develop #41

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jkuhl merged 210 commits from develop into master 2026-05-07 16:01:02 +02:00

Conversation 0 Commits 210 Files changed 37 +5533 -398

jkuhl commented 2026-05-07 09:36:34 +02:00

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Mayor overhaul:

• use Path type
• introduce testing
• introduce integrity checks of repository
• start abstracting the data layer to allow for different trackers
• use different default path for CLI commands
• restructure filters for record finding

Mayor overhaul: - use Path type - introduce testing - introduce integrity checks of repository - start abstracting the data layer to allow for different trackers - use different default path for CLI commands - restructure filters for record finding

jkuhl added 208 commits 2026-05-07 09:36:34 +02:00

communicate when files are downloaded d8ec6ef40e

add thin wrapper for getting files 0f499f080a

tell the user when the database is downloading 1e2f419243

Merge pull request 'fest/get_wrapper' (#6) from fest/get_wrapper into develop ... acab85df82

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/6

start refactor for data backend by only improting datalad into one submodule 44ab402c6c

test/first (#8) ... d70e8d32ce

Introducing first very simple tests for tools.py

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/8

add tests for init and version cli commands 7d8cf4274c

add two more trivial tests 574877c744

test init by itself 0af1b4e4a4

install git-annex in setup 9fd55b3d56

add simple test for listing ensembles and projects e81d10d08a

add coverage report e82b6b292c

add .coverage 3cd02a36a4

add coverage testing 64cdcb1122

add ruff tests 602324f84f

ruff compatible to YTT,E,W,F d137f67e10

Merge pull request 'test/more' (#9) from test/more into develop ... 04559cc95f

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/9

add ruff workflow f342aef951

no matrix e2a3e7c727

set python version to 3.12 4447b2ebe6

correct sfcf ruff errors ecfab2a897

Merge pull request 'test/ruff' (#10) from test/ruff into develop ... ce4d6d3dd5

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/10
Add a ruff workflow

correct mypy issues 4546688d97

correct mypy issues II c46eb68305

add mypy 854431997e

add mypy workflow 5109cbd4ab

correct typo 235a613057

Merge pull request 'test/mypy' (#11) from test/mypy into develop ... 5ec8ea682e

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/11

lint e262142e6c

chore: cleanup e57a761205

add tracker module, moularize tracking system 3963b07c5f

implement save method d5a48b91f0

create config on init 057f214e33

rename getter method 15fd97af8e

Merge branch 'develop' into refactor/data_backend 641c612a59

chore: cleanup 2100d90511

import correct file as tracker 3b64d8457b

correct syntax 18843f4d9f

remove duplicate method 38d00316e1

typing 28ea48ad66

add thin create wrapper 7240d29b46

import save from tracker 6c9b88a22f

remove config import 8993fbe4c1

correct typing errors d104d994f8

rename tracker create 59519eae3b

make file arg optional 07173e4999

use init, not create b0ef8c3fc0

cleaner implementation 294df0a6c9

change cached to be string 1264a09ed0

add option to not track b3256e0b7c

roll out save replacement 2537fea06c

throw error if not config file found aa51d5d786

avoid looking for a tracker before config exists 821bc14f4b

expose tracker option in cli c1aef6cdf2

nicer indents 1c06383f76

typing f83eab785c

use config in initialization 4b55227642

implement dynamic db name from config 0626b34337

be more careful with definitions 303dbdd2dc

add more simple init tests 0be5cb18e2

assert more vars in config 3e6c7a4fdb

remove temporary non-datalad implementation bc57087a5a

roll out tracker unlock implementation 00ec9f7f8a

lint df25acfe0a

docstrings 8f8f9b472a

Merge pull request 'refactor/data_backend' (#12) from refactor/data_backend into develop ... 155e6d952e

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/12

add docstrings for input files 029239c701

comment get_specs 3cd7896ae1

comment retruns of extract t0 and t1 54006f46f5

finish a first pitch of docstrings 4631769e81

Merge pull request 'docs/update' (#15) from docs/update into develop ... 5e712b64cf

