syncmoss 0.3.0__tar.gz → 0.4.0__tar.gz

{syncmoss-0.3.0 → syncmoss-0.4.0}/.github/workflows/_Tests.yml

@@ -74,7 +74,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install wheels/*.whl
-          pip install pytest
+          pip install pytest pytest-xdist
 
       - name: Install runtime dependencies + pytest (source checkout)
         if: inputs.install == 'source'
@@ -82,7 +82,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
-          pip install pytest
+          pip install pytest pytest-xdist
 
       - name: Run the test-suite
         shell: bash
@@ -103,4 +103,7 @@ jobs:
           if [ "$INSTALL" = "wheel" ]; then cd "$(mktemp -d)"; fi
 
           python -c "import syncmoss.syncmoss_main as m; print('syncmoss from:', m.__file__)"
-          python -m pytest "$GITHUB_WORKSPACE/tests" "${args[@]}"
+          # -n 0 forces a SERIAL run: pyproject sets -n auto for local use,
+          # which oversubscribes a small CI runner. xdist is installed above
+          # only so that this flag parses.
+          python -m pytest "$GITHUB_WORKSPACE/tests" -n 0 "${args[@]}"

{syncmoss-0.3.0 → syncmoss-0.4.0}/.gitignore

@@ -162,3 +162,11 @@ minimi_optimization_notes.txt
 # suite still covers the model end-to-end via the SCDW golden case, plus its
 # param-count and locked-angle checks (test_model_io / test_thick_gui).
 tests/test_sdw_grid.py
+
+# SMS instrumental-function study against the ESRF (temperature, angle) dataset
+# on N:\SL_studies: analysis scripts, cached intermediate fits and the figures
+# they produce. Local-only -- it needs a network share that is not part of the
+# repo, and its outputs are large. The conclusions that matter are tracked in
+# docs/sms_instrumental_function.md; the calibration it produced is in
+# sms_theory.FEBO3_BS_CALIBRATION and instrumental_io.ESRF_STANDARD_LINE_WIDTH.
+sms_study/

{syncmoss-0.3.0 → syncmoss-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: syncmoss
-Version: 0.3.0
+Version: 0.4.0
 Summary: SYNCmoss — Mössbauer spectroscopy analysis application
 Author: Sergey Yaroslavtsev
 License: MIT

{syncmoss-0.3.0 → syncmoss-0.4.0}/pyproject.toml

@@ -73,7 +73,21 @@ local_scheme = "no-local-version"
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
-addopts = "-q --basetemp=./.pytest_tmp"
+# -n 6: almost every test here spends its time in ONE process doing physics
+# (a fit, a calibration, an instrumental-function search), so a serial run
+# leaves most of the machine idle -- measured 351 s serial against 116 s on 8
+# workers for the calibration + instrumental set.
+#
+# A FIXED 6, not "auto". Each worker builds its own QApplication, PhysicsApp
+# and numba-compiled model, so the suite is limited by MEMORY, not by cores:
+# "auto" resolves to one worker per core (22 here) and dies during start-up
+# with an execnet EOFError once the machine runs out. The same ceiling bit the
+# 83-spectrum study, where 10 parallel fits OOM'd and 6 did not.
+#
+# CI overrides this with -n 0 (see .github/workflows/_Tests.yml): the runners
+# are small, where even 6 oversubscribes. Use -n 0 locally too when debugging,
+# since xdist swallows live output.
+addopts = "-q --basetemp=./.pytest_tmp -n 6"
 markers = [
     "gui: builds the PySide6 GUI; runs head-less via QT_QPA_PLATFORM=offscreen (set in tests/conftest.py)",
     "slow: slow tests (numba compilation / fitting)",

{syncmoss-0.3.0 → syncmoss-0.4.0}/syncmoss/Calibration.py

@@ -102,6 +102,7 @@ import numpy as np
 
 import syncmoss.minimi_lib as mi
 import syncmoss.models as m5
+import syncmoss.sms_theory as smst
 from syncmoss.constants import (number_of_baseline_parameters, ALPHA_FE_FIELD,
                                 TESLA_PER_MMS, LINE_RATIO_25, LINE_RATIO_34,
                                 NAT_WIDTH)
@@ -532,11 +533,16 @@ def Calibration(dir_path, Cal_file, pool, VVV, INS, JN, x0, MulCo, Vel_start=1,
             return m5.TI(x, p, model, JN, pool, x0, MulCo, INS, [], [], Norm=Norm)
 
