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icecube / flarestack

Unbinned likelihood analysis code for astroparticle physics datasets
https://flarestack.readthedocs.io/en/latest/?badge=latest
MIT License
8 stars 7 forks source link

Trouble Running Flarestack on Ubuntu 20.04 #38

Closed AdvaitDhingra closed 3 years ago

AdvaitDhingra commented 3 years ago

Describe the bug When I run 

python -m unittest discover tests/

In the flarestack folder in my terminal, it throws me me errors saying there is no module named numpy, even though I ran sudo pip3 install -U numpy

It also tells me that there is invalid syntax in some places. What can I do? To Reproduce Steps to reproduce the behavior:

  1. Run 'python -m unittest discover tests/'
  2. Use Ubuntu 20.04
  3. See error: 
    
advait@advait-dhingra:~/Documents/Coding/flarestack$ python -m unittest discover tests/
EEEEEEEEEEEEEEEEEEEEE
======================================================================
ERROR: test_likelihood_spatial (unittest.loader.ModuleImportFailure)
----------------------------------------------------------------------
ImportError: Failed to import test module: test_likelihood_spatial
Traceback (most recent call last):
File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests
module = self._get_module_from_name(name)
File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name
__import__(name)
File "/home/advait/Documents/Coding/flarestack/tests/test_likelihood_spatial.py", line 2, in <module>
from flarestack.data.public import icecube_ps_3_year
File "flarestack/__init__.py", line 1, in <module>
from flarestack.core.minimisation import MinimisationHandler
File "flarestack/core/minimisation.py", line 73
raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for "
                                                                                      ^
SyntaxError: invalid syntax

====================================================================== ERROR: test_util_custom_dataset (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_util_custom_dataset Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_util_custom_dataset.py", line 6, in from flarestack.data.public import icecube_ps_3_year File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_likelihood_standard_matrix (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_likelihood_standard_matrix Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_likelihood_standard_matrix.py", line 6, in from flarestack.data.public import icecube_ps_3_year File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_asimov_estimator (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_asimov_estimator Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_asimov_estimator.py", line 5, in import numpy as np ImportError: No module named numpy

====================================================================== ERROR: test_mh_fit_weights (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_mh_fit_weights Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_mh_fit_weights.py", line 6, in from flarestack.data.public import icecube_ps_3_year File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_simulate_catalogue (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_simulate_catalogue Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_simulate_catalogue.py", line 6, in from flarestack.utils import load_catalogue File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_util_astronomy (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_util_astronomy Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_util_astronomy.py", line 6, in from flarestack.analyses.tde.shared_TDE import tde_catalogue_name File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_mh_flare (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_mh_flare Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_mh_flare.py", line 6, in from flarestack import MinimisationHandler, analyse File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_cosmo_rates (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_cosmo_rates Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_cosmo_rates.py", line 3, in import numpy as np ImportError: No module named numpy

====================================================================== ERROR: test_full_analysis_chain (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_full_analysis_chain Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_full_analysis_chain.py", line 58 "name": f"{base_name}/{gamma}/", ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_submitter (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_submitter Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_submitter.py", line 5, in from flarestack.shared import flux_to_k File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_likelihood_standard (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_likelihood_standard Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_likelihood_standard.py", line 6, in import numpy as np ImportError: No module named numpy

====================================================================== ERROR: test_likelihood_standard_overlapping (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_likelihood_standard_overlapping Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_likelihood_standard_overlapping.py", line 6, in from flarestack.data.public import icecube_ps_3_year File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_mh_fixed_weights (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_mh_fixed_weights Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_mh_fixed_weights.py", line 6, in from flarestack.data.public import icecube_ps_3_year File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_time_pdfs (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_time_pdfs Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_time_pdfs.py", line 6, in from flarestack.data.public import icecube_ps_3_year File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_cosmo (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_cosmo Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_cosmo.py", line 6, in from flarestack.cosmo import get_diffuse_flux_at_1GeV, get_diffuse_flux_at_100TeV, \ File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_mh_large_catalogue (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_mh_large_catalogue Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_mh_large_catalogue.py", line 6, in from flarestack.data.public import icecube_ps_3_year File "flarestack/init.py", line 1, in from flarestack.core.minimisation import MinimisationHandler File "flarestack/core/minimisation.py", line 73 raise Exception(f"MinimisationHandler dictionary contained both 'fixed_scale' key for " ^ SyntaxError: invalid syntax

====================================================================== ERROR: test_energy_pdfs (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_energy_pdfs Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_energy_pdfs.py", line 7, in import numpy as np ImportError: No module named numpy

====================================================================== ERROR: test_negative_ns (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_negative_ns Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_negative_ns.py", line 6, in import numpy as np ImportError: No module named numpy

====================================================================== ERROR: test_simcube (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_simcube Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_simcube.py", line 5, in import numpy as np ImportError: No module named numpy

====================================================================== ERROR: test_likelihood_fixed_energy (unittest.loader.ModuleImportFailure)

ImportError: Failed to import test module: test_likelihood_fixed_energy Traceback (most recent call last): File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests module = self._get_module_from_name(name) File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name import(name) File "/home/advait/Documents/Coding/flarestack/tests/test_likelihood_fixed_energy.py", line 53 "name": f"tests/test_fixed_energy/{sindec:.2f}/", ^ SyntaxError: invalid syntax

Ran 21 tests in 0.001s

FAILED (errors=21)



**Expected behavior**
I would expect the tests to succeed
robertdstein commented 3 years ago

There is a problem in the python environment, unrelated to flarestack. Flarestack only works with python 3. Here python 2 is apparently being used, as can be seen from lines in the error e.g:

File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name

Possibly the wrong python installation is being used.

AdvaitDhingra commented 3 years ago

Ohh ok thanks