easydiffraction 0.12.0__tar.gz → 0.13.0__tar.gz

{easydiffraction-0.12.0 → easydiffraction-0.13.0}/.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

{easydiffraction-0.12.0 → easydiffraction-0.13.0}/.github/copilot-instructions.md

@@ -44,6 +44,10 @@
 - Type-annotate all public function signatures.
 - Docstrings on all public classes and methods (numpy style). These must
   include sections Parameters, Returns and Raises, where applicable.
+- Docstring summary must be a single line no longer than 72 characters
+  (the `max-doc-length` setting in `pyproject.toml`). If the summary
+  does not fit, shorten the wording rather than wrapping to a second
+  line.
 - Prefer flat over nested, explicit over clever.
 - Write straightforward code; do not add defensive checks for unlikely
   edge cases.
@@ -173,6 +177,15 @@
 
 ## Workflow
 
+- Use a two-phase workflow for all non-trivial changes:
+  - **Phase 1 — Implementation:** implement the change (source code,
+    docs, architecture updates). Do not create new tests or run existing
+    tests. Present the implementation for review and iterate until
+    approved.
+  - **Phase 2 — Verification:** once the implementation is approved, add
+    or update tests, then run linting (`pixi run fix`, `pixi run check`)
+    and all test suites (`pixi run unit-tests`,
+    `pixi run integration-tests`, `pixi run script-tests`).
 - All open issues, design questions, and planned improvements are
   tracked in `docs/architecture/issues_open.md`, ordered by priority.
   When an issue is fully implemented, move it from that file to
@@ -180,9 +193,12 @@
   architecture, update the relevant sections of
   `docs/architecture/architecture.md`.
 - After changes, run linting and formatting fixes with `pixi run fix`.
-  Do not check what was auto-fixed, just accept the fixes and move on.
-  Then, run linting and formatting checks with `pixi run check` and
-  address any remaining issues until the code is clean.
+  This also regenerates `docs/architecture/package-structure-full.md`
+  and `docs/architecture/package-structure-short.md` automatically — do
+  not edit those files by hand. Do not check what was auto-fixed, just
+  accept the fixes and move on. Then, run linting and formatting checks
+  with `pixi run check` and address any remaining issues until the code
+  is clean.
 - After changes, run unit tests with `pixi run unit-tests`.
 - After changes, run integration tests with
   `pixi run integration-tests`.

{easydiffraction-0.12.0 → easydiffraction-0.13.0}/.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

{easydiffraction-0.12.0 → easydiffraction-0.13.0}/.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: |

{easydiffraction-0.12.0 → easydiffraction-0.13.0}/.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/

{easydiffraction-0.12.0 → easydiffraction-0.13.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: easydiffraction
-Version: 0.12.0
+Version: 0.13.0
 Summary: Diffraction data analysis
 Project-URL: Homepage, https://easydiffraction.org
 Project-URL: Documentation, https://easyscience.github.io/diffraction-lib

