Rename 'report', 'util' + miscellaneous clean-ups

[khaeru]

• Use preferred module names per message-ix-models and genno:
  • ixmp.reporting → ixmp.report.
  • reporting.computations → report.operator (cf. Change term ‘computations’? khaeru/genno#34, Add an Operator class khaeru/genno#98).
  • ixmp.utils → ixmp.util.
• Provide .util.DeprecatedPathFinder to support imports from the previous locations and raise deprecation warnings.
• Improve documentation:
  • Address >100 Sphinx "nitpicks"—missing or unresolveable references, typos, errors, etc.; mainly in old code, identified with make SPHINXOPTS="-n" html.
  • Add .. automodule:: ixmp for the top-level module; this allows other projects to link to :mod:'ixmp' directly via intersphinx.
  • Add a documentation page for the command-line interface.
  • Update documentation links to genno.Computer and genno.operator.
• Close Adjust for mypy --no-implicit-optional #465.
• Close error in read_sol_from_gdx #98.

Items related to TODOs and FIXMEs in message_ix, message-ix-models, and message_data:

• Add the reporting operators from_url(), get_ts(), and remove_ts() (currently in message-ix-models).
• Close Add indexed_by= arg to Scenario.par_list() etc. #402.
• Add a CLI command "ixmp platform copy"; currently sits downstream in message_data.model.transport.cli here.
• Update JDBCBackend to handle some work-arounds that currently sit downstream:
  • Unit "" cannot be added with Oracle driver (currently in message-ix-models here). Closes Adding dimensionless unit through add_units() leads to an error #425.
  • Items cannot be initialized with a non-empty list of index sets, even if the list matches the one hard-coded in the ixmp_source Java code (currently in message_ix here).

Miscellaneous housekeeping:

• Add Python 3.12 placeholders to CI and packaging files; see Support Python 3.12 #501

How to review

• Read the generated docs:
  • Ensure the migration notes are clear.
  • Look for missing links or content.
• Note the CI checks all pass.
• Run downstream (message_ix, message-ix-models, message_data) test suites; confirm tests pass and appropriate warnings are raised.

PR checklist

• Continuous integration checks all ✅
• Add or expand tests; coverage checks both ✅
• Add, expand, or update documentation.
• Update release notes.

[codecov]

Codecov Report

Merging #500 (a8819d1) into main (f419427) will increase coverage by 0.3%.
The diff coverage is 100.0%.

Additional details and impacted files

@@           Coverage Diff           @@
##            main    #500     +/-   ##
=======================================
+ Coverage   98.5%   98.8%   +0.3%     
=======================================
  Files         42      44      +2     
  Lines       4554    4747    +193     
=======================================
+ Hits        4489    4694    +205     
+ Misses        65      53     -12     

Files	Coverage Δ
ixmp/__init__.py	100.0% <100.0%> (ø)
ixmp/_config.py	96.7% <100.0%> (ø)
ixmp/backend/__init__.py	100.0% <ø> (ø)
ixmp/backend/base.py	100.0% <100.0%> (ø)
ixmp/backend/io.py	98.5% <100.0%> (ø)
ixmp/backend/jdbc.py	97.2% <100.0%> (+1.9%)	⬆️
ixmp/cli.py	100.0% <100.0%> (ø)
ixmp/core/platform.py	98.9% <100.0%> (ø)
ixmp/core/scenario.py	98.3% <100.0%> (+0.4%)	⬆️
ixmp/core/timeseries.py	98.7% <100.0%> (ø)
... and 21 more