Fix peak profile function and parameter names

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.10.1-40-g29e2ccf
+_commit: v0.10.1-41-g508666e
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/diffraction-app
 app_doi: 10.5281/zenodo.18163581

.github/workflows/pypi-test.yml

@@ -49,6 +49,7 @@ jobs:
         run: pixi init easydiffraction
 
       - name: Set the minimum system requirements
+        working-directory: easydiffraction
         run: pixi project system-requirements add macos 14.0
 
       - name: Add Python 3.14 from Conda

.github/workflows/test.yml

@@ -99,12 +99,27 @@ jobs:
             echo
             echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
 
-            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
 
             echo "Running tests in environment: $env"
             pixi run --environment $env unit-tests
           done
 
+      - name: Run functional tests
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
+
+            echo "Running tests in environment: $env"
+            pixi run --environment $env functional-tests
+          done
+
       - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }}
         shell: bash
         run: |
@@ -114,7 +129,7 @@ jobs:
             echo
             echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
 
-            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
 
             echo "Running tests in environment: $env"
             pixi run --environment $env integration-tests ${{ needs.env-prepare.outputs.pytest-marks }}
@@ -263,6 +278,25 @@ jobs:
             cd ..
           done
 
+      - name: Run functional tests
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            echo "Entering pixi project directory easydiffraction_py$py_ver"
+            cd easydiffraction_py$py_ver
+
+            echo "Running tests"
+            pixi run python -m pytest ../tests/functional/ --color=yes -v
+
+            echo "Exiting pixi project directory"
+            cd ..
+          done
+
       - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }}
         shell: bash
         run: |

.gitignore

@@ -49,3 +49,4 @@ CMakeLists.txt.user*
 # Used to fetch tutorials data during their runtime. Need to have '/' at
 # the beginning to avoid ignoring 'data' module in the src/.
 /data/
+/tmp/

docs/architecture/ROADMAP.md

@@ -50,12 +50,12 @@ Legend:
 
 ### Atomic Displacement Parameters (ADP)
 
-| Feature                                         | LIB         | APP |
-| ----------------------------------------------- | ----------- | --- |
-| Isotropic Biso                                  | ✅          | 🗓  |
-| Isotropic Uiso                                  | 🗓          | ✅  |
-| Anisotropic Bani _B11, B22, B33, B12, B13, B23_ | 🗓`highest` | 🗓  |
-| Anisotropic Uani _U11, U22, U33, U12, U13, U23_ | 🗓          | 🗓  |
+| Feature                                         | LIB | APP |
+| ----------------------------------------------- | --- | --- |
+| Isotropic Biso                                  | ✅  | 🗓  |
+| Isotropic Uiso                                  | 🚧  | ✅  |
+| Anisotropic Bani _B11, B22, B33, B12, B13, B23_ | 🚧  | 🗓  |
+| Anisotropic Uani _U11, U22, U33, U12, U13, U23_ | 🚧  | 🗓  |
 
 ---
 
@@ -110,9 +110,9 @@ Legend:
 | Feature                                                  | LIB | APP |
 | -------------------------------------------------------- | --- | --- |
 | Wavelength                                               | ✅  | ✅  |
-| Second wavelength                                        | 🚧  | 🗓  |
+| Second wavelength                                        | 🗓  | 🗓  |
 | 2θ offset                                                | ✅  | ✅  |
-| Sample displacement correction (FullProf _SyCos, SySin_) | 🚧  | 🗓  |
+| Sample displacement correction (FullProf _SyCos, SySin_) | 🗓  | 🗓  |
 
 ### Instrument — Time-of-Flight
 
@@ -123,9 +123,6 @@ Legend:
 
