Test suite tidy (handley-lab#319)

* Removed fastkde from test_samples

* bump version to 2.1.1

* Added bump version script for convenience

* Moved astropy to skip rather than fail, and marked all fastkde

* removed erroneous kind check

* Added utils

* More updates for other conditional skipping

* Changed getdist to be an importerror

* Moved importerrors into the function itself

* bump version to 2.1.2

* update merged changes to new `fastkde_skipif` functionality

* Corrected merge of fastkde keys

* Caught importerror

* Renamed skipif functions

* Converted xfails to xskips

* Reverted tests

* Reordered fastkde

* converted xfails to skips

* Removed final xskips

* reinstated xskips

---------

Co-authored-by: Lukas Hergt <[email protected]>

README.rst

@@ -2,7 +2,7 @@
 anesthetic: nested sampling post-processing
 ===========================================
 :Authors: Will Handley and Lukas Hergt
-:Version: 2.1.4
+:Version: 2.1.5
 :Homepage: https://github.com/handley-lab/anesthetic
 :Documentation: http://anesthetic.readthedocs.io/
 

anesthetic/_version.py

@@ -1 +1 @@
-__version__ = '2.1.4'
+__version__ = '2.1.5'

anesthetic/convert.py

@@ -15,7 +15,10 @@ def to_getdist(samples):
     getdist_samples : :class:`getdist.mcsamples.MCSamples`
         getdist equivalent samples
     """
-    import getdist
+    try:
+        import getdist
+    except ModuleNotFoundError:
+        raise ImportError("You need to install getdist to use to_getdist")
     labels = np.char.strip(samples.get_labels().astype(str), '$')
     samples = samples.drop_labels()
     ranges = samples.agg(['min', 'max']).T.apply(tuple, axis=1).to_dict()

anesthetic/plot.py

@@ -16,14 +16,6 @@
 from scipy.special import erf
 from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
 from matplotlib.axes import Axes
-try:
-    from astropy.visualization import hist
-except ImportError:
-    pass
-try:
-    from anesthetic.kde import fastkde_1d, fastkde_2d
-except ImportError:
-    pass
 import matplotlib.cbook as cbook
 import matplotlib.lines as mlines
 from matplotlib.ticker import MaxNLocator, AutoMinorLocator
@@ -768,8 +760,9 @@ def fastkde_plot_1d(ax, data, *args, **kwargs):
     q = quantile_plot_interval(q=q)
 
     try:
+        from anesthetic.kde import fastkde_1d
         x, p, xmin, xmax = fastkde_1d(data, xmin, xmax)
-    except NameError:
+    except ImportError:
         raise ImportError("You need to install fastkde to use fastkde")
     p /= p.max()
     i = ((x > quantile(x, q[0], p)) & (x < quantile(x, q[-1], p)))
@@ -971,10 +964,11 @@ def hist_plot_1d(ax, data, *args, **kwargs):
 
     if isinstance(bins, str) and bins in ['knuth', 'freedman', 'blocks']:
         try:
+            from astropy.visualization import hist
             h, edges, bars = hist(data, ax=ax, bins=bins,
                                   range=range, histtype=histtype,
                                   color=color, *args, **kwargs)
-        except NameError:
+        except ImportError:
             raise ImportError("You need to install astropy to use astropyhist")
     else:
         h, edges, bars = ax.hist(data, weights=weights, bins=bins,
@@ -1048,10 +1042,11 @@ def fastkde_contour_plot_2d(ax, data_x, data_y, *args, **kwargs):
     kwargs.pop('q', None)
 
     try:
+        from anesthetic.kde import fastkde_2d
         x, y, pdf, xmin, xmax, ymin, ymax = fastkde_2d(data_x, data_y,
                                                        xmin=xmin, xmax=xmax,
                                                        ymin=ymin, ymax=ymax)
-    except NameError:
+    except ImportError:
         raise ImportError("You need to install fastkde to use fastkde")
 
     levels = iso_probability_contours(pdf, contours=levels)

anesthetic/read/ultranest.py

@@ -2,10 +2,6 @@
 import os
 import json
 from anesthetic.samples import NestedSamples
-try:
-    import h5py
-except ImportError:
-    pass
 
 
 def read_ultranest(root, *args, **kwargs):
@@ -23,6 +19,10 @@ def read_ultranest(root, *args, **kwargs):
     num_params = len(labels)
 
     filepath = os.path.join(root, 'results', 'points.hdf5')
+    try:
+        import h5py
+    except ImportError:
+        raise ImportError('h5py is required to read UltraNest results')
     with h5py.File(filepath, 'r') as fileobj:
         points = fileobj['points']
         _, ncols = points.shape