easydiffraction-0.13.0/docs/architecture/ROADMAP.md

@@ -0,0 +1,382 @@
+# EasyDiffraction Development Roadmap
+
+LIB – Python library API  
+APP – graphical application  
+CLI – command-line interface
+
+Legend:
+
+- ✅ done
+- 🚧 work in progress
+- 🗓 planned
+  - 🗓`highest` Urgent. Needs attention ASAP
+  - 🗓`high` Should be prioritized soon
+  - 🗓`medium` Normal/default priority
+  - 🗓`low` Low importance
+  - 🗓`lowest` Very low urgency
+- — not applicable / not implemented
+
+---
+
+# 1. Sample Model
+
+## 1.1 Crystal Structure Parameters
+
+### Space Group
+
+| Feature                            | LIB | APP |
+| ---------------------------------- | --- | --- |
+| Hermann-Mauguin space-group symbol | ✅  | ✅  |
+| Space group IT number              | 🗓  | 🗓  |
+| IT coordinate system code          | ✅  | ✅  |
+
+### Cell
+
+| Feature           | LIB | APP |
+| ----------------- | --- | --- |
+| Lengths _a, b, c_ | ✅  | ✅  |
+| Angles _α, β, γ_  | ✅  | ✅  |
+
+### Atom Sites
+
+| Feature                                        | LIB | APP |
+| ---------------------------------------------- | --- | --- |
+| Neutron scattering lengths (tabulated, CrysPy) | ✅  | ✅  |
+| X-ray scattering factors (tabulated, CrysPy)   | ✅  | ✅  |
+| Custom neutron scattering length               | 🗓  | 🗓  |
+| Fractional coordinates _x, y, z_               | ✅  | ✅  |
+| Occupancy                                      | ✅  | ✅  |
+| Symmetry _wyckoff_letter_                      | ✅  | ✅  |
+
+### Atomic Displacement Parameters (ADP)
+
+| Feature                                         | LIB | APP |
+| ----------------------------------------------- | --- | --- |
+| Isotropic Biso                                  | ✅  | 🗓  |
+| Isotropic Uiso                                  | 🚧  | ✅  |
+| Anisotropic Bani _B11, B22, B33, B12, B13, B23_ | 🚧  | 🗓  |
+| Anisotropic Uani _U11, U22, U33, U12, U13, U23_ | 🚧  | 🗓  |
+
+---
+
+## 1.2 Magnetic Structure Parameters
+
+| Feature                                                 | LIB | APP |
+| ------------------------------------------------------- | --- | --- |
+| EPIC (Magnetic space groups, unpolarized and polarized) | 🗓  | 🗓  |
+
+---
+
+# 2. Experiment Model
+
+## 2.1 Powder Diffraction
+
+### Fitting Methods
+
+| Feature                               | LIB | APP |
+| ------------------------------------- | --- | --- |
+| Rietveld refinement (full pattern)    | ✅  | ✅  |
+| Le Bail refinement (profile matching) | 🗓  | 🗓  |
+
+### Linked Phases
+
+| Feature      | LIB | APP |
+| ------------ | --- | --- |
+| Scale factor | ✅  | ✅  |
+
+### Excluded Regions
+
+| Feature                                   | LIB | APP |
+| ----------------------------------------- | --- | --- |
+| Multiple regions<br>_start/end positions_ | ✅  | 🗓  |
+
+---
+
+### Background
+
+| Feature                                           | LIB | APP |
+| ------------------------------------------------- | --- | --- |
+| Line segments type<br>_x, y_                      | ✅  | ✅  |
+| Chebyshev polynomial type<br>_order, coefficient_ | ✅  | 🗓  |
+
+### Preferred Orientation
+
+| Feature                                    | LIB      | APP |
+| ------------------------------------------ | -------- | --- |
+| Basic preferred orientation model (CrysPy) | 🗓`high` | 🗓  |
+
+### Instrument — Constant Wavelength
+
+| Feature                                                  | LIB | APP |
+| -------------------------------------------------------- | --- | --- |
+| Wavelength                                               | ✅  | ✅  |
+| Second wavelength                                        | 🗓  | 🗓  |
+| 2θ offset                                                | ✅  | ✅  |
+| Sample displacement correction (FullProf _SyCos, SySin_) | 🗓  | 🗓  |
+
+### Instrument — Time-of-Flight
+
+| Feature                                                       | LIB | APP |
+| ------------------------------------------------------------- | --- | --- |
+| 2θ bank                                                       | ✅  | ✅  |
+| d → TOF conversion<br>_reciprocal, offset, linear, quadratic_ | ✅  | ✅  |
+
+### Peak Profile — Constant Wavelength
+
+| 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)                                  | ✅    | ✅  |
+| Thompson-Cox-Hastings Pseudo-Voigt + Finger-Cox-Jephcoat asymmetry<br>_Gaussian broadening U, V, W. Lorentzian broadening X, Y<br>Finger-Cox-Jephcoat asymmetry 1, 2_<br>(CrysFML) | ✅/🗓 | 🗓  |
+
