[uellue]

Changes

• Fix tests that didn't check what they claimed, e.g. the overfocus fit and invert_focus()
• Model4DSTEM.derive() uses dataclasses.replace(), normalize_types() names the field in errors
• Solvers share their least-squares setup, validate their input and are documented
• UDFs calculate their transformation matrices per task
• One helper for the affine maps of the Numba kernels
• Calibration UI split into smaller methods, its calculations moved into tested functions
• CalibratedDataset moved to dataset.py, still importable from ui
• jeol_dm4 reads each DM4 file once and is tested with fake tags
• Seeded random test inputs, underfocus in random models, non-square shapes in correction tests
• Apptainer image and pinned requirements updated to Python 3.14, CI tests the pins again
• Coverage configuration moved to pyproject.toml, setup.cfg and test_requirements.txt removed
• CLAUDE.md: model code stays SymPy-compatible, numeric versions via lambdify()

Behavior changes

• semiconv is the slope at the source everywhere, back-projection and simulation used it as an angle (see Model4DSTEM docstring)
• solve_coords_points() returns a flip factor of exactly ±1, also when starting with the wrong sign
• solve_camera_length() returns the specimen-to-detector distance for any overfocus, diffraction_angle is renamed to twotheta
• solve_tilt_descan_error_points() requires at least three points, solve_coords_points() at least one
• make_overfocus_loss_function() raises ValueError for a starting model in focus
• The UI passes fix points to the solvers as float64 instead of float32
• Model4DSTEM.derive() only accepts keyword arguments and keeps fields of subclasses
• Model4DSTEM.normalize_types() rejects strings
• lambdify(args=...) works
• UDFs no longer accept back_mat, corr_mat and ref_model, and accept models with JAX or NumPy scalars
• UDFs log a warning for a singular matrix and raise ValueError for scans that aren't 2D
• jeol_dm4 functions take DM4 tags instead of an open file, CalibratedJEOLDM4.dm4 is removed
• CalibratedJEOLDM4.microscope_info() ignores the thumbnail
• The UI instructions name the plots by their titles, and the sections are reordered to match
• optax moved from the common to the test extra

Review notes

• f22dd3a adds a type dispatch for cos/sin and c2e741c replaces it with lambdify() at the call sites, so the net change is in the tests
• The UI refactor commits were checked with a script that compares data sources, figures, widgets, callbacks and layout over 111 interaction steps; it isn't part of this PR
• The Apptainer image wasn't built; the pinned requirements pass the test suite
• Branch lambdify-model builds on this branch

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 96.04520% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.80%. Comparing base (f8f8d1b) to head (7daa7ae).

Files with missing lines	Patch %	Lines
src/microscope_calibration/util/jeol_dm4.py	91.04%	5 Missing and 1 partial ⚠️
src/microscope_calibration/udf/stem_overfocus.py	90.00%	3 Missing ⚠️
src/microscope_calibration/ui.py	97.67%	2 Missing and 1 partial ⚠️
src/microscope_calibration/util/optimize.py	96.87%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #69      +/-   ##
==========================================
+ Coverage   87.94%   93.80%   +5.86%     
==========================================
  Files          13       14       +1     
  Lines        2015     2002      -13     
  Branches      171      173       +2     
==========================================
+ Hits         1772     1878     +106     
+ Misses        203       83     -120     
- Partials       40       41       +1     

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[uellue]

Example notebooks seem to work!