Add pore analyser to md kits #172

DSeiferth · 2024-10-08T11:21:29Z

Hi MDA community,

I would like to add PoreAnalyser. https://www.sciencedirect.com/science/article/pii/S0006349524004491?via%3Dihub
I have written the tests not with pytest and might need some help with the test section in the metadata file.

DSeiferth · 2024-10-08T13:27:27Z

There seem to be problems with python3.13:
AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?

I have added python requirements <=3.12.
In my CI, I can succsefully install PoreAnalyser with python version 3.9 - 3.12
How can I restart the failed tests?
I have published a new pip installable version of PoreAnalyser where I have specified the python requirements.

orbeckst · 2024-10-08T20:23:26Z

Restarting CI by closing and reopening... (or you could make a minimal change to the PR...)

orbeckst · 2024-10-08T20:25:52Z

@fiona-naughton could you please handle this kit?

Feel free to ask me any hole-related questions (or maybe @lilyminium , too?)

mdakits/PoreAnalyser/metadata.yaml

orbeckst · 2024-10-08T21:59:57Z

mdakits/PoreAnalyser/metadata.yaml

+
+## str: the development status of the MDAKit
+## See https://pypi.org/classifiers/ for development status classifiers.
+#development_status: Production/Stable


I'd add it — there's no shame in labelling it as alpha or beta. Or stable or mature ;-)

mdakits/PoreAnalyser/metadata.yaml

orbeckst · 2024-10-08T22:06:32Z

Not sure why Python 3.13 is installed. @IAlibay said on Discord he'll look into it.

IAlibay · 2024-10-13T04:23:48Z

Not sure why Python 3.13 is installed. @IAlibay said on Discord he'll look into it.

Should be fixed with b9f0439
Was a long standing bug/typo that didn't show up until Python updated.

DSeiferth · 2024-10-14T09:48:17Z

The tests yesterday failed again. Python 3.13 is used and version 0.0.7 is downloaded instead of version 0.0.9.
https://pypi.org/project/PoreAnalyser/#history

orbeckst · 2024-10-14T17:30:25Z

@IAlibay is there something that needs to be done in this PR to have your fix take effect?

IAlibay · 2024-10-15T19:39:51Z

@DSeiferth @orbeckst if you merge main into this branch it might work (I don't have edit access to do this).

…erth/MDAKits into add_PoreAnalyser_to_MDKits

orbeckst · 2024-10-15T19:52:07Z

Thanks @IAlibay. Had to do it locally as there was no update button on GH. Let's see if it dones anything good.

orbeckst · 2024-10-15T19:55:18Z

Fails https://github.com/MDAnalysis/MDAKits/actions/runs/11353355295/job/31578167467?pr=172#step:5:38

Run conda-incubator/setup-miniconda@v2
Gathering Inputs...
Creating bootstrap condarc file in /home/runner/.condarc...
Ensuring installer...
Running installer...
  /usr/bin/bash /home/runner/work/_temp/d66cef9c-7e50-4396-a36e-c75bbb19560b.sh -f -b -p /usr/share/miniconda3
  PREFIX=/usr/share/miniconda3
  
