Merge branch 'release-0.5.0'

CHANGELOG.rst

@@ -37,8 +37,22 @@ the author interprets the terms below as follows:
   API is stable.
   The package is available on PyPI (and perhaps conda).
 
-
-0.4.0 - 2020-xx-xx (beta release)
+0.5.0 - 2020-03-29 (beta release)
+---------------------------------
+Changed
+^^^^^^^
+* add_lorentzians moved from nmr.plt to nmr.math.
+  Besides being more appropriate here,
+  it fixes a problem where importing from nmrsim.plt also requires importing
+  from matplotlib/Tkinter.
+  Some environments
+  (some Unix systems; BeeWare's Briefcase packaging tool)
+  do not have Tkinter available.
+* nmrsim.plt will substitute the matplotlib "Agg" backend for "TkAgg"
+  if tkinter is not found on the users system, and print a warning message
+  that plots will not be visible.
+
+0.4.0 - 2020-02-22 (beta release)
 ---------------------------------
 Changed
 ^^^^^^^

README.rst

@@ -5,7 +5,7 @@ Click the "**Launch Binder**" link above to see how **nmrsim** can be used in Ju
 
 `Documentation on Read the Docs <https://nmrsim.readthedocs.io/>`_
 
-nmrsim (version 0.4.0 beta)
+nmrsim (version 0.5.0 beta)
 ============================
 
 **nmrsim** is a Python library for the simulation of solution-state nuclear magnetic resonance (NMR) spectra.

docs/source/conf.py

@@ -25,9 +25,9 @@
 author = 'Geoffrey M. Sametz'
 
 # The short X.Y version
-version = '0.4'
+version = '0.5'
 # The full version, including alpha/beta/rc tags
-release = '0.4.0-beta'
+release = '0.5.0-beta'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/introduction.rst

@@ -1,4 +1,4 @@
-Introduction to nmrsim v0.4.0 (beta)
+Introduction to nmrsim v0.5.0 (beta)
 =====================================
 
 **nmrsim** is a library of tools for simulating NMR spectra, starting from
@@ -13,8 +13,13 @@ feature that you would like to see, or a barrier to you using this library,
 feel free to open an issue on GitHub or to send the author email
 (sametz at udel dot edu).
 
-The project is inspired by the program `WINDNMR <https://www.chem.wisc.edu/areas/reich/plt/windnmr.htm>`_ by Hans
-Reich. The goal for Version 1.0 of **nmrsim** is to provide Python tools for the same types of simulations that
-WINDNMR did: first- and second-order simulation of spin-1/2 spin systems, plus simulation of some dynamic NMR (DNMR)
-lineshapes. A longer-term goal is to expand the toolset (e.g. to allow higher-spin nuclei, or new DNMR models).
+The project is inspired by the program
+`WINDNMR <https://www.chem.wisc.edu/areas/reich/plt/windnmr.htm>`_
+by Hans Reich.
+The goal for Version 1.0 of **nmrsim** is to provide Python tools
+for the same types of simulations that WINDNMR did:
+first- and second-order simulation of spin-1/2 spin systems,
+plus simulation of some dynamic NMR (DNMR) lineshapes.
+A longer-term goal is to expand the toolset
+(e.g. to allow higher-spin nuclei, or new DNMR models).
 

nmrsim/__init__.py

@@ -62,4 +62,4 @@
 
 from ._classes import Multiplet, SpinSystem, Spectrum  # noqa: F401
 
-__version__ = '0.4.0'
+__version__ = '0.5.0'

nmrsim/_classes.py

@@ -7,8 +7,7 @@
 import numpy as np
 
 from nmrsim.firstorder import first_order_spin_system, multiplet
-from nmrsim.math import reduce_peaks
-from nmrsim.plt import add_lorentzians
+from nmrsim.math import reduce_peaks, add_lorentzians
 from nmrsim.qm import qm_spinsystem
 from nmrsim._utils import low_high
 

nmrsim/math.py

@@ -146,6 +146,35 @@ def lorentz(v, v0, I, w):
     return scaling_factor * I * ((0.5 * w) ** 2 / ((0.5 * w) ** 2 + (v - v0) ** 2))
 
