mc3 3.2.0__tar.gz → 3.3.0__tar.gz

mc3-3.3.0/.github/workflows/python-package.yml

@@ -0,0 +1,47 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Tests
+
+on:
+  push:
+    branches: [ "*" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    - cron: '0 12 1 * *'
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        os: [ubuntu-latest]
+
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Install package
+      run: |
+        python -m pip install -e .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest tests -v

mc3-3.3.0/MANIFEST.in

@@ -0,0 +1,12 @@
+include MANIFEST.in
+include CONTRIBUTING.md
+include README.md
+include LICENSE
+include pyproject.toml
+include requirements.txt
+include pytest.ini
+include .readthedocs.yml
+include .github/workflows/python-package.yml
+include tests/*
+include docs/*
+include examples/*.py

{mc3-3.2.0 → mc3-3.3.0}/PKG-INFO

@@ -1,37 +1,19 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: mc3
-Version: 3.2.0
+Version: 3.3.0
 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.
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in
-        all copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-        THE SOFTWARE.
-        
+License-Expression: MIT
 Project-URL: Homepage, https://github.com/pcubillos/mc3
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy>=1.23.5
+Requires-Dist: numpy>=2.0.0
 Requires-Dist: scipy>=1.5.4
 Requires-Dist: matplotlib>=3.3.4
 Provides-Extra: test
 Requires-Dist: pytest>=6.0; extra == "test"
+Dynamic: license-file
 
 # mc3: Multi-core Markov-chain Monte Carlo
 > A Python implementation of the Markov-chain Monte Carlo algorithm.

mc3-3.3.0/docs/docs_requirements.txt

@@ -0,0 +1,6 @@
+sphinx==8.1.3
+sphinx-rtd-theme>=2.0.0
+nbsphinx
+sphinx_copybutton
+ipython>=8.17
+

{mc3-3.2.0 → mc3-3.3.0}/docs/get_started.rst

@@ -6,7 +6,7 @@ Getting Started
 System Requirements
 -------------------
 
-``mc3`` is compatible with Python 3.9+, and has been `tested
+``mc3`` is compatible with Python 3.10+, and is `tested
 <https://github.com/pcubillos/mc3/actions/workflows/python-package.yml>`_ to work on Unix/Linux and OS X machines.
 
 Install

{mc3-3.2.0 → mc3-3.3.0}/docs/index.rst

@@ -40,7 +40,7 @@ mc3: Multi-Core Markov-Chain Monte Carlo
 
 .. note::
 
-    Got  Python3.9+? Simply install as: ``pip install mc3``
+    Compatible with Python3.10.  Install as: ``pip install mc3``
 
 
 Features

{mc3-3.2.0 → mc3-3.3.0}/mc3/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 from .sampler_driver import *

{mc3-3.2.0 → mc3-3.3.0}/mc3/__main__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 import sys

{mc3-3.2.0 → mc3-3.3.0}/mc3/chain.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 import sys

{mc3-3.2.0 → mc3-3.3.0}/mc3/fit_driver.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.3.0}/mc3/mcmc_driver.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.3.0}/mc3/plots/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 from .plot_functions import *

{mc3-3.2.0 → mc3-3.3.0}/mc3/plots/colors.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 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 → mc3-3.3.0}/mc3/plots/plot_functions.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.3.0}/mc3/plots/posterior.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [
@@ -140,6 +140,8 @@ def _histogram(
         hist_kw['facecolor'] = 'none'
 
     for i in range(npars):
+        if np.any(np.isnan(posterior[:,i])):
+            continue
         ax = axes[i]
         if clear:
             ax.clear()
@@ -193,6 +195,7 @@ 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 +209,19 @@ 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 +229,30 @@ 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 +312,11 @@ 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 +509,7 @@ 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()
@@ -521,6 +535,7 @@ class Marginal(object):
             bins=25, fontsize=11, linewidth=1.5,
             axes=None,
             show_texts=True, show_estimates=True,
+            alpha=0.6,
         ):
         self.source = source
         self.fig = None
@@ -532,6 +547,7 @@ class Marginal(object):
         self.bestp = bestp
         self.ranges = ranges
         self.theme = theme
+        self.alpha = alpha
 
         if nx is None or ny is None:
             # Default layout:
@@ -618,6 +634,7 @@ class Marginal(object):
             hpd_min, self.source.low_bounds, self.source.high_bounds,
             self.linewidth, self.theme,
             self.orientation,
+            alpha=self.alpha,
             top_pad=1.25,
         )
         _plot_marginal(self)
@@ -625,6 +642,62 @@ class Marginal(object):
         if savefile is not None:
             self.fig.savefig(savefile, dpi=300)
 
