Adjust failing nightly tests for #653

[khaeru]

Since about 2022-11-08, nightly test jobs have failed with messages like the following. See logs 1, 2.

FAILED message_ix/tests/test_nightly.py::test_scenario[CD_Links_SSP2_baseline] - AssertionError: assert False
 +  where False = functools.partial(<function isclose at 0x7f465a8d6170>, rtol=3e-06)(3870157.5, 3869529.75)
 +    where functools.partial(<function isclose at 0x7f465a8d6170>, rtol=3e-06) = eval('partial(np.isclose, rtol=3e-6)')
FAILED message_ix/tests/test_nightly.py::test_scenario[CD_Links_SSP2_v2_1000] - AssertionError: assert False
 +  where False = functools.partial(<function isclose at 0x7f465a8d6170>, rtol=3e-06)(3358441.5, 3359089.0)
 +    where functools.partial(<function isclose at 0x7f465a8d6170>, rtol=3e-06) = eval('partial(np.isclose, rtol=3e-6)')

Per this Slack thread (private):

• @gidden @OFR-IIASA @behnam-zakeri suspect the cause was Correct levelized_cost calculation #653.
• To resolve the issue:
  • Confirm that the changes in the objective function value and other LP solution values are as anticipated in Correct levelized_cost calculation #653.
  • Document any implications for downstream applications of message_ix, particularly in message_data.
  • Adjust the tests or the test data with the expected results.

May be related to #667, #668, or #669.

[khaeru]

@gidden @OFR-IIASA @behnam-zakeri —I assigned all three of you, but please remove 1 or 2 when you decide who in particular will address this.

If that's to be done through #669, please remember basic housekeeping:

• Assign the PR to the person responsible.
• Add it to the "MESSAGEix team" project tracker.
• Apply any relevant labels.