renamed bond to cubids

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/PennLINC/bond/issues.
+Report bugs at https://github.com/PennLINC/cubids/issues.
 
 If you are reporting a bug, please include:
 
@@ -38,14 +38,14 @@ and "help wanted" is open to whoever wants to implement it.
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-BOnD could always use more documentation, whether as part of the
-official BOnD docs, in docstrings, or even on the web in blog posts,
+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
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/PennLINC/bond/issues.
+The best way to send feedback is to file an issue at https://github.com/PennLINC/cubids/issues.
 
 If you are proposing a feature:
 
@@ -57,17 +57,17 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `bond` for local development.
+Ready to contribute? Here's how to set up `cubids` for local development.
 
-1. Fork the `bond` repo on GitHub.
+1. Fork the `cubids` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone [email protected]:your_name_here/bond.git
+    $ 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::
 
-    $ mkvirtualenv bond
-    $ cd bond/
+    $ mkvirtualenv cubids
+    $ cd cubids/
     $ python setup.py develop
 
 4. Create a branch for local development::
@@ -79,7 +79,7 @@ Ready to contribute? Here's how to set up `bond` for local development.
 5. When you're done making changes, check that your changes pass flake8 and the
    tests, including testing other Python versions with tox::
 
-    $ flake8 bond tests
+    $ flake8 cubids tests
     $ python setup.py test or pytest
     $ tox
 
@@ -103,15 +103,15 @@ 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/PennLINC/bond/pull_requests
+   https://travis-ci.com/PennLINC/cubids/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----
 
 To run a subset of tests::
 
-$ pytest tests.test_bond
+$ pytest tests.test_cubids
 
 
 Deploying

Dockerfile

@@ -37,7 +37,7 @@ RUN npm install -g yarn && \
 #     yarn && \
 #     cd bids-validator && npm install -g
 
-COPY . /src/BOnD
-RUN pip3 install --no-cache-dir "/src/BOnD"
+COPY . /src/CuBIDS
+RUN pip3 install --no-cache-dir "/src/CuBIDS"
 
 ENTRYPOINT [ "/bin/bash"]

MANIFEST.in

@@ -5,7 +5,7 @@ include LICENSE
 include README.rst
 
 recursive-include tests *
-recursive-include bond/testdata *
+recursive-include cubids/testdata *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 

Makefile

@@ -48,7 +48,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 lint: ## check style with flake8
-	flake8 bond tests
+	flake8 cubids tests
 
 test: ## run tests quickly with the default Python
 	pytest
@@ -57,15 +57,15 @@ test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source bond -m pytest
+	coverage run --source cubids -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/bond.rst
+	rm -f docs/cubids.rst
 	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ bond
+	sphinx-apidoc -o docs/ cubids
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
 	$(BROWSER) docs/_build/html/index.html

README.rst

@@ -1,19 +1,19 @@
 ==================
-BOnD: BIDS On Disk
+CuBIDS: BIDS On Disk
 ==================
 
 
-.. image:: https://img.shields.io/pypi/v/bond.svg
-        :target: https://pypi.python.org/pypi/bond
+.. image:: https://img.shields.io/pypi/v/cubids.svg
+        :target: https://pypi.python.org/pypi/cubids
 
-.. image:: https://img.shields.io/travis/PennLINC/bond.svg
-        :target: https://travis-ci.com/PennLINC/bond
+.. image:: https://img.shields.io/travis/PennLINC/cubids.svg
+        :target: https://travis-ci.com/PennLINC/cubids
 
-.. image:: https://readthedocs.org/projects/bond/badge/?version=latest
-        :target: https://bond.readthedocs.io/en/latest/?badge=latest
+.. image:: https://readthedocs.org/projects/cubids/badge/?version=latest
+        :target: https://cubids.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status
 
-``BOnD`` is designed to facilitate the curation and sanity-checking of BIDS
+``CuBIDS`` is designed to facilitate the curation and sanity-checking of BIDS
 datasets that live on a hard drive. Its has many functions that help curators
 follow the Three Steps of Curation. These steps are
 
@@ -26,5 +26,5 @@ follow the Three Steps of Curation. These steps are
 Step 1: Ensure the data is valid BIDS
 -------------------------------------
 
-The BOnD class has a call to a containerized version of the BIDS Validator. The
+The CuBIDS class has a call to a containerized version of the BIDS Validator. The
 output of the BIDS validator is collected and converted to a convenient Python object.

bond/__init__.py → cubids/__init__.py

@@ -1,7 +1,7 @@
-"""Top-level package for BOnD."""
+"""Top-level package for CuBIDS."""
 
 __author__ = """PennLINC"""
 __email__ = '[email protected]'
 __version__ = '0.1.0'
 
-from .bond import BOnD
+from .cubids import CuBIDS