fixed/updated visualization annotations

- fix #133
- added missing versionadded to visualization
- regenerated figures for docs with corrected units
- minor doc fixes

CHANGES

@@ -13,17 +13,19 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/2021 xiki-tempula
+06/01/2021 xiki-tempula, orbeckst
 
   * 0.4.1
 
 Enhancements
 
 Deprecations
+  - Last release that supports Python 3.5 and 2.7.
 
 Fixes
   - The plotting function assumes that the default unit is kcal/mol where it is
     kT (issue #124, PR #123).
+  - invalid escape sequence in plotting annotations (issue #133)
 
 Changes
 

src/alchemlyb/visualisation/convergence.py

@@ -17,9 +17,9 @@ def plot_convergence(forward, forward_error, backward, backward_error,
     backward_error : List
         A list of error from the last X% of data.
     units : str
-        The label for the unit of the estimate. Default: `kT`
+        The label for the unit of the estimate. Default: "kT"
     ax : matplotlib.axes.Axes
-        Matplotlib axes object where the plot will be drawn on. If ax=None,
+        Matplotlib axes object where the plot will be drawn on. If ``ax=None``,
         a new axes will be generated.
 
     Returns
@@ -30,11 +30,13 @@ def plot_convergence(forward, forward_error, backward, backward_error,
     Note
     ----
     The code is taken and modified from
-    : `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_
+    `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
 
     The units variable is for labelling only. Changing it doesn't change the
-    unit of the underlying variable, which is in the unit of kT. The
-    scaling_factor is used to change the number to the desired unit.
+    unit of the underlying variable, which is in the unit of :math:`kT`.
+
+
+    .. versionadded:: 0.4.0
     """
     if ax is None: # pragma: no cover
         fig, ax = plt.subplots(figsize=(8, 6))
@@ -64,7 +66,7 @@ def plot_convergence(forward, forward_error, backward, backward_error,
     plt.xticks(r_ts[::2], fontsize=10)
     plt.yticks(fontsize=10)
 
-    ax.legend((line1[0], line2[0]), (r'$Forward$', r'$Reverse$'), loc=9,
+    ax.legend((line1[0], line2[0]), ('Forward', 'Reverse'), loc=9,
                     prop=FP(size=18), frameon=False)
     ax.set_xlabel(r'Fraction of the simulation time', fontsize=16,
                   color='#151B54')

src/alchemlyb/visualisation/dF_state.py

@@ -4,7 +4,7 @@
 lambda states can be ploted to assess the quality of the estimation.
 
 The code for producing the dF states plot is modified based on
-: `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
+`Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
 
 """
 
@@ -30,7 +30,7 @@ def plot_dF_state(estimators, labels=None, colors=None, units='kT',
     colors : List
         list of colors for plotting different estimators.
     units : str
-        The unit of the estimate. Default: `kT`
+        The unit of the estimate. Default: "kT"
     orientation : string
         The orientation of the figure. Can be `portrait` or `landscape`
     nb : int
@@ -44,11 +44,13 @@ def plot_dF_state(estimators, labels=None, colors=None, units='kT',
     Note
     ----
     The code is taken and modified from
-    : `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_
+    `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
 
     The units variable is for labelling only. Changing it doesn't change the
-    unit of the underlying variable, which is in the unit of kT.
+    unit of the underlying variable, which is in the unit of :math:`kT`.
 
