Add precautionary checks to Model.initialize_items

[khaeru]

This PR adds changes necessary for iiasa/message_ix#190. In particular, it ensures that the Model.initialize() method is always called when a Scenario is cloned or loaded.

This helps in the following way:

• In that PR, MESSAGE.initialize() is expanded to add sets and parameters related to storage to any existing Scenario that lacks them. E.g. in test_legacy_version, an old Scenario is loaded that lacks the storage parameters. Solving that Scenario with the updated MESSAGE GAMS code fails, because the items expected are not found.
• The code in this PR ensures that MESSAGE.initialize() is invoked when that Scenario is loaded: https://github.com/behnam-zakeri/message_ix/blob/43a98fe3e416bf1fe61af54f3243052dc162f23d/message_ix/tests/test_legacy_version.py#L15-L16

Also:

• Model.initialize_items() checks whether the returned object is in a checked-out state when it is received, and leaves the object in the same state.
• Backend.init_ts() and Backend.init_s() are consolidated and simplified.
• Scenario.__init__() now chains through its parent method, TimeSeries.__init__().
• Made some follow-up changes to Add ixmp show-versions #320. test_show_versions would load pyam and message_data, which both change the pint 'application registry'; this would cause the ixmp reporting tests related to units to fail, depending on which subset of tests was run.

How to review

• Note that CI passes.
• Run with Implementation of generic storage equations message_ix#190 and confirm the message_ix test test_legacy_version passes.

PR checklist

• Tests added.
• Documentation added.
• Release notes updated.

[codecov]

Codecov Report

Merging #315 into master will increase coverage by 0.12%.
The diff coverage is 99.25%.

@@            Coverage Diff             @@
##           master     #315      +/-   ##
==========================================
+ Coverage   97.43%   97.56%   +0.12%     
==========================================
  Files          41       41              
  Lines        4292     4353      +61     
==========================================
+ Hits         4182     4247      +65     
+ Misses        110      106       -4     

Impacted Files	Coverage Δ
ixmp/model/gams.py	97.67% <ø> (+4.34%)	⬆️
ixmp/core.py	95.63% <95.45%> (-0.18%)	⬇️
ixmp/backend/base.py	98.63% <100.00%> (-0.02%)	⬇️
ixmp/backend/jdbc.py	95.17% <100.00%> (+0.44%)	⬆️
ixmp/model/base.py	100.00% <100.00%> (ø)
ixmp/model/dantzig.py	100.00% <100.00%> (+4.76%)	⬆️
ixmp/reporting/utils.py	95.83% <100.00%> (+0.18%)	⬆️
ixmp/testing.py	94.15% <100.00%> (+0.23%)	⬆️
ixmp/tests/backend/test_base.py	98.27% <100.00%> (-0.03%)	⬇️
ixmp/tests/reporting/test_computations.py	100.00% <100.00%> (ø)
... and 8 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update fd7f77b...4ddee80. Read the comment docs.

[behnam-zakeri]

Thanks @khaeru for imprving the code to account for temporary and/or new items introduced in a development branch. I see this very useful, as the user can add these new/temporary items in one place message_ix.models.py and make sure that the entire ixmp-message_ix ecosystem will handle these items as expected. I tested this in combination with #190 in message_ix and it works well.