GuilloteauQ/study-docker-repro-longevity
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Author SHA1 Message Date
antux18
aab563fbfe Fixed shi_welder (wrong path to Git repos). 2024-07-24 16:17:11 +02:00
antux18
8687bb03f4 Switching from pip freeze to pip list because of inconsistent output mentionned in #18, close #22. Adding albab_k9db config. 2024-07-24 11:34:05 +02:00
antux18
4329e333ea Added shi_welder, renamed OAR timeout error. 2024-07-24 10:13:53 +02:00
antux18
cc50349cf5 Almost solved the removing of bash login messages from outputs (#18) but still needs some work ("dace" pip package incorrectly displayed for deinsum). 2024-07-23 21:04:34 +02:00
antux18
5ba63ad50e Fixed merge. 2024-07-23 17:27:10 +02:00
antux18
687b777912 Merge remote-tracking branch 'origin/workflow_config' 2024-07-23 17:26:03 +02:00
antux18
35f8b4c369 Merge branch 'main' of https://forge.chapril.org/GuilloteauQ/study-docker-repro-longevity 2024-07-23 09:38:24 +02:00
antux18
557f766a02 Removing global variables, closing #19. 2024-07-23 09:38:03 +02:00
Quentin Guilloteau
944b1bf6f9 checkpoint in case of reaching walltime 2024-07-21 17:32:04 +02:00
Quentin Guilloteau
ef257e6026 add prefix to config 2024-07-21 16:14:58 +02:00
Quentin Guilloteau
566eb778f2 fix execution on grid5000 from namespace 2024-07-21 16:13:52 +02:00
Quentin Guilloteau
318955865c typo 2024-07-21 16:12:40 +02:00
Quentin Guilloteau
dd6eb9bcbb now using tmp dir to decompress the artifact 2024-07-21 16:11:55 +02:00
Quentin Guilloteau
8ed548c435 first try for g5k execution 2024-07-20 15:41:56 +02:00
antux18
cc605943a9 Added a comment section for artifacts configuration. Moved hints to the Nickel contract. 2024-07-19 17:05:46 +02:00
Quentin Guilloteau
d7749369b4 move artifacts_nickel and artifacts_json to artifacts/nickel and artifacts/json 2024-07-19 16:38:18 +02:00
Quentin Guilloteau
9769f6b533 Add config for snakemake 2024-07-19 16:33:27 +02:00
antux18
9a29c526fb Small doc fixes. 2024-07-19 16:23:39 +02:00
antux18
a7bf9cee94 Written a doc for the output. Removed the "type" attribute from the Nickel contract, closing #17. 2024-07-19 16:18:49 +02:00
antux18
1861f44f1e Removed the "type" attribute in the misc_package description. 2024-07-19 15:28:58 +02:00
antux18
cb98727554 Added artifacts_json to git ignore and deleting, closing #15. Deleted old YAML files. Added hints on the config template. 2024-07-19 15:23:00 +02:00
antux18
57ff34e8b9 Written Nickel + JSON artifact config files from their YAML version. Handling unknown errors during image building. 2024-07-18 17:56:57 +02:00
antux18
d791064183 Added Nickel constraint on values. 2024-07-17 14:56:38 +02:00
antux18
6897091c0d Modified README according to changes. 2024-07-16 17:58:13 +02:00
antux18
75056727e5 Fixing quotes for formatted strings. 2024-07-16 17:53:34 +02:00
antux18
f2cfceffb0 When no cache dir is specified, cache is disabled. 2024-07-16 17:50:55 +02:00
antux18
1aaa77cba3 Fixed Nickel contract and check files. Fixed input/output files in Snakefile. 2024-07-16 17:35:09 +02:00
antux18
69e447ab0a Fixed Nickel config files. Added artifact hash log on Snakefile + modified some variables names. Switched from 'tgz' to 'tar' for archive type. 2024-07-16 16:47:17 +02:00
antux18
842f9d32a7 Added license. 2024-07-16 16:04:02 +02:00
antux18
83a6930593 Merge pull request 'integrate nickel in workflow' (#11) from nickel_workflow into main 
Reviewed-on: #11
 2024-07-16 15:37:13 +02:00
antux18
82af4bd521 Written a doc. Changing the name of the variables related to the hash log. 2024-07-16 15:34:15 +02:00
Quentin Guilloteau
4432a93123 integrate nickel in workflow 2024-07-16 13:59:44 +02:00
antux18
f068fb91d0 Added artifact hash logging, closing #3. 2024-07-16 12:04:29 +02:00
antux18
0841823096 Switched from YAML to JSON, closing #8. 2024-07-16 11:01:08 +02:00
antux18
5a8d7905c6 Fixed merge. 2024-07-16 10:32:54 +02:00
antux18
73b6cd1e70 Merge branch 'main' of https://forge.chapril.org/GuilloteauQ/study-docker-repro-longevity 2024-07-16 10:32:19 +02:00
antux18
e06831bd78 Merge branch 'start_workflow' 2024-07-16 10:31:18 +02:00
antux18
fd7c11483f Fixed example YAML to fit 'main'. 2024-07-16 10:29:46 +02:00
antux18
127c5c5ef4 Merge pull request 'Add POC for using nickel as a configuration lang' (#2) from nickel into main 
Reviewed-on: #2
 2024-07-16 10:24:20 +02:00
antux18
9a01db7faf Now using f-strings, closing #6. Made path-related cmd args required, closing #7. Used variables in check_env for readability, closing #5. 2024-07-16 10:20:04 +02:00
antux18
da114662ba Added stdout to output. Fixed log. Opening build_status file in append mode. Added verbose flag to run script. 2024-07-15 11:28:38 +02:00
antux18
0e6b181310 Continued work on buildstatus_saver. Removed headers for CSV files, closing #4. 2024-07-15 11:00:08 +02:00
antux18
2ad37f46f2 Initial support for Docker errors parsing. 2024-07-12 17:50:19 +02:00
antux18
23c4f7ede4 Added support for cache. Added run and clean scripts. 2024-07-12 12:10:03 +02:00
antux18
27d0331c06 Added logging to a file. 2024-07-12 11:21:14 +02:00
antux18
2f779d0ab0 - Config files now contain 1 Dockerfile only. 
- Removed support for running ECG with multiple config files at the same time: will be called with a single one only
- Removed storage management of outputs, paths are now given using command line args.
- Started working on cache support.
 2024-07-11 17:14:58 +02:00
Quentin Guilloteau
46b7d349c3 Add POC for using nickel as a configuration lang 
The `check.ncl` file contains the commands what we could use directly from snakemake to validate the configs and generate the json/yaml for ecg
 2024-07-11 16:05:08 +02:00
Quentin Guilloteau
28126f8b3e basic workflow for ecg 2024-07-11 15:17:16 +02:00
Quentin Guilloteau
3737dd29e6 add start of workflow to extract non blacklisted artifacts 2024-07-11 13:37:07 +02:00
Quentin Guilloteau
1d6cec18ff create folder to store artifacts yamls 2024-07-11 13:36:22 +02:00