Cannot initiate fit -- name 'pmn' is not defined

[keheintz]

Hello,

I have just tried installing and running Bagpipes, but I get the following error, which seems to suggest that PyMultiNest is not loaded correctly: Bagpipes: fitting object

---

NameError Traceback (most recent call last) /var/folders/91/z2qvcffn6b5ccndf82s32_fh0000gn/T/ipykernel_56739/1459370564.py in ----> 1 fit = load_results(run_id)

/var/folders/91/z2qvcffn6b5ccndf82s32_fh0000gn/T/ipykernel_56739/2772977949.py in load_results(run_id) 6 #set_model_type(run_id) 7 fit = pipes.fit(observed_galaxy, fit_instructions, run=run_id) ----> 8 fit.fit() 9 fit.posterior.get_advanced_quantities() # posterior.model_galaxy 10 return fit

/opt/anaconda3/lib/python3.9/site-packages/bagpipes/fitting/fit.py in fit(self, verbose, n_live, use_MPI) 120 start_time = time.time() 121 --> 122 with warnings.catch_warnings(): 123 warnings.simplefilter("ignore") 124 pmn.run(self.fitted_model.lnlike,

NameError: name 'pmn' is not defined

However, this bit in the .fit file seems to be compiled ok without complaining though, so I'm not sure what the issue could be: try: import pymultinest as pmn

except (ImportError, RuntimeError, SystemExit) as e: print("Bagpipes: PyMultiNest import failed, fitting will be unavailable.")

Any ideas for a fix?

Thanks! Kasper

[ACCarnall]

Hi Kasper, did you try installing MultiNest yourself? It doesn't get installed by default with the code. Usually the easiest way to get it is via conda.

[keheintz]

Hi Adam, yes I should have installed it following bagpipes installation docs -- or do you have to install pymultinest separately / after installing MultiNest?

[keheintz]

Update: It looks like it can read the pymultinest import now after installing it with conda.

However, now I get the following error from reading in Bagpipes:

ModuleNotFoundError Traceback (most recent call last) Input In [1], in <cell line: 4>() 2 import pandas as pd 3 import numpy as np ----> 4 import bagpipes as pipes

File /opt/anaconda3/lib/python3.9/site-packages/bagpipes/init.py:3, in 1 from future import print_function, division, absolute_import ----> 3 from . import models 4 from . import fitting 5 from . import filters

File /opt/anaconda3/lib/python3.9/site-packages/bagpipes/models/init.py:3, in 1 from future import print_function, division, absolute_import ----> 3 from . import making 5 from .stellar_model import stellar 6 from .dust_emission_model import dust_emission

File /opt/anaconda3/lib/python3.9/site-packages/bagpipes/models/making/init.py:4, in 1 from future import print_function, division, absolute_import 3 from . import igm_inoue2014 ----> 4 from . import make_cloudy_models

File /opt/anaconda3/lib/python3.9/site-packages/bagpipes/models/making/make_cloudy_models.py:9, in 5 import sys 7 from astropy.io import fits ----> 9 from ... import utils 10 from ... import config 12 from ..model_galaxy import model_galaxy

File /opt/anaconda3/lib/python3.9/site-packages/bagpipes/utils.py:5, in 3 import os 4 import numpy as np ----> 5 from astropy.cosmology import FlatLambdaCDM 8 def make_dirs(run="."): 9 """ Make local Bagpipes directory structure in working dir. """

File /opt/anaconda3/lib/python3.9/site-packages/astropy/cosmology/init.py:13, in 2 """ astropy.cosmology contains classes and functions for cosmological 3 distance measures and other cosmology-related calculations. 4 (...) 8 9 """ 11 from . import core, flrw, funcs, parameter, units, utils # noqa F401 ---> 13 from . import io # needed before 'realizations' # noqa: F401 # isort: split 14 from . import realizations 15 from .core import * # noqa F401, F403

