Note on typos and problems with the tutorials to be modified

[camurria]

This note is to keep track of the typos/errors/warnings in the tutorials.

Warnings (no action needed, they can be ignored, just taking notes in case students ask):

• Tutorial 1.2 (and all the others that import gwpy): running with a local installation of the updated igwn-py39 the user gets a warning coming from UserWarning: Wswiglal-redir-stdio when importing gwpy. To avoid the warning it can be disabled with

import warnings
warnings.filterwarnings("ignore", "Wswiglal-redir-stdio")

or

import lal
lal.swig_redirect_standard_output_error(True)

• Tutorials that import pycbc: using a local installation of the environment with pycbc 2.4.0, Windows user report the following warning:

libkmod: ERROR ../libkmod/libkmod-module.c:1668 kmod_module_new_from_loaded: could not open /proc/modules: No such file or directory
Error: could not get list of modules: No such file or directory

• Tutorial 3.1: running with a local installation of the updated igwn-py39 the user gets a warning coming from pandas

Typos:

• Tutorial 3.2: In the first line with pip install lalsuite= ->lalsuite==

Conflict with packages versions:

• The last version of igwn-py39 uses lalsuite=7.21 while at the top of the tutorials of Day_3 it is suggested to install lalsuite=7.22. I'd recommend to follow igwn-py39 current versions.
• the file environment.yml used for the light-weight conda installation (see step 3 of the Setup instructions) contains still the versions used in 2023 of all the packages and it needs to be aligned with the tutorials. As a note, we have tried to update environment.yml and create a new environment but if we use lalsuite=7.22 it would create a conflict and make the packages installation impossible.
• The extension_topic tutorials require packages not included in igwn-py39, probably we can leave the setup instructions as they are and just be aware that the students need to add some of the packages if they want to run the additional tutorials.
• Some mentors have got errors when running jupyter notebook after installing the environment igwn-py39. It seems related to the use of firefox as browser. A possible solution is to install jupytext and nbclassic and clear the cache

[duboism]

Note that PR #8 updates environment.yaml and requirements.txt to match the packages in the current igwn-py39 (which means switching back to lalsuite==7.21).

So it addresses some of the points raised here:

• the first typo
• the first 2 conflicts

I haven't looked much at Extension Topics.

[duboism]

While working on #10, I faced problems when running pesummary.io.read (see cell 5):

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[6], line 5
      3 if os.path.exists(pe_path): 
      4     print('Parameter estimation file found in: ' + pe_path + '\nOpening it.')
----> 5     pe_data = read(pe_path, package="gw")
      6 else: 
      7     print('Error: parameter estimation file not found in: ' + pe_path + 
      8           '\n You need to download the PE file manually from the GWOSC: ' + 
      9           'https://www.gwosc.org/eventapi/html/'+ catalog + '/' + evt)

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/io/read.py:111, in read(path, package, file_format, skymap, strain, cls, checkpoint, **kwargs)
    108 elif checkpoint:
    109     return OTHER["pickle"](path, **kwargs)
--> 111 module = importlib.import_module("pesummary.{}.file.read".format(package))
    112 return getattr(module, "read")(path, file_format=file_format, **kwargs)

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/importlib/__init__.py:127, in import_module(name, package)
    125             break
    126         level += 1
--> 127 return _bootstrap._gcd_import(name[level:], package, level)

File <frozen importlib._bootstrap>:1030, in _gcd_import(name, package, level)

File <frozen importlib._bootstrap>:1007, in _find_and_load(name, import_)

File <frozen importlib._bootstrap>:986, in _find_and_load_unlocked(name, import_)

File <frozen importlib._bootstrap>:680, in _load_unlocked(spec)

File <frozen importlib._bootstrap_external>:850, in exec_module(self, module)

File <frozen importlib._bootstrap>:228, in _call_with_frames_removed(f, *args, **kwds)

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/gw/file/read.py:3
      1 # Licensed under an MIT style license -- see LICENSE.md
----> 3 from pesummary.gw.file.formats.lalinference import LALInference
      4 from pesummary.gw.file.formats.bilby import Bilby
      5 from pesummary.gw.file.formats.default import Default

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/gw/file/formats/lalinference.py:8
      5 import h5py
      6 import numpy as np
----> 8 from pesummary.gw.file.formats.base_read import GWRead, GWSingleAnalysisRead
      9 from pesummary.utils.utils import logger
     10 from pesummary.utils.decorators import open_config

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/gw/file/formats/base_read.py:5
      3 import numpy as np
      4 from pesummary.gw.file.standard_names import standard_names
----> 5 from pesummary.core.file.formats.base_read import (
      6     Read, SingleAnalysisRead, MultiAnalysisRead
      7 )
      8 from pesummary.utils.utils import logger
      9 from pesummary.utils.samples_dict import SamplesDict

