Major rework based on Sympy and TEMGYM Core

.github/workflows/ci.yml

@@ -16,12 +16,10 @@ concurrency:
 jobs:
   tests:
     strategy:
+      fail-fast: false
       matrix:
-        python_version: ["3.10", "3.11", "3.12"]
+        python_version: ["3.14", ]
         os: [ubuntu-latest, windows-latest, macos-14]
-        exclude:
-          - os: macos-14
-            python_version: "3.9"
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v7
@@ -30,7 +28,7 @@ jobs:
         with:
           python-version: '${{ matrix.python_version }}'
       - name: install the package
-        run: python3 -m pip install uv && uv pip install --system .[test]
+        run: python3 -m pip install uv && uv pip install --system .[test,common,diffraction,gui]
       - name: run pytest
         run: pytest --cov=microscope_calibration --cov-report=xml --cov-report=term tests/
       - name: submit code coverage
@@ -39,6 +37,7 @@ jobs:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   pinned-requirements:
+    if: false  # skip job
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v7
@@ -47,22 +46,23 @@ jobs:
         with:
           python-version: '3.11'
       - name: install the package
-        run: python3 -m pip install uv && uv pip install --system .[test] -r packaging/requirements.txt
+        run: python3 -m pip install uv && uv pip install --system .[test,common,diffraction,gui] -r packaging/requirements.txt
       - name: run pytest
         run: pytest --cov=microscope_calibration --cov-report=xml --cov-report=term tests/
 
   numba_coverage:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v7
-      - name: 'Choose Python version 3.12'
+      - name: 'Choose Python version 3.14'
         uses: actions/setup-python@v7
         with:
-          python-version: '3.12'
+          python-version: '3.14'
       - name: install the package
-        run: python3 -m pip install uv && uv pip install --system .[test]
+        run: python3 -m pip install uv && uv pip install --system .[test,common,diffraction,gui]
       - name: run pytest
-        run: NUMBA_DISABLE_JIT=1 pytest --cov=microscope_calibration --cov-report=xml --cov-report=term tests/
+        # Run only marked tests since many functional tests are very slow without Numba
+        run: NUMBA_DISABLE_JIT=1 pytest --cov=microscope_calibration --cov-report=xml --cov-report=term -m with_numba tests/
       - name: submit code coverage
         uses: codecov/codecov-action@v7
         env:

.pre-commit-config.yaml

@@ -8,12 +8,15 @@ repos:
   - id: end-of-file-fixer
   - id: check-yaml
   - id: check-added-large-files
-- repo: https://github.com/pycqa/flake8
-  rev: 7.4.1
+    exclude: prototypes/clcalib.ipynb
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.16.10
   hooks:
-  - id: flake8
+  - id: ruff-check
+    args: [--fix]
+  - id: ruff-format
 - repo: https://github.com/asottile/pyupgrade
   rev: v3.21.2
   hooks:
     - id: pyupgrade
-      args: ["--py39-plus"]
+      args: ["--py314-plus"]

