Deprecate copytree method

[shandave]

Description

Deprecate copytree method

Motivation and Context

Resolves #432

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.

[shandave]

@bdice I deprecated the copytree method, but I'm not sure how to perform step 3 mentioned in your proposed solution.

[codecov]

Codecov Report

Merging #439 (911d7eb) into master (d3bb558) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #439      +/-   ##
==========================================
+ Coverage   77.06%   77.08%   +0.01%     
==========================================
  Files          42       42              
  Lines        5765     5768       +3     
  Branches     1129     1129              
==========================================
+ Hits         4443     4446       +3     
  Misses       1034     1034              
  Partials      288      288              

Impacted Files	Coverage Δ
signac/contrib/project.py	86.97% <100.00%> (ø)
signac/syncutil.py	76.39% <100.00%> (+0.44%)	⬆️

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[bdice]

@bdice I deprecated the copytree method, but I'm not sure how to perform step 3 mentioned in your proposed solution.

@shandave Thank you for the pull request! Step 3 is basically just a “find and replace” operation. Anywhere that the code says syncutil.copytree should be changed to shutil.copytree. We appreciate your contribution!

[b-butler]

@shandave I noticed there are a couple of references to syncutil.copytree remaining in signac/contrib/project.py lines 1439 and 1451.

[bdice]

@shandave I noticed you pushed a commit. Please tag the assigned reviewers in a comment when you're ready for someone to review again. Please add a note to the changelog and add yourself to the contributors list as you did for signac-flow. Thank you again! 😄

[shandave]

Thank You @bdice , @b-butler and @cbkerr for reviewing my commit and suggesting the changes; I would like to review my commit again, I have made all the changes suggested in the comment.

[b-butler]

@shandave I still see multiple uses of syncutil.copytree in signac/contrib/project.py. In the clone method of the Project class. This should default to shutil.copytree now.

[shandave]

Thank You @b-butler for reviewing. I have made the suggested changes.

[bdice]

@shandave The pre-checks are failing:

signac/contrib/project.py:25:1: F401 '..syncutil' imported but unused
signac/contrib/project.py:1497:35: F821 undefined name 'shutil'

You need to remove the import of syncutil and add import shutil. You should install pre-commit with these instructions to catch problems like these: https://docs.signac.io/projects/core/en/latest/support.html#set-up-a-development-environment

Also please update the changelog and contributors list.

[shandave]

Thank You @bdice for giving me an opportunity to contribute in signac. I have made the suggested changes. Thank you again for helping me out.

[bdice]

Great work @shandave! Thanks for your persistence. I have two small changes to apply. I will go ahead and make those changes, and approve this PR. Once a second reviewer approves the PR, we will merge it.

[b-butler]

LGTM