  Transaction
  
    Prefix: /usr/share/miniconda3/envs/_virtual_specs_checks
  
    All requested packages already installed
  
  Dry run. Not executing the transaction.
  Unpacking payload ...
  Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2
  Extracting charset-normalizer-3.3.2-pyhd8ed1ab_0.conda
  Extracting colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
  Extracting distro-1.9.0-pyhd8ed1ab_0.conda
  Extracting frozendict-2.4.4-py312h66e93f0_1.conda
  Extracting hpack-4.0.0-pyh9f0ad1d_0.tar.bz2
  Extracting hyperframe-6.0.1-pyhd8ed1ab_0.tar.bz2
  Extracting idna-3.10-pyhd8ed1ab_0.conda
  Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda
  Extracting libmamba-1.5.9-h4cc3d14_0.conda
  Extracting packaging-24.1-pyhd8ed1ab_0.conda
  Extracting platformdirs-4.3.6-pyhd8ed1ab_0.conda
  Extracting pluggy-1.5.0-pyhd8ed1ab_0.conda
  Extracting pycosat-0.6.6-py312h98912ed_0.conda
  Extracting pycparser-2.22-pyhd8ed1ab_0.conda
  Extracting pysocks-1.7.1-pyha2e5f31_6.tar.bz2
  Extracting ruamel.yaml.clib-0.2.8-py312h98912ed_0.conda
  Extracting setuptools-74.1.2-pyhd8ed1ab_0.conda
  Extracting truststore-0.9.2-pyhd8ed1ab_0.conda
  Extracting wheel-0.44.0-pyhd8ed1ab_0.conda
  Extracting cffi-1.17.1-py312h06ac9bb_0.conda
  Extracting h2-4.1.0-pyhd8ed1ab_0.tar.bz2
  Extracting jsonpatch-1.33-pyhd8ed1ab_0.conda
  Extracting libmambapy-1.5.9-py312h7fb9e8e_0.conda
  Extracting pip-24.2-pyh8b19718_1.conda
  Extracting ruamel.yaml-0.18.6-py312h98912ed_0.conda
  Extracting tqdm-4.66.5-pyhd8ed1ab_0.conda
  Extracting zstandard-0.23.0-py312hef9b889_1.conda
  Extracting conda-package-streaming-0.10.0-pyhd8ed1ab_0.conda
  Extracting urllib3-2.2.3-pyhd8ed1ab_0.conda
  Extracting conda-package-handling-2.3.0-pyh7900ff3_0.conda
  Extracting requests-2.32.3-pyhd8ed1ab_0.conda
  Extracting conda-24.7.1-py312h7900ff3_0.conda
  Extracting conda-libmamba-solver-24.7.0-pyhd8ed1ab_0.conda
  Extracting mamba-1.5.9-py312h9460a1c_0.conda
  Warning: Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at [https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.](https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/)
  Warning: ERROR: executing pre_install.sh failed
  
  ERROR: executing pre_install.sh failed
Error: The process '/usr/bin/bash' failed with exit code 1

orbeckst · 2024-10-15T20:00:56Z

From the error messages I have no idea why the installer is failing.

Looking back at b9f0439 I note that it only fixes gh-ci-cron.yaml so I am not even sure how it would affect the running of gh-ci.yaml.

orbeckst · 2024-10-15T20:03:46Z

I opened #213.

IAlibay · 2024-10-15T20:14:29Z

Looking back at b9f0439 I note that it only fixes gh-ci-cron.yaml so I am not even sure how it would affect the running of gh-ci.yaml.

There was a follow-up fix that I did when I fixed the registry entry for zaartraj, but I'll have a look at what's happening here.

IAlibay · 2024-10-15T20:33:09Z

@DSeiferth the pyproject.toml for poreanalyzer states 'numpy >=1.0, <1.23.0', however the minimum supported version of numpy for python 3.12 is 1.26.0. You also state in your pyproject.toml that you support all the way through to python 3.12, can you weigh on this please?

mdakits/PoreAnalyser/metadata.yaml

…erth/MDAKits into add_PoreAnalyser_to_MDKits

DSeiferth · 2024-10-16T12:24:46Z

@DSeiferth the pyproject.toml for poreanalyzer states 'numpy >=1.0, <1.23.0', however the minimum supported version of numpy for python 3.12 is 1.26.0. You also state in your pyproject.toml that you support all the way through to python 3.12, can you weigh on this please?

Thanks for spotting this, Irfan.
https://github.com/DSeiferth/PoreAnalyser/actions/runs/11236327945/job/31236196270
When I built PoreAnalyser with my CI, it downloaded numpy-1.26.4.

In the requirements.txt file, there was no <1.23 requirement (in the setup file either). Only in the pyproject.toml file.
I have removed the <1.23 requirement and published a new package version!

