Fix for logL_birth (handley-lab#324)

* Fix for logL_birth * bump version to 2.1.5 * bump version to 2.1.6 * now avoiding dropna where possible and reducing code repetition * version bump to 2.2.2 * Dropping all infs with warnings * Corrected bump_version script * Added a scatter kind * fix mistakenly changed DOI in README * check for inf directly instead of indirectly using isfinite, since nans are actually ok here * add `pytest.warns` to tests to explicitly check for the existance of the newly added warnings and to keep our pytest output clean * Update samples.py for pep8 * version bump to 2.5.2 * bump version to 2.7.4 * Removed obselete test for handley-lab#96 * Update README.rst version to 2.8.5 * Update _version.py to 2.8.5 * bump version to 2.8.6 * bump version to 2.8.7 * bump version to 2.8.8 * bump version to 2.8.9 --------- Co-authored-by: Lukas Hergt <[email protected]> Co-authored-by: Lukas Hergt <[email protected]>
AdamOrmondroyd · Apr 9, 2024 · 79c7bb6 · 79c7bb6
1 parent 16083c4
commit 79c7bb6
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Showing 5 changed files with 38 additions and 28 deletions.
diff --git a/README.rst b/README.rst
@@ -2,7 +2,7 @@
 anesthetic: nested sampling post-processing
 ===========================================
 :Authors: Will Handley and Lukas Hergt
-:Version: 2.8.8
+:Version: 2.8.9
 :Homepage: https://github.com/handley-lab/anesthetic
 :Documentation: http://anesthetic.readthedocs.io/
 

diff --git a/anesthetic/_version.py b/anesthetic/_version.py
@@ -1 +1 @@
-__version__ = '2.8.8'
+__version__ = '2.8.9'
diff --git a/anesthetic/samples.py b/anesthetic/samples.py
@@ -174,8 +174,11 @@ def plot_1d(self, axes=None, *args, **kwargs):
         for x, ax in axes.items():
             if x in self and kwargs['kind'] is not None:
                 xlabel = self.get_label(x)
-                self[x].plot(ax=ax, xlabel=xlabel, logx=x in logx,
-                             *args, **kwargs)
+                if np.isinf(self[x]).any():
+                    warnings.warn(f"column {x} has inf values.")
+                selfx = self[x].replace([-np.inf, np.inf], np.nan)
+                selfx.plot(ax=ax, xlabel=xlabel, logx=x in logx,
+                           *args, **kwargs)
                 ax.set_xlabel(xlabel)
             else:
                 ax.plot([], [])
@@ -239,6 +242,9 @@ def plot_2d(self, axes=None, *args, **kwargs):
                 - 'hist_1d': 1d histograms down the diagonal
                 - 'hist_2d': 2d histograms in lower triangle
                 - 'hist': 1d & 2d histograms in lower & diagonal
+                - 'scatter_2d': 2d scatter in lower triangle
+                - 'scatter': 1d histograms down diagonal
+                             & 2d scatter in lower triangle
 
             Feel free to add your own to this list!
             Default:
@@ -337,16 +343,24 @@ def plot_2d(self, axes=None, *args, **kwargs):
                     if x in self and y in self and lkwargs['kind'] is not None:
                         xlabel = self.get_label(x)
                         ylabel = self.get_label(y)
+                        if np.isinf(self[x]).any():
+                            warnings.warn(f"column {x} has inf values.")
                         if x == y:
-                            self[x].plot(ax=ax.twin, xlabel=xlabel,
-                                         logx=x in logx,
-                                         *args, **lkwargs)
+                            selfx = self[x].replace([-np.inf, np.inf], np.nan)
+                            selfx.plot(ax=ax.twin, xlabel=xlabel,
+                                       logx=x in logx,
+                                       *args, **lkwargs)
                             ax.set_xlabel(xlabel)
                             ax.set_ylabel(ylabel)
                         else:
-                            self.plot(x, y, ax=ax, xlabel=xlabel,
-                                      logx=x in logx, logy=y in logy,
-                                      ylabel=ylabel, *args, **lkwargs)
+                            if np.isinf(self[x]).any():
+                                warnings.warn(f"column {y} has inf values.")
+                            selfxy = self[[x, y]]
+                            selfxy = self.replace([-np.inf, np.inf], np.nan)
+                            selfxy = selfxy.dropna(axis=0)
+                            selfxy.plot(x, y, ax=ax, xlabel=xlabel,
+                                        logx=x in logx, logy=y in logy,
+                                        ylabel=ylabel, *args, **lkwargs)
                             ax.set_xlabel(xlabel)
                             ax.set_ylabel(ylabel)
                     else:
@@ -370,6 +384,8 @@ def plot_2d(self, axes=None, *args, **kwargs):
         'hist': {'diagonal': 'hist_1d', 'lower': 'hist_2d'},
         'hist_1d': {'diagonal': 'hist_1d'},
         'hist_2d': {'lower': 'hist_2d'},
+        'scatter': {'diagonal': 'hist_1d', 'lower': 'scatter_2d'},
+        'scatter_2d': {'lower': 'scatter_2d'},
     }
 
