Changes for pandas 2.1 (#335)

* pandas have removed teardown method, use plt.close instead

* something funky going on with loc and masks, first pass

* version bump

* restrict pandas version to <2.2.0

* add extra space

* stick to ~=2.1 for now

* update workflows to use 3.9 as minimum requirement, and 3.11 for building docs etc

* autoupdate docs

* correct python version in minimum dependencies name

* cast filled in labels to same type as given labels

* test removing autoclass from PlotAccessor

* Revert "test removing autoclass from PlotAccessor"

This reverts commit 9468521.

* try removing examples from PlotAccessor docstring

* remove the accidentally added doc `show-inheritance` stuff for select modules

* revert the cutting out of the examples section from the PlotAccessor docs

* preload pandas for autodoc for examples in docstrings

* move PlotAccessor stuff from samples into weighted_pandas, where it should have arguably been in the first place

* also used anesthetic plotting for labelled_pandas

* change mask instead

* use .to_numpy() on other mask

* some ilocs in test_plot.py due to label deprecation

* return restriction to >=pandas2.0

* ['A'] instead of .iloc[0] so no line break needed

* erroneous version to re trigger

* Restored correct version number

* erroneous version to re trigger

* Restored correct version number

* remove anesthetic PlotAccessor from labelled_pandas, so now just a patch update

---------

Co-authored-by: lukashergt <[email protected]>
Co-authored-by: Will Handley <[email protected]>

.github/workflows/CI.yaml

@@ -40,7 +40,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
         with:
-          python-version: '3.8'
+          python-version: '3.11'
       - name: Upgrade pip and install doc requirements
         run: |
           python -m pip install --upgrade pip
@@ -56,7 +56,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
         extras: [true, false]
         include:
           - os: macos-latest
@@ -94,7 +94,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
         include:
           - os: macos-latest
             python-version: '3.11'
@@ -126,10 +126,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Install pypa/build
         run: python -m pip install build --user
       - name: Build a binary wheel and a source tarball
@@ -146,10 +146,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install dependencies
         run: |

.github/workflows/build.yaml

@@ -35,10 +35,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Install pypa/build
         run: python -m pip install build --user
       - name: Build a binary wheel and a source tarball
@@ -53,10 +53,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

README.rst

@@ -2,7 +2,7 @@
 anesthetic: nested sampling post-processing
 ===========================================
 :Authors: Will Handley and Lukas Hergt
-:Version: 2.3.4
+:Version: 2.3.5
 :Homepage: https://github.com/handley-lab/anesthetic
 :Documentation: http://anesthetic.readthedocs.io/
 

anesthetic/_version.py

@@ -1 +1 @@
-__version__ = '2.3.4'
+__version__ = '2.3.5'

anesthetic/labelled_pandas.py

@@ -117,7 +117,8 @@ def get_labels_map(self, axis=0, fill=True):
                 labels_map = index.to_frame().droplevel(labs)[labs]
                 if fill:
                     replacement = labels_map.loc[labels_map == ''].index
-                    labels_map.loc[labels_map == ''] = replacement
+                    labels_map.loc[labels_map == ''] = replacement.astype(
+                        labels_map.loc[labels_map != ''].dtype)
                 return labels_map
             else:
                 return index.to_series()

anesthetic/samples.py

@@ -16,14 +16,9 @@
 from anesthetic.gui.plot import RunPlotter
 from anesthetic.weighted_pandas import WeightedDataFrame, WeightedSeries
 from anesthetic.labelled_pandas import LabelledDataFrame, LabelledSeries
-from pandas.core.accessor import CachedAccessor
 from anesthetic.plot import (make_1d_axes, make_2d_axes,
                              AxesSeries, AxesDataFrame)
 from anesthetic.utils import adjust_docstrings
-import anesthetic.weighted_pandas
-from anesthetic.plotting import PlotAccessor
-anesthetic.weighted_pandas._WeightedObject.plot =\
-    CachedAccessor("plot", PlotAccessor)
 
 
 class WeightedLabelledDataFrame(WeightedDataFrame, LabelledDataFrame):
@@ -172,8 +167,6 @@ def __init__(self, *args, **kwargs):
     def _constructor(self):
         return Samples
 
