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lpsinger / ligo.skymap

Localization of gravitational-wave transients. Mirror of https://git.ligo.org/lscsoft/ligo.skymap
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Add astroquery (back) in the requirements #4

Closed Janna112358 closed 4 years ago

Janna112358 commented 4 years ago

Add "astroquery>=0.3.10" to the requirements in setup.cfg. Without it, running "ligo-skymap-plot --help" results in the following error after installing from source:

pkg_resources.DistributionNotFound: The 'beautifulsoup4>=4.3.2' distribution was not found and is required by astroquery

Adding the requirement and re-installing fixes this issue.

lpsinger commented 4 years ago

Would you please give me instructions for reproducing this issue? I cannot reproduce it in a clean (Docker) environment using the latest version of ligo.skymap (0.3.1):

$ docker run --rm -it python bash
root@a1255912bd82:/# pip install ligo.skymap
Collecting ligo.skymap
  Downloading ligo.skymap-0.3.1-cp38-cp38-manylinux2014_x86_64.whl (22.2 MB)
     |████████████████████████████████| 22.2 MB 256 kB/s 
Collecting ptemcee
  Downloading ptemcee-1.0.0.tar.gz (17 kB)
Collecting h5py
  Downloading h5py-2.10.0-cp38-cp38-manylinux1_x86_64.whl (2.9 MB)
     |████████████████████████████████| 2.9 MB 1.6 MB/s 
Collecting healpy
  Downloading healpy-1.13.0-cp38-cp38-manylinux1_x86_64.whl (11.9 MB)
     |████████████████████████████████| 11.9 MB 1.4 MB/s 
Collecting tqdm>=4.27.0
  Downloading tqdm-4.46.1-py2.py3-none-any.whl (63 kB)
     |████████████████████████████████| 63 kB 1.7 MB/s 
Collecting astroplan>=0.5
  Downloading astroplan-0.6.tar.gz (271 kB)
     |████████████████████████████████| 271 kB 2.9 MB/s 
Collecting networkx
  Downloading networkx-2.4-py3-none-any.whl (1.6 MB)
     |████████████████████████████████| 1.6 MB 927 kB/s 
Collecting pillow>=2.5.0
  Downloading Pillow-7.1.2-cp38-cp38-manylinux1_x86_64.whl (2.1 MB)
     |████████████████████████████████| 2.1 MB 1.0 MB/s 
Collecting scipy>=0.14
  Downloading scipy-1.4.1-cp38-cp38-manylinux1_x86_64.whl (26.0 MB)
     |████████████████████████████████| 26.0 MB 1.8 MB/s 
Collecting pytz
  Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB)
     |████████████████████████████████| 510 kB 2.3 MB/s 
Collecting astropy-healpix>=0.3
  Downloading astropy_healpix-0.5-cp38-cp38-manylinux2010_x86_64.whl (204 kB)
     |████████████████████████████████| 204 kB 2.0 MB/s 
Collecting lalsuite>=6.53
  Downloading lalsuite-6.70-cp38-cp38-manylinux2014_x86_64.whl (29.0 MB)
     |████████████████████████████████| 29.0 MB 1.1 MB/s 
Collecting ligo-segments>=1.2.0
  Downloading ligo-segments-1.2.0.tar.gz (48 kB)
     |████████████████████████████████| 48 kB 3.5 MB/s 
Collecting reproject>=0.3.2
  Downloading reproject-0.7.1-cp38-cp38-manylinux2010_x86_64.whl (1.3 MB)
     |████████████████████████████████| 1.3 MB 1.8 MB/s 
Collecting astropy!=4.0.1,>=3.1
  Downloading astropy-4.0.1.post1-cp38-cp38-manylinux1_x86_64.whl (6.5 MB)
     |████████████████████████████████| 6.5 MB 847 kB/s 
Collecting numpy!=1.15.3,>=1.14
  Downloading numpy-1.18.5-cp38-cp38-manylinux1_x86_64.whl (20.6 MB)
     |████████████████████████████████| 20.6 MB 1.7 MB/s 
Collecting matplotlib>=3.0.2
  Downloading matplotlib-3.2.1-cp38-cp38-manylinux1_x86_64.whl (12.4 MB)
     |████████████████████████████████| 12.4 MB 2.5 MB/s 
Collecting python-ligo-lw
  Downloading python-ligo-lw-1.6.0.tar.gz (2.3 MB)
     |████████████████████████████████| 2.3 MB 748 kB/s 
Collecting lscsoft-glue>=2.0.0
  Downloading lscsoft-glue-2.0.0.tar.gz (1.6 MB)
     |████████████████████████████████| 1.6 MB 746 kB/s 
Collecting ligo-gracedb>=2.0.1
  Downloading ligo-gracedb-2.6.1.tar.gz (2.5 MB)
     |████████████████████████████████| 2.5 MB 970 kB/s 
Collecting six
  Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting decorator>=4.3.0
  Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting python-dateutil
  Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
     |████████████████████████████████| 227 kB 1.2 MB/s 
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.2.0-cp38-cp38-manylinux1_x86_64.whl (92 kB)
     |████████████████████████████████| 92 kB 65 kB/s 
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
     |████████████████████████████████| 67 kB 551 kB/s 
Collecting cycler>=0.10
  Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting pyyaml
  Downloading PyYAML-5.3.1.tar.gz (269 kB)
     |████████████████████████████████| 269 kB 479 kB/s 
Collecting pyOpenSSL
  Downloading pyOpenSSL-19.1.0-py2.py3-none-any.whl (53 kB)
     |████████████████████████████████| 53 kB 665 kB/s 
Collecting future>=0.15.0
  Downloading future-0.18.2.tar.gz (829 kB)
     |████████████████████████████████| 829 kB 591 kB/s 
Collecting cryptography>=1.7.2
