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. khaeru/genno#34, 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 #465.
• Close #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 #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 #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 #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

• [x] Continuous integration checks all ✅

• [x] ~Add or expand tests;~ coverage checks both ✅
• [x] Add, expand, or update documentation.

• [x] Update release notes.

[codecov[bot]]

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

```diff @@ 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](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa) | Coverage Δ | | |---|---|---| | [ixmp/\_\_init\_\_.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9fX2luaXRfXy5weQ==) | `100.0% <100.0%> (ø)` | | | [ixmp/\_config.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9fY29uZmlnLnB5) | `96.7% <100.0%> (ø)` | | | [ixmp/backend/\_\_init\_\_.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9iYWNrZW5kL19faW5pdF9fLnB5) | `100.0% <ø> (ø)` | | | [ixmp/backend/base.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9iYWNrZW5kL2Jhc2UucHk=) | `100.0% <100.0%> (ø)` | | | [ixmp/backend/io.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9iYWNrZW5kL2lvLnB5) | `98.5% <100.0%> (ø)` | | | [ixmp/backend/jdbc.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9iYWNrZW5kL2pkYmMucHk=) | `97.2% <100.0%> (+1.9%)` | :arrow_up: | | [ixmp/cli.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9jbGkucHk=) | `100.0% <100.0%> (ø)` | | | [ixmp/core/platform.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9jb3JlL3BsYXRmb3JtLnB5) | `98.9% <100.0%> (ø)` | | | [ixmp/core/scenario.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9jb3JlL3NjZW5hcmlvLnB5) | `98.3% <100.0%> (+0.4%)` | :arrow_up: | | [ixmp/core/timeseries.py](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC9jb3JlL3RpbWVzZXJpZXMucHk=) | `98.7% <100.0%> (ø)` | | | ... and [21 more](https://app.codecov.io/gh/iiasa/ixmp/pull/500?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa) | |