bin/bump_version.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+from utils import run
+from packaging import version
+import sys
+
+vfile = "anesthetic/_version.py"
+README = "README.rst"
+
+current_version = run("cat", vfile)
+current_version = current_version.split("=")[-1].strip().strip("'")
+current_version = version.parse(current_version)
+
+if len(sys.argv) > 1:
+    update_type = sys.argv[1]
+else:
+    update_type = "micro"
+
+major = current_version.major
+minor = current_version.minor
+micro = current_version.micro
+
+if update_type == "micro":
+    micro+=1
+elif update_type == "minor":
+    minor+=1
+    micro=0
+elif update_type == "major":
+    major+=1
+    minor=0
+    micro=0
+
+new_version = version.parse(f"{major}.{minor}.{micro}")
+
+for f in [vfile, README]:
+    run("sed", "-i", f"s/{current_version}/{new_version}/g", f)
+
+run("git", "add", vfile, README)
+run("git", "commit", "-m", f"bump version to {new_version}")

bin/check_version.py

@@ -2,17 +2,11 @@
 import sys
 import subprocess
 from packaging import version
-from utils import unit_incremented
+from utils import unit_incremented, run
+
 vfile = "anesthetic/_version.py"
 README = "README.rst"
 
-
-def run(*args):
-    return subprocess.run(args, text=True,
-                          stdout=subprocess.PIPE,
-                          stderr=subprocess.PIPE).stdout
-
-
 current_version = run("cat", vfile)
 current_version = current_version.split("=")[-1].strip().strip("'")
 

bin/utils.py

@@ -1,4 +1,12 @@
 from packaging import version
+import subprocess
+
+
+def run(*args):
+    """Run a bash command and return the output in Python."""
+    return subprocess.run(args, text=True,
+                          stdout=subprocess.PIPE,
+                          stderr=subprocess.PIPE).stdout
 
 
 def unit_incremented(a, b):

tests/test_convert.py

@@ -1,20 +1,19 @@
 from anesthetic import read_chains
 from anesthetic.convert import to_getdist
 from numpy.testing import assert_array_equal
+from utils import getdist_mark_xfail
 
 
+@getdist_mark_xfail
 def test_to_getdist():
-    try:
-        anesthetic_samples = read_chains('./tests/example_data/gd')
-        getdist_samples = to_getdist(anesthetic_samples)
+    anesthetic_samples = read_chains('./tests/example_data/gd')
+    getdist_samples = to_getdist(anesthetic_samples)
 
-        assert_array_equal(getdist_samples.samples, anesthetic_samples)
-        assert_array_equal(getdist_samples.weights,
-                           anesthetic_samples.get_weights())
+    assert_array_equal(getdist_samples.samples, anesthetic_samples)
+    assert_array_equal(getdist_samples.weights,
+                       anesthetic_samples.get_weights())
 
-        for param, p in zip(getdist_samples.getParamNames().names,
-                            anesthetic_samples.drop_labels().columns):
+    for param, p in zip(getdist_samples.getParamNames().names,
+                        anesthetic_samples.drop_labels().columns):
 
-            assert param.name == p
-    except ModuleNotFoundError:
-        pass
+        assert param.name == p

tests/test_gui.py

@@ -1,12 +1,8 @@
-import sys
 import anesthetic.examples._matplotlib_agg  # noqa: F401
 from anesthetic import read_chains
 import pytest
 import pandas._testing as tm
-try:
-    import h5py  # noqa: F401
-except ImportError:
-    pass
+from utils import skipif_no_h5py
 
 
 @pytest.fixture(autouse=True)
@@ -16,10 +12,8 @@ def close_figures_on_teardown():
 
 @pytest.mark.parametrize('root', ["./tests/example_data/pc",
                                   "./tests/example_data/mn",
-                                  "./tests/example_data/un"])
+                                  skipif_no_h5py("./tests/example_data/un")])
 def test_gui(root):
-    if 'un' in root and 'h5py' not in sys.modules:
-        pytest.skip("`h5py` not in sys.modules, but needed for ultranest.")
     samples = read_chains(root)
     plotter = samples.gui()
 
@@ -65,10 +59,8 @@ def test_gui(root):
 
 @pytest.mark.parametrize('root', ["./tests/example_data/pc",
                                   "./tests/example_data/mn",
-                                  "./tests/example_data/un"])
+                                  skipif_no_h5py("./tests/example_data/un")])
 def test_gui_params(root):
-    if 'un' in root and 'h5py' not in sys.modules:
-        pytest.skip("`h5py` not in sys.modules, but needed for ultranest.")
     samples = read_chains(root)
     params = samples.columns.get_level_values(0).to_list()
     plotter = samples.gui()
@@ -80,10 +72,8 @@ def test_gui_params(root):
 
 @pytest.mark.parametrize('root', ["./tests/example_data/pc",
                                   "./tests/example_data/mn",
-                                  "./tests/example_data/un"])
+                                  skipif_no_h5py("./tests/example_data/un")])
 def test_slider_reset_range(root):
-    if 'un' in root and 'h5py' not in sys.modules:
-        pytest.skip("`h5py` not in sys.modules, but needed for ultranest.")
     plotter = read_chains(root).gui()
     plotter.evolution.reset_range(-3, 3)
     assert plotter.evolution.ax.get_xlim() == (-3.0, 3.0)