+
+    .. versionadded:: 0.4.0
     '''
     try:
         len(estimators)
@@ -176,7 +178,7 @@ def plot_dF_state(estimators, labels=None, colors=None, units='kT',
             plt.yticks(fontsize=10)
             ax.xaxis.set_ticks([])
             for i in x + 0.5 * width * len(estimators):
-                ax.annotate('$\mathrm{%d-%d}$' % (i, i + 1), xy=(i, 0),
+                ax.annotate(r'$\mathrm{%d-%d}$' % (i, i + 1), xy=(i, 0),
                             xycoords=('data', 'axes fraction'), xytext=(0, -2),
                             size=10, textcoords='offset points', va='top',
                             ha='center')
@@ -193,11 +195,12 @@ def plot_dF_state(estimators, labels=None, colors=None, units='kT',
                          fancybox=True)
         plt.title('The free energy change breakdown', fontsize=12)
         plt.xlabel('States', fontsize=12, color='#151B54')
-        plt.ylabel('$\Delta G$ ' + units, fontsize=12, color='#151B54')
+        plt.ylabel(r'$\Delta G$ ({})'.format(units), fontsize=12, color='#151B54')
     elif orientation == 'portrait':
         leg = ax.legend(lines, labels, loc=0, ncol=2,
                         prop=FP(size=8),
-                        title='$\mathrm{\Delta G\/%s\/}\mathit{vs.}\/\mathrm{lambda\/pair}$' % units,
+                        title=r'$\Delta G$ ({})'.format(units) +
+                              r'$\mathit{vs.}$ lambda pair',
                         fancybox=True)
 
     leg.get_frame().set_alpha(0.5)

src/alchemlyb/visualisation/mbar_matrix.py

@@ -6,7 +6,7 @@
 quality of the overlap matrix is by plotting it.
 
 The code for producing the overlap matrix plot is taken from
-: `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
+`Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
 
 """
 from __future__ import division
@@ -24,9 +24,9 @@ def plot_mbar_overlap_matrix(matrix, skip_lambda_index=[], ax=None):
         :attr:`~alchemlyb.estimators.MBAR.overlap_matrix`
     skip_lambda_index : List
         list of lambda indices to be omitted from plotting process.
-        Default: [].
+        Default: ``[]``.
     ax : matplotlib.axes.Axes
-        Matplotlib axes object where the plot will be drawn on. If ax=None,
+        Matplotlib axes object where the plot will be drawn on. If ``ax=None``,
         a new axes will be generated.
 
     Returns
@@ -37,7 +37,10 @@ def plot_mbar_overlap_matrix(matrix, skip_lambda_index=[], ax=None):
     Note
     ----
     The code is taken and modified from
-    : `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_
+    `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
+
+
+    .. versionadded:: 0.4.0
 
     '''
     # Compute the size of the figure, if ax is not given.
@@ -60,8 +63,11 @@ def plot_mbar_overlap_matrix(matrix, skip_lambda_index=[], ax=None):
             else:
                 ii = ("{:.2f}".format(matrix[j, i])[1:])
             alf = matrix[j, i] / max_prob
-            ax.fill_between([i, i + 1], [size - j, size - j], [size - (j + 1), size - (j + 1)], color='k', alpha=alf)
-            ax.annotate(ii, xy=(i, j), xytext=(i + 0.5, size - (j + 0.5)), size=8, textcoords='data', va='center',
+            ax.fill_between([i, i + 1], [size - j, size - j],
+                            [size - (j + 1), size - (j + 1)], color='k',
+                            alpha=alf)
+            ax.annotate(ii, xy=(i, j), xytext=(i + 0.5, size - (j + 0.5)),
+                        size=8, textcoords='data', va='center',
                         ha='center', color=('k' if alf < 0.5 else 'w'))
 
