analyze aggregate size

[aligh92]

developed code for issue #2789 i.e to analyze the aggregate size
Changes made in this Pull Request:

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?
• New code proposal

[aligh92]

@lilyminium Thank you so much for looking into that. It is weird, I did that on my computer, I do not know why it did not transfer here!!! Anyway, I made the change again, let's see how it works.

[aligh92]

@lilyminium Thank you again for previous help. Currently, I have a problem with these two I guess. Any help is appreciated.
1-https://dev.azure.com/mdanalysis/mdanalysis/_build/results?buildId=951&view=logs&j=1cdae27b-58e8-5c64-01e2-519b6cdf4b73&t=c13e15da-7c65-5b3c-5c17-f011eed8e1e8&l=443
2-https://dev.azure.com/mdanalysis/mdanalysis/_build/results?buildId=951&view=logs&j=b3e715e3-855a-545e-22f2-ec20d10eac17&t=18ebbd08-144c-517e-f71d-909fbbe1f815&l=384

[lilyminium]

The error is odd. I think it's failing to read the xtc offsets?

    @pytest.fixture()
    def atomgroup():
>       return mda.Universe(Asph_gro, Asph_xtc).select_atoms('resname AsphC')

... [more error log, until it dies in np.load] ...
                # Try a pickle
                if not allow_pickle:
>                   raise ValueError("Cannot load file containing pickled data "
                                     "when allow_pickle=False")

@jbarnoud may be the one to ask here. The rest of the tests pass so it's likely not because of something with your file.

[aligh92]

@lilyminium Thank you so much for looking into the errors. I really appreciate your help and time.

Dear @jbarnoud,
Could you please look into this error and check if there is something wrong, please?
Looking forward to hearing from you,

[aligh92]

Dear @orbeckst

I am wondering if you can help me with this issue. I could run the test locally but it seems there is some small issue here.

Any help is appreciated.
Thank you in advance,
Best regards,
Ali

[jbarnoud]

From a quick look at the error message, it looks like there is an issue reading the offset for the test XTC file, indeed. As it only complains about the file introduced in this PR, I doubt there is an issue with the general system producing and reading the file (though it remains a possibility, of course). However, looking at the files introduced here, I do not see what could cause the problem if you can run the tests locally. Could you do the following test locally:

• if the offset file exists for Asph_xtc (hidden file next to the trajectory with a similar name to the trajectory and a .npz extension), delete it
• create a universe for the trajectory (the offset should be recreated)
• create another universe for the trajectory (the offset should be loaded)

If this works, then I do not know what the problem is. If it fails somewhere, then there is probably an issue with the trajectory. My hypothesis (and it is a not very substantiated one) is that the tests pass locally for you because you have an offset file already while the CI would not have that file.

[aligh92]

Dear @jbarnoud,

Thank you so much for your reply. I am looking to that based on your comments and I will get back to you as soon as possible.

Best regards

[aligh92]

Dear @jbarnoud,
I deleted the .npz file and ran the pytest again. It went through successfully and the .npz file was build by itself again. I am not sure if this is what you meant. Please see the attached screenshot which is the output of local pytest.

[jbarnoud]

These are OK, they are warnings that have nothing to do with your PR. I will restart the failing tests to see if it is not just a fluke. On 5 Oct 2020 03:11, aligh92 <notifications@github.com> wrote: Dear @jbarnoud, I deleted the .npz file and ran the pytest again. It went through successfully and the .npz file was build by itself again. I am not sure if this is what you meant. Please see the attached screenshot which is the output of local pytest. —You are receiving this because you were mentioned.Reply to this email directly, view it on GitHub, or unsubscribe.

[jbarnoud]

@aligh92 I did not manage to just re-run the pipeline to see if it works by just insisting. So I added a commit to your branch fixing an indentation error. The pipelines are running again now, we will see if it works any better.

[aligh92]

Dear @jbarnoud ,

Looks like we still have a problem. The main problem that I saw before and it is still there is related to the attached photo. Please advice me.

[orbeckst]

Aggregate size analysis might be a good fit for a MDAKit (independent analysis package linked to MDAnalysis).

@aligh92 would you be interested in pursuing that route?

[aligh92]

Hi Oliver, I am so sorry for the late reply. I would be very pleased to have my code published and functional for future people's use. Could you please let me know how and what can I do to fit that to the MDAKit? Looking forward to hearing from you, Best regards, Ali

…

On Thu, Oct 28, 2021 at 4:21 PM Oliver Beckstein ***@***.***> wrote: Aggregate size analysis might be a good fit for a MDAKit <https://www.mdanalysis.org/2021/08/31/CZI-EOSS4/#2-launching-the-mdakits-ecosystem> (independent analysis package linked to MDAnalysis). @aligh92 <https://github.com/aligh92> would you be interested in pursuing that route? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2822 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOY2YRHBKI6AG6DCRHVFGSTUJGLUZANCNFSM4OQD5EXA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[orbeckst]

@aligh92 , good to hear that you're interested in doing an MDAKit. For right now I added the MDAKit label to the PR and issue.

We are working on guidelines. We'll have a document for discussion soon and then we'd really like to hear from developers like you what they think. We'll also be very happy if you'd want to try it out and give feedback on the process.

[aligh92]

Thank you so much Oliver, I just should mention that I am not very good with GitHub and I need probably a bit of assistance there if I need to do any action. That was probably one of the main reasons that I could not publish my code in the first place. Because I still can not understand why I could not add my code to the MDAnalysis package itself. Best regards, Ali

…

On Mon, Nov 1, 2021 at 7:07 PM Oliver Beckstein ***@***.***> wrote: @aligh92 <https://github.com/aligh92> , good to hear that you're interested in doing an MDAKit. For right now I added the MDAKit label to the PR and issue. We are working on guidelines. We'll have a document for discussion soon and then we'd really like to hear from developers like you what they think. We'll also be very happy if you'd want to try it out and give feedback on the process. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2822 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOY2YRDKW4IMIKWBWQUWAKTUJ4B75ANCNFSM4OQD5EXA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[hmacdope]

Closing as stale, feel free to re-open if you want to continue.