[Bug]: asd available channels not logged

MaxGamill-Sheffield commented 3 weeks ago

Checklist

[X] Re-run analysis with topostats process --core 1.
[X] Describe the bug.
[X] Include the configuration file.
[X] Copy of the output.
[X] The exact command that failed. This is what you typed at the command line, including any options.
[X] TopoStats version, this is reported by topostats --version
[X] Operating System and Python Version

Describe the bug

With the switch toAFMReader for asd i/o. The broad exception statement printing the warning for "Channel not found, skipping the image" is super-seeding the available channel message in AFMReader.asd

Copy of the output

screenshot_2024-06-06_at_10 36 58

Include the configuration file

N/A

To Reproduce

No response

TopoStats Version

Git main branch

Python Version

3.11

Operating System

MacOS M1/M2 (post-2021)

Python Packages

No response

ns-rse commented 3 weeks ago

This hasn't been merged to main yet.

You can get information as to the version in the current Virtual Environment. Ideally a fresh pip install -e . should be done to ensure this is accurate.

❱ pip install -e .
❱ pip show topostats
Name: topostats
Version: 2.2.post1.dev190+g389fb1045
Summary: Automated Analysis for Atomic Force Microscopy Images of Biomolecules
Home-page: 
Author: 
Author-email: TopoStats Team <topostats@sheffield.ac.uk>, Alice Pyne <a.l.pyne@sheffield.ac.uk>, Sylvia Whittle <sylvia.whittle@sheffield.ac.uk>, Neil Shephard <n.shephard@sheffield.ac.uk>, Max Gamill <mcgamill1@sheffield.ac.uk>, Jean Du <mdu12@sheffield.ac.uk>
License: GNU Lesser GPLv3 only
Location: /home/neil/.virtualenvs/tmp-1b71451da46dd36/lib/python3.12/site-packages
Editable project location: /home/neil/work/git/hub/AFM-SPM/TopoStats
Requires: AFMReader, h5py, igor2, matplotlib, numpy, pandas, pyfiglet, pySPM, pyyaml, ruamel.yaml, schema, scikit-image, scipy, seaborn, snoop, tifffile, tqdm
Required-by:

...and because we are dynamically setting version using setuptools_scm it appends the last tag with the post1.dev190+g389fb1045 which indicates the number of commits ahead and the hash of the last commit on that branch.

Or as per the issue template topostats --version reports this and it can be copy pasted.

❱ topostats --version
Installed version of TopoStats: 2.2.post1.dev190+g389fb1045

MaxGamill-Sheffield commented 3 weeks ago

Yep, just made a new PR for it. I forgot the keywords would close the accidental PR. Also because of testing on one branch ns-rse/851... then applying the changes to another main I thought the package list and commit version may have been more confusing.

AFM-SPM / TopoStats