-    plot = CachedAccessor("plot", PlotAccessor)
-
     def plot_1d(self, axes=None, *args, **kwargs):
         """Create an array of 1D plots.
 

anesthetic/weighted_pandas.py

@@ -13,6 +13,8 @@
 from anesthetic.utils import (compress_weights, neff, quantile,
                               temporary_seed, adjust_docstrings)
 from pandas.core.dtypes.missing import notna
+from pandas.core.accessor import CachedAccessor
+from anesthetic.plotting import PlotAccessor
 
 
 class WeightedGroupBy(GroupBy):
@@ -141,6 +143,9 @@ def __init__(self, *args, **kwargs):
         if weights is not None:
             self.set_weights(weights, inplace=True)
 
+    plot = CachedAccessor("plot", PlotAccessor)
+    """:meta private:"""
+
     def isweighted(self, axis=0):
         """Determine if weights are actually present."""
         return 'weights' in self._get_axis(axis).names
@@ -207,7 +212,7 @@ def set_weights(self, weights, axis=0, inplace=False, level=None):
     def _rand(self, axis=0):
         """Random number for consistent compression."""
         seed = hash_pandas_object(self._get_axis(axis)).sum() % 2**32
-        with temporary_seed(seed):
+        with temporary_seed(int(seed)):
             return np.random.rand(self.shape[axis])
 
     def reset_index(self, level=None, drop=False, inplace=False,

docs/source/conf.py

@@ -121,6 +121,7 @@ def get_version(short=False):
 plot_include_source = True
 plot_html_show_source_link = False
 plot_html_show_formats = False
+plot_pre_code = "import numpy as np; from matplotlib import pyplot as plt; import pandas as pd"
 
 
 # -- Options for HTML output -------------------------------------------------

pyproject.toml

@@ -33,7 +33,7 @@ requires-python = ">=3.8"
 dependencies = [
     "scipy",
     "numpy",
-    "pandas~=2.0.0",
+    "pandas>=2.0.0",
     "matplotlib>=3.6.1,<3.8.0",
 ]
 classifiers = [

tests/test_gui.py

@@ -1,13 +1,14 @@
+import matplotlib.pyplot as plt
 import anesthetic.examples._matplotlib_agg  # noqa: F401
 from anesthetic import read_chains
 import pytest
-import pandas._testing as tm
 from utils import skipif_no_h5py
 
 
 @pytest.fixture(autouse=True)
 def close_figures_on_teardown():
-    tm.close()
+    yield
+    plt.close("all")
 
 
 @pytest.mark.parametrize('root', ["./tests/example_data/pc",

tests/test_plot.py

@@ -9,7 +9,6 @@
                              scatter_plot_2d, quantile_plot_interval,
                              basic_cmap, AxesSeries, AxesDataFrame)
 from numpy.testing import assert_array_equal
-import pandas._testing as tm
 
 from matplotlib.axes import SubplotBase
 from matplotlib.contour import ContourSet
@@ -25,7 +24,8 @@
 
 @pytest.fixture(autouse=True)
 def close_figures_on_teardown():
-    tm.close()
+    yield
+    plt.close("all")
 
 
 def test_AxesObjects():
@@ -97,18 +97,18 @@ def test_make_1d_axes():
 
     # Check ncol argument
     fig, axes = make_1d_axes(paramnames, ncol=2)
-    nrows, ncol = axes[0].get_subplotspec().get_gridspec().get_geometry()
+    nrows, ncol = axes.iloc[0].get_subplotspec().get_gridspec().get_geometry()
     assert ncol == 2
 
     # Check gridspec argument
     grid = gs.GridSpec(2, 2, width_ratios=[3, 1], height_ratios=[3, 1])
     g00 = grid[0, 0]
     fig, axes = make_1d_axes(paramnames, subplot_spec=g00)
-    assert g00 is axes[0].get_subplotspec().get_topmost_subplotspec()
+    assert g00 is axes.iloc[0].get_subplotspec().get_topmost_subplotspec()
 
