Changeset 3fb9404 in sasmodels

Timestamp:

Jan 24, 2018 4:41:33 PM (7 years ago)

Author:

Paul Kienzle <pkienzle@…>

Branches:

master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

49284e1, 4c8cf97

Parents:

0d5a655 (diff), fefc185 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'master' of github.com:sasview/sasmodels

Files:

• appveyor.yml (modified) (5 diffs)
• doc/developer/overview.rst (modified) (2 diffs)
• doc/genapi.py (modified) (1 diff)
• doc/guide/orientation/orientation.rst (modified) (1 diff)
• sasmodels/guyou.py (moved) (moved from explore/guyou.py)
• sasmodels/jitter.py (moved) (moved from explore/jitter.py) (4 diffs)

appveyor.yml

@@ -4 +4 @@
   # /E:ON and /V:ON options are not enabled in the batch script interpreter
   # See: http://stackoverflow.com/a/13751649/163740
-  CMD_IN_ENV: "cmd /E:ON /V:ON /C obvci_appveyor_python_build_env.cmd"
+  # 2018-01-19 PAK: probably irrelevant now that we are using tinycc rather than msvc
+  #CMD_IN_ENV: "cmd /E:ON /V:ON /C obvci_appveyor_python_build_env.cmd"
 
   # Workaround for https://github.com/conda/conda-build/issues/636
@@ -22 +23 @@
     - TARGET_ARCH: "x86"
       CONDA_PY: "35"
-      PY_CONDITION: "python >=3.5"
+      PY_CONDITION: "python >=3.5,<3.6"
       CONDA_INSTALL_LOCN: "C:\\Miniconda35"
     - TARGET_ARCH: "x64"
@@ -34 +35 @@
     - TARGET_ARCH: "x64"
       CONDA_PY: "35"
-      PY_CONDITION: "python >=3.5"
+      PY_CONDITION: "python >=3.5,<3.6"
       CONDA_INSTALL_LOCN: "C:\\Miniconda35-x64"
 
@@ -43 +44 @@
 
 install:
-    # Set the CONDA_NPY, although it has no impact on the actual build. We need this because of a test within conda-build.
+    # Set the CONDA_NPY, although it has no impact on the actual build. 
+    # We need this because of a test within conda-build.
     - cmd: set CONDA_NPY=19
 
     # Remove cygwin (and therefore the git that comes with it).
-    - cmd: rmdir C:\cygwin /s /q
+    # 2018-01-19 PAK: irrelevant since we already pulled the repo
+    #- cmd: rmdir C:\cygwin /s /q
+
+    # Set the conda path; would be nice to do this
+    - cmd: path %CONDA_INSTALL_LOCN%\Scripts;%PATH%
 
     # Use the pre-installed Miniconda for the desired arch
@@ -56 +62 @@
     # so that we can update it. Then we remove it so that
     # we can do a proper activation.
-    - cmd: set "OLDPATH=%PATH%"
-    - cmd: set "PATH=%CONDA_INSTALL_LOCN%\\Scripts;%CONDA_INSTALL_LOCN%\\Library\\bin;%PATH%"
     - cmd: conda update --yes --quiet conda python
-    - cmd: set "PATH=%OLDPATH%"
     - cmd: call %CONDA_INSTALL_LOCN%\Scripts\activate.bat
-
-    - cmd: conda config --add channels conda-forge
-    - cmd: conda config --set show_channel_urls true
-    - cmd: conda update --yes --quiet conda
-    - cmd: conda install --yes --quiet obvious-ci
-    - cmd: conda install --yes --quiet numpy toolchain scipy cython cffi
+    #- cmd: conda config --add channels conda-forge
+    #- cmd: conda config --set show_channel_urls true
+    #- cmd: conda install --yes --quiet obvious-ci
+    # 2018-01-19 PAK: skipping toolchain cython and cffi (these were for pyopencl?)
+    - cmd: conda install --yes --quiet numpy scipy
+    # 2018-01-19 PAK: skipping pyopencl; this would be needed for deploy but maybe not for test
     #- cmd: conda install --yes --channel conda-forge pyopencl
+    # 2018-01-19 PAK: 3rd party packages might need msvc, so %CMD_IN_ENV% may be needed for pip
     - cmd: pip install bumps unittest-xml-reporting tinycc
 
 build_script:
     # Build the project
-    - "%CMD_IN_ENV% python setup.py build"
+    # 2018-01-19 PAK: maybe need one of this if using msvc?
+    #- "%CMD_IN_ENV% python setup.py build"
+    #- cmd /E:ON /V:ON /C obvci_appveyor_python_build_env.cmd python setup.py build
+    - python setup.py build
 
