Can't install pyradex on latest (and any) anaconda

[SmirnGreg]

Dear Adam,

I can't install pyradex and make it to go through tests. I am installing it into conda environment since I don't have root access on most machines.

Steps to reproduce:

conda create -n pyradex_demo anaconda python=3.7
conda activate pyradex_demo      
git clone --recursive https://github.com/keflavich/pyradex.git
cd pyradex
pip install astroquery
pip install https://github.com/astropy/specutils/archive/master.zip
python setup.py install_radex install_myradex install

python runtests.py  # raises   File "_pytest.config", line 187, in addini AssertionError
pytest # raises Failed: [pytest] section in setup.cfg files is no longer supported, change to [tool:pytest] instead.

rm setup.cfg        
pytest   
# ==================================== test session starts ====================================
#platform linux -- Python 3.7.3, pytest-4.3.1, py-1.8.0, pluggy-0.9.0
#rootdir: /home/smirnov/pyradex, inifile:
#plugins: remotedata-0.3.1, openfiles-0.3.2, doctestplus-0.3.0, arraydiff-0.3
#collected 22 items                                                                          

#pyradex/tests/test_fjdu.py FF                                                         [  9%]
#pyradex/tests/test_radex.py .FF......F..F..F                                          [ 81%]
#pyradex/tests/test_radex_install.py F                                                 [ 86%]
#pyradex/tests/test_radex_myradex_consistency.py FF                                    [ 95%]
#pyradex/tests/test_synthspec.py

ipython

Python 3.7.3 (default, Mar 27 2019, 22:11:17) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.4.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: import pyradex 
   ...: import numpy as np 
   ...: R = pyradex.Radex(collider_densities={'oH2':900,'pH2':100}, column=1e16, species='co'
   ...: , temperature=20) 
   ...: Tlvg = R(escapeProbGeom='lvg') 
   ...: Tslab = R(escapeProbGeom='slab') 
   ...: Tsphere = R(escapeProbGeom='sphere') 
   ...: Tlvg[:3].pprint() 
   ...: Tslab[:3].pprint() 
   ...: Tsphere[:3].pprint()                                                                 
/home/smirnov/pyradex/pyradex/core.py:910: RuntimeWarning: invalid value encountered in true_divide
  frac_level_diff = level_diff/self.level_population
         Tex                    tau            frequency  ...      brightness     T_B
          K                                       GHz     ... erg / (cm2 Hz s sr)  K 
---------------------- ---------------------- ----------- ... ------------------- ---
 3.433046369148207e-15  9.472345744143519e-20 115.2712018 ...                 0.0 0.0
3.2016068866791967e-15  3.786530681495501e-20     230.538 ...                 0.0 0.0
1.4043485108295587e-15 2.4326869586205468e-20 345.7959899 ...                 0.0 0.0
         Tex                    tau            frequency  ...      brightness     T_B
          K                                       GHz     ... erg / (cm2 Hz s sr)  K 
---------------------- ---------------------- ----------- ... ------------------- ---
 3.433046369148207e-15  9.472345744143519e-20 115.2712018 ...                 0.0 0.0
3.2016068866791967e-15  3.786530681495501e-20     230.538 ...                 0.0 0.0
1.4043485108295587e-15 2.4326869586205468e-20 345.7959899 ...                 0.0 0.0
         Tex                    tau            frequency  ...      brightness     T_B
          K                                       GHz     ... erg / (cm2 Hz s sr)  K 
---------------------- ---------------------- ----------- ... ------------------- ---
 3.433046369148207e-15  9.472345744143519e-20 115.2712018 ...                 0.0 0.0
3.2016068866791967e-15  3.786530681495501e-20     230.538 ...                 0.0 0.0
1.4043485108295587e-15 2.4326869586205468e-20 345.7959899 ...                 0.0 0.0

This looks very different from what is in the readme, and started to work only after I have installed RADEX from https://personal.sron.nl/~vdtak/radex/index.shtml

Before that, and on other machine without RADEX, I get the following:

Type 'copyright', 'credits' or 'license' for more information
IPython 7.4.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import pyradex
   ...: import numpy as np
   ...: R = pyradex.Radex(collider_densities={'oH2':900,'pH2':100}, column=1e16, species='co', temperature=20)
   ...: Tlvg = R(escapeProbGeom='lvg')
   ...: Tslab = R(escapeProbGeom='slab')
   ...: Tsphere = R(escapeProbGeom='sphere')
   ...: Tlvg[:3].pprint()
   ...: Tslab[:3].pprint()
   ...: Tsphere[:3].pprint()
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-1-5897764a5c29> in <module>
      1 import pyradex
      2 import numpy as np
----> 3 R = pyradex.Radex(collider_densities={'oH2':900,'pH2':100}, column=1e16, species='co', temperature=20)
      4 Tlvg = R(escapeProbGeom='lvg')
      5 Tslab = R(escapeProbGeom='slab')

~/pyradex/pyradex/core.py in __init__(self, collider_densities, density, total_density, temperature, species, column, column_per_bin, tbackground, deltav, abundance, datapath, escapeProbGeom, outfile, logfile, debug, mu, source_area)
    290                 raise ValueError("Data path %s was not successfully stored;"
    291                                  " instead %s was." % (datapath,self.datapath))
--> 292         self.species = species
    293         if self.molpath == b'':
    294             raise ValueError("Must set a species name.")

