mc3 3.2.0__tar.gz → 3.2.1__tar.gz

{mc3-3.2.0 → mc3-3.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: mc3
-Version: 3.2.0
+Version: 3.2.1
 Summary: Multi-core Markov-chain Monte Carlo package
 Author-email: Patricio Cubillos <patricio.cubillos@oeaw.ac.at>
 License: Copyright (c) 2015-2022 Patricio Cubillos and contributors.

{mc3-3.2.0 → mc3-3.2.1}/mc3/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 from .sampler_driver import *

{mc3-3.2.0 → mc3-3.2.1}/mc3/__main__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 import sys

{mc3-3.2.0 → mc3-3.2.1}/mc3/chain.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 import sys

{mc3-3.2.0 → mc3-3.2.1}/mc3/fit_driver.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.2.1}/mc3/mcmc_driver.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.2.1}/mc3/plots/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 from .plot_functions import *

{mc3-3.2.0 → mc3-3.2.1}/mc3/plots/colors.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [
@@ -105,6 +105,7 @@ def rainbow_text(ax, texts, fontsize, colors=None, loc='above'):
     fig = ax.get_figure()
     t = ax.transAxes
     x = 0.02
+    horizontalalignment = 'left'
     if loc == 'above':
         y = 1.02
         verticalalignment = 'bottom'
@@ -113,11 +114,18 @@ def rainbow_text(ax, texts, fontsize, colors=None, loc='above'):
         y = 0.97
         verticalalignment = 'top'
         bbox = {'facecolor':'white', 'alpha':0.5, 'pad':0.0, 'edgecolor':'none'}
+    elif loc == 'under':
+        y = -0.04
+        x = 0.97
+        verticalalignment = 'top'
+        horizontalalignment = 'right'
+        bbox = None
+
     printed_texts = []
     for string, col in zip(texts, colors):
         text = ax.text(
             x, y, string, color=col, transform=t,
-            ha='left', va=verticalalignment,
+            ha=horizontalalignment, va=verticalalignment,
             size=fontsize,
             bbox=bbox,
         )

{mc3-3.2.0 → mc3-3.2.1}/mc3/plots/plot_functions.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.2.1}/mc3/plots/posterior.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [
@@ -193,6 +193,7 @@ def _pairwise(
         hist, hist_xran, axes, ranges, estimates,
         palette, nlevels, absolute_dens, lmax,
         linewidth, theme, alpha=0.8, clear=True,
+        swap_axes=False,
     ):
     """
     Lowest-lever routine to plot pair-wise posterior distributions.
@@ -206,13 +207,19 @@ def _pairwise(
     for icol in range(npars-1):
         for irow in range(icol, npars-1):
             ax = axes[irow,icol]
+            if swap_axes:
+                row, col = icol, irow+1
+                histo = hist[col-1,row].T
+            else:
+                row, col = irow+1, icol
+                histo = hist[row-1,col]
             if clear:
                 ax.clear()
             extent = (
-                hist_xran[icol,0],
-                hist_xran[icol,-1],
-                hist_xran[irow+1,0],
-                hist_xran[irow+1,-1],
+                hist_xran[col, 0],
+                hist_xran[col, -1],
+                hist_xran[row, 0],
+                hist_xran[row, -1],
             )
             levels = np.zeros(nlevels+1)
             levels[1:] = np.linspace(1.0, lmax[irow,icol], nlevels)
@@ -220,29 +227,30 @@ def _pairwise(
             colors[0,3] = 0.0
             colors[1,3] = 0.75*alpha
             cont = ax.contourf(
-                hist[irow,icol],
+                histo,
                 colors=colors, levels=levels,
                 origin='lower', extent=extent,
             )
-            edge_color = to_rgba(theme.color, alpha=0.65)
-            for c in cont.collections:
-                c.set_edgecolor(edge_color)
-                c.set_linewidth(0.1)
-            cont.collections[0].set_edgecolor((1,1,1,0))
-            if estimates[icol] is not None:
+            edge_color = to_rgba(theme.color, alpha=0.25)
+            edge_colors = [edge_color for _ in cont.get_paths()]
+            edge_colors[0] = (1,1,1,0)
+            cont.set_edgecolor(edge_colors)
+            cont.set_linewidth(0.1)
+
+            if estimates[col] is not None:
                 ax.axvline(
-                    estimates[icol],
+                    estimates[col],
                     dashes=(9,2), lw=linewidth, color=theme.dark_color,
                 )
-            if estimates[irow+1] is not None:
+            if estimates[row] is not None:
                 ax.axhline(
-                    estimates[irow+1],
+                    estimates[row],
                     dashes=(9,2), lw=linewidth, color=theme.dark_color,
                 )
-            if ranges[icol] is not None:
-                ax.set_xlim(ranges[icol])
-            if ranges[irow] is not None:
-                ax.set_ylim(ranges[irow+1])
+            if ranges[col] is not None:
+                ax.set_xlim(ranges[col])
+            if ranges[row] is not None:
+                ax.set_ylim(ranges[row])
 