examples/AuEntryWithCollCode163723.cif

@@ -0,0 +1,250 @@
+
+#(C) 2025 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure.  All rights reserved.
+data_163723-ICSD
+_database_code_ICSD 163723
+_audit_creation_date 2009-08-01
+_chemical_name_common Gold
+_chemical_formula_structural Au
+_chemical_formula_sum Au1
+_chemical_name_structure_type Cu
+_exptl_crystal_density_diffrn 19.39
+_citation_title 'Isothermal section of the Ce - Au - Sb system at 870 K'
+loop_
+_citation_id
+_citation_journal_full
+_citation_year
+_citation_journal_volume
+_citation_page_first
+_citation_page_last
+_citation_journal_id_ASTM
+primary 'Journal of Alloys and Compounds' 2009 479 184 188 JALCEU
+loop_
+_citation_author_citation_id
+_citation_author_name
+primary 'Salamakha, L.P.'
+primary 'Bauer, E.'
+primary 'Mudryi, S.I.'
+primary 'Goncalves, A.P.'
+primary 'Almeida, M.'
+primary 'Noel, H.'
+_cell_length_a 4.0709(2)
+_cell_length_b 4.0709(2)
+_cell_length_c 4.0709(2)
+_cell_angle_alpha 90.
+_cell_angle_beta 90.
+_cell_angle_gamma 90.
+_cell_volume 67.46
+_cell_formula_units_Z 4
+_space_group_name_H-M_alt 'F m -3 m'
+_space_group_IT_number 225
+loop_
+_space_group_symop_id
+_space_group_symop_operation_xyz
+1 'z, y, -x'
+2 'y, x, -z'
+3 'x, z, -y'
+4 'z, x, -y'
+5 'y, z, -x'
+6 'x, y, -z'
+7 'z, -y, x'
+8 'y, -x, z'
+9 'x, -z, y'
+10 'z, -x, y'
+11 'y, -z, x'
+12 'x, -y, z'
+13 '-z, y, x'
+14 '-y, x, z'
+15 '-x, z, y'
+16 '-z, x, y'
+17 '-y, z, x'
+18 '-x, y, z'
+19 '-z, -y, -x'
+20 '-y, -x, -z'
+21 '-x, -z, -y'
+22 '-z, -x, -y'
+23 '-y, -z, -x'
+24 '-x, -y, -z'
+25 '-z, -y, x'
+26 '-y, -x, z'
+27 '-x, -z, y'
+28 '-z, -x, y'
+29 '-y, -z, x'
+30 '-x, -y, z'
+31 '-z, y, -x'
+32 '-y, x, -z'
+33 '-x, z, -y'
+34 '-z, x, -y'
+35 '-y, z, -x'
+36 '-x, y, -z'
+37 'z, -y, -x'
+38 'y, -x, -z'
+39 'x, -z, -y'
+40 'z, -x, -y'
+41 'y, -z, -x'
+42 'x, -y, -z'
+43 'z, y, x'
+44 'y, x, z'
+45 'x, z, y'
+46 'z, x, y'
+47 'y, z, x'
+48 'x, y, z'
+49 'z, y+1/2, -x+1/2'
+50 'y, x+1/2, -z+1/2'
+51 'x, z+1/2, -y+1/2'
+52 'z, x+1/2, -y+1/2'
+53 'y, z+1/2, -x+1/2'
+54 'x, y+1/2, -z+1/2'
+55 'z, -y+1/2, x+1/2'
+56 'y, -x+1/2, z+1/2'
+57 'x, -z+1/2, y+1/2'
+58 'z, -x+1/2, y+1/2'
+59 'y, -z+1/2, x+1/2'
+60 'x, -y+1/2, z+1/2'
+61 '-z, y+1/2, x+1/2'
+62 '-y, x+1/2, z+1/2'
+63 '-x, z+1/2, y+1/2'
+64 '-z, x+1/2, y+1/2'
+65 '-y, z+1/2, x+1/2'
+66 '-x, y+1/2, z+1/2'
+67 '-z, -y+1/2, -x+1/2'
+68 '-y, -x+1/2, -z+1/2'
+69 '-x, -z+1/2, -y+1/2'
+70 '-z, -x+1/2, -y+1/2'
+71 '-y, -z+1/2, -x+1/2'
+72 '-x, -y+1/2, -z+1/2'
+73 '-z, -y+1/2, x+1/2'
+74 '-y, -x+1/2, z+1/2'
+75 '-x, -z+1/2, y+1/2'
+76 '-z, -x+1/2, y+1/2'
+77 '-y, -z+1/2, x+1/2'
+78 '-x, -y+1/2, z+1/2'
+79 '-z, y+1/2, -x+1/2'
+80 '-y, x+1/2, -z+1/2'
+81 '-x, z+1/2, -y+1/2'
+82 '-z, x+1/2, -y+1/2'
+83 '-y, z+1/2, -x+1/2'
+84 '-x, y+1/2, -z+1/2'
+85 'z, -y+1/2, -x+1/2'
+86 'y, -x+1/2, -z+1/2'
+87 'x, -z+1/2, -y+1/2'
+88 'z, -x+1/2, -y+1/2'
+89 'y, -z+1/2, -x+1/2'
+90 'x, -y+1/2, -z+1/2'
+91 'z, y+1/2, x+1/2'
+92 'y, x+1/2, z+1/2'
+93 'x, z+1/2, y+1/2'
+94 'z, x+1/2, y+1/2'
+95 'y, z+1/2, x+1/2'
+96 'x, y+1/2, z+1/2'
+97 'z+1/2, y, -x+1/2'
+98 'y+1/2, x, -z+1/2'
+99 'x+1/2, z, -y+1/2'
+100 'z+1/2, x, -y+1/2'
+101 'y+1/2, z, -x+1/2'
+102 'x+1/2, y, -z+1/2'
+103 'z+1/2, -y, x+1/2'
+104 'y+1/2, -x, z+1/2'
+105 'x+1/2, -z, y+1/2'
