Update species->mass field following specification change #631

ml-evs · 2020-12-17T17:26:36Z

Closes #630 following changes introduced in Materials-Consortia/OPTIMADE#344.

optimade/adapters/structures/aiida.py

codecov · 2020-12-21T10:26:41Z

Codecov Report

Merging #631 (76b70c7) into master (2f4d721) will increase coverage by 0.00%.
The diff coverage is 97.05%.

@@           Coverage Diff           @@
##           master     #631   +/-   ##
=======================================
  Coverage   93.18%   93.19%           
=======================================
  Files          61       62    +1     
  Lines        3362     3381   +19     
=======================================
+ Hits         3133     3151   +18     
- Misses        229      230    +1

Flag	Coverage Δ
project	`93.19% <97.05%> (+<0.01%)`	⬆️
validator	`65.83% <14.70%> (-0.32%)`	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
optimade/adapters/structures/ase.py	`96.96% <85.71%> (-3.04%)`	⬇️
optimade/adapters/structures/aiida.py	`100.00% <100.00%> (ø)`
optimade/adapters/structures/cif.py	`100.00% <100.00%> (ø)`
optimade/adapters/structures/jarvis.py	`100.00% <100.00%> (ø)`
optimade/adapters/structures/proteindatabank.py	`100.00% <100.00%> (ø)`
optimade/adapters/structures/pymatgen.py	`100.00% <100.00%> (ø)`
optimade/adapters/warnings.py	`100.00% <100.00%> (ø)`
optimade/models/structures.py	`96.38% <100.00%> (+0.02%)`	⬆️

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CasperWA · 2020-12-21T10:43:32Z

@ml-evs To sum up:

I've reverted the change I did to the ASE adapter, since it was correct, as we're not taking species with multiple chemical_symbols into account.
I've added another "special species" for testing the adapters, specifically only using it for the AiiDA adapter for now.
The calculation of an AiiDA Kind mass is done by multiplying each mass with the concentration and summing it all up.
Thinking about this, I'm not completely sure this is correct, but I might be messing it all up in my own head thinking about chemistry, whereas this is not really chemistry... Hmm. Let's perhaps discuss on slack?

CasperWA · 2020-12-21T12:21:14Z

Further updates:

Created specific adapter Warnings and used them for the fallback AiiDA mass setting warning, as well as for the general warning when a Python package cannot be found in the current environment when trying to use the adapter for said package.
Updated pytest.ini to ignore a sleugh of Warnings.

CasperWA · 2020-12-21T12:22:43Z

Maybe the adapter Warnings should not subclass the server base Warning? But then the doc string for said base Warning should definitely be updated.

optimade/adapters/structures/aiida.py

ml-evs · 2021-02-17T12:08:23Z

Is there anything still holding this up @CasperWA? I'd completely forgotten about it, but we should have really gotten this into the last openapi schema update ready for spec v1.0.1

CasperWA · 2021-02-17T12:19:05Z

Is there anything still holding this up @CasperWA? I'd completely forgotten about it, but we should have really gotten this into the last openapi schema update ready for spec v1.0.1

I need to dig into it again before I can answer that question. But from a quick look it seems it's all about just testing your suggestion and that it catches the correct edge cases?

ml-evs · 2021-02-17T12:19:55Z

Is there anything still holding this up @CasperWA? I'd completely forgotten about it, but we should have really gotten this into the last openapi schema update ready for spec v1.0.1

I need to dig into it again before I can answer that question. But from a quick look it seems it's all about just testing your suggestion and that it catches the correct edge cases?

I would be strongly in favour of splitting this PR into the model changes and the adapter changes, so that we can get the model changes in before the meeting today...

Fix masses creation for AiiDA StructureData to take concentration into account.

Subclassing `optimade.server.warnings.OptimadeWarning`. Use new warnings in all adapters for reporting if adapter package is not installed. Use new warning for AiiDA if mass is set to the fallback value of 1.0. Update tests accordingly. Update pytest.ini to avoid printing a lot of the warnings messages.

CasperWA · 2021-02-17T21:37:03Z

I would consider this all good to go.

ml-evs added schema Concerns the schema models priority/high Issue or PR with a consensus of high priority models For issues related to the pydantic models directly OPTIMADE v1.0 A label for tagging issues/PRs that are required for compliance with v1.0 of the OPTIMADE spec labels Dec 17, 2020

ml-evs force-pushed the ml-evs/close_#630 branch 2 times, most recently from 5e75077 to b13de87 Compare December 17, 2020 22:46

ml-evs commented Dec 17, 2020

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ml-evs marked this pull request as ready for review December 17, 2020 22:54

CasperWA force-pushed the ml-evs/close_#630 branch from 7f2a19f to 8148ed8 Compare December 21, 2020 10:40

ml-evs commented Dec 21, 2020

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ml-evs mentioned this pull request Feb 17, 2021

Update species->mass field #710

Closed

ml-evs and others added 7 commits February 17, 2021 22:22

Update species model with new mass field format

88a4203

Updated test data with new mass format

2922ac0

Update adapters to use mass lists

72ebbf4

Properly convert list of masses to AiiDA

ea17ca5

Add test for AiiDA with masses

27e459d

Fix masses creation for AiiDA StructureData to take concentration into account.

Add warning for fallback AiiDA mass setting

59d998e

CasperWA force-pushed the ml-evs/close_#630 branch from 4ec270b to 76b70c7 Compare February 17, 2021 21:36

CasperWA approved these changes Feb 17, 2021

View reviewed changes

ml-evs merged commit 04659d4 into master Feb 19, 2021

ml-evs deleted the ml-evs/close_#630 branch February 19, 2021 19:43

dependabot bot mentioned this pull request Mar 8, 2021

Update optimade requirement from ~=0.13.1 to ~=0.13.3 CasperWA/voila-optimade-client#271

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Update species->mass field following specification change #631

Update species->mass field following specification change #631

ml-evs commented Dec 17, 2020

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CasperWA commented Feb 17, 2021

Update species->mass field following specification change #631

Update species->mass field following specification change #631

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