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ACCarnall / bagpipes

Bagpipes is a state of the art code for generating realistic model galaxy spectra and fitting these to spectroscopic and photometric observations. Users should install with pip, not by cloning the repository.
http://bagpipes.readthedocs.io
GNU General Public License v3.0
71 stars 37 forks source link

`pipes.fit.fit` breaks after numpy update #42

Closed Nikhil0504 closed 1 year ago

Nikhil0504 commented 1 year ago

I have been using bagpipes with an old version of numpy but after updating the version of numpy, bagpipes fitting breaks. I tested it out with the sample scripts and also with my own datasets and none of them work anymore.

Here is my conda environment version dump

# packages in environment at /opt/homebrew/Caskroom/miniforge/base/envs/astroJWST:
#
# Name                    Version                   Build  Channel
_ipython_minor_entry_point 8.7.0                hb6b4a82_0    conda-forge
alabaster                 0.7.12                   pypi_0    pypi
alexandria                2.27.0          py310h0c5bc17_1    astrorama
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h8e9501a_3    conda-forge
asdf                      2.14.4             pyhd8ed1ab_0    conda-forge
asdf-astropy              0.3.0              pyhd8ed1ab_0    conda-forge
asdf-coordinates-schemas  0.1.0              pyhd8ed1ab_0    conda-forge
asdf-standard             1.0.3              pyhd8ed1ab_0    conda-forge
asdf-transform-schemas    0.3.0              pyhd8ed1ab_0    conda-forge
asdf-unit-schemas         0.1.0              pyhd8ed1ab_0    conda-forge
asdf-wcs-schemas          0.1.1              pyhd8ed1ab_0    conda-forge
astroalign                2.4.1                    pypi_0    pypi
astropy                   5.2.1           py310hf1a086a_0    conda-forge
astropy-healpix           0.7             py310hf1a086a_2    conda-forge
astroquery                0.4.6              pyhd8ed1ab_0    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
babel                     2.10.3                   pypi_0    pypi
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
backports.zoneinfo        0.2.1           py310hbe9552e_7    conda-forge
bagpipes                  1.0.0                    pypi_0    pypi
beautifulsoup4            4.12.0             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc2                    2.0.0                    pypi_0    pypi
boost                     1.74.0          py310hd0bb7a8_5    conda-forge
boost-cpp                 1.74.0               h1cb353e_8    conda-forge
bottleneck                1.3.7           py310hf1a086a_0    conda-forge
brotli                    1.0.9                h1a8c8d9_8    conda-forge
brotli-bin                1.0.9                h1a8c8d9_8    conda-forge
brotlipy                  0.7.0           py310h8e9501a_1005    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.18.1               h3422bc3_0    conda-forge
ca-certificates           2022.12.7            h4653dfc_0    conda-forge
casa-formats-io           0.2.1                    pypi_0    pypi
ccfits                    2.6                  hd2274d6_0    astrorama
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h2399d43_3    conda-forge
cfitsio                   3.470                ha83d327_7    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
configobj                 5.0.8              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7           py310h2887b22_0    conda-forge
corner                    2.2.1                    pypi_0    pypi
coverage                  7.2.2           py310h8e9501a_0    conda-forge
cryptography              39.0.2          py310hfc83b78_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.33                  pypi_0    pypi
cytoolz                   0.12.0          py310h8e9501a_1    conda-forge
dask-core                 2023.3.1           pyhd8ed1ab_0    conda-forge
debugpy                   1.6.4           py310h0f1eb42_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
deepdish                  0.3.7                    pypi_0    pypi
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.6                    pypi_0    pypi
docutils                  0.19                     pypi_0    pypi
echo                      0.8.0                    pypi_0    pypi
elements                  6.0.1           py310h6f341cb_5    astrorama
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
et-xmlfile                1.1.0                    pypi_0    pypi
exceptiongroup            1.1.1              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
fast-histogram            0.11                     pypi_0    pypi
fftw                      3.3.10          nompi_h3046061_106    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
fonttools                 4.39.2          py310h8e9501a_0    conda-forge
freetype                  2.12.1               hd633e50_1    conda-forge
freetype-py               2.3.0                    pypi_0    pypi
fsspec                    2023.3.0           pyhd8ed1ab_1    conda-forge
glue-core                 1.6.0                    pypi_0    pypi
glue-vispy-viewers        1.0.5                    pypi_0    pypi
glueviz                   1.2.0                    pypi_0    pypi
gsl                       2.7                  h6e638da_0    conda-forge
gwcs                      0.18.3             pyhd8ed1ab_0    conda-forge
h5py                      3.7.0                    pypi_0    pypi
hsluv                     5.0.3                    pypi_0    pypi
html5lib                  1.1                pyh9f0ad1d_0    conda-forge
hypothesis                6.70.0             pyha770c72_0    conda-forge
icu                       70.1                 h6b3803e_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagecodecs-lite          2019.12.3       py310hf1a086a_6    conda-forge
imageio                   2.26.0             pyh24c5eb1_0    conda-forge