+106 'z+1/2, -x, y+1/2'
+107 'y+1/2, -z, x+1/2'
+108 'x+1/2, -y, z+1/2'
+109 '-z+1/2, y, x+1/2'
+110 '-y+1/2, x, z+1/2'
+111 '-x+1/2, z, y+1/2'
+112 '-z+1/2, x, y+1/2'
+113 '-y+1/2, z, x+1/2'
+114 '-x+1/2, y, z+1/2'
+115 '-z+1/2, -y, -x+1/2'
+116 '-y+1/2, -x, -z+1/2'
+117 '-x+1/2, -z, -y+1/2'
+118 '-z+1/2, -x, -y+1/2'
+119 '-y+1/2, -z, -x+1/2'
+120 '-x+1/2, -y, -z+1/2'
+121 '-z+1/2, -y, x+1/2'
+122 '-y+1/2, -x, z+1/2'
+123 '-x+1/2, -z, y+1/2'
+124 '-z+1/2, -x, y+1/2'
+125 '-y+1/2, -z, x+1/2'
+126 '-x+1/2, -y, z+1/2'
+127 '-z+1/2, y, -x+1/2'
+128 '-y+1/2, x, -z+1/2'
+129 '-x+1/2, z, -y+1/2'
+130 '-z+1/2, x, -y+1/2'
+131 '-y+1/2, z, -x+1/2'
+132 '-x+1/2, y, -z+1/2'
+133 'z+1/2, -y, -x+1/2'
+134 'y+1/2, -x, -z+1/2'
+135 'x+1/2, -z, -y+1/2'
+136 'z+1/2, -x, -y+1/2'
+137 'y+1/2, -z, -x+1/2'
+138 'x+1/2, -y, -z+1/2'
+139 'z+1/2, y, x+1/2'
+140 'y+1/2, x, z+1/2'
+141 'x+1/2, z, y+1/2'
+142 'z+1/2, x, y+1/2'
+143 'y+1/2, z, x+1/2'
+144 'x+1/2, y, z+1/2'
+145 'z+1/2, y+1/2, -x'
+146 'y+1/2, x+1/2, -z'
+147 'x+1/2, z+1/2, -y'
+148 'z+1/2, x+1/2, -y'
+149 'y+1/2, z+1/2, -x'
+150 'x+1/2, y+1/2, -z'
+151 'z+1/2, -y+1/2, x'
+152 'y+1/2, -x+1/2, z'
+153 'x+1/2, -z+1/2, y'
+154 'z+1/2, -x+1/2, y'
+155 'y+1/2, -z+1/2, x'
+156 'x+1/2, -y+1/2, z'
+157 '-z+1/2, y+1/2, x'
+158 '-y+1/2, x+1/2, z'
+159 '-x+1/2, z+1/2, y'
+160 '-z+1/2, x+1/2, y'
+161 '-y+1/2, z+1/2, x'
+162 '-x+1/2, y+1/2, z'
+163 '-z+1/2, -y+1/2, -x'
+164 '-y+1/2, -x+1/2, -z'
+165 '-x+1/2, -z+1/2, -y'
+166 '-z+1/2, -x+1/2, -y'
+167 '-y+1/2, -z+1/2, -x'
+168 '-x+1/2, -y+1/2, -z'
+169 '-z+1/2, -y+1/2, x'
+170 '-y+1/2, -x+1/2, z'
+171 '-x+1/2, -z+1/2, y'
+172 '-z+1/2, -x+1/2, y'
+173 '-y+1/2, -z+1/2, x'
+174 '-x+1/2, -y+1/2, z'
+175 '-z+1/2, y+1/2, -x'
+176 '-y+1/2, x+1/2, -z'
+177 '-x+1/2, z+1/2, -y'
+178 '-z+1/2, x+1/2, -y'
+179 '-y+1/2, z+1/2, -x'
+180 '-x+1/2, y+1/2, -z'
+181 'z+1/2, -y+1/2, -x'
+182 'y+1/2, -x+1/2, -z'
+183 'x+1/2, -z+1/2, -y'
+184 'z+1/2, -x+1/2, -y'
+185 'y+1/2, -z+1/2, -x'
+186 'x+1/2, -y+1/2, -z'
+187 'z+1/2, y+1/2, x'
+188 'y+1/2, x+1/2, z'
+189 'x+1/2, z+1/2, y'
+190 'z+1/2, x+1/2, y'
+191 'y+1/2, z+1/2, x'
+192 'x+1/2, y+1/2, z'
+loop_
+_atom_type_symbol
+_atom_type_oxidation_number
+Au0+ 0
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_symmetry_multiplicity
+_atom_site_Wyckoff_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_B_iso_or_equiv
+_atom_site_occupancy
+Au1 Au0+ 4 a 0 0 0 . 1.
+#End of TTdata_163723-ICSD

examples/defocused_wide.json

@@ -0,0 +1 @@
+{"0": "/storage/er-c-data/adhoc/livecalibration/2026-08-27-CEA-JEOL/raw/MicroscopeCal/mag60kX_cl80cm_ca150um_z150um_roi.dm4", "1": {"overfocus": 0.00012542767535846512, "scan_pixel_pitch": 2.2362875995440845e-08, "scan_center": {"y": 64.0, "x": 64.0}, "scan_rotation": 0.0, "camera_length": 1.26, "detector_pixel_pitch": 5.9999999999999995e-05, "detector_center": {"y": 256.0, "x": 256.0}, "semiconv": 0.001, "flip_factor": 0.9993577283544929, "descan_error": {"pxo_pxi": 0.0, "pxo_pyi": 0.0, "pyo_pxi": 0.0, "pyo_pyi": 0.0, "sxo_pxi": -1148.5746728148993, "sxo_pyi": 62.21862729837022, "syo_pxi": -78.29870984334525, "syo_pyi": -1417.6246735609502, "offpxi": 0.0, "offpyi": 0.0, "offsxi": -0.00042827525992734233, "offsyi": 0.0007292625394919069}, "detector_rotation": -0.7305988596863205}}