+    def overplot(self, posts, labels=None, nlevels=4, alpha=0.4, axes_mask=None):
+        """
+        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.
+        """
+        all_posts = [self.source] + list(posts)
+        for i,post in enumerate(posts):
+            estimates = post.estimates
+            if not self.show_estimates:
+                estimates = [None for _ in estimates]
+            hpd_min = None
+            if '_like' in self.statistics:
+                hpd_min = self.source.hpd_min
+
+            _histogram(
+                post.posterior, estimates, self.ranges,
+                self.hist_axes, self.bins,
+                post.pdf, post.xpdf,
+                hpd_min, post.low_bounds, post.high_bounds,
+                self.linewidth, post.theme,
+                post.orientation, alpha=alpha,
+                clear=False,
+            )
+        if not self.show_texts:
+            return
+        text_cols = [post.theme.color for post in all_posts]
+        for text in self.stats_texts:
+            text.set_visible(False)
+        self.stats_texts = []
+
+        for j in range(self.npars):
+            stats_texts = [
+                '' if post.mask[j] else rf'{post.tex_estimates[j]}'
+                for post in all_posts
+            ]
+            self.stats_texts += colors.rainbow_text(
+                self.hist_axes[j], stats_texts, self.fontsize, text_cols,
+            )
+
 
 class Figure(Marginal):
     """A mostly-interactive pair-wise posterior plotting object."""
@@ -640,10 +713,11 @@ class Figure(Marginal):
             bins=25, nlevels=6, fontsize=None, linewidth=None,
             show_texts=True, show_estimates=True,
             show_colorbar=True,
+            figure=None,
             fignum=None,
         ):
         self.source = source
-        self.fig = None
+        self.fig = figure
         self.pair_axes = None
         self.hist_axes = None
         self.posterior = posterior
@@ -756,6 +830,7 @@ class Figure(Marginal):
             self.lmax,
             self.linewidth,
             self.theme,
+            swap_axes=self.orientation=='upper right',
         )
 
         # The colorbar:
@@ -879,7 +954,7 @@ class Figure(Marginal):
                 post.posterior, estimates, self.ranges, self.hist_axes,
                 self.bins, post.pdf, post.xpdf,
                 hpd_min, post.low_bounds, post.high_bounds,
-                self.linewidth, post.theme, post.orientation, alpha=0.5,
+                self.linewidth, post.theme, post.orientation, alpha=alpha,
                 clear=False,
             )
         if not self.show_texts:
@@ -989,7 +1064,7 @@ class StatisticsUpdate(ShareUpdate):
             )
 
 
-class Posterior(object):
+class Posterior():
     """
     Classification of posterior plotting tools.
 
@@ -1035,6 +1110,7 @@ class Posterior(object):
             show_texts=True, show_estimates=True,
             show_colorbar=True,
             seed=314159,
+            mask=None,
         ):
         self.figures = []
         nsamples, self.npars = np.shape(posterior)
@@ -1076,7 +1152,9 @@ class Posterior(object):
             self.bestp = bestp
         self.statistics = statistics
         self.quantile = quantile
-
+        if mask is None:
+            mask = np.ones(self.npars, bool)
+        self.mask = mask
 
     def plot(
             self, plot_marginal=True,
@@ -1088,6 +1166,7 @@ class Posterior(object):
             show_texts=None, show_estimates=None,
             show_colorbar=None,
             savefile=None,
+            nlevels=None,
         ):
         """
         Plot marginal histograms and pairwise posteriors.
@@ -1101,6 +1180,8 @@ class Posterior(object):
             show_texts = self.show_texts
         if show_colorbar is None:
             show_colorbar = self.show_colorbar
+        if nlevels is None:
+            nlevels = 6
 
         fig = Figure(
             self,
@@ -1119,7 +1200,8 @@ class Posterior(object):
             show_texts=show_texts,
             show_estimates=show_estimates,
             show_colorbar=show_colorbar,
-            # bins=25, nlevels=20,
+            # bins=25,
+            nlevels=nlevels,
         )
         self.figures.append(fig)
         fig.plot(figure=figure, savefile=savefile)
@@ -1130,7 +1212,9 @@ class Posterior(object):
             self, fignum=None, axes=None, quantile=None,
             nx=None, ny=None,
             savefile=None,
+            fontsize=11, linewidth=1.5,
             show_texts=None, show_estimates=None,
+            alpha=0.6,
         ):
         """
         Plot histogram of marginal posteriors.
@@ -1139,6 +1223,8 @@ class Posterior(object):
             show_estimates = self.show_estimates
         if show_texts is None:
             show_texts = self.show_texts
+        if quantile is None:
+            quantile = self.quantile
 
         fig = Marginal(
             self,
@@ -1146,8 +1232,12 @@ class Posterior(object):
             self.ranges, self.theme,
             statistics=self.statistics,
             nx=nx, ny=ny,
+            quantile=quantile,
+            fontsize=fontsize,
+            linewidth=linewidth,
             show_texts=show_texts,
             show_estimates=show_estimates,
+            alpha=alpha,
         )
         self.figures.append(fig)
         fig.plot(savefile=savefile, fignum=fignum, axes=axes)

{mc3-3.2.0 → mc3-3.3.0}/mc3/sampler_driver.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.0 → mc3-3.3.0}/mc3/stats/__init__.py

@@ -1,15 +1,17 @@
-# Copyright (c) 2015-2023 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 from .gelman import *
 from .stats import *
 from .time_averaging import *
+from .dwt import *
 from .prayer import *
 
 __all__ = (
     gelman.__all__
   + stats.__all__
   + time_averaging.__all__
+  + dwt.__all__
   + prayer.__all__
     )