search

logsdail / carmm

Scripts for creation, manipulation and analysis of geometric and electronic structure of molecular models
GNU General Public License v3.0
5 stars 17 forks source link

30 update codebase to work with Python 3.8 (and thus ase v3.23) #163

Closed logsdail closed 1 month ago

logsdail commented 3 months ago

Testing to updated codebase with ASE release

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 97.93103% with 3 lines in your changes missing coverage. Please review.

Project coverage is 89.38%. Comparing base (5e7334c) to head (68e195b).

Files Patch % Lines
carmm/run/aims_calculator.py 94.11% 1 Missing :warning:
examples/run_aims.py 66.66% 1 Missing :warning:
examples/utils_python_env_check.py 96.96% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #163 +/- ## ========================================== + Coverage 89.10% 89.38% +0.27% ========================================== Files 81 82 +1 Lines 3286 3382 +96 ========================================== + Hits 2928 3023 +95 - Misses 358 359 +1 ``` | [Flag](https://app.codecov.io/gh/logsdail/carmm/pull/163/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Andrew+Logsdail) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/logsdail/carmm/pull/163/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Andrew+Logsdail) | `89.38% <97.93%> (+0.27%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Andrew+Logsdail#carryforward-flags-in-the-pull-request-comment) to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

logsdail commented 3 months ago

Noting here that the docs runs with Python 3.9 - should we standardise to this version, perhaps?

logsdail commented 3 months ago

So I think after discussion today at a Group meeting, this has become an "update Python version to the most suitable for our HPC architectures".

Current Python compatibility of code: Python 3.7 (i.e., CI tests work to this version)

Current HPC system Python provisions: Hawk: 3.7 (used currently, default), 3.9.2, 3.10.4, 3.11.2 Isambard: 3.7.3.2 (used currently), 3.8.5.1 (default) Young: 3.6 (used currently), 3.7.0, 3.7.2, 3.7.4, 3.8.0, 3.8.6 (default), 3.9.0, 3.9.1, 3.9.6, 3.9.10, 3.11.3, 3.11.4 ARCHER2: 3.6.15 (used currently) 3.9.13.1 (default) 3.10.10

logsdail commented 3 months ago

So I think after discussion today at a Group meeting, this has become an "update Python version to the most suitable for our HPC architectures".

Current Python compatibility of code: Python 3.7 (i.e., CI tests work to this version)

Current HPC system Python provisions: Hawk: 3.7 (used currently, default), 3.9.2, 3.10.4, 3.11.2 Isambard: 3.7.3.2 (used currently), 3.8.5.1 (default) Young: 3.6 (used currently), 3.7.0, 3.7.2, 3.7.4, 3.8.0, 3.8.6 (default), 3.9.0, 3.9.1, 3.9.6, 3.9.10, 3.11.3, 3.11.4 ARCHER2: 3.6.15 (used currently) 3.9.13.1 (default) 3.10.10

My take home from this is the minimum we should go to is 3.8 or 3.9, but certainly not towards the high numbers.

logsdail commented 1 month ago

@PavelStishenko as suggested I've put a tag on the mainline version, and once merged we'll bumpy the minor version number.

ikowalec commented 1 month ago

I suggest a second review before merge.

logsdail commented 1 month ago

@ikowalec thanks for comments - all addressed. Does someone else want to do a second review, please?

logsdail commented 1 month ago

@GaryLZW I simplified the analyse_counterpoise test, as the checking for ASE now happens in get_aims_calculator. The CI tests pass but you might want to check if the code works correctly for further use cases.

GaryLZW commented 1 month ago

@GaryLZW I simplified the analyse_counterpoise test, as the checking for ASE now happens in get_aims_calculator. The CI tests pass but you might want to check if the code works correctly for further use cases.

This looks fine to me^^

FirasAssa commented 1 month ago

During my project the following changes were made: The err_handler folder was removed and a utils folder was created in its place A python_env_check file was created with python_env_check() and is_env_python() inside Implemented python_env_check() in anylyse_forces example Implemented python_env_check() in analyse_calculator Restricted mace-torch to 0.3.4, because it was failing on v3.7 Updated CatLearn to the most recent version to fix import error in mlneb.py, by getting the version of CatLearn directly from Git

Thinks still to do after the project: In python v3.8 ci-test there are 4 places where .BadConfiguration Error occurs. Presumably it is the same type of problem that can be fixed in one go Errors: ERROR analyse_counterpoise.py - ase.calculators.calculator.BadConfiguration: No configuration of aims ERROR run_aims.py - ase.calculators.calculator.BadConfiguration: No configuration of aims ERROR run_workflows_ReactAims.py - ase.calculators.calculator.BadConfiguration: No configuration of aims ERROR run_workflows_ReactAims_parallel.py - ase.calculators.calculator.BadConfiguration: No configuration of aims

logsdail commented 1 month ago

[like] Andrew Logsdail reacted to your message:

From: FirasAssa @.> Sent: Sunday, August 4, 2024 9:13:06 PM To: logsdail/carmm @.> Cc: Andrew Logsdail @.>; State change @.> Subject: Re: [logsdail/carmm] 30 update codebase to work with Python 3.8 (and thus ase v3.23) (PR #163)

External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.

During my project the following changes were made: The err_handler folder was removed and a utils folder was created in its place A python_env_check file was created with python_env_check() and is_env_python() inside Implemented python_env_check() in anylyse_forces example Implemented python_env_check() in analyse_calculator Restricted mace-torch to 0.3.4, because it was failing on v3.7 Updated CatLearn to the most recent version to fix import error in mlneb.py, by getting the version of CatLearn directly from Git

Thinks still to do after the project: In python v3.8 ci-test there are 4 places where .BadConfiguration Error occurs. Presumably it is the same type of problem that can be fixed in one go Errors: ERROR analyse_counterpoise.py - ase.calculators.calculator.BadConfiguration: No configuration of aims ERROR run_aims.py - ase.calculators.calculator.BadConfiguration: No configuration of aims ERROR run_workflows_ReactAims.py - ase.calculators.calculator.BadConfiguration: No configuration of aims ERROR run_workflows_ReactAims_parallel.py - ase.calculators.calculator.BadConfiguration: No configuration of aims

— Reply to this email directly, view it on GitHubhttps://github.com/logsdail/carmm/pull/163#issuecomment-2267678961, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AFMK4MYUDKHIE4IDSR2UDILZP2KOFAVCNFSM6AAAAABIWCQXZCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRXGY3TQOJWGE. You are receiving this because you modified the open/close state.Message ID: @.***>