Change config handling #410

mschwoer · 2024-12-16T10:29:37Z

change the handling of the config. The idea is to have a config dumped to disk that is fully self-contained, i.e. no additional CLI parameters are required.
strictly forbid to add new keys (as they would not be understood by AlphaDIA anyway), this requires change the modifications section
refactor what is passed to SearchPlan

See the updated docs for the motivation :-)

alphadia/constants/default.yaml

GeorgWa

Looks good!

alphadia/cli.py

alphadia/constants/multistep.yaml

alphadia/libtransform.py

alphadia/search_plan.py

alphadia/workflow/base.py

alphadia/workflow/config.py

docs/guides/transfer-dimethyl.md

install mono in CI

GeorgWa

LGTM

…fig_handling # Conflicts: # .github/workflows/_run_tests.yml # alphadia/cli.py # alphadia/search_plan.py # misc/pip_install.sh

mschwoer requested a review from GeorgWa December 16, 2024 10:31

mschwoer commented Dec 18, 2024

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alphadia/constants/default.yaml Show resolved Hide resolved

mschwoer force-pushed the change_config_handling branch from e7f8988 to 6c8854b Compare December 18, 2024 16:39

GeorgWa reviewed Dec 18, 2024

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mschwoer force-pushed the change_config_handling branch from ea3c760 to 25c4bc0 Compare December 19, 2024 06:37

mschwoer added 12 commits December 20, 2024 15:48

forbid adding new config keys

e28585d

introduce ConfigKeys

debc910

add missing parameters to config

31e0fd6

adapt docu

6033c78

change modifications structure

cdb9d0a

map cli parameters to a config dict

9bdee95

parse cli parameters config dict

aea776b

parse cli parameters config dict

ac41a02

minor improvements

c1e85a1

add config dumping

9cf125b

rename and adapt tests

9990b96

fix tests

82dfe46

mschwoer force-pushed the change_config_handling branch from 70560fa to 82dfe46 Compare December 20, 2024 14:48

mschwoer changed the base branch from rename_plan to refactor_config December 20, 2024 14:49

mschwoer marked this pull request as ready for review December 20, 2024 14:51

fix string constants

607fcf3

mschwoer requested a review from mo-sameh December 20, 2024 15:38

mschwoer added the breaking-change label Dec 20, 2024

mschwoer added 5 commits December 20, 2024 17:41

make empty cli args not part of cli_config

25dcce0

adapt keys in e2e test cases

d5a06fb

fix tests

3ad6582

install mono in CI

fb3b49b

install mono in CI

fix leftover renamings

5b9af14

GeorgWa self-requested a review December 21, 2024 18:45

GeorgWa approved these changes Dec 21, 2024

View reviewed changes

mschwoer added 7 commits December 23, 2024 13:56

custom errors on config errors

4a0fe82

allow same names in config as cli parameters

f8db8a6

fix multistep config

1cedea9

Merge remote-tracking branch 'origin/refactor_config' into change_con…

00ad59c

…fig_handling # Conflicts: # .github/workflows/_run_tests.yml # alphadia/cli.py # alphadia/search_plan.py # misc/pip_install.sh

resolve conflicts

f232ffd

resolve conflicts

c56956e

make exceptions more explicit

68b6b30

Base automatically changed from refactor_config to development January 9, 2025 10:23

mschwoer added 2 commits January 9, 2025 11:48

Merge branch 'development' into change_config_handling

4980188

fix merge issues

c23115d

mschwoer merged commit 8f32e51 into development Jan 9, 2025
5 checks passed

mschwoer deleted the change_config_handling branch January 9, 2025 11:14

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Change config handling #410

Change config handling #410

mschwoer commented Dec 16, 2024 •

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Change config handling #410

Change config handling #410

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mschwoer commented Dec 16, 2024 •

edited

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