Face lift

[yarikoptic]

• modern Python packaging: Update Python packaging #326
• maybe even pre-commit with whatever goodnesses we use for dandi-cli including black (only few PRs ATM): Add & apply pre-commit and linting #329
• autoreleasing, probably intuit auto would be enough: Set up auto #346
• Use a src/ layout: Use a src/ layout #332
• Set up local testing with tox: Add testing via tox #334
• Set up local linting with tox: Add & apply pre-commit and linting #329
• Run linting as part of CI: Run linting as part of CI #333
• tox environment for building docs: Enable building docs locally via tox -e docs #357
• Type annotations
• Remove dependency on simplejson: Replace simplejson with stdlib json #337
• Remove Python 2-specific __future__ imports: Remove Python 2-specific __future__ imports #335
• Remove use of six: Remove uses of six #336
• Do something with profiler.py and rest-server.py in repo root (Turn them into tox envs?)
  • rest-server.py was taken care of by Clean up Docker-related files #351.
  • profiler.py was deleted by Delete profiler.py #362.
• Clean up README.rst markup: Clean up README.rst markup #340
• Ensure that pytest is only used by test code, and then move it to the test dependencies: Add testing via tox #334
• Shorten rows of asterisks around license notices to < 80 columns: Shorten overly-long lines of punctuation #345
• Replace uses of tmpdir test fixture with tmp_path: Replace tmpdir fixture with tmp_path #339
• Ensure all commented-out sys.path manipulations are gone
• Configure pytest to fail on warnings: Make pytest error on warnings #341
• Use build instead of setup.py in pythonpublish.yml: Use build in pythonpublish.yml #330
• Run tests on pushes to master in addition to pull requests: Run tests in CI on pushes & merges to master #331
• Measure test coverage: Measure test coverage #344
• Make tests write temp files to temp directories instead of using the current directory (Write test.ttl into temp dir(s) #323): Write test temp files to temp directories #343
• The setup fixture in nidm/experiment/tests/test_query.py seems to depend on another test having previously created the cmu_a.nidm.ttl file. Fix this dependency.: Write test temp files to temp directories #343
• nidm/experiment/tools/tests/test_nidm_lingreg.py: Replace call_click_command() with appropriate use of click.testing.CliRunner: Clean up Click testing #352
• Cut down on the use of global variables Moved to dedicated issue: Eliminate the use of global variables throughout the code #361
• Replace %-formatting and str.format() with f-strings: Improve string formatting syntax #364
• Update/clean up Dockerfiles: Clean up Docker-related files #351
• Remove README.md files in code directories and move their contents (if any) to docstrings of adjacent __init__.py files: Prune README.md files from code directories #338
• Fix the test workflow so that there are actually Junit files to upload
  • Upload step deleted instead by Do not try to upload nonexisting junit artifacts #372
• Update all actions used by workflows to the latest versions, and configure Dependabot to keep them up to date: Update workflow actions versions and keep them up to date with Dependabot #350
• Replace uses of urllib.request with requests: Replace uses of urllib.request with requests #359
• Cut down on code duplication in nidm/experiment/tools/
• Remove the giant comments like these from source files and list their authors in a CONTRIBUTORS file: Pare down giant comment blocks that largely do what Git already does #363
• Replace restLog in src/nidm/experiment/tools/rest.py with an actual logger
• Replace most/all uses of tempfile.gettempdir() with tempfile.mkdtemp()
• Eliminate excessive whitespace printed out at ends of lines and around tab characters
• anything else good which comes to mind ;)

[jwodder]

@yarikoptic Should we maybe make this into a GitHub project with multiple issues instead of just one issue with a lot of tasks?

[yarikoptic]

wow the description grew, I didn't notice, time flies ;-) !
On one hand -- I don't mind you taking any approach you would like to make you more efficient etc. On the other -- I just love this checklist which could easily serve later as a condensed and easily copy pasteable template for one of us or someone else.
So if you like -- create separate issues, but checklist is as fine with me.

[jwodder]

@yarikoptic It turns out that projects have to be created at the organization level, and I apparently don't have permission to create projects for incf-nidash.