Add letter checking for release version

[braffes]

Hi again,

It should be interesting, if the comparison between version works with version which contains letter.

For example, currently I have:

2021-07-02 17:04:09,964 DEBUG [root][MainThread] found a release 4.1a
2021-07-02 17:04:09,964 DEBUG [root][MainThread] compare next release 4.1c
2021-07-02 17:04:09,964 DEBUG [root][MainThread] compare release major,minor,etc. : 4 >? 4
2021-07-02 17:04:09,964 DEBUG [root][MainThread] compare release major,minor,etc. : 1c >? 1a
2021-07-02 17:04:09,964 DEBUG [root][MainThread] compare next release 4.2a
2021-07-02 17:04:09,964 DEBUG [root][MainThread] compare release major,minor,etc. : 4 >? 4
2021-07-02 17:04:09,964 DEBUG [root][MainThread] compare release major,minor,etc. : 2a >? 1a
2021-07-02 17:04:09,964 DEBUG [root][MainThread] compare next release 4.2c
2021-07-02 17:04:09,964 DEBUG [root][MainThread] compare release major,minor,etc. : 4 >? 4
2021-07-02 17:04:09,964 DEBUG [root][MainThread] compare release major,minor,etc. : 2c >? 1a
2021-07-02 17:04:10,070 INFO  [root][MainThread] Workflow:DownloadService:CleanSession
2021-07-02 17:04:10,073 INFO  [root][MainThread] Session:RemoteRelease:4.1a
2021-07-02 17:04:10,073 INFO  [root][MainThread] Session:Release:4.1a
2021-07-02 17:04:10,073 INFO  [root][MainThread] Workflow:Start:download
2021-07-02 17:04:10,074 INFO  [root][MainThread] Workflow:wf_download

As we see, when the version contains letters, the verification doesn't work.

Thanks for you attention,

Brice

[osallou]

More complex to do.
Code was quite simple, comparing ints

Letters should be detected, and compared, in different patterns...

[braffes]

Maybe the following module can do the jobs:
https://packaging.pypa.io/en/latest/version.html

Without a new module, it should be more complicated ...

[osallou]

could be, will investiguate

now, anyway, will not work in all cases, if versions do not follow some patterns

[braffes]

It seems there is an other issue with the current algorithm.

2021-07-05 13:07:28,183 DEBUG [root][MainThread] found a release 2.1.1
2021-07-05 13:07:28,183 DEBUG [root][MainThread] compare next release 2.0.2
2021-07-05 13:07:28,183 DEBUG [root][MainThread] compare release major,minor,etc. : 2 >? 2
2021-07-05 13:07:28,183 DEBUG [root][MainThread] compare release major,minor,etc. : 0 >? 1
2021-07-05 13:07:28,183 DEBUG [root][MainThread] compare release major,minor,etc. : 2 >? 1
2021-07-05 13:07:28,183 DEBUG [root][MainThread] found newer release 2.0.2
2021-07-05 13:07:28,184 INFO  [root][MainThread] Workflow:DownloadService:CleanSession
2021-07-05 13:07:28,185 INFO  [root][MainThread] Session:RemoteRelease:2.0.2
2021-07-05 13:07:28,185 INFO  [root][MainThread] Session:Release:2.0.2

The good algorithm should stop after comparing 0 >?1, but this is not the case.

[osallou]

Hum, need complete recheck of the algo...
Was made quickly for a specific need

[osallou]

Hi, i will be off for some time (holidays), feel frree to submit a pr for this issue meanwhile i you feel so ;-) Else will manage this after my holidays :-) I will follow requests Le lun. 5 juil. 2021 à 13:20, Brice Raffestin ***@***.***> a écrit :

…

It seems there is an other issue with the current algorithm. 2021-07-05 13:07:28,183 DEBUG [root][MainThread] found a release 2.1.1 2021-07-05 13:07:28,183 DEBUG [root][MainThread] compare next release 2.0.2 2021-07-05 13:07:28,183 DEBUG [root][MainThread] compare release major,minor,etc. : 2 >? 2 2021-07-05 13:07:28,183 DEBUG [root][MainThread] compare release major,minor,etc. : 0 >? 1 2021-07-05 13:07:28,183 DEBUG [root][MainThread] compare release major,minor,etc. : 2 >? 1 2021-07-05 13:07:28,183 DEBUG [root][MainThread] found newer release 2.0.2 2021-07-05 13:07:28,184 INFO [root][MainThread] Workflow:DownloadService:CleanSession 2021-07-05 13:07:28,185 INFO [root][MainThread] Session:RemoteRelease:2.0.2 2021-07-05 13:07:28,185 INFO [root][MainThread] Session:Release:2.0.2 The good algorithm should stop after comparing 0 >?1, but this is not the case. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#127 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAH2AYQE6XNMZCV473ANQ33TWGIRNANCNFSM47W5CMGQ> .

