Merge branch 'master' into TwoYukawa

.github/workflows/test.yml

@@ -9,13 +9,13 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -59,3 +59,12 @@ jobs:
       if: ${{ matrix.os == 'ubuntu-latest' }}
       run: |
         make -j 4 -C doc SPHINXOPTS="-W --keep-going -n" html
+
+    - name: Publish samodels docs
+      if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10'}}
+      uses: actions/upload-artifact@v3
+      with:
+        name: sasmodels-docs-${{ matrix.os }}-${{ matrix.python-version }}
+        path: |
+          doc/_build/html
+        if-no-files-found: error

CHANGES.rst

@@ -1,6 +1,27 @@
 Release notes
 =============
 
+v1.0.7 2023-02-??
+------------------
+* Doc upate: corefunc and optimizer documentation
+* Doc update: various models (cylinder, gel_fit, paracrystal, core_shell_ellipsoid)
+* Fix error in BCC and FCC paracrystaline models
+* Fix rare race condition causing errors
+* Fix to allow multiple scattering scripts to run
+* Fix problem with models containing complex amplitudes not compiling on the fly
+* Restructuring and cross-linking of sasmodels docs
+* Update web links and contributor list
+
+v1.0.6 2022-03-17
+------------------
+* implements generalized 3D description of magnetic SANS
+* adds Boucher-type SLD profile to the selection in the model spherical_sld
+* improves naming conventions of constants in magnetic SANS
+* composite mixture models with multiplicity are now allowed
+* improvements to the superball model
+* fix to bug in magnetic SLD calculations
+* updates to documentation
+
 v1.0.5 2021-01-26
 ------------------
 * fix probelm with P(Q) scaling when using a shell type form factors

LICENSE.txt

@@ -1,4 +1,5 @@
-Copyright (c) 2009-2021, SasView Developers
+Copyright (c) 2009-2022, SasView Developers
+
 
 All rights reserved.
 

doc/conf.py

@@ -27,7 +27,6 @@
 
 nitpick_ignore = [
     ('py:class', 'argparse.Namespace'),
-    ('py:class', 'bumps.parameter.Parameter'),
     ('py:class', 'collections.OrderedDict'),
     ('py:class', 'cuda.Context'),
     ('py:class', 'cuda.Function'),
@@ -51,10 +50,16 @@
     ('py:class', 'Data1D'),
     ('py:class', 'Data2D'),
     ('py:class', 'Kernel'),
+    ('py:class', 'KernelModel'),
     ('py:class', 'ModelInfo'),
     ('py:class', 'module'),
     ('py:class', 'SesansData'),
     ('py:class', 'SourceModule'),
+    # KernelModel and Calculator breaking on git actions tests, even though
+    # KernelModel is already listed. astropy example sometimes includes full
+    # path to complaining symbol. Let's see if that helps here:
+    ('py:class', 'sasmodels.compare.Calculator'),
+    ('py:class', 'sasmodels.kernel.KernelModel'),
 ]
 
 # -- General configuration -----------------------------------------------------

doc/genmodel.py

@@ -46,6 +46,7 @@
 import re
 import shutil
 import argparse
+import subprocess
 
 # CRUFT: python 2.7 backport of makedirs(path, exist_ok=False)
 if sys.version_info[0] >= 3:
@@ -148,8 +149,10 @@ def make_figure(model_info, opts):
     """
     import matplotlib.pyplot as plt
 
+    print("Build model")
     model = core.build_model(model_info)
 
