Dataclass material refactor

.github/workflows/test.yml

@@ -19,10 +19,10 @@ jobs:
           # pure python wheels
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.config.py }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.config.py }}
 
@@ -66,7 +66,7 @@ jobs:
     # See the following for how to upload to a release
     #  https://eugene-babichenko.github.io/blog/2020/05/09/github-actions-cross-platform-auto-releases/
     - name: Archive artifacts
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: artifacts
         path: |
@@ -80,7 +80,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Retrieve all artifacts
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: artifacts
 

.github/workflows/unstable.yml

@@ -20,10 +20,10 @@ jobs:
           # all using to stable abi
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.config.py }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.config.py }}
 
@@ -60,7 +60,7 @@ jobs:
     # See the following for how to upload to a release
     #  https://eugene-babichenko.github.io/blog/2020/05/09/github-actions-cross-platform-auto-releases/
     - name: Archive artifacts
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: artifacts
         path: |
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Retrieve all artifacts
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: artifacts
 

.gitignore

@@ -9,9 +9,13 @@
 .idea
 *.pyd
 *.pyc
+**/__pycache__/
+**/node_modules/
+/refl1d/webview/client/dist/
 *.swp
 *.so
 *.bak
+refl1d-webview-client*.tgz
 /build/
 /dist/
 /refl1d.egg-info/

MANIFEST.in

@@ -14,6 +14,11 @@ include master_builder.py
 include refl1d.iss
 include setup_py2exe.py
 include refl1d/lib/*.h refl1d/lib/erf.c
-
+recursive-include refl1d/webview/client/dist *.html *.js *.css *.svg *.png
+recursive-include refl1d/webview/client/src *.html *.js *.css *.svg *.png *.vue
+include refl1d/webview/client/*.html
+include refl1d/webview/client/*.js
+include refl1d/webview/client/*.json
+include refl1d/webview/client/*.txt
 # Delete files
 #prune this that

extra/build_conda_packed.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+ENV_NAME="isolated-base"
+PYTHON_VERSION="3.10"
+DIRNAME="refl1d"
+
+eval "$(conda shell.bash hook)"
+conda activate base || { echo 'failed: conda not installed'; exit 1; }
+
+conda install -y conda-pack
+conda create -n "$ENV_NAME" -y "python=$PYTHON_VERSION"
+conda-pack -n "$ENV_NAME" -f -o "$ENV_NAME.tar.gz"
+
+# unpack the new environment, that contains only python + pip
+tmpdir=$(mktemp -d)
+destdir="$tmpdir/$DIRNAME"
+mkdir "$destdir"
+tar -xzf "$ENV_NAME.tar.gz" -C "$destdir"
+
+# activate the unpacked environment and install pip packages
+conda deactivate
+WORKING_DIRECTORY=$(pwd)
+cd "$tmpdir"
+source "$DIRNAME/bin/activate"
+pip install --no-input numba
+pip install --no-input git+https://github.com/bumps/bumps@dataclass_overlay
+pip install --no-input git+https://github.com/reflectometry/refl1d@webview
+pip install -r https://raw.githubusercontent.com/reflectometry/refl1d/webview/webview-requirements
+source "$DIRNAME/bin/deactivate"
+
+# zip it back up
+tar -czf "$WORKING_DIRECTORY/refl1d-webview-$(uname -s)-$(uname -m).tar.gz" "$DIRNAME"

refl1d/errors.py

@@ -161,7 +161,7 @@ def calc_errors(problem, points):
     # TODO: return sane datastructure
     # Make a hashable version of model which just contains the name
     # attribute, which is all that the rest of this code accesses.
-    models = [_HashableModel(m) for m in _experiments(problem)]
+    models = [_HashableModel(m, i) for i, m in enumerate(_experiments(problem))]
 
     profiles = {h: [v[k] for v in profiles] for k, h in enumerate(models)}
     slabs = {h: [v[k] for v in slabs] for k, h in enumerate(models)}
@@ -179,8 +179,8 @@ def calc_errors(problem, points):
 
 class _HashableModel:
     name: str
-    def __init__(self, model):
-        self.name = model.name
+    def __init__(self, model, index):
+        self.name = model.name if model.name is not None else f"M{index}"
     def __str__(self):
         return f"model {self.name}"
 