 
 def _plot_marginal(obj):
@@ -302,7 +310,11 @@ def _plot_pairwise(obj):
     for icol in range(npars-1):
         for irow in range(icol, npars-1):
             ax = obj.pair_axes[irow,icol]
-            h = nx*irow + icol + 1 + npars*int(obj.plot_marginal)
+            if obj.orientation == 'vertical':
+                h = nx*irow + icol + 1 + npars*int(obj.plot_marginal)
+            else:
+                h = 2 + (nx+int(obj.plot_marginal))*icol + irow - icol
+
             ax_position = subplot(
                 obj.rect, obj.margin, h, nx, nx, obj.ymargin, dry=True,
             )
@@ -495,7 +507,7 @@ class RangeUpdate(SoftUpdate):
         setattr(obj.source, var_name, value)
 
 
-class Marginal(object):
+class Marginal():
     """A mostly-interactive marginal posterior plotting object."""
     # Soft-update properties:
     pnames = SoftUpdate()
@@ -625,6 +637,48 @@ class Marginal(object):
         if savefile is not None:
             self.fig.savefig(savefile, dpi=300)
 
+    def overplot(self, post, labels=None, nlevels=4, alpha=0.4):
+        """
+        Overplot additional posteriors in the same figure.
+
+        This method is still work in progress!
+        Note that a call to self.update() or even soft updates
+        will remove all/some of the overplot data. In such case
+        the user would need to make a new call to self.overplot().
+        It is also recommended to set show_estimates=False to
+        prevent over-crowding the figures.
+
+        Parameters
+        ----------
+        posts: 1D iterable of Posterior objects
+            Currently there are no checks that these new posteriors
+            have the same parameters (nor same statistics) as self.
+            The user needs to make sure they are all compartible.
+        labels: 1D iterable of strings
+            Labels for each posterior.  Note that if provided, the
+            length of labels has to be one more than posts, because
+            it also contains the label for self.
+        """
+        if '_like' in post.statistics:
+            hpd_min = post.hpd_min
+        else:
+            hpd_min = None
+
+        estimates = post.estimates
+        if not self.show_estimates:
+            estimates = [None for _ in estimates]
+
+        _histogram(
+            post.posterior, estimates, post.ranges,
+            self.hist_axes, self.bins,
+            post.pdf, post.xpdf,
+            hpd_min, post.low_bounds, post.high_bounds,
+            self.linewidth, post.theme,
+            post.orientation,
+            top_pad=1.25,
+            clear=False,
+        )
+
 
 class Figure(Marginal):
     """A mostly-interactive pair-wise posterior plotting object."""
@@ -756,6 +810,7 @@ class Figure(Marginal):
             self.lmax,
             self.linewidth,
             self.theme,
+            swap_axes=self.orientation=='upper right',
         )
 
         # The colorbar:

{mc3-3.2.0 → mc3-3.2.1}/mc3/sampler_driver.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.2.1}/mc3/stats/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 from .gelman import *

{mc3-3.2.0 → mc3-3.2.1}/mc3/stats/gelman.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.2.1}/mc3/stats/prayer.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.2.1}/mc3/stats/stats.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [
@@ -611,7 +611,7 @@ def dwt_daub4(array, inverse=False):
     return dwt.daub4(np.array(array), isign)
 
 
-class Loglike(object):
+class Loglike():
     """
     Wrapper to compute log(likelihood)
 
@@ -1041,7 +1041,7 @@ def summary_stats(post, mc3_output=None, filename=None):
 
     # Central quantile:
     f.write(
-        '\nCentral quintile credible intervals:\n'
+        '\nCentral quantile credible intervals:\n'
         ' 2sigma_low     1sigma_low     1sigma_up      2sigma_up      '
         'Parameter\n'
     )

{mc3-3.2.0 → mc3-3.2.1}/mc3/stats/time_averaging.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.2.1}/mc3/utils/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 from .utils import *

{mc3-3.2.0 → mc3-3.2.1}/mc3/utils/log.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.2.1}/mc3/utils/utils.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.2.1}/mc3/version.py

@@ -1,9 +1,9 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 # mc3 Version:
 MC3_VER = 3  # Major version
 MC3_MIN = 2  # Minor version
-MC3_REV = 0  # Revision
+MC3_REV = 1  # Revision
 
 __version__ = f'{MC3_VER}.{MC3_MIN}.{MC3_REV}'

{mc3-3.2.0 → mc3-3.2.1}/mc3.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: mc3
-Version: 3.2.0
+Version: 3.2.1
 Summary: Multi-core Markov-chain Monte Carlo package
 Author-email: Patricio Cubillos <patricio.cubillos@oeaw.ac.at>
 License: Copyright (c) 2015-2022 Patricio Cubillos and contributors.

