mc3 3.2.1__tar.gz → 3.3.1__tar.gz

mc3-3.3.1/.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

mc3-3.3.1/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

{mc3-3.2.1 → mc3-3.3.1}/PKG-INFO

@@ -1,37 +1,19 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: mc3
-Version: 3.2.1
+Version: 3.3.1
 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.
-        
-        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
+Requires-Dist: matplotlib>=3.8.0
 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.

mc3-3.3.1/docs/docs_requirements.txt

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

{mc3-3.2.1 → mc3-3.3.1}/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

{mc3-3.2.1 → mc3-3.3.1}/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

{mc3-3.2.1 → mc3-3.3.1}/mc3/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 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 *

{mc3-3.2.1 → mc3-3.3.1}/mc3/__main__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 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

{mc3-3.2.1 → mc3-3.3.1}/mc3/chain.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 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

{mc3-3.2.1 → mc3-3.3.1}/mc3/fit_driver.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.1 → mc3-3.3.1}/mc3/mcmc_driver.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.1 → mc3-3.3.1}/mc3/plots/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 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 *

{mc3-3.2.1 → mc3-3.3.1}/mc3/plots/colors.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.1 → mc3-3.3.1}/mc3/plots/plot_functions.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.1 → mc3-3.3.1}/mc3/plots/posterior.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [
@@ -114,9 +114,9 @@ def hist_2D(posterior, ranges, nbins):
 def _histogram(
         posterior, estimates, ranges, axes,
         nbins, pdf, xpdf, hpd_min, low_bounds, high_bounds,
-        linewidth, theme, orientation, alpha=0.6,
-        top_pad=1.05,
-        clear=True,
+        linewidth, theme, orientation,
+        normalization='density',
+        alpha=0.6, top_pad=1.05, clear=True,
     ):
     """
     Lowest-lever routine to plot marginal posterior distributions.
@@ -128,18 +128,17 @@ def _histogram(
     )
 
     hist_kw = {
-        'bins': nbins,
         'linewidth': linewidth,
         'orientation': orientation,
         'facecolor': to_rgba(theme.light_color, alpha=alpha),
         'edgecolor': theme.color,
-        'histtype': 'stepfilled',
-        'density': True,
     }
     if has_credible_interval:
         hist_kw['facecolor'] = 'none'
 
     for i in range(npars):
+        if np.any(np.isnan(posterior[:,i])):
+            continue
         ax = axes[i]
         if clear:
             ax.clear()
@@ -152,7 +151,13 @@ def _histogram(
             fill_between = ax.fill_betweenx
             axline = ax.axhline
 
-        vals, bins, h = ax.hist(posterior[:,i], range=ranges[i], **hist_kw)
+        vals, bins = np.histogram(
+            posterior[:,i], bins=nbins, density=True, range=ranges[i],
+        )
+        if normalization == 'top':
+            vals /= np.amax(vals)
+        ax.stairs(vals, bins, fill=True, **hist_kw)
+
         # Plot the credible intervals as shaded areas:
         if has_credible_interval:
             vals = np.r_[0, vals, 0]
@@ -533,6 +538,8 @@ class Marginal():
             bins=25, fontsize=11, linewidth=1.5,
             axes=None,
             show_texts=True, show_estimates=True,
+            normalization=None,
+            alpha=0.6,
         ):
         self.source = source
         self.fig = None
@@ -543,7 +550,11 @@ class Marginal():
         self.pnames = pnames
         self.bestp = bestp
         self.ranges = ranges
+        if normalization is None:
+            normalization = 'density'
+        self.normalization = normalization
         self.theme = theme
+        self.alpha = alpha
 
         if nx is None or ny is None:
             # Default layout:
@@ -629,7 +640,8 @@ class Marginal():
             self.source.pdf, self.source.xpdf,
             hpd_min, self.source.low_bounds, self.source.high_bounds,
             self.linewidth, self.theme,
-            self.orientation,
+            self.orientation, self.normalization,
+            alpha=self.alpha,
             top_pad=1.25,
         )
         _plot_marginal(self)
@@ -637,7 +649,7 @@ class Marginal():
         if savefile is not None:
             self.fig.savefig(savefile, dpi=300)
 
-    def overplot(self, post, labels=None, nlevels=4, alpha=0.4):
+    def overplot(self, posts, labels=None, nlevels=4, alpha=0.4, axes_mask=None):
         """
         Overplot additional posteriors in the same figure.
 
