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JPBergsma/partial data #1812

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JPBergsma/partial data #1812

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JPBergsma
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PR to implement the partial data mechanism and the JSON lines return format as described in PR#467, and PR#481

@JPBergsma
Addded meta field to entry model
eecc878
@JPBergsma
Added validator for meta field.
6ed4a5d
@JPBergsma
Merge branch 'master' into JPBergsma/add_metadata
5e0ace4
@JPBergsma
Update pyyaml version in requirements.txt
ef1ca3c
@JPBergsma
Update requirements.txt
89ac0fe
@JPBergsma
Update requirements.txt
f229be1
@JPBergsma
Merge branch 'master' into JPBergsma/add_metadata
fcc501c
@JPBergsma
Remove test structures to get an idea of what triggers yaml import er…
a195fb5 
…ror on github.
@JPBergsma
Readding meta field to test_good_structures.
07d77fe
@JPBergsma
Readding meta field to test_structures.json.
2848dd3
@JPBergsma
Added handling None for property_metadata to validator + small correc…
80c4dc4 
…tionds.
@JPBergsma
Added test for validator per entry meta field.
d55abec
@JPBergsma
Added test for presence metadata field in test_structures.py.
ff545bb
@JPBergsma
Remove metadata fields when the fields that they belong to are not re…
e0d6ff3 
…turned.
@JPBergsma
add extra test for bad prefix.
191fbba
@JPBergsma
Merge branch 'master' into JPBergsma/add_metadata
8764e34
@JPBergsma
Test if dependancy conflict causes error.
6251e48
@JPBergsma
Merge branch 'master' into JPBergsma/add_metadata
c6be5ca
@JPBergsma
Revert "Test if dependancy conflict causes error."
bf9692a 
This reverts commit 6251e48.
@JPBergsma
Revert "Revert "Test if dependancy conflict causes error.""
0864911 
This reverts commit bf9692a.
@JPBergsma
Merge branch 'JPBergsma/add_metadata' of https://github.com/JPBergsma…
03f91f1 
…/optimade-python-tools into JPBergsma/add_metadata
@JPBergsma
correct version httpx.
eb953ad
@JPBergsma
commenting out validator to see if this resolves issue github.
2879fac
@JPBergsma
Slowly reassembling validator to see if this resolves issue github.
18e2ef1
@JPBergsma
Slowly reassembling validator to see if this resolves issue github.
7fc1906
@JPBergsma
Slowly reassembling validator to see if this resolves issue github.
b622414
@JPBergsma
Slowly reassembling validator to see if this resolves issue github.
95bf11b
@JPBergsma
Slowly reassembling validator to see if this resolves issue github.
7c02f38
@JPBergsma
Slowly reassembling validator to see if this resolves issue github.
2b52248
@JPBergsma
Slowly reassembling validator to see if this resolves issue github.
20e228d
@JPBergsma JPBergsma changed the title Jp bergsma/partial data JPBergsma/partial data Oct 13, 2023
JPBergsma and others added 15 commits October 13, 2023 17:44
@JPBergsma
Trying to determine why jsonlines is not impoeted properly on github.
ca2a0f2
@JPBergsma
Update requirements-client.txt (Materials-Consortia#1813)
cf45488 
removed duplicate requirement
@JPBergsma
Merge branch 'master' of https://github.com/JPBergsma/optimade-python…
2466fb1 
…-tools
@JPBergsma
Merge branch 'master' into JPBergsma/add_metadata
ff25f14
@JPBergsma
Merge branch 'JPBergsma/add_metadata' into JPBergsma/Partial_data
1dbd07a
@ml-evs @CasperWA
Modernize all Python 3.8 annotations (Materials-Consortia#1815)
8510ffa 
* Use Python 3.9 as the 'base' CI version for linting

* Update pre-commit hooks

* Run `pyupgrade --py39-plus` to upgrade legacy annotations

* Add `--exit-non-zero-on-fix` for ruff

Co-authored-by: Casper Welzel Andersen <[email protected]>

* Use f-string over format

Co-authored-by: Casper Welzel Andersen <[email protected]>

---------

Co-authored-by: Casper Welzel Andersen <[email protected]>
@JPBergsma
Merging with master.
44d8789
@JPBergsma
merging with metadata branch
563948e
@JPBergsma
backporting bugfixes from of the JPBergsma/trajectory_endpoint branch.
4fe22a2
@JPBergsma
Expanded model partial_data.
870018d
@JPBergsma
Expanded model partial_data.
da11332
@JPBergsma
Clarified why field is named describedby and not described_by.
61361b8
@JPBergsma
Removed unneccesary empty line
e4c2293
@JPBergsma
Somehow the line setting the filepointer to 0 has gone missing.
e04387f
@JPBergsma
Skip partial_data tests for elastic search for which it has not been …
bf29459 
…implemented yet.
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codecov bot commented Oct 19, 2023 •
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Codecov Report

Attention: Patch coverage is 94.16667% with 35 lines in your changes missing coverage. Please review.

Project coverage is 90.65%. Comparing base (f28a6e1) to head (bf29459).
Report is 11 commits behind head on 0.25.x.

Files Patch % Lines
optimade/server/entry_collections/mongo.py 81.63% 18 Missing ⚠️
optimade/server/routers/utils.py 87.09% 8 Missing ⚠️
optimade/adapters/jsonl.py 89.65% 3 Missing ⚠️
optimade/models/entries.py 96.72% 2 Missing ⚠️
optimade/server/routers/structures.py 66.66% 2 Missing ⚠️
optimade/client/cli.py 66.66% 1 Missing ⚠️
optimade/filtertransformers/elasticsearch.py 66.66% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           0.25.x    #1812      +/-   ##
==========================================
- Coverage   90.77%   90.65%   -0.12%     
==========================================
  Files          74       78       +4     
  Lines        4629     4956     +327     
==========================================
+ Hits         4202     4493     +291     
- Misses        427      463      +36
Flag Coverage Δ
project 90.65% <94.16%> (-0.12%) ⬇️
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Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
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@ml-evs ml-evs changed the base branch from master to 0.25.x October 23, 2023 12:56
@ml-evs
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ml-evs commented Oct 23, 2023

Hi @JPBergsma, I've just changed the base branch of this PR and others to the new 0.25.x branch until we can port things over. I would suggest you keep working as you see fit, and we can then try to port your changes over to the new format once finished.

@ml-evs ml-evs mentioned this pull request Mar 21, 2024
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@ml-evs ml-evs added the OPTIMADE v1.2 This label describes actions that have to be taken to be complient with OPTIMADE 1.2 label Jun 11, 2024
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@CasperWA CasperWA Awaiting requested review from CasperWA CasperWA will be requested when the pull request is marked ready for review CasperWA is a code owner

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@markus1978 markus1978 Awaiting requested review from markus1978 markus1978 will be requested when the pull request is marked ready for review markus1978 is a code owner

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