imagesize                 1.4.1                    pypi_0    pypi
importlib-metadata        6.1.0              pyha770c72_0    conda-forge
importlib-resources       5.12.0             pyhd8ed1ab_0    conda-forge
importlib_metadata        6.1.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.19.2             pyh736e0ef_0    conda-forge
ipympl                    0.9.3              pyhd8ed1ab_0    conda-forge
ipython                   8.7.0              pyhd1c38e8_0    conda-forge
ipython-genutils          0.2.0                    pypi_0    pypi
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.4              pyhd8ed1ab_0    conda-forge
jaraco.classes            3.2.3              pyhd8ed1ab_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jmespath                  1.0.1              pyhd8ed1ab_0    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0           py310hbe9552e_8    conda-forge
jupyter_client            7.4.8              pyhd8ed1ab_0    conda-forge
jupyter_console           6.6.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.1.0           py310hbe9552e_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.5.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab                3.5.1              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.20.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.5              pyhd8ed1ab_0    conda-forge
keyring                   23.13.1         py310hbe9552e_0    conda-forge
kiwisolver                1.4.4           py310h2887b22_1    conda-forge
krb5                      1.20.1               h69eda48_0    conda-forge
lcms2                     2.15                 hd835a16_1    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
levmar                    2.6                  h58d6552_8    astrorama
libblas                   3.9.0           16_osxarm64_openblas    conda-forge
libbrotlicommon           1.0.9                h1a8c8d9_8    conda-forge
libbrotlidec              1.0.9                h1a8c8d9_8    conda-forge
libbrotlienc              1.0.9                h1a8c8d9_8    conda-forge
libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
libcurl                   7.88.1               h9049daf_1    conda-forge
libcxx                    14.0.6               h2692d47_0    conda-forge
libdeflate                1.17                 h1a8c8d9_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           12_2_0_hd922786_31    conda-forge
libgfortran5              12.2.0              h0eea778_31    conda-forge
libjpeg-turbo             2.1.5.1              h1a8c8d9_0    conda-forge
liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
libnghttp2                1.52.0               hae82a92_0    conda-forge
libopenblas               0.3.21          openmp_hc731615_3    conda-forge
libpng                    1.6.39               h76d750c_0    conda-forge
libprotobuf               3.21.12              hb5ab8b9_0    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.40.0               h76d750c_0    conda-forge
libssh2                   1.10.0               h7a5bd25_3    conda-forge
libtiff                   4.5.0                hdc14d85_5    conda-forge
libwebp-base              1.3.0                h1a8c8d9_0    conda-forge
libxcb                    1.13              h9b22ae9_1004    conda-forge
libzlib                   1.2.13               h03a7124_4    conda-forge
llvm-openmp               16.0.0               h7cfbb63_0    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
log4cpp                   1.1.3             hbdafb3b_1003    conda-forge
lxml                      4.9.1                    pypi_0    pypi
markdown-it-py            2.2.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.2           py310h8e9501a_0    conda-forge
matplotlib                3.6.2           py310hb6292c7_0    conda-forge
matplotlib-base           3.6.2           py310h78c5c2f_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
more-itertools            9.1.0              pyhd8ed1ab_0    conda-forge
mpi4py                    3.1.4                    pypi_0    pypi
mpl-scatter-density       0.7                      pypi_0    pypi
msgpack                   1.0.4                    pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclassic                 0.5.3              pyhb4ecaf3_3    conda-forge
nbclient                  0.7.2              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.9              pyhd8ed1ab_0    conda-forge
nbformat                  5.8.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h07bb92c_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
notebook                  6.5.3              pyha770c72_0    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
numexpr                   2.8.4                    pypi_0    pypi
numpy                     1.24.2          py310h3d2048e_0    conda-forge
numpydoc                  1.5.0                    pypi_0    pypi
onnxruntime-cpp           1.12.1               hc2310fa_1    conda-forge
openjpeg                  2.5.0                hbc2ba62_2    conda-forge
openpyxl                  3.0.10                   pypi_0    pypi
openssl                   3.1.0                h03a7124_0    conda-forge
packaging                 22.0               pyhd8ed1ab_0    conda-forge
pandas                    1.1.5                    pypi_0    pypi
pandoc                    2.19.2               hce30654_2    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
partd                     1.3.0              pyhd8ed1ab_0    conda-forge
pcigale                   2022.1                    dev_0    <develop>
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pgplot                    5.2.2             h507632e_1008    conda-forge
photutils                 1.6.0           py310hf1a086a_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0           py310h07496d3_2    conda-forge