     if skip_lambda_index:
@@ -70,11 +76,16 @@ def plot_mbar_overlap_matrix(matrix, skip_lambda_index=[], ax=None):
     else:
         ks = range(size)
     for i in range(size):
-        ax.annotate(ks[i], xy=(i + 0.5, 1), xytext=(i + 0.5, size + 0.5), size=10, textcoords=('data', 'data'),
+        ax.annotate(ks[i], xy=(i + 0.5, 1), xytext=(i + 0.5, size + 0.5),
+                    size=10, textcoords=('data', 'data'),
                     va='center', ha='center', color='k')
-        ax.annotate(ks[i], xy=(-0.5, size - (size - 0.5)), xytext=(-0.5, size - (i + 0.5)), size=10, textcoords=('data', 'data'),
+        ax.annotate(ks[i], xy=(-0.5, size - (size - 0.5)),
+                    xytext=(-0.5, size - (i + 0.5)),
+                    size=10, textcoords=('data', 'data'),
                     va='center', ha='center', color='k')
-    ax.annotate('$\lambda$', xy=(-0.5, size - (size - 0.5)), xytext=(-0.5, size + 0.5), size=10, textcoords=('data', 'data'),
+    ax.annotate(r'$\lambda$', xy=(-0.5, size - (size - 0.5)),
+                xytext=(-0.5, size + 0.5),
+                size=10, textcoords=('data', 'data'),
                 va='center', ha='center', color='k')
     ax.plot([0, size], [0, 0], 'k-', lw=4.0, solid_capstyle='butt')
     ax.plot([size, size], [0, size], 'k-', lw=4.0, solid_capstyle='butt')

src/alchemlyb/visualisation/ti_dhdl.py

@@ -5,7 +5,7 @@
 thoroughly.
 
 The code for producing the dhdl plot is modified based on
-: `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
+`Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
 
 """
 from __future__ import division
@@ -29,9 +29,9 @@ def plot_ti_dhdl(dhdl_data, labels=None, colors=None, units='kT',
         list of colors for plotting all the alchemical transformations.
         Default: ['r', 'g', '#7F38EC', '#9F000F', 'b', 'y']
     units : str
-        The label for the unit of the estimate. Default: `kT`
+        The label for the unit of the estimate. Default: "kT"
     ax : matplotlib.axes.Axes
-        Matplotlib axes object where the plot will be drawn on. If ax=None,
+        Matplotlib axes object where the plot will be drawn on. If ``ax=None``,
         a new axes will be generated.
 
     Returns
@@ -42,11 +42,13 @@ def plot_ti_dhdl(dhdl_data, labels=None, colors=None, units='kT',
     Note
     ----
     The code is taken and modified from
-    : `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_
+    `Alchemical Analysis <https://github.com/MobleyLab/alchemical-analysis>`_.
 
     The units variable is for labelling only. Changing it doesn't change the
-    unit of the underlying variable, which is in the unit of kT.
+    unit of the underlying variable, which is in the unit of :math:`kT`.
 
+
+    .. versionadded:: 0.4.0
     '''
     # Make it into a list
     # separate_dhdl method is used so that the input for the actual plotting
@@ -94,7 +96,7 @@ def plot_ti_dhdl(dhdl_data, labels=None, colors=None, units='kT',
             raise ValueError(
                 'Number of colors ({}) should be larger than the number of data ({})'.format(
                     len(labels), len(dhdl_list)))
-        
+
     # Get the real data out
     xs, ndx, dx = [0], 0, 0.001
     min_y, max_y = 0, 0
@@ -171,9 +173,10 @@ def getInd(r=ri, z=[0]):
             ax.yaxis.set_minor_locator(AML())
     ax.grid(which='both', color='w', lw=0.25, axis='y', zorder=12)
     ax.set_ylabel(
-        r'$\mathrm{\langle{\frac{ \partial U } { \partial \lambda }}\rangle_{\lambda}\/%s}$' % units,
+        r'$\langle{\frac{\partial U}{\partial\lambda}}\rangle_{\lambda}$' +
+        '({})'.format(units),
         fontsize=20, color='#151B54')
-    ax.annotate('$\mathit{\lambda}$', xy=(0, 0), xytext=(0.5, -0.05), size=18,
+    ax.annotate(r'$\mathit{\lambda}$', xy=(0, 0), xytext=(0.5, -0.05), size=18,
                 textcoords='axes fraction', va='top', ha='center',
                 color='#151B54')
     lege = ax.legend(prop=FP(size=14), frameon=False, loc=1)