Remove or use dead code

[sverhoeven]

Fixes #19

[codacy-production]

Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation	Diff coverage
✅ +1.11% (target: -1.00%)	✅ ∅

Coverage variation details

	Coverable lines	Covered lines	Coverage
Common ancestor commit (360e5d2)	2157	673	31.20%
Head commit (3104a82)	2083 (-74)	673 (+0)	32.31% (+1.11%)

Coverage variation is the difference between the coverage for the head and common ancestor commits of the pull request branch: <coverage of head commit> - <coverage of common ancestor commit>

Diff coverage details

	Coverable lines	Covered lines	Diff coverage
Pull request (#39)	0	0	∅ (not applicable)

Diff coverage is the percentage of lines that are covered by tests out of the coverable lines that the pull request added or modified: <covered lines added or modified>/<coverable lines added or modified> * 100%

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[BSchilperoort]

I removed the rot_search.py script in 3104a82, because it has not worked on any release of powerfit. In 1.1.4 it didn't exist yet, and the file was included in 2.0.0, but the rotate_grid function did not exist in _powerfit.pyx at that release.

So it hasn't worked in >9 years.

[AnnaEngel98]

I just discussed the other scripts with Alexandre. The rest can also be removed as we are not using it

[amjjbonvin]

Thinking of the directory content, shouldn’t we add a small example to it? Or point to the online tutorial (once updated)?

[BSchilperoort]

@AnnaEngel98 I also found out that the "rotate_grid3d" OpenCL kernel is unused, and contains a (known) bug;

powerfit/src/powerfit_em/correlators/kernels.cl

Lines 148 to 149 in 360e5d2

	// TODO fix why nan = 1 * 1 + 0 * 0, instead of 1
	printf("c1 = c01 * dy1 + c11 * dy: %f = %f * %f + %f * %f\n", c1, c01, dy1, c11, dy);

The result of this operation are NaN values.

Instead, the rotate_image3d kernel is used to rotate the grid (which does lead to the same results on CPU and GPU). But this rotate_grid openCL kernel & python function remain in the code. Seeing as it's unused code that's not needed, shall I just remove this?

[AnnaEngel98]

Yeah if it is unused and buggy it can definitely be removed

[codacy-production]

Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation	Diff coverage
❌ -5.18% (target: -1.00%)	✅ 33.33%

Coverage variation details

	Coverable lines	Covered lines	Coverage
Common ancestor commit (360e5d2)	2157	673	31.20%
Head commit (f0e6bf4)	1991 (-166)	518 (-155)	26.02% (-5.18%)

Coverage variation is the difference between the coverage for the head and common ancestor commits of the pull request branch: <coverage of head commit> - <coverage of common ancestor commit>

Diff coverage details

	Coverable lines	Covered lines	Diff coverage
Pull request (#39)	3	1	33.33%

Diff coverage is the percentage of lines that are covered by tests out of the coverable lines that the pull request added or modified: <covered lines added or modified>/<coverable lines added or modified> * 100%

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[Copilot]

Pull Request Overview

Removes significant amounts of dead/unused code across the powerfit_em package, including unused imports, commented-out code, and entire script files.

• Removed unused imports across multiple files to clean up dependencies
• Deleted commented-out code sections and debug print statements in test files
• Removed entire script files and test modules that appear to be no longer used

Reviewed Changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/test_powerfitter.py	Removed unused imports and large sections of commented/skipped test code
tests/test_kernels.py	Deleted entire test file (201 lines)
tests/test__powerfit.py	Deleted entire test file (82 lines)
tests/run_tests.py	Deleted entire test utility file (7 lines)
src/powerfit_em/scripts/rot_search.py	Deleted entire script file (98 lines)
src/powerfit_em/scripts/fsc-curve.py	Deleted entire script file (23 lines)
src/powerfit_em/scripts/atom2dens.py	Deleted entire script file (20 lines)
src/powerfit_em/scripts/init.py	Deleted entire script module (104 lines)
src/powerfit_em/report.py	Removed unused import of FileType
src/powerfit_em/helpers.py	Removed unused imports (os, errno, pi, volume module)
src/powerfit_em/correlators/kernels.cl	Removed large rotate_grid3d kernel function (153 lines)
src/powerfit_em/correlators/gpu.py	Removed unused import get_normalization_factor
src/powerfit_em/correlators/cpu.py	Removed unused import get_normalization_factor
src/powerfit_em/correlators/clkernels.py	Removed unused imports and rotate_grid3d method

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