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.1.1              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
pooch                     1.7.0              pyhd8ed1ab_0    conda-forge
poppy                     1.0.3                    pypi_0    pypi
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.36             pyha770c72_0    conda-forge
prompt_toolkit            3.0.36               hd8ed1ab_0    conda-forge
protobuf                  4.21.12         py310h0f1eb42_0    conda-forge
psutil                    5.9.4           py310h8e9501a_0    conda-forge
pthread-stubs             0.4               h27ca646_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pvextractor               0.3                      pypi_0    pypi
py-cpuinfo                9.0.0                    pypi_0    pypi
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyerfa                    2.0.0.2         py310hf1a086a_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyopengl                  3.1.6                    pypi_0    pypi
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3          py310h8e9501a_0    conda-forge
pysiaf                    0.18.0                   pypi_0    pypi
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytest                    7.2.2              pyhd8ed1ab_0    conda-forge
pytest-arraydiff          0.3                        py_0    conda-forge
pytest-astropy            0.10.0             pyhd8ed1ab_0    conda-forge
pytest-astropy-header     0.1.2                      py_0    conda-forge
pytest-cov                4.0.0              pyhd8ed1ab_0    conda-forge
pytest-doctestplus        0.12.1             pyhd8ed1ab_0    conda-forge
pytest-filter-subpackage  0.1.1                      py_0    conda-forge
pytest-mock               3.10.0             pyhd8ed1ab_0    conda-forge
pytest-openfiles          0.5.0                      py_0    conda-forge
pytest-remotedata         0.4.0              pyhd8ed1ab_0    conda-forge
python                    3.10.8          h3ba56d0_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    2_cp310    glueviz
pytz                      2022.5                   pypi_0    pypi
pyvo                      1.4.1              pyhd8ed1ab_0    conda-forge
pywavelets                1.4.1           py310hf1a086a_0    conda-forge
pyyaml                    6.0             py310h8e9501a_5    conda-forge
pyzmq                     24.0.1          py310hc407298_1    conda-forge
qtconsole                 5.4.0                    pypi_0    pypi
qtpy                      2.3.0                    pypi_0    pypi
radio-beam                0.3.4                    pypi_0    pypi
re2                       2023.03.02           hc5e2d97_0    conda-forge
readline                  8.1.2                h46ed386_0    conda-forge
reproject                 0.9             py310hf1a086a_0    astropy
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rich                      13.3.2             pyhd8ed1ab_0    conda-forge
scikit-image              0.19.3          py310h2b830bf_2    conda-forge
scikit-learn              1.2.2           py310ha00a7cd_0    conda-forge
scipy                     1.10.1          py310ha0d8a01_0    conda-forge
semantic_version          2.10.0             pyhd8ed1ab_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
sep                       1.2.1                    pypi_0    pypi
setuptools                65.5.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0                    pypi_0    pypi
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sourcextractor            0.19            py310hf695b33_2    astrorama
spectral-cube             0.6.0                    pypi_0    pypi
sphinx                    5.3.0                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.2                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.2                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.0.0                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      1.0.3                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.5                    pypi_0    pypi
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
synphot                   1.1.1                    pypi_0    pypi
tables                    3.8.0                    pypi_0    pypi
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tifffile                  2020.6.3                   py_0    conda-forge
tinycss2                  1.1.1                    pypi_0    pypi
tk                        8.6.12               he1e0b03_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2             py310h8e9501a_1    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
traitlets                 5.7.1              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
unicodedata2              15.0.0          py310h8e9501a_0    conda-forge
urllib3                   1.26.12                  pypi_0    pypi
vispy                     0.12.2.dev12             pypi_0    pypi
wcslib                    7.3                  h2b4298d_1    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webbpsf                   1.1.0                    pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.5              pyhd8ed1ab_0    conda-forge
xlrd                      2.0.1                    pypi_0    pypi
xorg-kbproto              1.0.7             h27ca646_1002    conda-forge
xorg-libx11               1.8.4                h1a8c8d9_0    conda-forge
xorg-libxau               1.0.9                h27ca646_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xorg-xextproto            7.3.0             h1a8c8d9_1003    conda-forge
xorg-xproto               7.0.31            h27ca646_1007    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
zeromq                    4.3.4                hbdafb3b_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h03a7124_4    conda-forge
zstd                      1.5.2                hf913c23_6    conda-forge

