[DOC] Add JOSS badges

[tsalo]

Closes #669.

Changes proposed in this pull request:

• Add JOSS badge to README.md and docs/index.rst.
• Add JOSS citation to README and docs/index.rst.
• Add JOSS citation to package-level duecredit decorator.
• Add JOSS citation as reference to tedana and t2smap workflow docstrings.
• Add JOSS citation to the tedana boilerplate.

[tsalo]

isort isn't running correctly 😭🤣

Traceback (most recent call last):
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/plugins/manager.py", line 161, in load_plugin
    self._load()
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/plugins/manager.py", line 138, in _load
    self._plugin = self.entry_point.load()
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/importlib_metadata/__init__.py", line 167, in load
    module = import_module(match.group('module'))
  File "/opt/conda/envs/tedana_py37/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8_isort.py", line 3, in <module>
    from isort import SortImports
ImportError: cannot import name 'SortImports' from 'isort' (/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/isort/__init__.py)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/envs/tedana_py37/bin/flake8", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/main/cli.py", line 22, in main
    app.run(argv)
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/main/application.py", line 375, in run
    self._run(argv)
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/main/application.py", line 363, in _run
    self.initialize(argv)
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/main/application.py", line 343, in initialize
    self.find_plugins(config_finder)
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/main/application.py", line 163, in find_plugins
    self.check_plugins.load_plugins()
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/plugins/manager.py", line 422, in load_plugins
    plugins = list(self.manager.map(load_plugin))
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/plugins/manager.py", line 309, in map
    yield func(self.plugins[name], *args, **kwargs)
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/plugins/manager.py", line 420, in load_plugin
    return plugin.load_plugin()
  File "/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/flake8/plugins/manager.py", line 168, in load_plugin
    raise failed_to_load
flake8.exceptions.FailedToLoadPlugin: Flake8 failed to load plugin "I00" due to cannot import name 'SortImports' from 'isort' (/opt/conda/envs/tedana_py37/lib/python3.7/site-packages/isort/__init__.py).
make: *** [Makefile:15: lint] Error 1

[jbteves]

Do we need to pin a particular version?

[notZaki]

I think the current PR installed flake8-isort-3.0.0 whereas the main branch used flake8-isort-4.0.0. Setting a minimum version to "flake8-isort>=4", here

tedana/tedana/info.py

Line 48 in 4d5c645

"flake8-isort",

might fix it. Not sure why it downgraded---for some reason, the most recent version of flake8 wants to use an older version of flake8-isort.

For reference, the logs of the environment are linked: [this PR] [main]
The installed versions are listed all the way at the bottom of the log.

EDIT: Issue 1409 on flake8's repo has some discussion on this. Looks like pip has trouble resolving the correct versions.

[notZaki]

The upstream issue should now be fixed, so re-running the build might fix it---unless if circle-ci decides to re-use the old cache, in which case, any edit to info.py should force it to start from a clean slate.

[codecov]

Codecov Report

Merging #815 (d789c3f) into main (5399ca5) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main     #815   +/-   ##
=======================================
  Coverage   93.27%   93.27%           
=======================================
  Files          27       27           
  Lines        2215     2217    +2     
=======================================
+ Hits         2066     2068    +2     
  Misses        149      149           

Impacted Files	Coverage Δ
tedana/workflows/t2smap.py	96.29% <ø> (ø)
tedana/__init__.py	100.00% <100.00%> (ø)
tedana/workflows/tedana.py	89.92% <100.00%> (+0.03%)	⬆️

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[tsalo]

Thanks @notZaki! It passed.

[jbteves]

LGTM, thanks @tsalo !

[jbteves]

We should add:

• duecredit
• citation on README
• citation on index.rst
• references in workflow

[tsalo]

@jbteves okay I think I got them all. I also cited the paper in the workflow boilerplate.

[jbteves]

Right now the first reference is numbered and subsequent ones are not. I lean towards asking that all of them be numbered rather than asking you to remove the first one's number, but I could go either way.

[tsalo]

Hm.. it wasn't numbered when I checked, but I guess that's because the Zenodo website was down at the time so the function must not have been working. I'll change it back.

[emdupre]

This LGTM ! TY, @tsalo !! 📖

[jbteves]

LGTM, thanks @tsalo !