~/pyradex/pyradex/base_class.py in species(self, species)
    125         self._species = species
    126         try:
--> 127             self.molpath = os.path.join(self.datapath,species+'.dat')
    128         except IOError:
    129             log.warn("Did not find data file for species {0} "

~/pyradex/pyradex/core.py in molpath(self, molfile)
    613         else:
    614             self.radex.impex.molfile[:] = ""
--> 615         utils.verify_collisionratefile(molfile)
    616         try:
    617             self.radex.impex.molfile[:len(molfile)] = molfile

~/pyradex/pyradex/utils.py in verify_collisionratefile(fn)
     69     from astroquery import lamda
     70
---> 71     if not os.path.exists(fn):
     72         raise IOError("File {0} does not exist.".format(fn))
     73

/anaconda3/envs/pyradex_demo/lib/python3.7/genericpath.py in exists(path)
     17     """Test whether a path exists.  Returns False for broken symbolic links"""
     18     try:
---> 19         os.stat(path)
     20     except OSError:
     21         return False

ValueError: embedded null byte

Is it expected? Does pyradex depend on pre-installed RADEX? Is it fine that tests don't run out of the box, and many of them fail if I run them manually?

I am sorry if I do something weird.

[keflavich]

the 'embedded null byte' issue is one I've seen but I thought I had fixed. I'll investigate; maybe there are py3.7 issues as I haven't tested against 3.7 yet

[keflavich]

it does look like some of the tests are broken. However, I'm pretty sure the code is working in most cases... I won't be able to fix the bugs for at least a day though

[SmirnGreg]

Thanks for your response. You don't have to rush for me, I don't have a time pressure now.

[keflavich]

I fixed a few of the bugs. I'm a little worried about the numerical differences in the README example, though - Jeff Mangum reported a similar issue, and I don't know what caused it. I want to validate against a clean RADEX run. That has to happen later, unfortunately. If you want to help with that, it would be welcome, though =)

[gianninapr]

I'm having the same issue listed by @SmirnGreg of the embedded null byte despite having installed RADEX and updated my data path within the MAKEFILE in RADEX. I used homebrew gcc to install my gfortran compiler. I'm running python version 3.6 , I can't get any of the simpler examples listed in the README file to run since they all give the same error

[keflavich]

Regarding the original issue, I just did a fresh install & run of the example using python 3.7:

import pyradex
import numpy as np
R = pyradex.Radex(collider_densities={'oH2':900,'pH2':100}, column=1e16, species='co', temperature=20)
Tlvg = R(escapeProbGeom='lvg')
Tslab = R(escapeProbGeom='slab')
Tsphere = R(escapeProbGeom='sphere')
Tlvg[:3].pprint()
Tslab[:3].pprint()
Tsphere[:3].pprint()

## -- End pasted text --
/Users/adam/miniconda3/lib/python3.7/site-packages/pyradex/core.py:910: RuntimeWarning: invalid value encountered in true_divide
  frac_level_diff = level_diff/self.level_population
       Tex                tau          frequency  upperstateenergy upperlevel lowerlevel    upperlevelpop       lowerlevelpop          brightness              T_B
        K                                 GHz            K                                                                        erg / (cm2 Hz s sr)           K
------------------ ------------------ ----------- ---------------- ---------- ---------- ------------------- ------------------- ---------------------- -----------------
13.290883580311629 1.1468849744920648 115.2712018             5.53     1          0       0.4690681835772442 0.23707418568311267 2.7509509930774456e-14 6.738597089663219
 9.818841145513437  3.001401907034107     230.538             16.6     2          1        0.253345500331731  0.4690681835772442   7.92657371926513e-14 4.854323769676796
 7.463146983160675  1.923670595076573 345.7959899            33.19     3          2      0.03837985573671704   0.253345500331731  6.197465478870997e-14  1.68695108408779
       Tex                tau          frequency  upperstateenergy upperlevel lowerlevel    upperlevelpop      lowerlevelpop          brightness              T_B
        K                                 GHz            K                                                                       erg / (cm2 Hz s sr)           K
------------------ ------------------ ----------- ---------------- ---------- ---------- ------------------- ------------------ ---------------------- ------------------
15.033255537705188 0.8822636119487622 115.2712018             5.53     1          0       0.4187667856349173 0.2016829184801295 2.7746969242628808e-14 6.7967639792879995
 12.96726846017353 2.2752960483725784     230.538             16.6     2          1       0.2973499665319058 0.4187667856349173  1.174470050344317e-13  7.192587975689052
 9.881878806224918 2.0596268711954067 345.7959899            33.19     3          2      0.07763119330763295 0.2973499665319058   1.20717013122686e-13 3.2859190075271423
       Tex                tau          frequency  upperstateenergy upperlevel lowerlevel    upperlevelpop       lowerlevelpop          brightness              T_B
        K                                 GHz            K                                                                        erg / (cm2 Hz s sr)           K
------------------ ------------------ ----------- ---------------- ---------- ---------- ------------------- ------------------- ---------------------- ------------------
12.643328614869603 1.2818237512839787 115.2712018             5.53     1          0       0.4930538787795504  0.2545664508826119 2.7244700714182203e-14  6.673730699068296
 8.479008281968543  3.401580205974277     230.538             16.6     2          1      0.22286520293005335  0.4930538787795504  6.189487914094684e-14 3.7905126940903053
  6.85804192779582 1.7288125158470458 345.7959899            33.19     3          2      0.02774741534234436 0.22286520293005335  4.779526844016607e-14   1.30098796329388

[keflavich]

When you say you installed RADEX, could you give more details? On my machine, I have not installed radex (at least, radex is not anywhere on my path).

If you're still having trouble, try running python setup.py install_radex install_myradex build install and put the full results in a gist. Mine looks like this