+    print("Set up figure")
     fig_height = 3.0 # in
     fig_left = 0.6 # in
     fig_right = 0.5 # in
@@ -167,8 +170,10 @@ def make_figure(model_info, opts):
         ax_width = ax_height/ratio # square axes
         fig = plt.figure(figsize=aspect)
         ax2d = fig.add_axes([0.5+ax_left, ax_bottom, ax_width, ax_height])
+        print("2D plot")
         plot_2d(model, opts, ax2d)
         ax1d = fig.add_axes([ax_left, ax_bottom, ax_width, ax_height])
+        print("1D plot")
         plot_1d(model, opts, ax1d)
         #ax.set_aspect('square')
     else:
@@ -182,11 +187,14 @@ def make_figure(model_info, opts):
         aspect = (fig_width, fig_height)
         fig = plt.figure(figsize=aspect)
         ax1d = fig.add_axes([ax_left, ax_bottom, ax_width, ax_height])
+        print("1D plot")
         plot_1d(model, opts, ax1d)
 
     if model_info.profile:
+        print("Profile inset")
         plot_profile_inset(model_info, ax1d)
 
+    print("Save")
     # Save image in model/img
     makedirs(joinpath(TARGET_DIR, 'img'), exist_ok=True)
     path = joinpath(TARGET_DIR, 'img', figfile(model_info))
@@ -290,7 +298,7 @@ def gen_docs(model_info, outfile):
         print('------------------------------------------------------------------')
         docstr += insertion
 
-    with open(outfile, 'w') as fid:
+    with open(outfile, 'w', encoding='utf-8') as fid:
         fid.write(docstr)
 
 def make_figure_cached(model_info, opts):
@@ -311,7 +319,9 @@ def make_figure_cached(model_info, opts):
     # check if we are caching
     cache_dir = os.environ.get('SASMODELS_BUILD_CACHE', None)
     if cache_dir is None:
+        print("Nothing cashed, creating...")
         make_figure(model_info, opts)
+        print("Made a figure")
         return
 
     # TODO: changing default parameters won't trigger a rebuild.
@@ -387,31 +397,57 @@ def process_model(py_file, force=False):
     }
 
     # Generate the RST file and the figure.  Order doesn't matter.
-    print("generating", rst_file)
+    print("generating rst", rst_file)
+    print("1: docs")
     gen_docs(model_info, rst_file)
+    print("2: figure", end='')
     if force:
+        print()
         make_figure(model_info, PLOT_OPTS)
     else:
+        print(" (cached)")
         make_figure_cached(model_info, PLOT_OPTS)
+    print("Done process_model")
+
     return rst_file
 
 def run_sphinx(rst_files, output):
     """
     Use sphinx to build *rst_files*, storing the html in *output*.
     """
+
+    print("Building index...")
+
     conf_dir = dirname(realpath(__file__))
     with open(joinpath(TARGET_DIR, 'index.rst'), 'w') as fid:
         fid.write(".. toctree::\n\n")
         for path in rst_files:
             fid.write("    %s\n"%basename(path))
+
+    print("Running sphinx command...")
+
     command = [
         sys.executable,
         "-m", "sphinx",
         "-c", conf_dir,
         TARGET_DIR,
         output,
     ]
-    os.system(" ".join(repr(s) for s in command))
+
+    process = subprocess.Popen(command, shell=False, stdout=subprocess.PIPE)
+
+    # Make sure we can see process output in real time
+    while True:
+
+        output = process.stdout.readline()
+
+        if process.poll() is not None:
+            break
+
+        if output:
+            print(output.strip())
+
+
 
 def main():
     """
@@ -442,19 +478,13 @@ def main():
         sys.exit(1)
     makedirs(TARGET_DIR, exist_ok=True)
 
-    if args.cpus == -1:
-        cpus = int(os.environ.get("SASMODELS_BUILD_CPUS", "0"))
-    else:
-        cpus = args.cpus
-    if cpus != 1 and not args.force:
-        import multiprocessing
-        p = multiprocessing.Pool(cpus if cpus > 0 else None)
-        rst_files = p.map(process_model, args.files)
-    else:
-        rst_files = [process_model(py_file, args.force)
+    print("** 'Normal' processing **")
+    rst_files = [process_model(py_file, args.force)
                      for py_file in args.files]
+    print("normal .rst file processing complete")
 
     if args.sphinx:
+        print("running sphinx")
         run_sphinx(rst_files, args.build)