 ### Peak Profile — Constant Wavelength
 
-CrysPy: Pseudo-Voigt from FullProf. Empirical asymmetry, 4 params (p1,
-p2, p3, p4) from FullProf.
-
 | Feature                                                                                                                                                                            | LIB   | APP |
 | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----- | --- |
 | Pseudo-Voigt + Empirical asymmetry<br>_Gaussian broadening U, V, W. Lorentzian broadening X, Y<br>Empirical asymmetry p1, p2, p3, p4_<br>(CrysPy)                                  | ✅    | ✅  |
@@ -144,14 +141,16 @@ CrysPy peak_shape options:
 | Feature                                                                                                                                                                                                                            | LIB | APP |
 | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --- | --- |
 | Jorgensen (back-to-back exponentials ⊗ Gaussian)<br>_Gaussian broadening σ₀, σ₁, σ₂<br>Back-to-back exponential rise α₀, α₁. Back-to-back exponential decay β₀, β₁_<br>(CrysPy)                                                    | ✅  | ✅  |
-| Jorgensen-Von Dreele (back-to-back exponentials ⊗ pseudo-Voigt)<br>_Gaussian broadening σ₀, σ₁, σ₂. Lorentzian broadening γ₀, γ₁, γ₂<br>Back-to-back exponential rise α₀, α₁. Back-to-back exponential decay β₀, β₁_<br>(CrysPy)   | 🗓  | ✅  |
-| Double back-to-back exponentials ⊗ pseudo-Voigt [Z-Rietveld type0m]<br>_Gaussian broadening σ₀, σ₁, σ₂. Lorentzian broadening γ₀, γ₁, γ₂<br>Rise α₁, α₂. Fast decay β₀₀, β₀₁. Slow decay β₁₀. Switching r₀₁, r₀₂, r₀₃_<br>(CrysPy) | 🗓  | 🗓  |
+| Jorgensen-Von Dreele (back-to-back exponentials ⊗ pseudo-Voigt)<br>_Gaussian broadening σ₀, σ₁, σ₂. Lorentzian broadening γ₀, γ₁, γ₂<br>Back-to-back exponential rise α₀, α₁. Back-to-back exponential decay β₀, β₁_<br>(CrysPy)   | ✅  | ✅  |
+| Double back-to-back exponentials ⊗ pseudo-Voigt [Z-Rietveld type0m]<br>_Gaussian broadening σ₀, σ₁, σ₂. Lorentzian broadening γ₀, γ₁, γ₂<br>Rise α₁, α₂. Fast decay β₀₀, β₀₁. Slow decay β₁₀. Switching r₀₁, r₀₂, r₀₃_<br>(CrysPy) | ✅  | 🗓  |
+| Ikeda-Carpenter ⊗ pseudo-Voigt<br>_Moderator pulse α₀, α₁, β₀, κ<br>Gaussian broadening σ². Lorentzian broadening γ_<br>(CrysFML)                                                                                                  | 🗓  | 🗓  |
 
 | TOF profile                                                         | TOF source                                                        | Performance |
 | ------------------------------------------------------------------- | ----------------------------------------------------------------- | ----------- |
 | Jorgensen (back-to-back exponentials ⊗ Gaussian)                    | Simpler TOF profile, including reactor-source TOF implementations | Fast        |
 | Jorgensen-Von Dreele (back-to-back exponentials ⊗ pseudo-Voigt)     | Spallation-source TOF                                             | Slower      |
 | Double back-to-back exponentials ⊗ pseudo-Voigt (Z-Rietveld type0m) | Spallation-source TOF; more elaborate asymmetric profile          | Slowest     |
+| Ikeda-Carpenter ⊗ pseudo-Voigt                                      | Spallation-source TOF; moderator pulse shape model                | Moderate    |
 
 ---
 
@@ -169,9 +168,8 @@ CrysPy peak_shape options:
 
 ### Extinction
 
-CrysPy's extinction is NOT Shelx-style. It's an analytical
-Becker-Coppens spherical model with Gauss or Lorentz mosaicity
-distribution
+CrysPy's extinction is an analytical Becker-Coppens spherical model with
+Gauss or Lorentz mosaicity distribution
 
 | Feature                                               | LIB | APP |
 | ----------------------------------------------------- | --- | --- |

docs/architecture/architecture.md

@@ -337,7 +337,7 @@ class PeakFactory(FactoryBase):
         frozenset({
             ('scattering_type', ScatteringTypeEnum.BRAGG),
             ('beam_mode', BeamModeEnum.TIME_OF_FLIGHT),
-        }): PeakProfileTypeEnum.PSEUDO_VOIGT_IKEDA_CARPENTER,
+        }): PeakProfileTypeEnum.JORGENSEN,
         frozenset({
             ('scattering_type', ScatteringTypeEnum.TOTAL),
         }): PeakProfileTypeEnum.GAUSSIAN_DAMPED_SINC,
@@ -389,26 +389,26 @@ from .line_segment import LineSegmentBackground
 