+### Peak Profile — Time-of-Flight
+
+CrysPy peak_shape options:
+
+- "Gauss": Jorgensen (back-to-back exponentials ⊗ Gaussian)
+- "pseudo-Voigt": Jorgensen-Von Dreele (back-to-back exponentials ⊗
+  pseudo-Voigt)
+- "type0m": Double back-to-back exponentials ⊗ pseudo-Voigt (Z-Rietveld
+  type 0m)
+
+| 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) | ✅  | 🗓  |
+| 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    |
+
+---
+
+## 2.1.2 Total Scattering (Pair Distribution Function)
+
+### Peak Profile
+
+| Feature                                                                                                | LIB | APP |
+| ------------------------------------------------------------------------------------------------------ | --- | --- |
+| GaussianDampedSinc type<br>_cutoff q. broadening q. sharpening δ₁, δ₂<br>damping q, particle diameter_ | ✅  | 🗓  |
+
+---
+
+## 2.2 Single Crystal Diffraction
+
+### Extinction
+
+CrysPy's extinction is an analytical Becker-Coppens spherical model with
+Gauss or Lorentz mosaicity distribution
+
+| Feature                                               | LIB | APP |
+| ----------------------------------------------------- | --- | --- |
+| Becker-Coppens, Gaussian model: _radius, mosaicity_   | ✅  | ✅  |
+| Becker-Coppens, Lorentzian model: _radius, mosaicity_ | ✅  | ✅  |
+| Anisotropic extinction correction                     | 🗓  | 🗓  |
+
+### Domains / Twinning
+
+| Feature                                           | LIB | APP |
+| ------------------------------------------------- | --- | --- |
+| Twinning / domains for single-crystal diffraction | 🗓  | 🗓  |
+
+### Instrument — Constant Wavelength
+
+| Feature               | LIB | APP |
+| --------------------- | --- | --- |
+| Wavelength            | ✅  | ✅  |
+| Half wavelength (λ/2) | 🗓  | 🗓  |
+
+### Instrument — Time-of-Flight
+
+| Feature                              | LIB | APP |
+| ------------------------------------ | --- | --- |
+| Individual wavelength per reflection | ✅  | 🗓  |
+
+## 2.3. Polarized Neutron Diffraction
+
+| Feature                                        | LIB | APP |
+| ---------------------------------------------- | --- | --- |
+| EPIC (powders and single crystals, FR and SNP) | 🗓  | 🗓  |
+
+---
+
+# 3. Multi-Dataset Support
+
+| Feature                           | LIB | APP |
+| --------------------------------- | --- | --- |
+| Multiple structural data blocks   | ✅  | ✅  |
+| Multiple experimental data blocks | ✅  | 🗓  |
+
+---
+
+# 4. Analysis (Fitting)
+
+### Refinement Algorithms
+
+| Feature                                                         | LIB | APP |
+| --------------------------------------------------------------- | --- | --- |
+| Levenberg–Marquardt (numerical derivatives)<br>LMFIT minimizer  | ✅  | ✅  |
+| Levenberg–Marquardt (analytical derivatives)<br>LMFIT minimizer | 🗓  | 🗓  |
+| Derivative-free minimization<br>DFO-LS minimizer                | ✅  | ✅  |
+| Bayesian analysis<br>BUMPS minimizer                            | 🗓  | 🗓  |
+
+### Fit Strategies
+
+| Feature                                                                                              | LIB | APP |
+| ---------------------------------------------------------------------------------------------------- | --- | --- |
+| Sequential fit of experimental data blocks                                                           | ✅  | 🗓  |
+| Joint fit of experimental data blocks within the same calculation engine                             | ✅  | 🗓  |
+| Joint fit of experimental data blocks using different calculation engines<br>(e.g. CrysPy + Pdffit2) | ✅  | 🗓  |
+| Custom weighting for joint fit: _weight per dataset_                                                 | ✅  | 🗓  |
+
+### Live Fitting
+
+| Feature                                        | LIB | APP |
+| ---------------------------------------------- | --- | --- |
+| Live fitting during real-time data acquisition | 🗓  | 🗓  |
+
+---
+
+# 5. Refinement Execution
+
+| Feature                                       | LIB | APP | CLI |
+| --------------------------------------------- | --- | --- | --- |
+| Scripted refinement workflow                  | ✅  | —   | —   |
+| GUI-driven refinement workflow                | —   | ✅  | —   |
+| Command-line refinement execution             | —   | —   | ✅  |
+| Parameter modification                        | ✅  | ✅  | —   |
+| Load individual structure or experiment files | ✅  | ✅  | —   |
