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.

[jwodder]

@yarikoptic Question: Currently, the pythontest.yml workflow tries to upload a Junit summary of the test results as a build artifact, but this summary is not generated by anything at the moment. Do we want to generate and make use of Junit summaries, or should we just get rid of the upload step?

[jwodder]

@yarikoptic Ping on the above question.

[yarikoptic]

@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.

sorry, missed this one . Unfortunately I don't have those superpowers either. @dbkeator, @cmaumet or @vsoch - could you invite/add us (@yarikoptic and @jwodder ) at the organizational level with enough privileges to create projects if you have those super-powers?

[yarikoptic]

@yarikoptic Question: Currently, the pythontest.yml workflow tries to upload a Junit summary of the test results as a build artifact, but this summary is not generated by anything at the moment. Do we want to generate and make use of Junit summaries, or should we just get rid of the upload step?

That file with that line was added in 825aa64 and nothing even at that state suggests using junit anything, so I guess it is indeed safe to just remove it . sent #372

[khelm]

Do you need to be an admin or just a member of incf-nidash? I can invite you, I think.

[yarikoptic]

Do you need to be an admin or just a member of incf-nidash? I can invite you, I think.

Thank you @khelm for chiming in! I don't know which level we need, so we could start "low". What if you add us at some basic "write" level?
Looking at https://github.com/organizations/datalad/settings/projects where we have projects enabled, comment says "This allows members to create projects for the datalad organization. Members can create projects to organize and track issues from any datalad-owned repository." so the hope is that as soon as we become members we should be able to create projects.

[khelm]

@yarikoptic and @jwodder I invited you both to the organization. We have the same permission level as you mention above. Is this new project going to be merged back into the original one?

[jwodder]

@khelm By "project," I mean a GitHub Project, not a repository.

[yarikoptic]

thank you! I accepted and I think I can create projects now, so I expect @jwodder can too (ping us if I am wrong).

[jwodder]

Project created: https://github.com/orgs/incf-nidash/projects/1

[khelm]

Ok, great and thanks for the clarification!

[yarikoptic]

@jwodder so much of great work was already done. Could we cut a release with some "release" PR? ;)