Confirm support for Python 3.13 and drop 3.8

[khaeru]

• Check/confirm that message-ix-models is compatible with the new version. This includes:
  • iiasa/ixmp#544
  • iiasa/message_ix#881
  • [x] Add an explicit CI job for ixmp/message-ix 3.9.0.
  • [x] Bump GAMS version in CI from 29.1.0 to 43.4.1.
• Drop support for Python 3.8, which reached end-of-life (no more updates, even security updates) "approximately [during, before, or after] October 2024" per PEP 569.
  • [x] Remove any code marked as for Python 3.8 compatibility only. Depending on these changes, part or all of the functionality may remain usable with Python 3.8 if users have extreme need.
  • [x] Make any general clean-ups or improvements possible with features available from Python 3.9.
    • [x] Type hint using generics, e.g. list[str] instead of from typing import List/List[str].
    • [x] Use from collections.abc import Sequence et al instead of deprecated from typing import Sequence.

How to review

• Read the diff and note that the CI checks all pass.

PR checklist

• [x] Continuous integration checks all ✅

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

• [x] Update doc/whatsnew.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 97.24138% with 4 lines in your changes missing coverage. Please review.

Project coverage is 75.6%. Comparing base (012b501) to head (0c40618). Report is 13 commits behind head on main.

Files with missing lines	Patch %	Lines
...ge_ix_models/util/compat/message_data/utilities.py	0.0%	2 Missing :warning:
message_ix_models/project/navigate/__init__.py	85.7%	1 Missing :warning:
message_ix_models/util/click.py	75.0%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #250 +/- ## ======================================= - Coverage 76.5% 75.6% -1.0% ======================================= Files 203 203 Lines 15578 15600 +22 ======================================= - Hits 11927 11801 -126 - Misses 3651 3799 +148 ``` | [Files with missing lines](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa) | Coverage Δ | | |---|---|---| | [message\_ix\_models/model/build.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Fbuild.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvYnVpbGQucHk=) | `100.0% <100.0%> (ø)` | | | [message\_ix\_models/model/disutility.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Fdisutility.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvZGlzdXRpbGl0eS5weQ==) | `100.0% <100.0%> (ø)` | | | [message\_ix\_models/model/emissions.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Femissions.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvZW1pc3Npb25zLnB5) | `98.0% <100.0%> (ø)` | | | [message\_ix\_models/model/macro.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Fmacro.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvbWFjcm8ucHk=) | `100.0% <100.0%> (ø)` | | | [message\_ix\_models/model/material/build.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Fmaterial%2Fbuild.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvbWF0ZXJpYWwvYnVpbGQucHk=) | `67.8% <100.0%> (+0.2%)` | :arrow_up: | | [message\_ix\_models/model/material/data\_aluminum.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Fmaterial%2Fdata_aluminum.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvbWF0ZXJpYWwvZGF0YV9hbHVtaW51bS5weQ==) | `90.5% <100.0%> (ø)` | | | [message\_ix\_models/model/material/data\_methanol.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Fmaterial%2Fdata_methanol.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvbWF0ZXJpYWwvZGF0YV9tZXRoYW5vbC5weQ==) | `92.0% <100.0%> (ø)` | | | [message\_ix\_models/model/material/data\_petro.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Fmaterial%2Fdata_petro.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvbWF0ZXJpYWwvZGF0YV9wZXRyby5weQ==) | `78.7% <100.0%> (-0.2%)` | :arrow_down: | | [message\_ix\_models/model/material/data\_steel.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Fmaterial%2Fdata_steel.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvbWF0ZXJpYWwvZGF0YV9zdGVlbC5weQ==) | `87.0% <100.0%> (ø)` | | | [message\_ix\_models/model/material/data\_util.py](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree&filepath=message_ix_models%2Fmodel%2Fmaterial%2Fdata_util.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-bWVzc2FnZV9peF9tb2RlbHMvbW9kZWwvbWF0ZXJpYWwvZGF0YV91dGlsLnB5) | `33.3% <100.0%> (+0.1%)` | :arrow_up: | | ... and [43 more](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa) | | ... and [4 files with indirect coverage changes](https://app.codecov.io/gh/iiasa/message-ix-models/pull/250/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa)

---

🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[khaeru]

adapt the snapshot-workflow file to use the newer GAMS version

Ah good catch—will do.