DSeiferth · 2024-10-18T07:23:27Z

mdakit-ci (PoreAnalyser, develop) installs PoreAnalyser==0.0.11 and then fails at this stage:
INFO: pip is looking at multiple versions of poreanalyser to determine which version is compatible with other requirements. This could take a while.
ERROR: Package 'poreanalyser' requires a different Python: 3.12.7 not in '<=3.12,>=3.6'

In my CI, the install with python 3.12.7 was successful build (3.12)

mdakit-ci (PoreAnalyser, latest) still downloads poreanalyser-0.0.7.
However, at pypi, the latest version is 0.0.11.

Co-authored-by: Oliver Beckstein <[email protected]>

DSeiferth added 3 commits October 8, 2024 11:22

add PoreAnalyser

0e3b5a9

del

d1fcd4c

add metadata

938904c

orbeckst closed this Oct 8, 2024

orbeckst reopened this Oct 8, 2024

orbeckst assigned fiona-naughton Oct 8, 2024

orbeckst added mdakit About an MDAKit. new create a new MDAKit labels Oct 8, 2024

orbeckst reviewed Oct 8, 2024

View reviewed changes

Merge branch 'add_PoreAnalyser_to_MDKits' of https://github.com/DSeif…

37c3481

…erth/MDAKits into add_PoreAnalyser_to_MDKits

orbeckst mentioned this pull request Oct 15, 2024

install-conda-env in GH CI broken #213

Closed

orbeckst reviewed Oct 15, 2024

View reviewed changes

mdakits/PoreAnalyser/metadata.yaml Outdated Show resolved Hide resolved

orbeckst reviewed Oct 15, 2024

View reviewed changes

mdakits/PoreAnalyser/metadata.yaml Outdated Show resolved Hide resolved

orbeckst reviewed Oct 15, 2024

View reviewed changes

mdakits/PoreAnalyser/metadata.yaml Outdated Show resolved Hide resolved

DSeiferth added 2 commits October 16, 2024 12:56

changes from pull request

5f2cd3d

Merge branch 'add_PoreAnalyser_to_MDKits' of https://github.com/DSeif…

79fad3c

…erth/MDAKits into add_PoreAnalyser_to_MDKits

change liscene to or later

62f866b

Update mdakits/PoreAnalyser/metadata.yaml

5ade7c8

Co-authored-by: Oliver Beckstein <[email protected]>

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add pore analyser to md kits #172

Add pore analyser to md kits #172

DSeiferth commented Oct 8, 2024

DSeiferth commented Oct 8, 2024

orbeckst commented Oct 8, 2024

orbeckst commented Oct 8, 2024

orbeckst Oct 8, 2024

orbeckst commented Oct 8, 2024

IAlibay commented Oct 13, 2024

DSeiferth commented Oct 14, 2024

orbeckst commented Oct 14, 2024

IAlibay commented Oct 15, 2024

orbeckst commented Oct 15, 2024

orbeckst commented Oct 15, 2024

orbeckst commented Oct 15, 2024

orbeckst commented Oct 15, 2024

IAlibay commented Oct 15, 2024

IAlibay commented Oct 15, 2024

DSeiferth commented Oct 16, 2024

DSeiferth commented Oct 18, 2024

Add pore analyser to md kits #172

Are you sure you want to change the base?

Add pore analyser to md kits #172

Conversation

DSeiferth commented Oct 8, 2024

DSeiferth commented Oct 8, 2024

orbeckst commented Oct 8, 2024

orbeckst commented Oct 8, 2024

orbeckst Oct 8, 2024

Choose a reason for hiding this comment

orbeckst commented Oct 8, 2024

IAlibay commented Oct 13, 2024

DSeiferth commented Oct 14, 2024

orbeckst commented Oct 14, 2024

IAlibay commented Oct 15, 2024

orbeckst commented Oct 15, 2024

orbeckst commented Oct 15, 2024

orbeckst commented Oct 15, 2024

orbeckst commented Oct 15, 2024

IAlibay commented Oct 15, 2024

IAlibay commented Oct 15, 2024

DSeiferth commented Oct 16, 2024

DSeiferth commented Oct 18, 2024