 ### 5.5 All Factories
 
-| Factory                      | Domain                 | Tags resolve to                                             |
-| ---------------------------- | ---------------------- | ----------------------------------------------------------- |
-| `BackgroundFactory`          | Background categories  | `LineSegmentBackground`, `ChebyshevPolynomialBackground`    |
-| `PeakFactory`                | Peak profiles          | `CwlPseudoVoigt`, `TofPseudoVoigtIkedaCarpenter`, …         |
-| `InstrumentFactory`          | Instruments            | `CwlPdInstrument`, `TofPdInstrument`, …                     |
-| `DataFactory`                | Data collections       | `PdCwlData`, `PdTofData`, `ReflnData`, `TotalData`          |
-| `ExtinctionFactory`          | Extinction models      | `BeckerCoppensExtinction`                                   |
-| `LinkedCrystalFactory`       | Linked-crystal refs    | `LinkedCrystal`                                             |
-| `ExcludedRegionsFactory`     | Excluded regions       | `ExcludedRegions`                                           |
-| `LinkedPhasesFactory`        | Linked phases          | `LinkedPhases`                                              |
-| `ExperimentTypeFactory`      | Experiment descriptors | `ExperimentType`                                            |
-| `CellFactory`                | Unit cells             | `Cell`                                                      |
-| `SpaceGroupFactory`          | Space groups           | `SpaceGroup`                                                |
-| `AtomSitesFactory`           | Atom sites             | `AtomSites`                                                 |
-| `AliasesFactory`             | Parameter aliases      | `Aliases`                                                   |
-| `ConstraintsFactory`         | Parameter constraints  | `Constraints`                                               |
-| `FitModeFactory`             | Fit-mode category      | `FitMode`                                                   |
-| `JointFitExperimentsFactory` | Joint-fit weights      | `JointFitExperiments`                                       |
-| `CalculatorFactory`          | Calculation engines    | `CryspyCalculator`, `CrysfmlCalculator`, `PdffitCalculator` |
-| `MinimizerFactory`           | Minimisers             | `LmfitMinimizer`, `DfolsMinimizer`, …                       |
+| Factory                      | Domain                 | Tags resolve to                                              |
+| ---------------------------- | ---------------------- | ------------------------------------------------------------ |
+| `BackgroundFactory`          | Background categories  | `LineSegmentBackground`, `ChebyshevPolynomialBackground`     |
+| `PeakFactory`                | Peak profiles          | `CwlPseudoVoigt`, `TofJorgensen`, `TofJorgensenVonDreele`, … |
+| `InstrumentFactory`          | Instruments            | `CwlPdInstrument`, `TofPdInstrument`, …                      |
+| `DataFactory`                | Data collections       | `PdCwlData`, `PdTofData`, `ReflnData`, `TotalData`           |
+| `ExtinctionFactory`          | Extinction models      | `BeckerCoppensExtinction`                                    |
+| `LinkedCrystalFactory`       | Linked-crystal refs    | `LinkedCrystal`                                              |
+| `ExcludedRegionsFactory`     | Excluded regions       | `ExcludedRegions`                                            |
+| `LinkedPhasesFactory`        | Linked phases          | `LinkedPhases`                                               |
+| `ExperimentTypeFactory`      | Experiment descriptors | `ExperimentType`                                             |
+| `CellFactory`                | Unit cells             | `Cell`                                                       |
+| `SpaceGroupFactory`          | Space groups           | `SpaceGroup`                                                 |
+| `AtomSitesFactory`           | Atom sites             | `AtomSites`                                                  |
+| `AliasesFactory`             | Parameter aliases      | `Aliases`                                                    |
+| `ConstraintsFactory`         | Parameter constraints  | `Constraints`                                                |
+| `FitModeFactory`             | Fit-mode category      | `FitMode`                                                    |
+| `JointFitExperimentsFactory` | Joint-fit weights      | `JointFitExperiments`                                        |
+| `CalculatorFactory`          | Calculation engines    | `CryspyCalculator`, `CrysfmlCalculator`, `PdffitCalculator`  |
+| `MinimizerFactory`           | Minimisers             | `LmfitMinimizer`, `DfolsMinimizer`, …                        |
 
 > **Note:** `ExperimentFactory` and `StructureFactory` are _builder_
 > factories with `from_cif_path`, `from_cif_str`, `from_data_path`, and
@@ -450,15 +450,15 @@ Tags are the user-facing identifiers for selecting types. They must be:
 