 
+def add_lorentzians(linspace, peaklist, w):
+    """
+    Given a numpy linspace, a peaklist of (frequency, intensity)
+    tuples, and a linewidth, returns an array of y coordinates for the
+    total line shape.
+
+    Arguments
+    ---------
+    linspace : array-like
+        Normally a numpy.linspace of x coordinates corresponding to frequency
+        in Hz.
+    peaklist : [(float, float)...]
+        A list of (frequency, intensity) tuples.
+    w : float
+        Peak width at half maximum intensity.
+
+    Returns
+    -------
+    [float...]
+        an array of y coordinates corresponding to intensity.
+    """
+    # TODO: consider naming, and confusion with .math.add_peaks
+    # TODO: function looks clunky. Refactor?
+    result = lorentz(linspace, peaklist[0][0], peaklist[0][1], w)
+    for v, i in peaklist[1:]:
+        result += lorentz(linspace, v, i, w)
+    return result
+
+
 def get_intensity(lineshape, x):
     """
     A crude method to find the intensity of data point closest to

nmrsim/plt.py

@@ -12,44 +12,30 @@
 * mplplot_lineshape: Creates a lineshape plot from provided x, y lineshape data
   and returns the x, y plot data.
 """
-
-import matplotlib.pyplot as plt
 import numpy as np
 
-from nmrsim.math import lorentz
+from nmrsim.math import add_lorentzians
 from nmrsim._utils import low_high
 
+# Pyplot assumes a TkAgg backend as a default. This can cause problems in
+# environments where Tkinter is not available (e.g. some Unix systems;
+# BeeWare's Briefcase packaging for Windows).
+import matplotlib
+try:
+    import tkinter as tk  # noqa: F401
+except ImportError:
+    matplotlib.use('Agg')
+    print('WARNING: Tkinter not found--plots will not display on screen!')
 
-def add_lorentzians(linspace, peaklist, w):
-    """
-    Given a numpy linspace, a peaklist of (frequency, intensity)
-    tuples, and a linewidth, returns an array of y coordinates for the
-    total line shape.
-
-    Arguments
-    ---------
-    linspace : array-like
-        Normally a numpy.linspace of x coordinates corresponding to frequency
-        in Hz.
-    peaklist : [(float, float)...]
-        A list of (frequency, intensity) tuples.
-    w : float
-        Peak width at half maximum intensity.
-
-    Returns
-    -------
-    [float...]
-        an array of y coordinates corresponding to intensity.
-    """
-    # TODO: consider naming, and confusion with .math.add_peaks
-    # TODO: function looks clunky. Refactor?
-    result = lorentz(linspace, peaklist[0][0], peaklist[0][1], w)
-    for v, i in peaklist[1:]:
-        result += lorentz(linspace, v, i, w)
-    return result
+import matplotlib.pyplot as plt
 
+# TODO: especially considering the possible swap to the 'Agg' backend,
+# makes more intuitive sense for plot functions to return a plot object
+# and not the coordinates.
 
 # TODO: possibly refactor plot routines to avoid repetitive code
+
+
 def mplplot(peaklist, w=1, y_min=-0.01, y_max=1, points=800, limits=None):
     """
     A matplotlib plot of the simulated lineshape for a peaklist.

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="nmrsim",
-    version="0.4.0rc1",
+    version="0.5.0",
     author="Geoffrey M. Sametz",
     author_email="[email protected]",
     description="A library for simulating nuclear magnetic resonance (NMR) spectra.",

tests/test_nmrsim.py

@@ -4,7 +4,7 @@
 from nmrsim import Multiplet, SpinSystem, Spectrum
 from nmrsim._classes import extract_components
 from nmrsim.firstorder import first_order_spin_system
-from nmrsim.plt import add_lorentzians
+from nmrsim.math import add_lorentzians
 from tests.accepted_data import SPECTRUM_RIOUX
 from tests.qm_arguments import rioux
 

tests/test_plt.py

@@ -1,7 +1,8 @@
 import numpy as np
 import pytest
 
-from nmrsim.plt import add_lorentzians, mplplot, mplplot_stick, mplplot_lineshape
+from nmrsim.plt import mplplot, mplplot_stick, mplplot_lineshape
+from nmrsim.math import add_lorentzians
 from tests.accepted_data import ADD_SIGNALS_DATASET
 from tests.dnmr_standards import TWOSPIN_SLOW