File_Writer for DigitalSurf files

[Attolight-NTappy]

Description of the change

This PR implements save support for digitalsurf file formats:

• Implement file_writer for the digitalsurf formats (.sur and .pro)
• Correct a minor bug causing some datasets being offset by a constant upon loading
• Improve documentation

Progress of the PR

• Change implemented (can be split into several points),
• update docstring (if appropriate),
• update user guide (if appropriate),
• add a changelog entry in the upcoming_changes folder (see upcoming_changes/README.rst),
• Check formatting of the changelog entry (and eventual user guide changes) in the docs/readthedocs.org:rosettasciio build of this PR (link in github checks)
• add tests,
• ready for review.

Minimal example of the bug fix or the new feature

import numpy as np
from rsciio.digitalsurf import file_writer,file_reader
md = { 'General': {},
       'Signal': {}}

ax  = {'name': 'X',
 'navigate': False,
 }

sd = {"data": np.arange(24)+111,
       "axes": [ax],
       "metadata": md,
       "original_metadata": {}}

file_writer("test.pro",sd)
file_reader('test.pro')[0]['data']
#array([111., 112., 113., 114., 115., 116., 117., 118., ... 133., 134.])

[codecov]

Codecov Report

Attention: Patch coverage is 97.51773% with 14 lines in your changes missing coverage. Please review.

Project coverage is 87.66%. Comparing base (e921e77) to head (1f5e4c5).
Report is 85 commits behind head on main.

Files with missing lines	Patch %	Lines
rsciio/digitalsurf/_api.py	97.50%	0 Missing and 14 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #280      +/-   ##
==========================================
+ Coverage   86.33%   87.66%   +1.33%     
==========================================
  Files          83       83              
  Lines       10672    11150     +478     
  Branches     2331     2414      +83     
==========================================
+ Hits         9214     9775     +561     
+ Misses        939      860      -79     
+ Partials      519      515       -4     

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[Attolight-NTappy]

This is now ready for review :)

[ericpre]

pre-commit.ci autofix

[ericpre]

This looks good, I didn't review in depth but this looks all sensible.
I made a few comments and maybe it would be good to increase the coverage? There are a couple of if block which are not coverage.

[Attolight-NTappy]

Thanks for review!

I made a few comments and maybe it would be good to increase the coverage? There are a couple of if block which are not coverage.

Alright, wait for it I'll push some new tests later today

[ericpre]

A test checking the list of functions in the public API needs to be updated:

rosettasciio/rsciio/tests/test_import.py

Lines 130 to 146 in 916c4b5

	if plugin["name"] == "MSA":
	assert dir(plugin_module) == [
	"file_reader",
	"file_writer",
	"parse_msa_string",
	]
	elif plugin["name"] == "QuantumDetector":
	assert dir(plugin_module) == [
	"file_reader",
	"load_mib_data",
	"parse_exposures",
	"parse_timestamps",
	]
	elif plugin["writes"] is False:
	assert dir(plugin_module) == ["file_reader"]
	else:
	assert dir(plugin_module) == ["file_reader", "file_writer"]

[ericpre]

parse_metadata needs to be part of the public API, this is the test that needs to be updated to take into account this change.

[Attolight-NTappy]

Ok. I thought you would not consider changing this. Hadn't realized some other modules where already deviating from the file_reader,file_writer norm
my bad

[Attolight-NTappy]

Ok finally I think we're there.

[ericpre]

Thank you @Attolight-NTappy, I push some tweaks to please ruff and improve the release note.

[Attolight-NTappy]

🤩