deprecate Project.index

[atravitz]

addresses issue #588

Description

Motivation and Context

Indexing is deprecated and we'd like to remove indexing.py in v 2.0, but to do so we need to remove dependencies in project.py.

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.

[codecov]

Codecov Report

Merging #591 (3023c03) into master (70d480e) will increase coverage by 0.00%.
The diff coverage is 100.00%.

❗ Current head 3023c03 differs from pull request most recent head e50af81. Consider uploading reports for the commit e50af81 to get more accurate results

@@           Coverage Diff           @@
##           master     #591   +/-   ##
=======================================
  Coverage   78.27%   78.27%           
=======================================
  Files          65       65           
  Lines        7069     7070    +1     
  Branches     1310     1310           
=======================================
+ Hits         5533     5534    +1     
  Misses       1231     1231           
  Partials      305      305           

Impacted Files	Coverage Δ
signac/contrib/project.py	85.30% <100.00%> (+0.01%)	⬆️

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[atravitz]

Looks like @bdice handled dependencies etc. in #593, so I'm just adding the deprecation message here.

[cbkerr]

thanks!

[bdice]

I added a changelog line. Merging. We will still need to go back and add deprecations to individual functions accepting an index argument. See #588 for a list of those methods.

[atravitz]

I added a changelog line. Merging. We will still need to go back and add deprecations to individual functions accepting an index argument. See #588 for a list of those methods.

@bdice I'm doing this now. Is there an easy way to only show a deprecation warning when a user passes the index argument? Otherwise I'll put it on all of the functions that are not already deprecated.

[bdice]

@atravitz We don't want to deprecate the whole method. Try something like this:

signac/signac/contrib/project.py

Line 169 in 0c5a096

warnings.warn(DOC_FILTER_WARNING, DeprecationWarning)

For example:

# At the top of the `project.py` file:
INDEX_DEPRECATION_WARNING = "The index argument is deprecated and will be removed in signac 2.0."

# In methods with an `index` argument, put this near the top of the method:
if index is not None:
    warnings.warn(INDEX_DEPRECATION_WARNING, DeprecationWarning)