  Downloading cryptography-2.9.2-cp35-abi3-manylinux2010_x86_64.whl (2.7 MB)
     |████████████████████████████████| 2.7 MB 937 kB/s 
Collecting cffi!=1.11.3,>=1.8
  Downloading cffi-1.14.0-cp38-cp38-manylinux1_x86_64.whl (409 kB)
     |████████████████████████████████| 409 kB 1.1 MB/s 
Collecting pycparser
  Downloading pycparser-2.20-py2.py3-none-any.whl (112 kB)
     |████████████████████████████████| 112 kB 1.1 MB/s 
Building wheels for collected packages: ptemcee, astroplan, ligo-segments, python-ligo-lw, lscsoft-glue, ligo-gracedb, pyyaml, future
  Building wheel for ptemcee (setup.py) ... done
  Created wheel for ptemcee: filename=ptemcee-1.0.0-py3-none-any.whl size=18550 sha256=1592fa6c4b2f543b79dd689d362c53812c1a21cf6129c6750d9e5498aa0a825f
  Stored in directory: /root/.cache/pip/wheels/37/c2/f9/a1874c709263ee601725a588da201a8818b83c3ab9cd49c7a0
  Building wheel for astroplan (setup.py) ... done
  Created wheel for astroplan: filename=astroplan-0.6-py3-none-any.whl size=100602 sha256=10528ea8f48cc2ecfaf720d752793a1453f073d08e4c03b61d30046661eff06c
  Stored in directory: /root/.cache/pip/wheels/e0/b4/06/ab844a77022d682457858943d44400e0089123be493eb98eeb
  Building wheel for ligo-segments (setup.py) ... done
  Created wheel for ligo-segments: filename=ligo_segments-1.2.0-cp38-cp38-linux_x86_64.whl size=113211 sha256=7d3615370fc460b5291061423ecb4ff062f1bb8a8b7285d49568b4175605bdea
  Stored in directory: /root/.cache/pip/wheels/84/51/4f/cbf827107836e22eee7c47f44b6ebdb9f6de78b74ccae8c323
  Building wheel for python-ligo-lw (setup.py) ... done
  Created wheel for python-ligo-lw: filename=python_ligo_lw-1.6.0-cp38-cp38-linux_x86_64.whl size=181113 sha256=761bfdb080d9a9a07438f95b6a36699096ee3b57c7595d97afc7c2bd32f7cc17
  Stored in directory: /root/.cache/pip/wheels/0c/c9/68/203a29fef3bdbec4e59dc465735d8ee6fe6a9bb9c7587dcc24
  Building wheel for lscsoft-glue (setup.py) ... done
  Created wheel for lscsoft-glue: filename=lscsoft_glue-2.0.0-cp38-cp38-linux_x86_64.whl size=420072 sha256=cb46308bcbda2476c4aae0a60be104e39236115a3be6fe78d267a2312115fa50
  Stored in directory: /root/.cache/pip/wheels/aa/c1/73/1abbf872b83e4a8680e835b467d14a2cb48d2218bcaa58f7b5
  Building wheel for ligo-gracedb (setup.py) ... done
  Created wheel for ligo-gracedb: filename=ligo_gracedb-2.6.1-py2.py3-none-any.whl size=2282869 sha256=651347cb857391067210f5858a62d43699314e5929539d8468b13794eae9eee8
  Stored in directory: /root/.cache/pip/wheels/a5/5f/99/cdb8758de5fcb968dfaaa9b74f8e33411facab0e76c250af69
  Building wheel for pyyaml (setup.py) ... done
  Created wheel for pyyaml: filename=PyYAML-5.3.1-cp38-cp38-linux_x86_64.whl size=572472 sha256=3dd4bcbb434f538d4358fe6e60916e7058eb649b24ccae1e179ed16ba6b903ba
  Stored in directory: /root/.cache/pip/wheels/13/90/db/290ab3a34f2ef0b5a0f89235dc2d40fea83e77de84ed2dc05c
  Building wheel for future (setup.py) ... done
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491058 sha256=6856cd874c982cc296497aa9d4cb6baf07f73418ba1f0be98885c545c293b4c3
  Stored in directory: /root/.cache/pip/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4
Successfully built ptemcee astroplan ligo-segments python-ligo-lw lscsoft-glue ligo-gracedb pyyaml future
Installing collected packages: numpy, ptemcee, six, h5py, scipy, kiwisolver, pyparsing, cycler, python-dateutil, matplotlib, astropy, healpy, tqdm, pytz, astroplan, decorator, networkx, pillow, astropy-healpix, ligo-segments, pycparser, cffi, cryptography, pyOpenSSL, lscsoft-glue, lalsuite, reproject, pyyaml, python-ligo-lw, future, ligo-gracedb, ligo.skymap
Successfully installed astroplan-0.6 astropy-4.0.1.post1 astropy-healpix-0.5 cffi-1.14.0 cryptography-2.9.2 cycler-0.10.0 decorator-4.4.2 future-0.18.2 h5py-2.10.0 healpy-1.13.0 kiwisolver-1.2.0 lalsuite-6.70 ligo-gracedb-2.6.1 ligo-segments-1.2.0 ligo.skymap-0.3.1 lscsoft-glue-2.0.0 matplotlib-3.2.1 networkx-2.4 numpy-1.18.5 pillow-7.1.2 ptemcee-1.0.0 pyOpenSSL-19.1.0 pycparser-2.20 pyparsing-2.4.7 python-dateutil-2.8.1 python-ligo-lw-1.6.0 pytz-2020.1 pyyaml-5.3.1 reproject-0.7.1 scipy-1.4.1 six-1.15.0 tqdm-4.46.1
root@a1255912bd82:/# ligo-skymap-plot --help
usage: ligo-skymap-plot [-h] [-o FILE.{pdf,png}] [--colormap CMAP]
                        [--help-colormap] [--figure-width INCHES]
                        [--figure-height INCHES] [--dpi PIXELS]
                        [--transparent [TRANSPARENT]] [--version]
                        [-l CRITICAL|ERROR|WARNING|INFO|DEBUG|NOTSET]
                        [--annotate] [--contour PERCENT [PERCENT ...]]
                        [--colorbar] [--radec deg deg]
                        [--inj-database FILE.sqlite] [--geo]
                        [--projection {mollweide,aitoff,globe,zoom}]
                        [--projection-center CENTER] [--zoom-radius RADIUS]
                        [INPUT.fits[.gz]]