@@ -229,7 +229,7 @@ def align_profiles(profiles, slabs, align):
                 for m in profiles.keys())
 
 def show_errors(errors, contours=CONTOURS, npoints=200,
-                align='auto', plots=1, save=None):
+                align='auto', plots=1, save=None, fig=None):
     """
     Plot the aligned profiles and the distribution of the residuals for
     profiles and residuals returned from calc_errors.
@@ -259,15 +259,20 @@ def show_errors(errors, contours=CONTOURS, npoints=200,
     """
     import matplotlib.pyplot as plt
 
+    if fig is not None and plots != 1:
+        raise ValueError("can only pass in a figure object if exactly 1 plot is requested")
+
     if plots == 0: # Don't create plots, just save the data
         _save_profile_data(errors, contours=contours, npoints=npoints,
                            align=align, save=save)
         _save_residual_data(errors, contours=contours, save=save)
     elif plots == 1: # Subplots for profiles/residuals
-        plt.subplot(211)
-        show_profiles(errors, contours=contours, npoints=npoints, align=align)
-        plt.subplot(212)
-        show_residuals(errors, contours=contours)
+        if fig is None:
+            fig = plt.gcf()
+        ax_profiles = fig.add_subplot(211)
+        show_profiles(errors, contours=contours, npoints=npoints, align=align, axes=ax_profiles)
+        ax_residuals = fig.add_subplot(212)
+        show_residuals(errors, contours=contours, axes=ax_residuals)
         if save:
             plt.savefig(save+"-err.png")
     elif plots == 2:  # Separate plots for profiles/residuals
@@ -296,24 +301,24 @@ def show_errors(errors, contours=CONTOURS, npoints=200,
                 plt.savefig(save+"-err%d.png"%fignum)
             fignum += 1
 
-def show_profiles(errors, align, contours, npoints):
+def show_profiles(errors, align, contours, npoints, axes=None):
     profiles, slabs, _, _ = errors
     if align is not None:
         profiles = align_profiles(profiles, slabs, align)
 
     if contours:
-        _profiles_contour(profiles, contours, npoints)
+        _profiles_contour(profiles, contours, npoints, axes=axes)
     else:
-        _profiles_overplot(profiles)
+        _profiles_overplot(profiles, axes=axes)
 
 
-def show_residuals(errors, contours):
+def show_residuals(errors, contours, axes=None):
     _, _, Q, residuals = errors
 
     if False and contours:
         _residuals_contour(Q, residuals, contours=contours)
     else:
-        _residuals_overplot(Q, residuals)
+        _residuals_overplot(Q, residuals, axes=axes)
 
 
 def _save_profile_data(errors, align, contours, npoints, save):
@@ -376,34 +381,36 @@ def _write_file(path, data, title, columns):
 def dark(color):
     return dhsv(color, dv=-0.2)
 
-def _profiles_overplot(profiles):
+def _profiles_overplot(profiles, axes=None):
     for model, group in profiles.items():
         name = model.name
         absorbing = any((L[2] != 1e-4).any() for L in group)
         magnetic = (len(group[0]) > 3)
         # Note: Use 3 colours per dataset for consistency
-        _draw_overplot(group, 1, name + ' rho')
+        _draw_overplot(group, 1, name + ' rho', axes=axes)
         if absorbing:
-            _draw_overplot(group, 2, name + ' irho')
+            _draw_overplot(group, 2, name + ' irho', axes=axes)
         else:
-            next_color()
+            next_color(axes=axes)
         if magnetic:
-            _draw_overplot(group, 3, name + ' rhoM')
+            _draw_overplot(group, 3, name + ' rhoM', axes=axes)
         else:
-            next_color()
-    _profile_labels()
+            next_color(axes=axes)
+    _profile_labels(axes=axes)
 
-def _draw_overplot(group, index, label):
+def _draw_overplot(group, index, label, axes=None):
     import matplotlib.pyplot as plt
+    if axes is None:
+        axes = plt.gca()
     alpha = 0.1
-    color = next_color()
+    color = next_color(axes=axes)
     for L in group[1:]:
-        plt.plot(L[0], L[index], '-', color=color, alpha=alpha)
+        axes.plot(L[0], L[index], '-', color=color, alpha=alpha)
     # Plot best
     L = group[0]
-    plt.plot(L[0], L[index], '-', label=label, color=dark(color))
+    axes.plot(L[0], L[index], '-', label=label, color=dark(color))
 