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/15

add a simple method to show the statistics of a record 0d6ad8f552

Merge pull request 'add a simple method to show the statistics of a record' (#18) from feat/cli_stat into develop ... 06b07bc590

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/18

fix the file finder for sfcf 60b56dfb25

Merge pull request 'fix the file finder for sfcf' (#19) from fix/sfcf_file_finder into develop ... 314234fed8

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/19

write explicit setup-uv link 875d7b9461

use older setup-uv action 540160c51f

explicit install-uv version 373f3476c0

fix: cli show stat failed for single values b2ac8939a3

fix file unlock b51a69bc69

add list for stat types 6b2db911bf

fix write measurement call and reporting to user a9cc2b3f48

fix when files are unlocked or saved 96731baeb9

silence readers 52f6b0f53c

use v6 of astral action 54b42040a9

update uv setup after runner upate 0e0153bd1d

older version again ca2eb081bb

use 6.4.0 67a9e4ea4b

use v5 53067f7c47

add setup python 4a821006ed

roll out changes f05caf572d

use python 3.12 for mypy and ruff 0c01d18ecb

fix type error for now 4853c0e414

fix invalid escape in docs 7ce9742ed5

fix typo in type annotations d302ae7e0d

set up git bd581c6c12

Throw errors when parmeter file is not set c6f3603fbf

setup local cache 6cfa51f878

remove cache envs 94b677262a

remove uv cache c2296f00ee

remove pip cache a5d6b978ea

fix list test b65ee83698

Merge pull request 'fix/uv-setup' (#21) from fix/uv-setup into develop ... 158fb1d08b

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/21

add further tests for tools 776e4a3d8d

replace config file name with var 7e76966d5f

add types 6bb48f151c

use Path in type annotations 92f307b83a

use Path in type annotations oat 2 97e30fa27d

add error messages 110ddaf3a1

use pathlib.Path for directories and files 8162758cec

lint 480c04e069

Merge pull request 'tests/tools' (#22) from tests/tools into develop ... 99ec6afdfc

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/22

rename init_tests 2396a657b2

add test for project alias lookup a57138dc50

fix alias db 8a8480af32

write first trivial find test bd34b7c378

add id lookup test f8566207e3

rewrite time filter d0d5f9aa87

add test for db lookup 29558a734b

linting and hotfix 402ca07edb

any hotfix b50ffc4c6b

some more db lookup c431145a23

add customtFilter 3fd557f3ee

customtFilter after general filters 3fe8e28a68

better type annotation fir id lookup 4516ca3149

hotfix ensure that path is a Path 2fd46d452b

HOTFIX: hand over path as str b8121811f9

HOTFIX: hand over path as str 2 38b4983fed

Merge branch 'develop' into tests/find a90b992326

add tests for time filter and find project, add a first check for integrity of the database cc14e68b44

add a docstring for time filter 81af9579dc

add more templates e8360c88b9

restructure: make code filter 1a1ac5121d

HOTFIX: strings for pyerrors 3 f98521b5a1

add docstrings for openQCD filter 4673751dc3

add very simple tests or code filter and openQCD filter, fix json par strings 8db8d46a06

correct minor typos in doc 3a1e41808b

remove unnecessary output when results are empty 7275fdd4f3

add an implementation to read the first ~200 bytes of the par file of openQCD's qcd2 5c37c06b13

add thin wrapper to accomodate for input conventions, add comments 5ea8326757

restruct: give each openQCD prog it's own file 71332264cf

restruct: introduce a file for flags e654d7c1bb

correct function names 9498c1dd73

rename functions, let write_measurement decide which file type is given 8394b1fdbd

lint 2660763232

Merge pull request 'feat/qcd2_par' (#27) from feat/qcd2_par into develop ... 8736755fea

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/27

TEMPFIX: allow ms1 to not have an in or par file 3b6a8be0cc

TEMPFIX: allow ms1 to not have an in or par file part 2 9b628abc69

TEMPFIX: allow ms1 to not have an in or par file part 3 16dcca3f3d

TEMPFIX: allow ms1 to not have an in or par file part 4 e3be65beec

Merge pull request 'remove unnecessary output when results are empty' (#28) from feat/empty_find into develop ... 8ff555a639