Plot an all-sky map on a Mollweide projection.
By default, plot in celestial coordinates (RA, Dec).

To plot in geographic coordinates (longitude, latitude) with major
coastlines overlaid, provide the ``--geo`` flag.

Public-domain cartographic data is courtesy of `Natural Earth
<http://www.naturalearthdata.com>`_ and processed with `MapShaper
<http://www.mapshaper.org>`_.

positional arguments:
  INPUT.fits[.gz]       Input FITS file (default: -)

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -l CRITICAL|ERROR|WARNING|INFO|DEBUG|NOTSET, --loglevel CRITICAL|ERROR|WARNING|INFO|DEBUG|NOTSET
  --annotate            annotate plot with information about the event
                        (default: False)
  --contour PERCENT [PERCENT ...]
                        plot contour enclosing this percentage of probability
                        mass [may be specified multiple times, default: none]
                        (default: None)
  --colorbar            Show colorbar (default: False)
  --radec deg deg       right ascension (deg) and declination (deg) to mark
                        (default: [])
  --inj-database FILE.sqlite
                        read injection positions from database (default: None)
  --geo                 Use a terrestrial reference frame with coordinates
                        (lon, lat) instead of the celestial frame with
                        coordinates (RA, dec) and draw continents on the map
                        (default: False)
  --projection {mollweide,aitoff,globe,zoom}
                        Projection style (default: mollweide)
  --projection-center CENTER
                        Specify the center for globe and zoom projections,
                        e.g. 14h 10d (default: None)
  --zoom-radius RADIUS  Specify the radius for zoom projections, e.g. 4deg
                        (default: None)

figure options:
  Options that affect figure output format

  -o FILE.{pdf,png}, --output FILE.{pdf,png}
                        output file, or - to plot to screen (default: -)
  --colormap CMAP       matplotlib colormap (default: cylon)
  --help-colormap       show support values for --colormap and exit
  --figure-width INCHES
                        width of figure in inches (default: 8)
  --figure-height INCHES
                        height of figure in inches (default: 6)
  --dpi PIXELS          resolution of figure in dots per inch (default: 300)
  --transparent [TRANSPARENT]
                        Save image with transparent background (default: 0)
root@a1255912bd82:/#
Janna112358 commented 4 years ago

Well, it seems that I cannot reproduce the issue anymore either. Previously I was simply cloning ligo.skymap, then creating a python3 virtualenv and installing with pip. I would get an error when running 'ligo-skymap-plot --help' but it does not happen anymore. No idea what was going on previously because doing the exact same thing now does not give me any issues. So ignore this I guess and if I encounter the issue again I will let you know.

lpsinger commented 4 years ago

Spooky! 👻 Please reopen if this reappears.