@@ -650,7 +662,7 @@ class Marginal():
 
         Parameters
         ----------
-        posts: 1D iterable of Posterior objects
+        posts: Posterior or 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.
@@ -659,25 +671,41 @@ class Marginal():
             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:
+        if isinstance(posts, Posterior):
+            posts = [posts]
+        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
 
-        estimates = post.estimates
-        if not self.show_estimates:
-            estimates = [None for _ in estimates]
+            _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, self.normalization, 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 = []
 
-        _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,
-        )
+        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):
@@ -694,10 +722,12 @@ class Figure(Marginal):
             bins=25, nlevels=6, fontsize=None, linewidth=None,
             show_texts=True, show_estimates=True,
             show_colorbar=True,
+            normalization=None,
+            figure=None,
             fignum=None,
         ):
         self.source = source
-        self.fig = None
+        self.fig = figure
         self.pair_axes = None
         self.hist_axes = None
         self.posterior = posterior
@@ -743,6 +773,9 @@ class Figure(Marginal):
         self.fontsize = fontsize
         self.linewidth = linewidth
         self.orientation = 'vertical'
+        if normalization is None:
+            normalization = 'density'
+        self.normalization = normalization
         self.show_texts = show_texts
         self.show_estimates = show_estimates
         self.show_colorbar = show_colorbar
@@ -849,7 +882,7 @@ class Figure(Marginal):
                 hpd_min,
                 self.source.low_bounds, self.source.high_bounds,
                 self.linewidth, self.theme,
-                self.orientation,
+                self.orientation, self.normalization,
             )
         _plot_pairwise(self)
 
@@ -869,7 +902,7 @@ class Figure(Marginal):
 
         Parameters
         ----------
-        posts: 1D iterable of Posterior objects
+        posts: Posterior or 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.
@@ -878,6 +911,8 @@ class Figure(Marginal):
             length of labels has to be one more than posts, because
             it also contains the label for self.
         """
+        if isinstance(posts, Posterior):
+            posts = [posts]
         all_posts = [self.source] + list(posts)
         for post in posts:
             post.hist_xran, post.hist, post.lmax = hist_2D(
@@ -934,7 +969,9 @@ 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,
+                normalization=self.normalization,
+                alpha=alpha,
                 clear=False,
             )
         if not self.show_texts:
@@ -1044,7 +1081,7 @@ class StatisticsUpdate(ShareUpdate):
             )
 
 
-class Posterior(object):
+class Posterior():
     """
     Classification of posterior plotting tools.
 
@@ -1089,7 +1126,9 @@ class Posterior(object):
             theme='blue', orientation='vertical',
             show_texts=True, show_estimates=True,
             show_colorbar=True,
+            normalization='density',
             seed=314159,
+            mask=None,
         ):
         self.figures = []
         nsamples, self.npars = np.shape(posterior)
@@ -1110,6 +1149,7 @@ class Posterior(object):
         self.ranges = ranges
         self.theme = theme
         self.orientation = orientation
+        self.normalization = normalization
         self.show_texts = show_texts
         self.show_estimates = show_estimates
         self.show_colorbar = show_colorbar
@@ -1131,7 +1171,9 @@ 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,
@@ -1143,6 +1185,7 @@ class Posterior(object):
             show_texts=None, show_estimates=None,
             show_colorbar=None,
             savefile=None,
+            nlevels=None,
         ):
         """
         Plot marginal histograms and pairwise posteriors.
@@ -1156,6 +1199,8 @@ 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,
@@ -1171,10 +1216,12 @@ class Posterior(object):
             fontsize=fontsize,
             figsize=figsize,
             fignum=fignum,
+            normalization=self.normalization,
             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)
@@ -1185,7 +1232,9 @@ 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.
@@ -1194,6 +1243,8 @@ 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,
@@ -1201,8 +1252,13 @@ class Posterior(object):
             self.ranges, self.theme,
             statistics=self.statistics,
             nx=nx, ny=ny,
+            quantile=quantile,
+            fontsize=fontsize,
+            linewidth=linewidth,
+            normalization=self.normalization,
             show_texts=show_texts,
             show_estimates=show_estimates,
+            alpha=alpha,
         )
         self.figures.append(fig)
         fig.plot(savefile=savefile, fignum=fignum, axes=axes)

{mc3-3.2.1 → mc3-3.3.1}/mc3/sampler_driver.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2015-2025 Patricio Cubillos and contributors.
+# Copyright (c) 2015-2026 Patricio Cubillos and contributors.
 # mc3 is open-source software under the MIT license (see LICENSE).
 
 __all__ = [

{mc3-3.2.1 → mc3-3.3.1}/mc3/stats/__init__.py

@@ -1,15 +1,17 @@
-# Copyright (c) 2015-2025 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__
     )