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/28

restruct for easier tests, test drop of sfcf params e95edcb093

add counter for measurements in tomls 6e886aa06d

fix mypy issue 74d99f8d5f

Merge pull request 'feat/nmeas' (#29) from feat/nmeas into develop ... 892430ae54

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/29

add NotImplemented warning for openQCD filter 6d1f8f7f1b

add second time integrity check 91938c3c5a

add wrapper functions to check for the validity of the database 0b8c041ee5

add test on whether paths are indeed unique 65cd55ec0a

use uniqueness for complete db check 85698c377b

fix import d8bb9e4080

fix time tests dc424c3e18

proper row interation b625bf9243

Merge branch 'develop' into tests/find 111e42adeb

Merge pull request 'tests/find' (#32) from tests/find into develop ... 27d23b2de8

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/32

prepare implementation 0b1ff3cbad

Merge branch 'develop' into cli/integrity 199e9579db

make integrity checks accassible from cli 23b5d066f7

Merge pull request 'cli/integrity' (#33) from cli/integrity into develop ... 4411f63984

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/33

add check for links to files b13136a248

show progress a little 29ebafc1c4

small logic issue 37ae818589

fix typing 0535e19bf0

add dry run for loading data using the integrity functions 083d7ee3ce

add empty return 51ae53aa02

Merge pull request 'integ/links' (#34) from integ/links into develop ... 702010c8fc

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/34

Introduce thin wrapper for SQL calls d6de8e6387

Merge pull request 'Introduce thin wrapper for SQL calls' (#35) from feat/thinsql into develop ... 7e33a689b7

Reviewed-on: #35

add FileNotFound to db tests 1b338b3f6c

Merge pull request 'add FileNotFound to db tests' (#36) from test/fnftools into develop ... 0d01df1ca4

Reviewed-on: #36

use CONFIG_FILENAMR 5649a0a38c

Merge pull request 'use CONFIG_FILENAME' (#37) from fix/constant_use into develop ... 30dba29426

Reviewed-on: #37

HOTFIX: paths in update_aliases 4e3327709e

throw error if library path is not found in get_db_file 2f83c1f9cb

check whether paths exist for import 6c99653fff

pathlib for concat 93ca059fc0

add integrity check for the config-file 656f99a13c

add docs, add check for needed paths c3bf36bf52

restruct: needed paths get extra check ba4624d843

neater UX 3247cdbc40

provide docstring for repo check a2a3346f51

Breaking change for CLI: change default path to current directory ac400aa901

Merge pull request 'Breaking change for CLI: change default path to current directory' (#38) from cli/default_path into develop ... b3ead47adb

Reviewed-on: #38

Merge branch 'develop' into feat/minteg b3a0c412f2

Merge pull request 'feat/minteg' (#39) from feat/minteg into develop ... 3aba39fd9d

Reviewed-on: #39

HOTFIX: nsure path casting in find and meas_io 08d25da188

HOTFIX: ensure path casting in tools fbf802959a

HOTFIX: ensure path casting in tracker 075cb2f756

add checks of the format of the paths in the database 4c4a5fd670

correct typing issues 3c09fb7f8c

get rid of circular import ac3eb272ad

get rid of circular imports part 2 46b97acf95

Give user a sense of the severity, add basic tests 3640f163fc

add test for has_valid_times a450601b80

add simple test for key uniqueness 9d0b922db9

add test whether the ensemble in the database is the one in meas_path 32987d5557

stramline, add tests for path_format check da62af835c

Merge pull request 'feat/path_check' (#40) from feat/path_check into develop ... 08de17e6ba

Reviewed-on: #40

jkuhl added 1 commit 2026-05-07 15:27:30 +02:00

bump version b088a28291

jkuhl added 1 commit 2026-05-07 15:33:15 +02:00

Merge branch 'master' into develop 18845b0998

jkuhl merged commit a2d11f8802 into master 2026-05-07 16:01:02 +02:00

jkuhl referenced this pull request from a commit 2026-05-07 16:01:03 +02:00

Merge pull request 'develop' (#41) from develop into master

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