Commit Graph

105 Commits

Author SHA1 Message Date
72a638cd17 Added conference date to Nickel contract + artifacts (close #29). Changes localhost to 127.0.0.1 in test artifact, because localhost doesn't work in a Nix environment. 2024-08-20 17:44:41 +02:00
37176178f1 Restored blacklist. 2024-08-19 19:09:41 +02:00
0a8b0c85c6 Fixed analysis part in Snakemake again, needs testing. Moved test and template artifacts back to parent folder. Changes analysis output dir. 2024-08-19 19:02:23 +02:00
ece5749b7a Fixed analysis in Snakefile. Started working on plotting part. 2024-08-19 16:37:51 +02:00
f6f20cb0d6 Integrated the whole analysis part to the Snakefile, but needs testing (#44). 2024-08-19 15:21:28 +02:00
e943be4efe Integrated softenv analysis to workflow. Changed input and output cmd options in analysis scripts to take multiple files at once. Moved test and template artifacts in an excluded folder. 2024-08-19 14:59:08 +02:00
1e5dd77cd8 Working on the integration of the analysis to the snakemake workflow. 2024-08-16 17:41:20 +02:00
744b3b0d35 Added doc for running the Snakemake workflow. 2024-08-15 12:32:39 +02:00
0bbed9d0f5 Adding missing changes from the previous commit because I wasn't in the root folder... 2024-08-15 12:23:34 +02:00
cb1a62217c The handling of the output of ECG and of ECG's own errors has been transfered to a new wrapper script that calls ECG. Now, ECG doesn't take an output log file as parameter, rather just write everything to the terminal. It is then retrieved by the wrapper scripts that writes the ouput to the given output log file, and logs any script crash. README has been updated according to these changes, and the verbose and log path options of ECG have been removed. Close #25.
Started integrating the analysis to the workflow, not done yet (#44).
Removed legacy line and bar plot scripts.
2024-08-15 12:16:53 +02:00
aad9318e6e Updated README with plot script and protocol. 2024-08-14 12:58:55 +02:00
13780c9f39 Finished bar plots. Merged bar and line plots into a single plot script. 2024-08-14 12:51:52 +02:00
b7a84c5a78 Improved the formatting of dates in R plots. Switched to a functionnal approach in the line plot. Broke the bar plot while trying to improve the formatting of dates :( Added the tidyverse R package to the Nix flake. 2024-08-09 18:31:17 +02:00
5aae58d680 Initial script for bar plotting. Continued line plot script (started in the last commit, but forgot to mention it). 2024-08-07 20:50:42 +02:00
e2903ffac1 Removed the headers from the output of the analysis, because they will have to be combined. So I made the columns deterministic. Added the supported package sources to the doc. Updated the protocol with the information from the doc + typos. 2024-08-07 19:51:21 +02:00
c816cbde2c Updated doc. 2024-08-07 17:32:46 +02:00
a5e32f9224 Added timestamp to each row of each analysis' result. Package changes analysis now specifies if a package source has no packages that changed. 2024-08-07 17:31:35 +02:00
3d6b6d1ade Updated doc with more details. 2024-08-07 16:51:19 +02:00
56c3682124 Finished the package changes analysis. 2024-08-07 12:26:36 +02:00
4b91a6cb5d Modified analysis according to the fact that logs for multiple executions of ECG will not be appended to the same file, rather written to a new file every time. Added a column for the artifact name in the artifact hash log for that reason. Updated README. Added sed as dependency for Nix. Started writing package changes analysis. 2024-08-07 11:22:54 +02:00
eae7c40d59 Added timestamp to every row in package list (close #38). 2024-08-06 16:59:36 +02:00
58dd52e403 Separated the analysis into 3 different scripts. 2024-08-06 16:50:07 +02:00
74228cd1c5 Now optional with a default value in the Nickel contract: version, comment, git_packages, misc_packages, python_venvs (close #30). 2024-08-06 11:44:38 +02:00
ac6c100c6b Fixed venv pkglist (close #21). 2024-08-05 18:22:38 +02:00
ab72ee398c output_analysis now takes multiple files and not just a single directory as argument for the analysis input (close #36). 2024-08-05 17:19:45 +02:00
cd9a9000d5 Adding a column with the name of the artifact in each row of the package list (close #37). 2024-08-05 17:04:42 +02:00
ea6d78dac2 Switched from an empty hash to indicate download failure to a hash equal to "-1". Fixed a bug where the cache folder would not be removed in case artifact download failed. 2024-08-05 16:29:07 +02:00
Quentin Guilloteau
199d1dc282 minor improvement to protocol 2024-08-02 17:49:55 +02:00
Quentin Guilloteau
43ceead6b0 Continue writing the protocol 2024-08-02 11:04:30 +02:00
Quentin Guilloteau
a24091b390 start writing protocol 2024-08-01 17:49:41 +02:00
114d0e5816 Added support for other virtualization techs in the Nickel contract (close #28). Added Nix dependency for Snakemake diagram generation. 2024-07-30 18:06:16 +02:00
ff2fc2d365 Added version number to the Nickel contracts and artifacts (close #27). 2024-07-29 16:39:30 +02:00
14ca1da160 Now handling the script's own crashes: saving to log and build status file (close #25). 2024-07-29 15:17:22 +02:00
e8b25b74a7 Added build status analysis. Now logging build status even if build is successful, to make analysis easier (as mentionned in #26). Added a new error type. 2024-07-26 19:00:25 +02:00
4db323fb03 Implemented artifact hash analysis. Switched to a table of tables instead of a single table to be able to identify multiple artifacts for the artifact analysis. 2024-07-26 17:01:59 +02:00
f25f5e356d Handling the case where artifact/misc packages cannot be downloaded. 2024-07-26 13:28:26 +02:00
8574c5e238 Softenv analysis written. 2024-07-26 12:58:00 +02:00
3c648c1a09 Written skeleton for output analysis (#26). Renamed some arguments of ECG. 2024-07-25 18:03:14 +02:00
e118cf3da1 Added the convention on config file name on the doc. 2024-07-25 09:32:52 +02:00
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