     # Check gridspec kwargs
     fig, axes = make_1d_axes(paramnames, gridspec_kw=dict(wspace=0.1))
-    ws = axes[0].get_subplotspec().get_gridspec().get_subplot_params().wspace
+    ws = axes['A'].get_subplotspec().get_gridspec().get_subplot_params().wspace
     assert ws == 0.1
 
     # Check figure kwargs
@@ -180,7 +180,7 @@ def test_make_2d_axes_inputs_outputs():
 
     # Check gridspec kwargs
     fig, axes = make_1d_axes(paramnames_x, gridspec_kw=dict(wspace=0.1))
-    ws = axes[0].get_subplotspec().get_gridspec().get_subplot_params().wspace
+    ws = axes['A'].get_subplotspec().get_gridspec().get_subplot_params().wspace
     assert ws == 0.1
 
     # Check figure kwargs

tests/test_reader.py

@@ -3,6 +3,7 @@
 import pytest
 import numpy as np
 from numpy.testing import assert_array_equal, assert_array_almost_equal
+import matplotlib.pyplot as plt
 from anesthetic.testing import assert_frame_equal
 from anesthetic import MCMCSamples, NestedSamples
 from anesthetic import read_chains
@@ -12,14 +13,14 @@
 from anesthetic.read.multinest import read_multinest
 from anesthetic.read.ultranest import read_ultranest
 from anesthetic.read.nestedfit import read_nestedfit
-import pandas._testing as tm
 from anesthetic.read.hdf import HDFStore, read_hdf
 from utils import pytables_mark_xfail, h5py_mark_xfail, getdist_mark_skip
 
 
 @pytest.fixture(autouse=True)
 def close_figures_on_teardown():
-    tm.close()
+    yield
+    plt.close("all")
 
 
 def test_read_getdist():

tests/test_samples.py

@@ -19,15 +19,15 @@
 from numpy.testing import (assert_array_equal, assert_array_almost_equal,
                            assert_array_less, assert_allclose)
 from pandas.testing import assert_frame_equal
-import pandas._testing as tm
 from matplotlib.colors import to_hex
 from scipy.stats import ks_2samp, kstest, norm
 from utils import skipif_no_fastkde, astropy_mark_xfail, fastkde_mark_skip
 
 
 @pytest.fixture(autouse=True)
 def close_figures_on_teardown():
-    tm.close()
+    yield
+    plt.close("all")
 
 
 def test_build_samples():
@@ -1478,7 +1478,7 @@ def test_groupby_stats():
     assert np.all(chains.corrwith(mcmc).get_weights() == [w1, w2])
 
     for chain in [1, 2]:
-        mask = mcmc.chain == chain
+        mask = (mcmc.chain == chain).to_numpy()
         assert_allclose(mcmc.loc[mask, params].mean(),
                         chains.mean().loc[chain])
         assert_allclose(mcmc.loc[mask, params].std(),
@@ -1520,7 +1520,7 @@ def test_groupby_stats():
     for col in params:
         if 'chain' not in col:
             for chain in [1, 2]:
-                mask = mcmc.chain == chain
+                mask = (mcmc.chain == chain).to_numpy()
                 assert_allclose(mcmc.loc[mask, col].mean(),
                                 chains[col].mean().loc[chain])
                 assert_allclose(mcmc.loc[mask, col].std(),

tests/test_scripts.py

@@ -1,12 +1,13 @@
+import matplotlib.pyplot as plt
 from anesthetic.scripts import gui
 from bin.utils import unit_incremented
 import pytest
-import pandas._testing as tm
 
 
 @pytest.fixture(autouse=True)
 def close_figures_on_teardown():
-    tm.close()
+    yield
+    plt.close("all")
 
 
 def test_gui():

tests/test_weighted_pandas.py

@@ -11,12 +11,12 @@
 from pandas.plotting._matplotlib.misc import (
     scatter_matrix as orig_scatter_matrix
 )
-import pandas._testing as tm
 
 
 @pytest.fixture(autouse=True)
 def close_figures_on_teardown():
-    tm.close()
+    yield
+    plt.close("all")
 
 
 @pytest.fixture