{mc3-3.2.0 → mc3-3.2.1}/setup.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 import os

{mc3-3.2.0 → mc3-3.2.1}/src_c/_binarray.c

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+// Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 // mc3 is open-source software under the MIT license (see LICENSE).
 
 #include <Python.h>

{mc3-3.2.0 → mc3-3.2.1}/src_c/_chisq.c

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+// Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 // mc3 is open-source software under the MIT license (see LICENSE).
 
 #include <Python.h>

{mc3-3.2.0 → mc3-3.2.1}/src_c/_dwt.c

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+// Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 // mc3 is open-source software under the MIT license (see LICENSE).
 
 #include <Python.h>

{mc3-3.2.0 → mc3-3.2.1}/src_c/_time_averaging.c

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+// Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 // mc3 is open-source software under the MIT license (see LICENSE).
 
 #include <Python.h>

{mc3-3.2.0 → mc3-3.2.1}/src_c/include/ind.h

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+// Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 // mc3 is open-source software under the MIT license (see LICENSE).
 
 /* Definitions for indexing Numpy arrays:                                   */

{mc3-3.2.0 → mc3-3.2.1}/src_c/include/stats.h

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+// Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 // mc3 is open-source software under the MIT license (see LICENSE).
 
 /******************************************************************

{mc3-3.2.0 → mc3-3.2.1}/src_c/include/wavelet.h

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+// Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 // mc3 is open-source software under the MIT license (see LICENSE).
 
 /**********************************************************************

{mc3-3.2.0 → mc3-3.2.1}/tests/test_fit.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # MC3 is open-source software under the MIT license (see LICENSE).
 
 import pytest

{mc3-3.2.0 → mc3-3.2.1}/tests/test_logging.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # MC3 is open-source software under the MIT license (see LICENSE).
 
 import pytest

{mc3-3.2.0 → mc3-3.2.1}/tests/test_mcmc.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 import os
@@ -233,14 +233,17 @@ def test_mcmc_gr_break_iterations(capsys):
 def test_mcmc_thin_gr_break_frac(capsys):
     nsamples = 1e4
     thin = 5
+    nchains = 3
     output = mc3.sample(
         data, uncert, func=quad, params=np.copy(params),
         sampler=sampler, indparams=[x],
         pstep=pstep, nsamples=nsamples, burnin=100, thinning=thin,
-        grtest=True, grbreak=1.1, grnmin=0.55)
+        nchains=nchains, grtest=True, grbreak=1.1, grnmin=0.55)
     captured = capsys.readouterr()
     assert output is not None
-    assert output['chisq'].size < nsamples/thin * 0.7
+    size = output['chisq'].size
+    expected_size = nsamples/thin * 0.9
+    assert size < expected_size
     assert "All parameters satisfy the GR convergence threshold of 1.1" \
            in captured.out
 
@@ -248,14 +251,18 @@ def test_mcmc_thin_gr_break_frac(capsys):
 def test_mcmc_gr_thin_break_iterations(capsys):
     nsamples = 1e4
     thin = 5
+    nchains = 3
     output = mc3.sample(
         data, uncert, func=quad, params=np.copy(params),
         sampler=sampler, indparams=[x],
         pstep=pstep, nsamples=nsamples, burnin=100, thinning=thin,
+        nchains=nchains,
         grtest=True, grbreak=1.1, grnmin=5000)
     captured = capsys.readouterr()
     assert output is not None
-    assert output['chisq'].size < nsamples/thin * 0.7
+    size = output['chisq'].size
+    expected_size = nsamples/thin * 0.9
+    assert size < expected_size
     assert "All parameters satisfy the GR convergence threshold of 1.1" \
            in captured.out
 

{mc3-3.2.0 → mc3-3.2.1}/tests/test_plots.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # MC3 is open-source software under the MIT license (see LICENSE).
 
 import pytest

{mc3-3.2.0 → mc3-3.2.1}/tests/test_stats.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # MC3 is open-source software under the MIT license (see LICENSE).
 
 import pytest

{mc3-3.2.0 → mc3-3.2.1}/tests/test_utils.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
 # MC3 is open-source software under the MIT license (see LICENSE).
 
 import pytest