[braffes]

Since the version 22.0 of packaging, my pull request broke the version check when an underscore is used :
Before 21.3 :

(biomaj) [biomaj-prod@maestro-biomaj-prod config]$ biomaj-cli.py --update --bank uniref30                                                                                              
2025-03-11 12:38:39,872 INFO  [root][MainThread] Log file: /opt/biomaj/log/uniref30/1741693119.8690608/uniref30.log                                                                    
2025-03-11 12:38:39,882 WARNI [root][MainThread] Bank:uniref30:Update
2025-03-11 12:38:39,883 INFO  [root][MainThread] Bank:uniref30:Release:latest
2025-03-11 12:38:39,884 INFO  [root][MainThread] Workflow:Start
2025-03-11 12:38:39,884 INFO  [root][MainThread] Workflow:Start:init
2025-03-11 12:38:39,884 INFO  [root][MainThread] Workflow:wf_init
2025-03-11 12:38:39,885 INFO  [root][MainThread] Workflow:Skip:check
2025-03-11 12:38:39,885 INFO  [root][MainThread] Workflow:Skip:depends
2025-03-11 12:38:39,885 INFO  [root][MainThread] Workflow:Skip:preprocess
2025-03-11 12:38:39,885 INFO  [root][MainThread] Workflow:Start:release
2025-03-11 12:38:39,885 INFO  [root][MainThread] Workflow:wf_release
2025-03-11 12:38:39,885 INFO  [root][MainThread] Workflow:wf_release:previous_session:2023_02                                                                                          
2025-03-11 12:38:39,885 INFO  [root][MainThread] Use remote: False
2025-03-11 12:38:39,885 INFO  [root][MainThread] Workflow:wf_release:DownloadSession:ea2125a8-da44-41d6-ae61-95a4a7ca5572                                                              
2025-03-11 12:38:40,243 INFO  [root][MainThread] Download was redirected to https://wwwuser.gwdguser.de/~compbiol/uniclust/ (4 redirection(s), took 0.10241s)                          
2025-03-11 12:38:40,243 WARNI [biomaj][MainThread] archive_check: unable to process check call for '/local/scratch/tmp/tmpkmp0qfnabiomaj/uniclust'                                     
2025-03-11 12:38:40,245 INFO  [root][MainThread] Workflow:DownloadService:CleanSession
2025-03-11 12:38:40,247 INFO  [root][MainThread] Workflow:wf_release:same_as_previous_session                                                                                          
2025-03-11 12:38:40,247 INFO  [root][MainThread] Workflow:wf_over
2025-03-11 12:38:40,248 INFO  [root][MainThread] Workflow:Skip:download
2025-03-11 12:38:40,248 INFO  [root][MainThread] Workflow:Skip:postprocess
2025-03-11 12:38:40,248 INFO  [root][MainThread] Workflow:Skip:publish
2025-03-11 12:38:40,248 INFO  [root][MainThread] Workflow:Skip:over
2025-03-11 12:38:40,258 INFO  [root][MainThread] Notify:biomaj@pasteur.fr
2025-03-11 12:38:40,259 INFO  [root][MainThread] BANK[uniref30] - STATUS[True] - UPDATE[False] - REMOVE[False] - RELEASE[2023_02]                                                      
Bank update request sent for uniref30

22.0 and after:

[...]
2025-03-11 12:42:21,834 INFO  [root][MainThread] Workflow:wf_release:DownloadSession:e49091ad-3c41-43ab-9184-5189cf0b56df
2025-03-11 12:42:22,447 INFO  [root][MainThread] Download was redirected to https://wwwuser.gwdguser.de/~compbiol/uniclust/ (4 redirection(s), took 0.066538s)
2025-03-11 12:42:22,447 WARNI [biomaj][MainThread] archive_check: unable to process check call for '/local/scratch/tmp/tmp3n1wvnknbiomaj/uniclust'
2025-03-11 12:42:22,448 ERROR [root][MainThread] Workflow:release:Exception:Invalid version: '2023_02'
Traceback (most recent call last):
  File "/opt/biomaj/lib/python3.11/site-packages/biomaj/workflow.py", line 130, in start
    self.session._session['status'][flow['name']] = getattr(self, 'wf_' + flow['name'])()
                                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/biomaj/lib/python3.11/site-packages/biomaj/workflow.py", line 794, in wf_release
    release = self.__findLastRelease(rels)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/biomaj/lib/python3.11/site-packages/biomaj/workflow.py", line 518, in __findLastRelease
    release_version = parse(release)
                      ^^^^^^^^^^^^^^
  File "/opt/biomaj/lib/python3.11/site-packages/packaging/version.py", line 52, in parse
    return Version(version)
           ^^^^^^^^^^^^^^^^
  File "/opt/biomaj/lib/python3.11/site-packages/packaging/version.py", line 197, in __init__
    raise InvalidVersion(f"Invalid version: '{version}'")
packaging.version.InvalidVersion: Invalid version: '2023_02'
2025-03-11 12:42:22,451 ERROR [root][MainThread] Error during task release
2025-03-11 12:42:22,451 INFO  [root][MainThread] Workflow:wf_over
2025-03-11 12:42:22,462 INFO  [root][MainThread] Notify:biomaj@pasteur.fr
2025-03-11 12:42:22,462 INFO  [root][MainThread] BANK[uniref30] - STATUS[False] - UPDATE[True] - REMOVE[False] - RELEASE[None]
An error occured:

Bank update request sent for uniref30
Failed to send update request for uniref30

At the moment, I just add a requirement on packaging module : "packaging<22"
I will try to find a better way to handle versioning, but I can't now.