From 057456ebf25c8ded2c2575df5522953407aaab25 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 24 Jan 2024 12:04:23 -0500 Subject: [PATCH] Update some docs. --- AUTHORS.rst | 14 +++++++---- CONTRIBUTING.rst | 61 ++++++++++++++++++++++++------------------------ HISTORY.rst | 23 ++++++++++++++++++ README.rst | 12 ++++++---- 4 files changed, 70 insertions(+), 40 deletions(-) diff --git a/AUTHORS.rst b/AUTHORS.rst index 81d4937b1..eb67a8e3e 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -4,14 +4,18 @@ Credits Development Lead ---------------- -* Sydney Covitz +* Taylor Salo Contributors ------------ -* Matt Cieslak - -* Tinashe Tapera +* Matt Cieslak Principal Investigator ---------------------- -* Theodore Satterthwaite +* Theodore Satterthwaite + +Previous Contributors +--------------------- +* Sydney Covitz (previous development lead) + +* Tinashe Tapera diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index e4f95ef1a..65a6e2ec6 100644 --- a/CONTRIBUTING.rst +++ b/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 git@github.com: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. diff --git a/HISTORY.rst b/HISTORY.rst index 0d1123c89..03ec01d9f 100644 --- a/HISTORY.rst +++ b/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) ------------------ diff --git a/README.rst b/README.rst index 36a2d0167..db0440b24 100644 --- a/README.rst +++ b/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 `_ 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 `_ \ No newline at end of file +For full documentation, please visit our +`ReadTheDocs `_ \ No newline at end of file