     def importance_sample(self, logL_new, action='add', inplace=False):

diff --git a/bin/bump_version.py b/bin/bump_version.py
@@ -8,6 +8,7 @@
 
 current_version = run("cat", vfile)
 current_version = current_version.split("=")[-1].strip().strip("'")
+escaped_version = current_version.replace(".", "\.")
 current_version = version.parse(current_version)
 
 if len(sys.argv) > 1:
@@ -33,9 +34,9 @@
 
 for f in [vfile, README]:
     if sys.platform == "darwin":  # macOS sed requires empty string for backup
-        run("sed", "-i", "", f"s/{current_version}/{new_version}/g", f)
+        run("sed", "-i", "", f"s/{escaped_version}/{new_version}/g", f)
     else:
-        run("sed", "-i", f"s/{current_version}/{new_version}/g", f)
+        run("sed", "-i", f"s/{escaped_version}/{new_version}/g", f)
 
 run("git", "add", vfile, README)
 run("git", "commit", "-m", f"bump version to {new_version}")
diff --git a/tests/test_samples.py b/tests/test_samples.py
@@ -418,6 +418,10 @@ def test_plot_2d_no_axes():
     assert axes.iloc[-1, 1].get_xlabel() == 'x1'
     assert axes.iloc[-1, 2].get_xlabel() == 'x2'
 
+    with pytest.warns(UserWarning):
+        axes = ns[['x0', 'logL_birth']].plot_2d()
+        axes = ns.drop_labels()[['x0', 'logL_birth']].plot_2d()
+
 
 def test_plot_1d_no_axes():
     np.random.seed(3)
@@ -431,6 +435,11 @@ def test_plot_1d_no_axes():
     assert axes.iloc[1].get_xlabel() == 'x1'
     assert axes.iloc[2].get_xlabel() == 'x2'
 
+    with pytest.warns(UserWarning):
+        axes = ns.plot_1d()
+        axes = ns[['x0', 'logL_birth']].plot_1d()
+        axes = ns.drop_labels()[['x0', 'logL_birth']].plot_1d()
+
 
 @pytest.mark.parametrize('kind', ['kde', 'hist', skipif_no_fastkde('fastkde')])
 def test_plot_logscale_1d(kind):
@@ -1213,22 +1222,6 @@ def test_hist_range_1d():
     assert x2 >= +1
 
 
-def test_contour_plot_2d_nan():
-    """Contour plots with nans arising from issue #96"""
-    np.random.seed(3)
-    ns = read_chains('./tests/example_data/pc')
-
-    ns.loc[:9, ('x0', '$x_0$')] = np.nan
-    with pytest.raises((np.linalg.LinAlgError, RuntimeError, ValueError)):
-        ns.plot_2d(['x0', 'x1'])
-
-    # Check this error is removed in the case of zero weights
-    weights = ns.get_weights()
-    weights[:10] = 0
-    ns.set_weights(weights, inplace=True)
-    ns.plot_2d(['x0', 'x1'])
-
-
 def test_compute_insertion():
     np.random.seed(3)
     ns = read_chains('./tests/example_data/pc')