         # The multi-line instrumental function displaces the apparent line
-        # positions by the intensity-weighted sum of the squared line shifts;
-        # the folded velocity axis is corrected by this at the very end.
+        # positions by its first moment (for the legacy sum of unit-area
+        # Gaussians: the intensity-weighted sum of the line shifts); the folded
+        # velocity axis is corrected by this at the very end. The theoretical
+        # SMS shapes compute the same moment in sms_theory.ins_centroid.
         INS_shift = 0
-        for i in range(0, int(len(INS) / 3)):
-            INS_shift += INS[i * 3 + 1] * INS[i * 3 + 2] ** 2
+        if smst.ins_kind(INS) == smst.KIND_GAUSS:
+            for i in range(0, int(len(INS) / 3)):
+                INS_shift += INS[i * 3 + 1] * INS[i * 3 + 2] ** 2
+        else:
+            INS_shift = smst.ins_centroid(INS)
     else:
         raise ValueError(f"unknown experimental method VVV={VVV!r} (expected 1 or 3)")
 

{syncmoss-0.3.0 → syncmoss-0.4.0}/syncmoss/constants.py

@@ -56,6 +56,26 @@ TESLA_PER_MMS = 1 / (2 * LINE_SHIFT_16)                 # 3.1097641 T per mm/s o
 LINE_RATIO_25 = LINE_SHIFT_25 / LINE_SHIFT_16           # 0.5789752
 LINE_RATIO_34 = LINE_SHIFT_34 / LINE_SHIFT_16           # 0.1579504
 
+# --- scattering-side 57Fe quantities (sms_theory.py) -----------------------
+# Everything below is DERIVED from the primitives above plus two new inputs,
+# ALPHA_IC and the universal hc; no 57Fe literal is repeated.
+#   ALPHA_IC -- internal conversion coefficient of the 14.4 keV level.
+#   HC_EV_A  -- h*c = 1239.8419843320026 eV nm (exact in SI since 2019).
+ALPHA_IC = 8.56
+HC_EV_A = 12398.419843320026                            # eV * Angstrom
+
+MMPS_TO_NEV = E0 / c * 10**9            # 48.0733 neV per (mm/s): E = E0 v/c
+GAMMA0_NEV = NAT_WIDTH * MMPS_TO_NEV    # 4.7112 neV, the natural width in neV
+MU_N_NEV_PER_T = mun / (E0_J / E0) * 10**9              # 31.4331 neV/T
+LAMBDA_A = HC_EV_A / E0                                 # 0.8603 A
+K_VEC_A = 2 * 3.141592653589793 / LAMBDA_A              # 7.3035 1/A
+R_E_A = 2.8179403262 * 10**-5                           # classical electron radius, A
+# Maximum resonant cross-section from the level scheme:
+#   sigma_0 = 2 pi lambdabar^2 (2 I_e + 1)/(2 I_g + 1) / (1 + alpha_ic)
+# equals `sigma` above (2.464e-22 m^2) to 0.02 %; sms_theory.selftest() checks it.
+SIGMA0_A2 = (2 * 3.141592653589793 * (LAMBDA_A / (2 * 3.141592653589793))**2
+             * (2 * 1.5 + 1) / (2 * 0.5 + 1) / (1 + ALPHA_IC))   # 0.024644 A^2
+
 # Linear polarization degree of the SMS (synchrotron) beam, 0..1. Only a default:
 # it is GUI-editable via Supp -> "Set polarization" and travels to the models as
 # the `pol` / `sms_pol` argument. 0.98 is a realistic synchrotron beam.

{syncmoss-0.3.0 → syncmoss-0.4.0}/syncmoss/fitting_io.py

@@ -343,7 +343,8 @@ def fit_single_spectrum(app, spectrum_file, pool, background=None, sequence_para
             # Load and concatenate all spectra
             A_list, B_list = [], []
             for i, spec_file in enumerate(spectrum_files):
-                A_temp, B_temp = load_spectrum(app, spec_file)
+                A_temp, B_temp = load_spectrum(
+                    app, spec_file, calibration_path=app.calibration_path)
                 A_temp, B_temp = A_temp[0], B_temp[0]
                 A_list.append(A_temp)
                 B_list.append(B_temp)
@@ -357,7 +358,8 @@ def fit_single_spectrum(app, spectrum_file, pool, background=None, sequence_para
             
         else:
             # Single spectrum fitting mode
-            A, B = load_spectrum(app, spectrum_file)
+            A, B = load_spectrum(app, spectrum_file,
+                                 calibration_path=app.calibration_path)
             A, B = A[0], B[0]  # Unpack from list
             A_list, B_list = [A], [B]