anesthetic
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Published
20 hours ago •
handley-lab
handley-lab
AttributeError in PolyChordLite example script
Having installed PolyChordLite (https://github.com/PolyChord/PolyChordLite), I ran the example script (https://github.com/PolyChord/PolyChordLite/blob/master/run_pypolychord.py).
PolyChord ran fine, but the Anesthetic plotter failed.
Error message:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[9], line 4
2 from anesthetic import NestedSamples
3 samples = NestedSamples(root= settings.base_dir + '/' + settings.file_root)
----> 4 fig, axes = samples.plot_2d(['p0','p1','p2','p3','r'])
5 fig.savefig('posterior.pdf')
7 except ImportError:
File ~/.conda/envs/polychordenv/lib/python3.9/site-packages/anesthetic/samples.py:351, in MCMCSamples.plot_2d(self, axes, *args, **kwargs)
348 local_kwargs[pos].update(kwargs)
350 if not isinstance(axes, pandas.DataFrame):
--> 351 fig, axes = make_2d_axes(axes, tex=self.tex,
352 upper=('upper' in types),
353 lower=('lower' in types),
354 diagonal=('diagonal' in types))
355 else:
356 fig = axes.values[~axes.isna()][0].figure
File ~/.conda/envs/polychordenv/lib/python3.9/site-packages/anesthetic/plot.py:200, in make_2d_axes(params, **kwargs)
198 axes[x][y].twin.set_ylim(0, 1.1)
199 axes[x][y].set_zorder(axes[x][y].twin.get_zorder() + 1)
--> 200 axes[x][y].lines = axes[x][y].twin.lines
201 axes[x][y].patches = axes[x][y].twin.patches
202 axes[x][y].collections = axes[x][y].twin.collections
AttributeError: can't set attribute
My environment details:
# packages in environment at /global/homes/u/ucapnje/.conda/envs/polychordenv:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
anesthetic 1.3.6 pypi_0 pypi
asttokens 2.0.5 pyhd3eb1b0_0
backcall 0.2.0 pyhd3eb1b0_0
blas 1.0 mkl
brotli 1.0.9 h5eee18b_7
brotli-bin 1.0.9 h5eee18b_7
ca-certificates 2023.01.10 h06a4308_0
certifi 2022.12.7 py39h06a4308_0
comm 0.1.2 py39h06a4308_0
contourpy 1.0.5 py39hdb19cb5_0
cycler 0.11.0 pyhd3eb1b0_0
dbus 1.13.18 hb2f20db_0
debugpy 1.5.1 py39h295c915_0
decorator 5.1.1 pyhd3eb1b0_0
entrypoints 0.4 py39h06a4308_0
executing 0.8.3 pyhd3eb1b0_0
expat 2.4.9 h6a678d5_0
fftw 3.3.9 h27cfd23_1
fontconfig 2.14.1 h52c9d5c_1
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.12.1 h4a9f257_0
getdist 1.4.2 pypi_0 pypi
giflib 5.2.1 h7b6447c_0
glib 2.69.1 he621ea3_2
gst-plugins-base 1.14.0 h8213a91_2
gstreamer 1.14.0 h28cd5cc_2
icu 58.2 he6710b0_3
intel-openmp 2021.4.0 h06a4308_3561
ipykernel 6.19.2 py39hb070fc8_0
ipython 8.10.0 py39h06a4308_0
jedi 0.18.1 py39h06a4308_1
jpeg 9e h7f8727e_0
jupyter_client 7.4.9 py39h06a4308_0
jupyter_core 5.2.0 py39h06a4308_0
kiwisolver 1.4.4 py39h6a678d5_0
krb5 1.19.4 h568e23c_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libbrotlicommon 1.0.9 h5eee18b_7
libbrotlidec 1.0.9 h5eee18b_7
libbrotlienc 1.0.9 h5eee18b_7
libclang 10.0.1 default_hb85057a_2
libdeflate 1.8 h7f8727e_5
