Merge branch 'RELEASE_next_minor' into RELEASE_next_major

.travis.yml

@@ -30,30 +30,32 @@ before_install:
 install:
 
   - if [[ $MINIMAL_ENV == 'False' ]] ; then
-      DEPS="nose numpy scipy matplotlib ipython h5py sympy scikit-learn dill natsort setuptools scikit-image cython lxml ipyparallel";
+      DEPS="numpy scipy matplotlib ipython h5py sympy scikit-learn dill natsort setuptools scikit-image cython lxml ipyparallel";
       conda create -n testenv --yes $DEPS;
       source activate testenv;
       conda install pip;
       python setup.py install;
-    else pip3 install .;
+      pip install pytest pytest-xdist;
+    else pip install pytest;
+    pip3 install .;
     fi
 
 script:
   - if [[ $MINIMAL_ENV == 'False' ]]; then
       python setup.py build_ext --inplace;
-      pip install coverage coveralls;
-      python continuous_integration/nosetest.py --with-coverage hyperspy.tests;
+      pip install coverage coveralls pytest-cov;
+      py.test --cov=hyperspy --pyargs hyperspy;
     else python3 setup.py build_ext --inplace;
       echo "available installed python libraries (pip3 list):"
       pip3 list;
-      pip3 install coverage coveralls;
-      python3 continuous_integration/nosetest.py --with-coverage hyperspy.tests;
+      pip3 install coverage coveralls pytest-cov;
+      py.test --cov=hyperspy --pyargs hyperspy.tests;
     fi
 
 after_success:
 - coveralls
 - if [[ $MINIMAL_ENV == 'False' ]]; then
-    if [[ $TRAVIS_OS_NAME == 'osx' ]]; then 
+    if [[ $TRAVIS_OS_NAME == 'osx' ]]; then
       python setup.py bdist_wheel;
     else python setup.py sdist;
     fi;

anaconda_hyperspy_environment.yml

@@ -7,7 +7,7 @@ dependencies:
 - ipyparallel
 - jupyter
 - matplotlib
-- nose
+- pytest
 - numpy
 - qt
 - scikit-image

appveyor.yml

@@ -4,7 +4,7 @@ shallow_clone: true
 environment:
 
   global:
-    TEST_DEPS: "nose wheel pip"
+    TEST_DEPS: "pytest pytest-cov wheel pip"
     NSIS_DIR: "%PROGRAMFILES(x86)%/NSIS"
 
 
@@ -67,7 +67,7 @@ test_script:
   # Run the project tests
   - ps: Add-AppveyorMessage "Running tests..."
   - "python setup.py build_ext --inplace"
-  - "python continuous_integration/nosetest.py hyperspy.tests"
+  - "py.test"
   - "python setup.py clean"
   - ps: Add-AppveyorMessage "Testing completed."
 
@@ -101,7 +101,7 @@ before_deploy:
   - ps: Add-AppveyorMessage "Setting up WinPython environment..."
   - ps: Start-FileDownload ('http://freefr.dl.sourceforge.net/project/nsis/NSIS%202/2.46/nsis-2.46-strlen_8192.zip') ../nsis_patch.zip
   - ps: if ((Get-FileHash '../nsis_patch.zip').Hash -ne '3BA22DDC0F14DBD75A9487EB6C9BD85F535E7038927D251103B97E0AAD94EEAD') { exit(1) }
-  - "7z x ../nsis_patch.zip -o%NSIS_DIR -aoa"
+  - "7z x ../nsis_patch.zip -o%NSIS_DIR% -aoa"
   - ps: Start-FileDownload ('http://nsis.sourceforge.net/mediawiki/images/e/eb/Textreplace.zip') ../Textreplace.zip
   - ps: if ((Get-FileHash '../Textreplace.zip').Hash -ne '6462C0C22E87E7C81DD9076D40ACC74C515243A56F10F4F8FE720F7099DB3BA2') { exit(1) }
   - "7z x ../Textreplace.zip -o%NSIS_DIR% -aoa"
@@ -116,6 +116,8 @@ before_deploy:
   - "%CMD_IN_ENV% python.exe -c \"import sys; print(sys.version)\""
   - "%CMD_IN_ENV% python.exe setup.py recythonize"
   - "%CMD_IN_ENV% python.exe setup.py install"
+  # Try to run twice as workaround for permission error
+  - "%CMD_IN_ENV% pip install hyperspyui || pip install hyperspyui"
   # setting back the config:
   - "ren %WP_INSTDIR%\\settings\\pydistutils_bak.cfg pydistutils.cfg"
   # Custom installer step

