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46 inconsistent handling of work function decay parameter processing vs output file naming#48

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46-inconsistent-handling-of-work-function-decay-parameter-processing-vs-output-file-naming
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46 inconsistent handling of work function decay parameter processing vs output file naming#48
GianmarcoMidena wants to merge 21 commits into
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46-inconsistent-handling-of-work-function-decay-parameter-processing-vs-output-file-naming

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@GianmarcoMidena GianmarcoMidena commented Jun 10, 2026

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Closes #46

@GianmarcoMidena GianmarcoMidena linked an issue Jun 10, 2026 that may be closed by this pull request
Inconsistent Handling of Work Function Decay Parameter: Processing vs Output File Naming #46
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ondrejkrejci
ondrejkrejci reviewed Jun 10, 2026
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@ondrejkrejci ondrejkrejci left a comment

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For now few comments, before I will approve. Thank you!

Comment thread pyPPSTM/visualization.py
Comment thread tests/test_plot_png.py Outdated

@ondrejkrejci ondrejkrejci Jun 10, 2026

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May I just ask here: It checks whether a png file was created? If, so what line checks it?

@GianmarcoMidena GianmarcoMidena Jun 10, 2026

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I'll refactor the code for better readability.

@GianmarcoMidena GianmarcoMidena Jun 10, 2026

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Done. Could you now see where the file creation is checked?

Comment thread tests/test_save_npy.py Outdated
@@ -0,0 +1,115 @@
from pathlib import Path

@ondrejkrejci ondrejkrejci Jun 10, 2026

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Are we still using npy, or the new npz?

@GianmarcoMidena GianmarcoMidena Jun 10, 2026

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npz

@ondrejkrejci ondrejkrejci Jun 10, 2026

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Shouldn't we call the file test_save_npz?

@GianmarcoMidena GianmarcoMidena Jun 10, 2026

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Yes, I'll rename it.

@GianmarcoMidena GianmarcoMidena Jun 10, 2026

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Done

Comment thread tests/test_save_xsf.py Outdated

@ondrejkrejci ondrejkrejci Jun 10, 2026

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as XSF is used from ppafm, I feel, that ppafm should be added to the minimal installation at the end.

@GianmarcoMidena GianmarcoMidena Jun 10, 2026

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So, does ppafm become a compulsory package for ppastm?

@ondrejkrejci ondrejkrejci Jun 10, 2026

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yes.

@GianmarcoMidena GianmarcoMidena Jun 10, 2026

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Added

Comment thread environment.yml
Comment thread environment_dev.yml
Comment thread environment_min.yml
@GianmarcoMidena
chore(deps): add ppafm as a required dependency
c6cb3b4
@GianmarcoMidena
chore: create automation testing directory
5effc01
@GianmarcoMidena
docs(readme): add test execution command
ddd8f6a
@GianmarcoMidena
test(visualization): verify scan PNG filename format
d706f34
@GianmarcoMidena
fix(visualization): align PNG naming with work function decay processing
4f22c13
@GianmarcoMidena
test(visualization): verify scan WSxM filename format
da49395
@GianmarcoMidena
fix(visualization): align WSxM naming with work function decay proces…
d1278ce 
…sing
@GianmarcoMidena
test(visualization): verify scan XSF filename format
6600920
@GianmarcoMidena
fix(visualization): align XSF naming with work function decay processing
f8a9cdb
@GianmarcoMidena
test(visualization): verify scan NPZ filename format
c1ae794
@GianmarcoMidena
fix(visualization): align NPZ naming with work function decay processing
c740bb9
@GianmarcoMidena
test(io): add package for testing generated output
a4fc067
@GianmarcoMidena
test(visualization): refactor NPZ filename format validation
7e89c37
@GianmarcoMidena
test(visualization): refactor XSF filename format validation
27f1746
@GianmarcoMidena
test(visualization): refactor PNG filename format validation
dbfc666
@GianmarcoMidena
test(visualization): refactor WSxM filename format validation
2ba7fd8
@GianmarcoMidena
refactor(io): rename save_npy to save_npz
1b69996
@GianmarcoMidena GianmarcoMidena force-pushed the 46-inconsistent-handling-of-work-function-decay-parameter-processing-vs-output-file-naming branch from e928bc0 to 1b69996 Compare June 10, 2026 15:15
ondrejkrejci
ondrejkrejci requested changes Jun 10, 2026
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@ondrejkrejci ondrejkrejci left a comment

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1 change (sorry for misunderstanding) and then it is good to go. Thanks!

Comment thread environment_min.yml
- ppafm==0.4.0

variables:
PPAFM_RECOMPILE: 1

@ondrejkrejci ondrejkrejci Jun 10, 2026

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For the min one, please remove the PPAFM_RECOMPILE as this is needed just for pytests and dev version, otherwise it should work normally.

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Inconsistent Handling of Work Function Decay Parameter: Processing vs Output File Naming

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