libedit 3.1.20221030 h5eee18b_0
libevent 2.1.12 h8f2d780_0
libffi 3.4.2 h6a678d5_6
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 11.2.0 h00389a5_1
libgfortran5 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libllvm10 10.0.1 hbcb73fb_5
libpng 1.6.37 hbc83047_0
libpq 12.9 h16c4e8d_3
libsodium 1.0.18 h7b6447c_0
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.5.0 hecacb30_0
libuuid 1.41.5 h5eee18b_0
libwebp 1.2.4 h11a3e52_0
libwebp-base 1.2.4 h5eee18b_0
libxcb 1.15 h7f8727e_0
libxkbcommon 1.0.1 hfa300c1_0
libxml2 2.9.14 h74e7548_0
libxslt 1.1.35 h4e12654_0
lz4-c 1.9.4 h6a678d5_0
matplotlib 3.6.2 py39h06a4308_0
matplotlib-base 3.6.2 py39h945d387_0
matplotlib-inline 0.1.6 py39h06a4308_0
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py39h7f8727e_0
mkl_fft 1.3.1 py39hd3c417c_0
mkl_random 1.2.2 py39h51133e4_0
mpi4py 3.1.4 pypi_0 pypi
munkres 1.1.4 py_0
ncurses 6.3 h5eee18b_3
nest-asyncio 1.5.6 py39h06a4308_0
nspr 4.33 h295c915_0
nss 3.74 h0370c37_0
numpy 1.23.5 py39h14f4228_0
numpy-base 1.23.5 py39h31eccc5_0
openssl 1.1.1t h7f8727e_0
packaging 22.0 py39h06a4308_0
pandas 1.0.5 pypi_0 pypi
parso 0.8.3 pyhd3eb1b0_0
pcre 8.45 h295c915_0
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 9.3.0 py39hace64e9_1
pip 22.3.1 py39h06a4308_0
platformdirs 2.5.2 py39h06a4308_0
ply 3.11 py39h06a4308_0
prompt-toolkit 3.0.36 py39h06a4308_0
psutil 5.9.0 py39h5eee18b_0
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
pygments 2.11.2 pyhd3eb1b0_0
pyparsing 3.0.9 py39h06a4308_0
pypolychord 1.20.1 pypi_0 pypi
pyqt 5.15.7 py39h6a678d5_1
pyqt5-sip 12.11.0 py39h6a678d5_1
python 3.9.16 h7a1cb2a_0
python-dateutil 2.8.2 pyhd3eb1b0_0
pytz 2023.2 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
pyzmq 23.2.0 py39h6a678d5_0
qt-main 5.15.2 h327a75a_7
qt-webengine 5.15.9 hd2b0992_4
qtwebkit 5.212 h4eab89a_4
readline 8.2 h5eee18b_0
scipy 1.9.3 py39h14f4228_0
setuptools 65.6.3 py39h06a4308_0
sip 6.6.2 py39h6a678d5_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.40.1 h5082296_0
stack_data 0.2.0 pyhd3eb1b0_0
tk 8.6.12 h1ccaba5_0
toml 0.10.2 pyhd3eb1b0_0
tornado 6.2 py39h5eee18b_0
traitlets 5.7.1 py39h06a4308_0
tzdata 2022g h04d1e81_0
wcwidth 0.2.5 pyhd3eb1b0_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.10 h5eee18b_1
zeromq 4.3.4 h2531618_0
zlib 1.2.13 h5eee18b_0
zstd 1.5.2 ha4553b6_0
Hi @NiallJeffrey,
anesthetic version 1.3.6 is fairly old by now, so my initial guess would be that it might no longer be compatible with newer versions of pandas and/or matplotlib.
We are pushing for the anesthetic 2.0.0 release, which will hopefully happen soon. That will probably also prompt a new PolyChord release.
Until then, I'd probably recommend installing the latest anesthetic 2.0.0 beta version and using the anesthetic plotting script from PolyChord 1.20.2, which has already been updated. But maybe @williamjameshandley has a different recommendation?