+| Project-based refinement                      | ✅  | ✅  | ✅  |
+| Save refinement results to project            | ✅  | ✅  | ✅  |
+
+---
+
+# 6. Constraints
+
+| Feature                        | LIB | APP   |
+| ------------------------------ | --- | ----- |
+| Automatic symmetry constraints | ✅  | ✅/🗓 |
+| User-defined constraints       | ✅  | 🗓    |
+
+---
+
+# 7. Data Management
+
+### Data Loading
+
+| Feature                         | LIB | APP | CLI |
+| ------------------------------- | --- | --- | --- |
+| Load structure from CIF         | ✅  | ✅  | —   |
+| Load experiment data from ASCII | ✅  | ✅  | —   |
+| Load experiment data from CIF   | ✅  | ✅  | —   |
+
+### Project Files
+
+| Feature                | LIB | APP | CLI |
+| ---------------------- | --- | --- | --- |
+| Load project from disk | ✅  | ✅  | ✅  |
+| Save project to disk   | ✅  | ✅  | ✅  |
+
+### SciCat Integration
+
+| Feature                  | LIB | APP | CLI |
+| ------------------------ | --- | --- | --- |
+| Load project from SciCat | 🗓  | 🗓  | —   |
+| Save project to SciCat   | 🗓  | 🗓  | —   |
+
+### External Resources
+
+| Feature                           | LIB | APP | CLI |
+| --------------------------------- | --- | --- | --- |
+| List available tutorial notebooks | —   | —   | ✅  |
+| Download tutorial notebooks       | —   | —   | ✅  |
+
+---
+
+# 8. Visualization
+
+## 8.1. Sample Model
+
+### Crystal Structure
+
+| Feature                                  | LIB | APP |
+| ---------------------------------------- | --- | --- |
+| Visualize unit cell                      | 🗓  | ✅  |
+| Visualize multiple unit cells            | 🗓  | 🗓  |
+| Visualize atom sites as spheres          | 🗓  | ✅  |
+| Visualize atoms occupied same position   | 🗓  | 🗓  |
+| Visualize bonds                          | 🗓  | 🗓  |
+| Visualize polyhedra                      | 🗓  | 🗓  |
+| Interactive mode<br>3D rotation, zooming | 🗓  | ✅  |
+| Orthogonal unit cell                     | 🗓  | ✅  |
+| Non-orthogonal unit cell                 | 🗓  | 🗓  |
+
+### Magnetic Structure
+
+| Feature                              | LIB | APP |
+| ------------------------------------ | --- | --- |
+| Visualize magnetic moments as arrows | 🗓  | 🗓  |
+
+## 8.2. Experiment
+
+### Powder Diffraction
+
+| Feature                              | LIB      | APP | CLI |
+| ------------------------------------ | -------- | --- | --- |
+| Plot experimental curve              | ✅       | ✅  | ✅  |
+| Plot calculated curve                | ✅       | ✅  | ✅  |
+| Plot residual curve                  | ✅       | ✅  | ✅  |
+| Plot Bragg peaks                     | 🗓`high` | ✅  | —   |
+| Interactive mode<br>zooming, panning | ✅       | ✅  | —   |
+
+### Single Crystal Diffraction
+
+| Feature                              | LIB | APP | CLI |
+| ------------------------------------ | --- | --- | --- |
+| Plot obs vs calc for reflections     | ✅  | ✅  | ✅  |
+| Interactive mode<br>zooming, panning | ✅  | ✅  | —   |
+
+## 8.3. Analysis
+
+| Feature                                              | LIB   | APP | CLI |
+| ---------------------------------------------------- | ----- | --- | --- |
+| Live update of plots on parameter change with slider | —     | ✅  | —   |
+| Live update of plots during refinement               | —     | ✅  | —   |
+| Parameter evolution (sequential refinement)          | ✅/🗓 | 🗓  | —   |
+
+### Fitting
+
+| Feature                                   | LIB | APP | CLI |
+| ----------------------------------------- | --- | --- | --- |
+| Live update of plots                      | —   | ✅  | —   |
+| Live update of fit quality (change in χ²) | ✅  | ✅  | ✅  |
+| Plot correlation between parameters       | ✅  | 🗓  | ✅  |
+
+---
+
+# 9. User documentation
+
+| Feature                             | LIB | APP   |
+| ----------------------------------- | --- | ----- |
+| New unified documentation structure | ✅  | 🗓    |
+| Introduction                        | ✅  | ✅/🗓 |
+| Installation and setup guide        | ✅  | ✅/🗓 |
+| User guide                          | ✅  | ✅/🗓 |
+| Tutorials                           | ✅  | 🗓    |
+| API reference                       | ✅  | —     |
+
+---
+
+# 10. Future Topics
+
+Here, we list features that are not sorted into the above categories,
+but are still on our radar for future development.
+
+- Restrains (soft constraints, e.g. bond lengths, angles)
+- Global optimization algorithms (e.g. simulated annealing)
+- Incommensurate structures
+- 2D Rietveld refinement