doc/user_guide/install.rst

@@ -243,37 +243,6 @@ In addition, since version 0.7.2 the lowess filter requires statsmodels.
 In Windows HyperSpy uses the Ipython's QtConsole and therefore Qt and PyQt or
 PySide are also required.
 
-
-In Debian/Ubuntu you can install the libraries as follows:
-
-.. code-block:: bash
-
-    $ sudo apt-get install python-numpy python-matplotlib ipython
-    ipython-notebook python-traits python-traitsui python-h5py
-    python-scikit-learn python-scikit-image python-nose
-    python-statsmodels python3-tqdm
-
-..
-    In Arch Linux, the following command should install the required packages to
-    get a fully functional installation:
-
-    .. code-block:: bash
-
-        $ sudo pacman -Sy python2 python2-numpy	python2-matplotlib	python2-pip
-        python2-traits python2-traitsui python2-h5py python2-scikit-learn python2-nose
-        python2-statsmodels python2-pillow python2-pyqt4 python2-pyqt5 python2-scipy
-        python2-pandas python2-setuptools ipython2	python2-jinja python2-pyzmq
-        python2-pyqt4 python2-tornado python2-sip python2-pygments python2-scikit-image
-
-        # Or, just run this command from the root hyperspy directory to import the
-        # list of packages and install automatically:
-        $ xargs sudo pacman -Sy --noconfirm < doc/package_lists/arch_linux_package_list.txt
-
-        # Once these are installed, go to the HyperSpy directory and run:
-        $ sudo pip2 install -e ./
-
-        # If desired, the python2-seaborn library can also be installed from AUR for prettier plotting
-
 .. _known-issues:
 
 Known issues

doc/user_guide/model.rst

@@ -124,6 +124,19 @@ parameters for spectroscopy than the one that ships with HyperSpy:
     ... centre=0,
     ... module="numpy")
 
+If the expression is inconvenient to write out in full (e.g. it's long and/or
+complicated), multiple substitutions can be given, separated by semicolumns.
+Both symbolic and numerical substitutions are allowed:
+
+.. code-block:: python
+
+    >>> expression = "h / sqrt(p2) ; p2 = 2 * m0 * e1 * x * brackets;"
+    >>> expression += "brackets = 1 + (e1 * x) / (2 * m0 * c * c) ;"
+    >>> expression += "m0 = 9.1e-31 ; c = 3e8; e1 = 1.6e-19 ; h = 6.6e-34"
+    >>> wavelength = hs.model.components1D.Expression(
+    ... expression=expression,
+    ... name="Electron wavelength with voltage")
+
 :py:class:`~._components.expression.Expression` uses `Sympy
 <http://www.sympy.org>`_ internally to turn the string into
 a funtion. By default it "translates" the expression using
@@ -523,15 +536,25 @@ For example:
             A	5.000000
             centre	0.000000
 
+.. deprecated:: 1.1.3
+    Setting the :py:attr:`~.component.Parameter.twin_function` and
+    :py:attr:`~.component.Parameter.twin_inverse_function` attributes. Set the
+    :py:attr:`~.component.Parameter.twin_function_expr` and
+    :py:attr:`~.component.Parameter.twin_inverse_function_expr` attributes
+    instead.
+
+.. versionadded:: 1.1.3
+    :py:attr:`~.component.Parameter.twin_function_expr` and
+    :py:attr:`~.component.Parameter.twin_inverse_function_expr`.
 