-def _profiles_contour(profiles, contours=CONTOURS, npoints=200):
+def _profiles_contour(profiles, contours=CONTOURS, npoints=200, axes=None):
     for model, group in profiles.items():
         name = model.name if model.name is not None else 'model'
         absorbing = any((L[2] > 1e-4).any() for L in group)
@@ -412,46 +419,52 @@ def _profiles_contour(profiles, contours=CONTOURS, npoints=200):
         z = np.hstack([line[0] for line in group])
         zp = np.linspace(np.min(z), np.max(z), npoints)
         # Note: Use 3 colours per dataset for consistency
-        _draw_contours(group, 1, name + ' rho', zp, contours)
+        _draw_contours(group, 1, name + ' rho', zp, contours, axes=axes)
         if absorbing:
-            _draw_contours(group, 2, name + ' irho', zp, contours)
+            _draw_contours(group, 2, name + ' irho', zp, contours, axes=axes)
         else:
-            next_color()
+            next_color(axes=axes)
         if magnetic:
-            _draw_contours(group, 3, name + ' rhoM', zp, contours)
+            _draw_contours(group, 3, name + ' rhoM', zp, contours, axes=axes)
         else:
-            next_color()
-    _profile_labels()
+            next_color(axes=axes)
+    _profile_labels(axes=axes)
 
-def _draw_contours(group, index, label, zp, contours):
+def _draw_contours(group, index, label, zp, contours, axes=None):
     import matplotlib.pyplot as plt
-    color = next_color()
+    if axes is None:
+        axes = plt.gca()
+    color = next_color(axes=axes)
     # Interpolate on common z
     fp = np.vstack([np.interp(zp, L[0], L[index]) for L in group])
     # Plot the quantiles
-    plot_quantiles(zp, fp, contours, color)
+    plot_quantiles(zp, fp, contours, color, axes=axes)
     # Plot the best
-    plt.plot(zp, fp[0], '-', label=label, color=dark(color))
+    axes.plot(zp, fp[0], '-', label=label, color=dark(color))
 
-def _profile_labels():
+def _profile_labels(axes=None):
     import matplotlib.pyplot as plt
-    plt.legend()
-    plt.xlabel(u'z (Å)')
-    plt.ylabel(u'SLD (10⁻⁶/Ų)')
+    if axes is None:
+        axes = plt.gca()
+    axes.legend()
+    axes.set_xlabel(u'z (Å)')
+    axes.set_ylabel(u'SLD (10⁻⁶/Ų)')
 
-def _residuals_overplot(Q, residuals):
+def _residuals_overplot(Q, residuals, axes=None):
     import matplotlib.pyplot as plt
+    if axes is None:
+        axes = plt.gca()
     alpha = 0.4
     shift = 0
     for m, r in residuals.items():
-        color = next_color()
-        plt.plot(Q[m], shift+r[:, 1:], '.', markersize=1, color=color, alpha=alpha)
-        plt.plot(Q[m], shift+r[:, 0], '.', label=m.name, markersize=1, color=dark(color))
+        color = next_color(axes=axes)
+        axes.plot(Q[m], shift+r[:, 1:], '.', markersize=1, color=color, alpha=alpha)
+        axes.plot(Q[m], shift+r[:, 0], '.', label=m.name, markersize=1, color=dark(color))
         # Use 3 colours from cycle so reflectivity matches rho for each dataset
-        next_color()
-        next_color()
+        next_color(axes=axes)
+        next_color(axes=axes)
         shift += 5
-    _residuals_labels()
+    _residuals_labels(axes=axes)
 
 def _residuals_contour(Q, residuals, contours=CONTOURS):
     import matplotlib.pyplot as plt
@@ -466,11 +479,13 @@ def _residuals_contour(Q, residuals, contours=CONTOURS):
         shift += 5
     _residuals_labels()
 
-def _residuals_labels():
+def _residuals_labels(axes=None):
     import matplotlib.pyplot as plt
-    plt.legend()
-    plt.xlabel(u'Q (1/Å)')
-    plt.ylabel(u'Residuals')
+    if axes is None:
+        axes = plt.gca()
+    axes.legend()
+    axes.set_xlabel(u'Q (1/Å)')
+    axes.set_ylabel(u'Residuals')
 
 # ==== Helper functions =====
 

refl1d/experiment.py

@@ -677,7 +677,7 @@ def __init__(self, samples=None, ratio=None, probe=None,
         self.probe = probe
         self.ratio = [Parameter.default(r, name="ratio %d"%i)
                       for i, r in enumerate(ratio)]
-        self.parts = [Experiment(s, probe, **kw) for s in samples]
+        self.parts = [Experiment(s, probe, name=s.name, **kw) for s in samples]
         self.coherent = coherent
         self.interpolation = interpolation
         self._substrate = self.samples[0][0].material