File /opt/anaconda3/lib/python3.9/site-packages/astropy/cosmology/io/init.py:9, in 4 """ 5 Read/Write/Interchange methods for astropy.cosmology. NOT public API. 6 """ 8 # Import to register with the I/O machinery ----> 9 from . import cosmology, ecsv, mapping, model, row, table, yaml

File /opt/anaconda3/lib/python3.9/site-packages/astropy/cosmology/io/cosmology.py:84, in 78 return itis 81 # =================================================================== 82 # Register ---> 84 convert_registry.register_reader("astropy.cosmology", Cosmology, from_cosmology) 85 convert_registry.register_writer("astropy.cosmology", Cosmology, to_cosmology) 86 convert_registry.register_identifier("astropy.cosmology", Cosmology, cosmology_identify)

File /opt/anaconda3/lib/python3.9/site-packages/astropy/io/registry/core.py:108, in UnifiedInputRegistry.register_reader(self, data_format, data_class, function, force, priority) 103 raise IORegistryError("Reader for format '{}' and class '{}' is " 104 'already defined' 105 ''.format(data_format, data_class.name)) 107 if data_class not in self._delayed_docs_classes: --> 108 self._updatedoc(data_class, 'read')

File /opt/anaconda3/lib/python3.9/site-packages/astropy/io/registry/base.py:418, in _UnifiedIORegistryBase._updatedoc(self, data_class, readwrite) 414 left_indent = ' ' * min(match.start() for match in matches if match) 416 # Get the available unified I/O formats for this class 417 # Include only formats that have a reader, and drop the 'Data class' column --> 418 format_table = self.get_formats(data_class, readwrite.capitalize()) 419 format_table.remove_column('Data class') 421 # Get the available formats as a table, then munge the output of pformat() 422 # a bit and put it into the docstring.

File /opt/anaconda3/lib/python3.9/site-packages/astropy/io/registry/core.py:404, in UnifiedIORegistry.get_formats(self, data_class, readwrite) 384 def get_formats(self, data_class=None, readwrite=None): 385 """ 386 Get the list of registered I/O formats as a ~astropy.table.Table. 387 (...) 402 Table of available I/O formats. 403 """ --> 404 return super().get_formats(data_class, readwrite)

File /opt/anaconda3/lib/python3.9/site-packages/astropy/io/registry/base.py:86, in _UnifiedIORegistryBase.get_formats(self, data_class, filter_on) 64 def get_formats(self, data_class=None, filter_on=None): 65 """ 66 Get the list of registered formats as a ~astropy.table.Table. 67 (...) 84 If filter_on is not None nor a registry name. 85 """ ---> 86 from astropy.table import Table 88 # set up the column names 89 colnames = ( 90 "Data class", "Format", 91 *[self._registries[k]["column"] for k in self._registries_order], 92 "Deprecated")

File /opt/anaconda3/lib/python3.9/site-packages/astropy/table/init.py:75, in 72 import astropy.io.misc.pandas.connect # noqa: F401 74 if optional_deps.HAS_ASDF_ASTROPY: ---> 75 import asdf_astropy.io.connect 76 else: 77 import astropy.io.misc.asdf.connect

ModuleNotFoundError: No module named 'asdf_astropy.io'

[ACCarnall]

Hmm, haven't seen that one before, what version of astropy are you running?

[keheintz]

I live to idiot-proof software! I have astropy.version = '5.1'

[ACCarnall]

Ok that's the same version as me. I'm pretty sure this is an astropy issue though, can you successfully run "from astropy.cosmology import FlatLambdaCDM" in a python terminal?

One potential shortcut to fixing this might be to make a new anaconda environment for bagpipes, whilst installing all the dependencies from scratch. I have a yml file that should do this for you, which I'll email. Try the instructions at https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file

[keheintz]

No, it actually outputs an error now (which it didn't before) so there indeed may be some issue cosmology astropy package.

But thanks for the .yml file! Will try installing in a new environment with that.