Changeset 587cbcd in sasmodels

Timestamp:

Apr 11, 2017 5:39:31 AM (7 years ago)

Author:

GitHub <noreply@…>

Branches:

master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

1cd24b4

Parents:

b2921d0 (diff), bccb40f (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.

git-author:

Andrew Jackson <andrew.jackson@…> (04/11/17 05:39:31)

git-committer:

GitHub <noreply@…> (04/11/17 05:39:31)

Message:

Merge pull request #40 from SasView?/ticket-695

Fix profile function to plot what the documentation says about the SL…

Files:

• sasmodels/models/onion.py (modified) (4 diffs)
• .gitattributes (added)
• .travis.yml (modified) (1 diff)
• appveyor.yml (added)
• sasmodels/kerneldll.py (modified) (4 diffs)
• sasmodels/kernelpy.py (modified) (1 diff)

sasmodels/models/onion.py

@@ -1 +1 @@
 r"""
 This model provides the form factor, $P(q)$, for a multi-shell sphere where
-the scattering length density (SLD) of the each shell is described by an
+the scattering length density (SLD) of each shell is described by an
 exponential, linear, or constant function. The form factor is normalized by
 the volume of the sphere where the SLD is not identical to the SLD of the
@@ -142 +142 @@
 
 For $A = 0$, the exponential function has no dependence on the radius (so that
-$\rho_\text{out}$ is ignored this case) and becomes flat. We set the constant
+$\rho_\text{out}$ is ignored in this case) and becomes flat. We set the constant
 to $\rho_\text{in}$ for convenience, and thus the form factor contributed by
 the shells is
@@ -346 +346 @@
             # flat shell
             z.append(z_current + thickness[k])
-            rho.append(sld_out[k])
+            rho.append(sld_in[k])
         else:
             # exponential shell
@@ -357 +357 @@
                 z.append(z_current+z_shell)
                 rho.append(slope*exp(A[k]*z_shell/thickness[k]) + const)
-
+    
     # add in the solvent
     z.append(z[-1])

.travis.yml

@@ -1 +1 @@
 language: python
-python:
-- '2.7'
+
+sudo:  false
+
+matrix:
+  include:
+    - os: linux
+      env:
+        - PY=2.7
+        - NUMPYSPEC=numpy
+    - os: linux
+      env:
+        - PY=3
+        - NUMPYSPEC=numpy
+    - os: osx
+      language: generic
+      env:
+        - PY=2.7
+        - NUMPYSPEC=numpy
+    - os: osx
+      language: generic
+      env:
+        - PY=3
+        - NUMPYSPEC=numpy
+
+# whitelist
 branches:
   only:
-  - master
-virtualenv:
-  system_site_packages: true
+    - master
+
+addons:
+  apt:
+    packages:
+      opencl-headers
+
 before_install:
-- sudo apt-get update;
-- sudo apt-get install python-numpy python-scipy
+  - echo $TRAVIS_OS_NAME
+
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi;
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+    fi;
+
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda update --yes conda
+
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+  - conda install --yes python=$PY $NUMPYSPEC scipy cython mako cffi
+
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+      pip install pyopencl;
+    fi;
+
 install:
-- pip install bumps
-- pip install unittest-xml-reporting
+  - pip install bumps
+  - pip install unittest-xml-reporting
+
 script:
 - export WORKSPACE=/home/travis/build/SasView/sasmodels/
 - python -m sasmodels.model_test dll all
+
 notifications:
   slack:

sasmodels/kerneldll.py

@@ -97 +97 @@
 
 if "SAS_COMPILER" in os.environ:
-    compiler = os.environ["SAS_COMPILER"]
+    COMPILER = os.environ["SAS_COMPILER"]
 elif os.name == 'nt':
-    # If vcvarsall.bat has been called, then VCINSTALLDIR is in the environment
-    # and we can use the MSVC compiler.  Otherwise, if tinycc is available
-    # the use it.  Otherwise, hope that mingw is available.
-    if "VCINSTALLDIR" in os.environ:
-        compiler = "msvc"
-    elif tinycc:
-        compiler = "tinycc"
+    if tinycc is not None:
+        COMPILER = "tinycc"
+    elif "VCINSTALLDIR" in os.environ:
+        # If vcvarsall.bat has been called, then VCINSTALLDIR is in the environment
+        # and we can use the MSVC compiler.  Otherwise, if tinycc is available
+        # the use it.  Otherwise, hope that mingw is available.
+        COMPILER = "msvc"
     else:
-        compiler = "mingw"
+        COMPILER = "mingw"
 else:
-    compiler = "unix"
+    COMPILER = "unix"
 
 ARCH = "" if ct.sizeof(ct.c_void_p) > 4 else "x86"  # 4 byte pointers on x86
-if compiler == "unix":
+if COMPILER == "unix":
     # Generic unix compile
     # On mac users will need the X code command line tools installed
@@ -123 +123 @@
         """unix compiler command"""
         return CC + [source, "-o", output, "-lm"]
-elif compiler == "msvc":
+elif COMPILER == "msvc":
     # Call vcvarsall.bat before compiling to set path, headers, libs, etc.
     # MSVC compiler is available, so use it.  OpenMP requires a copy of
@@ -139 +139 @@
         """MSVC compiler command"""
         return CC + ["/Tp%s"%source] + LN + ["/OUT:%s"%output]
-elif compiler == "tinycc":
+elif COMPILER == "tinycc":
     # TinyCC compiler.
     CC = [tinycc.TCC] + "-shared -rdynamic -Wall".split()
@@ -145 +145 @@
         """tinycc compiler command"""
         return CC + [source, "-o", output]
-elif compiler == "mingw":
+elif COMPILER == "mingw":
     # MinGW compiler.
     CC = "gcc -shared -std=c99 -O2 -Wall".split()

sasmodels/kernelpy.py

@@ -235 +235 @@
             # exclude all q for that NaN.  Even better would be to have an
             # INVALID expression like the C models, but that is too expensive.
-            Iq = form()
+            Iq = np.asarray(form(), 'd')
             if np.isnan(Iq).any(): continue