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release: merge dev with main for release 3.0.0 #561

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wants to merge 187 commits into from
Closed

release: merge dev with main for release 3.0.0 #561

wants to merge 187 commits into from

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gcroci2
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@gcroci2 gcroci2 commented Jan 25, 2024

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DaniBodor and others added 30 commits September 22, 2023 20:16
@DaniBodor
rename Query class to DeepRankQuery
e6feec0
@DaniBodor
make DeepRankQuery a dataclass with common args
87e6156
@DaniBodor
improve readability of DeepRankQuery methods
d6112aa
@DaniBodor
create generic SingleResidueVariantQuery
068a03d 
build function not updated yet and AtomicQuery not deleted yet
@DaniBodor
merge SRV build methods
0b0f4f0 
atomic and residue builds now depend on `resolution` argument
@DaniBodor
merge both PPI queries into single dataclass
0ece474
@DaniBodor
improve readability of PPI helper functions
908f3e9
@DaniBodor
default distance_cutoff dependent on situation
985be65
@DaniBodor
update and refactor tests, notebooks, and READMEs
8630e05 
_generate_testdata.ipynb is not properly tested, because
I don't currently have the correct data on my disc
@DaniBodor
remove obsolete hydrogenation code
95ce32d
@DaniBodor
replace _load_ppi_atoms function
17eb287 
only requires a single line of code anyway
@DaniBodor
remove _get_atom_node_key method
2f08eee 
as discussed in issue #490
@gcroci2
update dev readme
fe86f62
@gcroci2
add relevant attributes to the Trainer and improve their logic
a5ad04a
@gcroci2
add tests for testing when no test is provided and when no mmodel is …
a094e2f 
…loaded/trained
@gcroci2
fix test_optim
a6209cb
@gcroci2
change dataset_train to train_data and update docs, for later functio…
d562513 
…nality refactor
@gcroci2
change dataset_train to train_data in all relevant scripts
fa45c60
@gcroci2
improve logic for handling both a pre-trained model and a dataset_tra…
fe18d3d 
…in when train is False in dataset.py
@gcroci2
add logic for handling the pre-trained model as input in DeeprankData…
f9b82de 
…set classes
@gcroci2
add tests for catching uncorrect pre-trained models
c21fe2b
@gcroci2
add folder for pretrained models in tests
fc5f6af
@gcroci2
update data paths in test_dataset.py
0a068b5
@gcroci2
implement inheritance in dataset from a pre-trained model
bcc5138
@gcroci2
add tests for inheritance from pre-trained model
5280ece
@gcroci2
add classes_to_index as inherited param and to the pre-trained model
7fcc033
@gcroci2
add classes_to_index to the tests' models
cc3d79a
@gcroci2
add classes_to_index's check to the tests
6b037ad
@gcroci2
save features_transform's lambdas as strings and load them as functio…
8e2496c 
…ns (much more reliable)
@gcroci2
update pre-trained models
11f826e
DaniBodor and others added 28 commits January 24, 2024 11:58
@DaniBodor
suggestions to README
486a8a1
@gcroci2
fix typos and edit subtitles
28b9735
@gcroci2
add toc to docs/installation.md
7a4ce85
@gcroci2
remove pyhon 3.11 from the CI
08a4013
@gcroci2
add extra input for testing release in the action.yml
0b63729
@gcroci2
remove line to run the ci
4521438
@gcroci2 @DaniBodor
Update docs/installation.md
ac12feb 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2 @DaniBodor
Update docs/installation.md
f1519d2 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Merge pull request #549 from DeepRank/534_conda_dssp_gcroci2
8718308 
build: switch to conda dssp installation
@gcroci2
Merge branch 'dev' into 539_action_for_testing_release_gcroci2
d6942f1
@gcroci2
add yml file for testing latest release
386e6ff
@gcroci2
update build names
65a8b45
@gcroci2
remove deeprank2 dir from env before installing latest release
5f24eef
@gcroci2
try to fix test-release input format
f9ecec7
@gcroci2
try to fix if condition
e9b4deb
@gcroci2
try to fix if cond
bba34e3
@gcroci2
use string for if cond on test package input
3dc2d99
@gcroci2
add pytest in latest version case
0a4ae17
@gcroci2
try to fix pytest installation
967e436
@gcroci2
make build latest release action run only when a release action is co…
974cb60 
…mpleted
@gcroci2
rename test-release input to pkg-installation-type
469139f
@gcroci2
improve description for pkg-installation-type
bdf94d8
@gcroci2
rename editable to repository
cc82882
@gcroci2
rename editable with github repo
6d832e2
@gcroci2
fix typo
6d0ca44
@gcroci2
Merge pull request #560 from DeepRank/539_action_for_testing_release_…
67ce748 
…gcroci2

ci: add GitHub action for testing the latest package version released on PyPi
@gcroci2
solve merge conflicts
2dae3ff
@gcroci2
merge dev with main
2d5ef8b
@gcroci2 gcroci2 closed this Jan 25, 2024
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Coverage Status

coverage: 84.446% (+84.4%) from 0.0%
when pulling 2d5ef8b on dev
into 8b5227f on main.

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3 participants
@gcroci2 @coveralls @DaniBodor