Deprecation of create_access_module method

[kidrahahjo]

Description

I have deprecated the create_access_module method but haven't adapted with its deprecation warning yet as no warnings were showing up on my local machine.

Motivation and Context

Fixes #303, fixes #317.

Types of Changes

• Documentation update
• Bug fix
• New feature
• Breaking change¹

¹The change breaks (or has the potential to break) existing functionality.

Checklist:

• I am familiar with the Contributing Guidelines.
• I agree with the terms of the Contributor Agreement.
• My name is on the list of contributors.
• My code follows the code style guideline of this project.
• The changes introduced by this pull request are covered by existing or newly introduced tests.

If necessary:

• I have updated the API documentation as part of the package doc-strings.
• I have created a separate pull request to update the framework documentation on signac-docs and linked it here.
• I have updated the changelog and added all related issue and pull request numbers for future reference (if applicable). See example below.

Example for a changelog entry: Fix issue with launching rockets to the moon (#101, #212).

[bdice]

@kidrahahjo Next steps:

• Make sure the deprecation warning appears when calling signac project --access, in addition to the Python API project.create_access_module(). It doesn't look like it's showing in the test output right now, but I'm not sure if it's just untested or if it's not showing for another reason.
• Hide this deprecation warning wherever it occurs in testing output, use pytest's "deprecated call" feature or something like that.
• Add access modules to the "Deprecated" section of the changelog for the next release.

[kidrahahjo]

@kidrahahjo Next steps:

• Make sure the deprecation warning appears when calling signac project --access, in addition to the Python API project.create_access_module(). It doesn't look like it's showing in the test output right now, but I'm not sure if it's just untested or if it's not showing for another reason.
• Hide this deprecation warning wherever it occurs in testing output, use pytest's "deprecated call" feature or something like that.
• Add access modules to the "Deprecated" section of the changelog for the next release.

@bdice Can I ignore the deprecation warning globally instead of using the pytest's "deprecated call" feature?

[codecov]

Codecov Report

Merging #308 into master will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #308      +/-   ##
==========================================
+ Coverage   76.18%   76.19%   +0.01%     
==========================================
  Files          43       43              
  Lines        7075     7078       +3     
==========================================
+ Hits         5390     5393       +3     
  Misses       1685     1685              

Impacted Files	Coverage Δ
signac/__main__.py	80.04% <100.00%> (+0.04%)	⬆️
signac/contrib/project.py	91.59% <100.00%> (+0.01%)	⬆️

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[tommy-waltmann]

LGTM

[bdice]

@kidrahahjo Ignoring the warning is not quite the same. Using pytest.deprecated_call ensures that the code actually triggers a deprecation warning. That means it is testable behavior.
https://docs.pytest.org/en/3.1.0/warnings.html#ensuring-function-triggers

[kidrahahjo]

@kidrahahjo Ignoring the warning is not quite the same. Using pytest.deprecated_call ensures that the code actually triggers a deprecation warning. That means it is testable behavior.
https://docs.pytest.org/en/3.1.0/warnings.html#ensuring-function-triggers

@bdice I will have a look and then do the changes where required. Thank you for providing the link.

[kidrahahjo]

@tommy-waltmann @zhou-pj
Even after testing the module test_shell.py without using pytest.deprecated_call(): then too it doesn't show up any warning. So the tests are failing. I don't know why the warning is now showing up. I think that this should not be merged until the deprecation warning starts showing up. Please help me with your views on this comment.

[tommy-waltmann]

@kidrahahjo There is nothing that immediately jumps out to me as the reason a warning is not being generated, you may have to experiment a little on your own machine as to why this is happening.

For example, you might run only this unit test and make sure, via pdb or a print statement, that the code does in fact enter the if args.access block. You might also want to check and make sure that the print statement right after the warnings.warn line is being printed to the console.

If neither of those work, you can try some of your own experiments to determine what is going on.

[kidrahahjo]

@tommy-waltmann @zhou-pj @bdice
I don't think that we should use pytest.deprecated_call() in the tests because as we are not calling the function directly rather we're running python -m signac project --access in the tests through the call method. If a user runs this command then he might get the warning. Please let me know if I'm going in the wrong direction.

[bdice]

@kidrahahjo I am going to push some changes. I finally figured out something that had been confusing me. I forgot that the deprecation warnings won't actually appear until __version__ >= deprecated_in. So until we release 1.5.0, the deprecation warnings will not appear. I kept thinking I would see deprecations appearing in the output but they didn't show up...

[bdice]

@glotzerlab/signac-maintainers Can I get a second opinion on this one-line fix for issue #317? I put it in this PR because it's related to deprecation warnings.

[bdice]

I verified that warnings are sent to stderr, not stdout.

[kidrahahjo]

@kidrahahjo I am going to push some changes. I finally figured out something that had been confusing me. I forgot that the deprecation warnings won't actually appear until __version__ >= deprecated_in. So until we release 1.5.0, the deprecation warnings will not appear. I kept thinking I would see deprecations appearing in the output but they didn't show up...

@bdice I tried with a code which had deprecated_in < __version__ but that too didn't get the warning.

[kidrahahjo]

I also tried using the print statement with file=sys.stdout. That too didn't work out for helping me debug. Can you let me know why that happened?

[bdice]

I approve. Thanks @kidrahahjo! I think this is ready to merge once I get a second opinion from someone on warnings in the signac CLI.