 **Peak tags**
 
-| Tag                                | Class                          |
-| ---------------------------------- | ------------------------------ |
-| `pseudo-voigt`                     | `CwlPseudoVoigt`               |
-| `split-pseudo-voigt`               | `CwlSplitPseudoVoigt`          |
-| `thompson-cox-hastings`            | `CwlThompsonCoxHastings`       |
-| `tof-pseudo-voigt`                 | `TofPseudoVoigt`               |
-| `tof-pseudo-voigt-ikeda-carpenter` | `TofPseudoVoigtIkedaCarpenter` |
-| `tof-pseudo-voigt-back-to-back`    | `TofPseudoVoigtBackToBack`     |
-| `gaussian-damped-sinc`             | `TotalGaussianDampedSinc`      |
+| Tag                                  | Class                              |
+| ------------------------------------ | ---------------------------------- |
+| `pseudo-voigt`                       | `CwlPseudoVoigt`                   |
+| `pseudo-voigt + empirical asymmetry` | `CwlPseudoVoigtEmpiricalAsymmetry` |
+| `thompson-cox-hastings`              | `CwlThompsonCoxHastings`           |
+| `jorgensen`                          | `TofJorgensen`                     |
+| `jorgensen-von-dreele`               | `TofJorgensenVonDreele`            |
+| `double-jorgensen-von-dreele`        | `TofDoubleJorgensenVonDreele`      |
+| `gaussian-damped-sinc`               | `TotalGaussianDampedSinc`          |
 
 **Instrument tags**
 
@@ -542,25 +542,25 @@ line-segment points.
 
 #### Singleton CategoryItems — factory-created (get all three)
 
-| Class                          | Factory                 |
-| ------------------------------ | ----------------------- |
-| `CwlPdInstrument`              | `InstrumentFactory`     |
-| `CwlScInstrument`              | `InstrumentFactory`     |
-| `TofPdInstrument`              | `InstrumentFactory`     |
-| `TofScInstrument`              | `InstrumentFactory`     |
-| `CwlPseudoVoigt`               | `PeakFactory`           |
-| `CwlSplitPseudoVoigt`          | `PeakFactory`           |
-| `CwlThompsonCoxHastings`       | `PeakFactory`           |
-| `TofPseudoVoigt`               | `PeakFactory`           |
-| `TofPseudoVoigtIkedaCarpenter` | `PeakFactory`           |
-| `TofPseudoVoigtBackToBack`     | `PeakFactory`           |
-| `TotalGaussianDampedSinc`      | `PeakFactory`           |
-| `BeckerCoppensExtinction`      | `ExtinctionFactory`     |
-| `LinkedCrystal`                | `LinkedCrystalFactory`  |
-| `Cell`                         | `CellFactory`           |
-| `SpaceGroup`                   | `SpaceGroupFactory`     |
-| `ExperimentType`               | `ExperimentTypeFactory` |
-| `FitMode`                      | `FitModeFactory`        |
+| Class                              | Factory                 |
+| ---------------------------------- | ----------------------- |
+| `CwlPdInstrument`                  | `InstrumentFactory`     |
+| `CwlScInstrument`                  | `InstrumentFactory`     |
+| `TofPdInstrument`                  | `InstrumentFactory`     |
+| `TofScInstrument`                  | `InstrumentFactory`     |
+| `CwlPseudoVoigt`                   | `PeakFactory`           |
+| `CwlPseudoVoigtEmpiricalAsymmetry` | `PeakFactory`           |
+| `CwlThompsonCoxHastings`           | `PeakFactory`           |
+| `TofJorgensen`                     | `PeakFactory`           |
+| `TofJorgensenVonDreele`            | `PeakFactory`           |
+| `TofDoubleJorgensenVonDreele`      | `PeakFactory`           |
+| `TotalGaussianDampedSinc`          | `PeakFactory`           |
+| `BeckerCoppensExtinction`          | `ExtinctionFactory`     |
+| `LinkedCrystal`                    | `LinkedCrystalFactory`  |
+| `Cell`                             | `CellFactory`           |
+| `SpaceGroup`                       | `SpaceGroupFactory`     |
+| `ExperimentType`                   | `ExperimentTypeFactory` |
+| `FitMode`                          | `FitModeFactory`        |
 
 #### CategoryCollections — factory-created (get all three)
 
@@ -889,7 +889,7 @@ expt = ExperimentFactory.from_data_path(
 )
 expt.instrument.calib_d_to_tof_offset = 0.0
 expt.instrument.calib_d_to_tof_linear = 7476.91
-expt.peak_profile_type = 'pseudo-voigt * ikeda-carpenter'
+expt.peak_profile_type = 'jorgensen'
 expt.peak.broad_gauss_sigma_0 = 3.0
 ```