1d925ca364
Now using the name of the config file (without ext) as image name, meaning the name of the config file should comply with Docker image naming rules (should be the case).
2024-07-25 09:27:30 +02:00
48d3da9c7d
Removed image name from the config file, now generated from the artifact URL ( close #24 ). Fixed the "--no-cache" option when using Docker cache.
2024-07-24 18:58:50 +02:00
d2768d5373
Added initial support for Python venvs, close #21 . Disabled the Docker build cache by default, and added an option to reenable it, close #23 . Removed conditions on the existance of git_packages and misc_packages, because the workflow enforces their existance with the Nickel artifact contract.
2024-07-24 18:05:31 +02:00
aab563fbfe
Fixed shi_welder (wrong path to Git repos).
2024-07-24 16:17:11 +02:00
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
4329e333ea
Added shi_welder, renamed OAR timeout error.
2024-07-24 10:13:53 +02:00
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
5ba63ad50e
Fixed merge.
2024-07-23 17:27:10 +02:00
687b777912
Merge remote-tracking branch 'origin/workflow_config'
2024-07-23 17:26:03 +02:00
35f8b4c369
Merge branch 'main' of https://forge.chapril.org/GuilloteauQ/study-docker-repro-longevity
2024-07-23 09:38:24 +02:00
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
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
9a29c526fb
Small doc fixes.
2024-07-19 16:23:39 +02:00
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
1861f44f1e
Removed the "type" attribute in the misc_package description.
2024-07-19 15:28:58 +02:00
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
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
d791064183
Added Nickel constraint on values.
2024-07-17 14:56:38 +02:00
6897091c0d
Modified README according to changes.
2024-07-16 17:58:13 +02:00
75056727e5
Fixing quotes for formatted strings.
2024-07-16 17:53:34 +02:00
f2cfceffb0
When no cache dir is specified, cache is disabled.
2024-07-16 17:50:55 +02:00
1aaa77cba3
Fixed Nickel contract and check files. Fixed input/output files in Snakefile.
2024-07-16 17:35:09 +02:00
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
842f9d32a7
Added license.
2024-07-16 16:04:02 +02:00
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
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
f068fb91d0
Added artifact hash logging, closing #3 .
2024-07-16 12:04:29 +02:00
0841823096
Switched from YAML to JSON, closing #8 .
2024-07-16 11:01:08 +02:00
5a8d7905c6
Fixed merge.
2024-07-16 10:32:54 +02:00
73b6cd1e70
Merge branch 'main' of https://forge.chapril.org/GuilloteauQ/study-docker-repro-longevity
2024-07-16 10:32:19 +02:00
e06831bd78
Merge branch 'start_workflow'
2024-07-16 10:31:18 +02:00
fd7c11483f
Fixed example YAML to fit 'main'.
2024-07-16 10:29:46 +02:00
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
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
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
0e6b181310
Continued work on buildstatus_saver. Removed headers for CSV files, closing #4 .
2024-07-15 11:00:08 +02:00
2ad37f46f2
Initial support for Docker errors parsing.
2024-07-12 17:50:19 +02:00
23c4f7ede4
Added support for cache. Added run and clean scripts.
2024-07-12 12:10:03 +02:00
27d0331c06
Added logging to a file.
2024-07-12 11:21:14 +02:00
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