 By default the coupling function is the identity function. However it is
 possible to set a different coupling function by setting the
-:py:attr:`~.component.Parameter.twin_function` and
-:py:attr:`~.component.Parameter.twin_inverse_function` attributes.  For
+:py:attr:`~.component.Parameter.twin_function_expr` and
+:py:attr:`~.component.Parameter.twin_inverse_function_expr` attributes.  For
 example:
 
-    >>> gaussian2.A.twin_function = lambda x: x**2
-    >>> gaussian2.A.twin_inverse_function = lambda x: np.sqrt(np.abs(x))
+    >>> gaussian2.A.twin_function_expr = "x**2"
+    >>> gaussian2.A.twin_inverse_function_expr = "sqrt(abs(x))"
     >>> gaussian2.A.value = 4
     >>> m.print_current_values()
     Components	Parameter	Value

hyperspy/_components/expression.py

@@ -19,6 +19,16 @@ def fn_wrapped(self, x):
     return fn_wrapped
 
 
+def _parse_substitutions(string, simultaneous=True):
+    import sympy
+    splits = map(str.strip, string.split(';'))
+    expr = sympy.sympify(next(splits))
+    # We substitute one by one manually, as passing all at the same time does
+    # not work as we want (subsitutions inside other substitutions do not work)
+    for sub in splits:
+        expr = expr.subs(*tuple(map(str.strip, sub.split('='))))
+    return expr
+
 class Expression(Component):
 
     """Create a component from a string expression.
@@ -34,7 +44,8 @@ class docstring.
         Parameters
         ----------
         expression: str
-            Component function in SymPy text expression format. See the SymPy
+            Component function in SymPy text expression format with
+            substitutions separated by `;`. See examples and the SymPy
             documentation for details. The only additional constraint is that
             the variable must be `x`. Also, in `module` is "numexpr" the
             functions are limited to those that numexpr support. See its
@@ -72,6 +83,17 @@ class docstring.
         ... x0=0,
         ... position="x0",)
 
+        Substitutions for long or complicated expressions are separated by
+        semicolumns:
+
+        >>> expr = 'A*B/(A+B) ; A = sin(x)+one; B = cos(y) - two; y = tan(x)'
+        >>> comp = hs.model.components1D.Expression(
+        ... expression=expr,
+        ... name='my function')
+        >>> comp.parameters
+        (<Parameter one of my function component>,
+         <Parameter two of my function component>)
+
         """
 
         import sympy
@@ -94,15 +116,15 @@ class docstring.
 
         if autodoc:
             self.__doc__ = _CLASS_DOC % (
-                name, sympy.latex(sympy.sympify(expression)))
+                name, sympy.latex(_parse_substitutions(expression)))
 
     def function(self, x):
         return self._f(x, *[p.value for p in self.parameters])
 
     def compile_function(self, module="numpy"):
         import sympy
         from sympy.utilities.lambdify import lambdify
-        expr = sympy.sympify(self._str_expression)
+        expr = _parse_substitutions(self._str_expression)
 
         rvars = sympy.symbols([s.name for s in expr.free_symbols], real=True)
         real_expr = expr.subs(

hyperspy/_signals/eels.py

@@ -75,8 +75,6 @@ def add_elements(self, elements, include_pre_edges=False):
 
         >>> s = hs.signals.EELSSpectrum(np.arange(1024))
         >>> s.add_elements(('C', 'O'))
-        Adding C_K subshell
-        Adding O_K subshell
 
         Raises
         ------
@@ -226,13 +224,16 @@ def align_zero_loss_peak(
 
         Examples
         --------
-        >>>> s_ll.align_zero_loss_peak()
+        >>> s_ll = hs.signals.EELSSpectrum(np.zeros(1000))
+        >>> s_ll.data[100] = 100
+        >>> s_ll.align_zero_loss_peak()
 
         Aligning both the lowloss signal and another signal
-        >>>> s_ll.align_zero_loss_peak(also_align=[s])
+        >>> s = hs.signals.EELSSpectrum(np.range(1000))
+        >>> s_ll.align_zero_loss_peak(also_align=[s])
 
         Aligning within a narrow range of the lowloss signal
-        >>>> s_ll.align_zero_loss_peak(signal_range=(-10.,10.))
+        >>> s_ll.align_zero_loss_peak(signal_range=(-10.,10.))
 
 
         See Also