 test_script:
     # Run the project tests
-    - "%CMD_IN_ENV% python -m sasmodels.model_test dll all"
+    # 2018-01-19 PAK: maybe need one of this if using msvc?
+    #- "%CMD_IN_ENV% python -m sasmodels.model_test dll all"
+    #- cmd /E:ON /V:ON /C obvci_appveyor_python_build_env.cmd python -m sasmoels.model_test dll all
+    - python -m sasmodels.model_test dll all

doc/developer/overview.rst

@@ -190 +190 @@
 *sasmodels.generate.PROJECTION*, with the default *PROJECTION=1* for
 equirectangular and *PROJECTION=2* for sinusoidal.  The more complicated
-Guyou and Postel projections are not implemented. See explore.jitter.draw_mesh
+Guyou and Postel projections are not implemented. See jitter.draw_mesh
 for details.
 
@@ -274 +274 @@
 code.
 
-*explore/jitter.py* is for exploring different options for handling
-orientation and orientation dispersity.  It uses *explore/guyou.py* to
+*sasmodels/jitter.py* is for exploring different options for handling
+orientation and orientation dispersity.  It uses *sasmodels/guyou.py* to
 generate the Guyou projection.
 

doc/genapi.py

@@ -69 +69 @@
     ('exception', 'Annotate exceptions'),
     ('generate', 'Model parser'),
+    ('jitter', 'Orientation explorer'),
+    ('guyou', 'Guyou map projection'),
     ('kernel', 'Evaluator type definitions'),
     ('kernelcl', 'OpenCL model evaluator'),

doc/guide/orientation/orientation.rst

@@ -52 +52 @@
 yaw angle $\theta$ about the $b$-axis and pitch angle $\phi$ about the
 $a$-axis.
+
+You can explore the view and jitter angles interactively using
+:func:`sasmodels.jitter.run`.  Enter the following into the python
+interpreter::
+
+    from sasmodels import jitter
+    jitter.run()
 
 More formally, starting with axes $a$-$b$-$c$ of the particle aligned

sasmodels/jitter.py

@@ -1 +1 @@
 #!/usr/bin/env python
 """
-Application to explore the difference between sasview 3.x orientation
-dispersity and possible replacement algorithms.
+Jitter Explorer
+===============
+
+Application to explore orientation angle and angular dispersity.
 """
 from __future__ import division, print_function
@@ -124 +126 @@
 def draw_parallelepiped(ax, size, view, jitter, steps=None, alpha=1):
     """Draw a parallelepiped."""
-    a,b,c = size
+    a, b, c = size
     x = a*np.array([ 1,-1, 1,-1, 1,-1, 1,-1])
     y = b*np.array([ 1, 1,-1,-1, 1, 1,-1,-1])
@@ -141 +143 @@
     x, y, z = transform_xyz(view, jitter, x, y, z)
     ax.plot_trisurf(x, y, triangles=tri, Z=z, color='w', alpha=alpha)
+
+    # Draw pink face on box.
+    # Since I can't control face color, instead draw a thin box situated just
+    # in front of the "a+" face.
+    if 1:
+        x = a*np.array([ 1,-1, 1,-1, 1,-1, 1,-1])
+        y = b*np.array([ 1, 1,-1,-1, 1, 1,-1,-1])
+        z = c*np.array([ 1, 1, 1, 1,-1,-1,-1,-1])
+        x, y, z = transform_xyz(view, jitter, abs(x)*1.05, y, z)
+        ax.plot_trisurf(x, y, triangles=tri, Z=z, color=[1,0.6,0.6], alpha=alpha)
 
     draw_labels(ax, view, jitter, [
@@ -608 +620 @@
     Show an interactive orientation and jitter demo.
 
-    *model_name* is one of the models available in :func:`select_model`.
+    *model_name* is one of: sphere, cylinder, ellipsoid, parallelepiped,
+    triaxial_ellipsoid, or bcc_paracrystal.
+
+    *size* gives the dimensions (a, b, c) of the shape.
+
+    *dist* is the type of dispersition: gaussian, rectangle, or uniform.
+
+    *mesh* is the number of points in the dispersion mesh.
+
+    *projection* is the map projection to use for the mesh: equirectangular,
+    sinusoidal, guyou, azimuthal_equidistance, or azimuthal_equal_area.
     """
     # projection number according to 1-order position in list, but