[com4]: Add thalweg computation option

[PaulaSp3]

The goal is to derive thalweg data for each flow path (release from one release cell or from all cells having the same release ID).
The location of a thalweg is derived as the center of zDelta or energy or flux of the locations within one generation.

So the computation within the flowCore.py is changed so that we remember and track which cells are hidden within each generation.

Please be aware that simulations with computing thalwegs increases the computation time and the consumed RAM.

Short description of the changed files:

• com4FlowPy/com4FlowPy.py

  • black formatter
  • allow thalweg calculation (input parameter handling)

• com4FlowPy/flowClass.py

  • compute flow energy as: flux * zdelta * 9.81

• com4FlowPy/flowCore.py

  • option for a calculation generation wise (considering the order of cells that are computed) -> different results!
  • get_start_idx, split_release (line 25-165):when thalweg is calculated for continuous release areas, check that all start cells belonging to one release area are computed in one Core

• com4FlowPy/flowPath.py

  • compute averaged values for each generation (e.g., x and y values -> location of thalweg)
  • save thalweg Data as pickle

• com4FlowPy/splitAndMerge.py

  • add a function that computes tiling extents, that do not split release cells that have the same release ID

• data/avaParabChannelPaperFP:

  • topo: parabola with channel

• in3Utils/geoTrans.py:

  • black formatter
  • indicesToCoords(): compute row and col to x and y (is there already a function for this computation? - I could not find it)

• runCom4FlowPy.py:

  • black formatter
  • allow thalweg computation (input parameters and path handling)

• runScripts/runRegionalThalweg2DPlot.py:

  • runscript for plotting com4 thalweg data

• runStandardTestsCom4FlowPy.py:

  • run "simple" benchmark test for com4FlowPy
  • data: avaParabChannelPaperFP and avaArzlerAlm
  • simulation results are compared and the difference of the simulation results is written into the report

PR Checklist

Please confirm before requesting review:

• I ran pytest locally without fails
• I added/updated tests where needed
• I updated documentation where needed

Confirm before the final merge/rebase into master

• Commits are sensibly squashed and rebased onto latest master
• Standardtest run without difference (with recompiled cython code)

[qltysh]

Analysis for project AvaFrame

❌ 11 blocking issues (39 total)

Tool	Category	Rule	Count
ripgrep	Lint	# TODO: we could put this checking part in an extra function, if we can move updateInfraDirGraph	10	❌
ruff	Style	Incorrect formatting, autoformat by running qlty fmt.	1	❌
qlty	Structure	Deeply nested control flow (level = 4)	19
qlty	Structure	Function with high complexity (count = 26): tileInputLayers	6
qlty	Duplication	Found 17 lines of similar code in 2 locations (mass = 140)	2
qlty	Structure	High total complexity (count = 71)	1

@qltysh one-click actions:

• Auto-fix formatting (qlty fmt && git push)

[qltysh]

Coverage Impact

⬇️ Merging this pull request will decrease total coverage on master by 1.65%.

Modified Files with Diff Coverage (6)

Rating	File	% Diff	Uncovered Line #s
	avaframe/com4FlowPy/flowCore.py	25.1%	56, 63, 107-487...
	avaframe/com4FlowPy/splitAndMerge.py	99.3%	332
	avaframe/com4FlowPy/flowClass.py	100.0%
	avaframe/com4FlowPy/com4FlowPy.py	0.0%	80-701
	avaframe/in3Utils/geoTrans.py	14.3%	2264-2269
	avaframe/com4FlowPy/flowPath.py	7.9%	40-84, 106-114...
	Total	32.2%

🤖 Increase coverage with AI coding...

In the `PS_thalweg_onlyFP` branch, add test coverage for this new code:

- `avaframe/com4FlowPy/com4FlowPy.py` -- Line 80-701
- `avaframe/com4FlowPy/flowCore.py` -- Lines 56, 63, 107-487, 599-600, 666-668, 723-1021, 1029, 1033-1039, 1050, 1057-1068, 1081, 1087, 1121, 1126-1132, 1141, 1147, and 1161-1194
- `avaframe/com4FlowPy/flowPath.py` -- Lines 40-84, 106-114, 117-138, 145-159, 182-195, 210-245, 265-270, 286-322, and 332-388
- `avaframe/com4FlowPy/splitAndMerge.py` -- Line 332
- `avaframe/in3Utils/geoTrans.py` -- Line 2264-2269

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• Total Coverage: Coverage for the whole repository, calculated as the sum of all File Coverage. Learn more.

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