please visit our
+`ReadTheDocs <https://cubids.readthedocs.io/en/latest/?badge=latest>`_