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/core/file/formats/base_read.py:7
      5 import h5py
      6 from pesummary.utils.parameters import MultiAnalysisParameters, Parameters
----> 7 from pesummary.utils.samples_dict import (
      8     MultiAnalysisSamplesDict, SamplesDict, MCMCSamplesDict, Array
      9 )
     10 from pesummary.utils.utils import logger
     12 __author__ = ["Charlie Hoy <charlie.hoy@ligo.org>"]

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/utils/samples_dict.py:20
     15 __author__ = ["Charlie Hoy <charlie.hoy@ligo.org>"]
     17 latex_labels.update(GWlatex_labels)
---> 20 class SamplesDict(Dict):
     21     """Class to store the samples from a single run
     22 
     23     Parameters
   (...)
    104     >>> fig.show()
    105     """
    106     def __init__(self, *args, logger_warn="warn", autoscale=True):

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/utils/samples_dict.py:425, in SamplesDict()
    414     for key, val in zip(self.parameters, _2d_array):
    415         self[key] = val
    417 @docstring_subfunction([
    418     'pesummary.core.plots.plot._1d_histogram_plot',
    419     'pesummary.gw.plots.plot._1d_histogram_plot',
    420     'pesummary.gw.plots.plot._ligo_skymap_plot',
    421     'pesummary.gw.plots.publication.spin_distribution_plots',
    422     'pesummary.core.plots.plot._make_corner_plot',
    423     'pesummary.gw.plots.plot._make_corner_plot'
    424 ])
--> 425 def plot(self, *args, type="marginalized_posterior", **kwargs):
    426     """Generate a plot for the posterior samples stored in SamplesDict
    427 
    428     Parameters
   (...)
    435         all additional kwargs are passed to the plotting function
    436     """
    437     return super(SamplesDict, self).plot(*args, type=type, **kwargs)

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/utils/decorators.py:245, in docstring_subfunction.<locals>.wrapper_function(func)
    243         module = ".".join(_subfunction[:-1])
    244         function = _subfunction[-1]
--> 245         module = importlib.import_module(module)
    246         original_docstring += "\n{}{}".format(
    247             subfunction + "\n" + "-" * len(subfunction) + "\n",
    248             getattr(module, function).__doc__
    249         )
    250 else:

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/importlib/__init__.py:127, in import_module(name, package)
    125             break
    126         level += 1
--> 127 return _bootstrap._gcd_import(name[level:], package, level)

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/gw/plots/publication.py:10
      8 from pesummary.gw.plots.bounds import default_bounds
      9 from pesummary.gw.plots.cmap import colormap_with_fixed_hue
---> 10 from pesummary.gw.conversions import mchirp_from_m1_m2, q_from_m1_m2
     11 import numpy as np
     12 import copy

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/gw/conversions/__init__.py:31
     29 from .remnant import *
     30 from .remnant import _final_from_initial_BBH
---> 31 from .snr import *
     32 from .snr import _ifo_snr
     33 from .spins import *

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/gw/conversions/snr.py:6
      4 from pesummary.utils.decorators import array_input
      5 from pesummary.utils.utils import logger
----> 6 from pesummary.gw.pycbc import optimal_snr, compute_the_overlap
      7 from pesummary.gw.conversions.angles import _dphi, _dpsi
      9 __author__ = [
     10     "Stephen Fairhurst <stephen.fairhurst@ligo.org>",
     11     "Rhys Green <rhys.green@ligo.org>",
     12     "Charlie Hoy <charlie.hoy@ligo.org>",
     13     "Cameron Mills <joseph.mills@ligo.org>"
     14 ]

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pesummary/gw/pycbc.py:10
      8 import numpy as np
      9 try:
---> 10     import pycbc.psd
     11     from pycbc.filter import sigma, overlap_cplx
     12     from pycbc import pnutils

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/site-packages/pycbc/__init__.py:149
    147     import multiprocessing
    148     if hasattr(multiprocessing, 'set_start_method'):
--> 149         multiprocessing.set_start_method('fork')
    150 else:
    151     HAVE_OMP = True

File ~/miniconda3/envs/igwn-py39-lw/lib/python3.9/multiprocessing/context.py:243, in DefaultContext.set_start_method(self, method, force)
    241 def set_start_method(self, method, force=False):
    242     if self._actual_context is not None and not force:
--> 243         raise RuntimeError('context has already been set')
    244     if method is None and force:
    245         self._actual_context = None

RuntimeError: context has already been set

It seems like a deep issue and I haven't been able to dig in it.

To workaround this, I had to import pycbc explicitly before pesummary. Did anybody get the same problem ?

I am using the igwn-py39 conda environment.

[camurria]

Hi @duboism , I confirm that I get the same error

[duboism]

@camurria, thanks for testing. I only tested Extension Topic A.1. Did you get the error on other notebooks ?