I am attaching the output that came out while running the example 3 notebook.

fit = pipes.fit(galaxy, fit_instructions)

fit.fit(verbose=False, use_MPI=True)

OUTPUT:


Bagpipes: fitting object 17433

 MultiNest Warning: no resume file found, starting from scratch
 *****************************************************
 MultiNest v3.10
 Copyright Farhan Feroz & Mike Hobson
 Release Jul 2015

 no. of live points =  400
 dimensionality =    6
 *****************************************************

 MultiNest Warning!
 Parameter            5  of mode            1  is converging towards the edge of the prior.

 MultiNest Warning!
 Parameter            5  of mode            1  is converging towards the edge of the prior.

 MultiNest Warning!
 Parameter            5  of mode            1  is converging towards the edge of the prior.

 MultiNest Warning!
 Parameter            5  of mode            1  is converging towards the edge of the prior.

 MultiNest Warning!
 Parameter            5  of mode            1  is converging towards the edge of the prior.

 MultiNest Warning!
 Parameter            5  of mode            1  is converging towards the edge of the prior.

 MultiNest Warning!
 Parameter            5  of mode            1  is converging towards the edge of the prior.

 MultiNest Warning!
 Parameter            5  of mode            1  is converging towards the edge of the prior.

 MultiNest Warning!
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Completed in 536.0 seconds.
 ln(ev)=  -48.958506784983591      +/-  0.30330781080861774     
 Total Likelihood Evaluations:       234416
 Sampling finished. Exiting MultiNest

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[6], line 3
      1 fit = pipes.fit(galaxy, fit_instructions)
----> 3 fit.fit(verbose=False, use_MPI=True)

File [/opt/homebrew/Caskroom/miniforge/base/envs/astroJWST/lib/python3.10/site-packages/bagpipes/fitting/fit.py:150](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/astroJWST/lib/python3.10/site-packages/bagpipes/fitting/fit.py:150), in fit.fit(self, verbose, n_live, use_MPI)
    148 with warnings.catch_warnings():
    149     warnings.simplefilter("ignore")
--> 150     dd.io.save(self.fname[:-1] + ".h5", self.results)
    152 os.system("rm " + self.fname + "*")
    154 self._print_results()

File [/opt/homebrew/Caskroom/miniforge/base/envs/astroJWST/lib/python3.10/site-packages/deepdish/io/hdf5io.py:584](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/astroJWST/lib/python3.10/site-packages/deepdish/io/hdf5io.py:584), in save(path, data, compression)
    582     idtable[id(data)] = '[/](https://file+.vscode-resource.vscode-cdn.net/)'
    583     for key, value in data.items():
--> 584         _save_level(h5file, group, value, name=key,
    585                     filters=filters, idtable=idtable)
    587 elif (_sns and isinstance(data, SimpleNamespace) and
    588       _dict_native_ok(data.__dict__)):
    589     idtable[id(data)] = '[/](https://file+.vscode-resource.vscode-cdn.net/)'

File [/opt/homebrew/Caskroom/miniforge/base/envs/astroJWST/lib/python3.10/site-packages/deepdish/io/hdf5io.py:250](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/astroJWST/lib/python3.10/site-packages/deepdish/io/hdf5io.py:250), in _save_level(handler, group, level, name, filters, idtable)
    246         _save_level(handler, new_group, entry, name=level_name,
    247                     filters=filters, idtable=idtable)
...

AttributeError: module 'numpy' has no attribute 'object'.
`np.object` was a deprecated alias for the builtin `object`. To avoid this error in existing code, use `object` by itself. Doing this will not modify any behavior and is safe. 
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
ACCarnall commented 1 year ago

Please see #32 , I'll try to get round to updating the code to use h5py instead of deepdish at some point.

ACCarnall commented 1 year ago

Just to note that I've now replaced deepdish with h5py from bagpipes v1.0.2, so hopefully the code should now again be compatible with the most recent versions of numpy.