Error with pystan

[gabriel-fontinele]

Hello, when I run the program the error message described below appears, and I apparently installed Pystan correctly, but when I go to import I can't, so if I just use import stan, then it works. Should I install the previous version of this module?

gabriel@gabriel-Aspire-A515-51G:~/astrosoft/pyproffit-master/validation$ python test_script.py WARNING: FITSFixedWarning: RADECSYS= 'FK5 ' / Equatorial system reference the RADECSYS keyword is deprecated, use RADESYSa. [astropy.wcs.wcs] File reading test passed Excluded 2 sources Region file test passed Applying high-pass filter /home/gabriel/miniconda3/lib/python3.10/site-packages/pyproffit/data.py:259: RuntimeWarning: invalid value encountered in divide img_smoothed = np.nan_to_num(np.divide(gsb, gsexp)) Interpolating in the masked regions Filling holes Dmfilth test passed Computing centroid and ellipse parameters using principal component analysis Will search for the centroid within a region of 20 arcmin centered on RA=55.5399, DEC=-53.5573 Denoising image... Running PCA... Centroid position: 276.6758121528362 282.19710486450094 Corresponding FK5 coordinates: 55.688756583569834 -53.62322183974974 Ellipse axis ratio and position angle: 1.167875137382187 -170.89745485625753 Centroid calculation test failed, difference RA=0.00359309 , difference DEC=0.00077744 Determining X-ray peak Coordinates of surface-brightness peak: 272.0 281.0 Corresponding FK5 coordinates: 55.72147733144434 -53.628226297404545 SB peak test passed Corresponding pixels coordinates: 277.18944608325205 282.3833169452636 Surface brightness profile test passed /home/gabriel/miniconda3/lib/python3.10/site-packages/pyproffit/fitting.py:58: VisibleDeprecationWarning: make_func_code is deprecated: Use of func_code attribute to declare parameters is deprecated. Use _parameters instead, which is a dict of parameter names to limits. self.func_code = iminuit.util.make_func_code(iminuit.util.describe(self.model)[1:]) ┌─────────────────────────────────────────────────────────────────────────┐ │ Migrad │ ├──────────────────────────────────┬──────────────────────────────────────┤ │ FCN = 120.7 │ Nfcn = 263 │ │ EDM = 4.05e-05 (Goal: 0.0002) │ │ ├──────────────────────────────────┼──────────────────────────────────────┤ │ Valid Minimum │ Below EDM threshold (goal x 10) │ ├──────────────────────────────────┼──────────────────────────────────────┤ │ No parameters at limit │ Below call limit │ ├──────────────────────────────────┼──────────────────────────────────────┤ │ Hesse ok │ Covariance accurate │ └──────────────────────────────────┴──────────────────────────────────────┘ ┌───┬──────┬───────────┬───────────┬────────────┬────────────┬─────────┬─────────┬───────┐ │ │ Name │ Value │ Hesse Err │ Minos Err- │ Minos Err+ │ Limit- │ Limit+ │ Fixed │ ├───┼──────┼───────────┼───────────┼────────────┼────────────┼─────────┼─────────┼───────┤ │ 0 │ beta │ 0.750 │ 0.022 │ │ │ │ │ │ │ 1 │ rc │ 4.23 │ 0.20 │ │ │ │ │ │ │ 2 │ norm │ -1.471 │ 0.015 │ │ │ │ │ │ │ 3 │ bkg │ -3.688 │ 0.015 │ │ │ │ │ │ └───┴──────┴───────────┴───────────┴────────────┴────────────┴─────────┴─────────┴───────┘ ┌──────┬─────────────────────────────────────┐ │ │ beta rc norm bkg │ ├──────┼─────────────────────────────────────┤ │ beta │ 0.000504 4.3e-3 -0.19e-3 0.21e-3 │ │ rc │ 4.3e-3 0.0404 -2.37e-3 1.55e-3 │ │ norm │ -0.19e-3 -2.37e-3 0.000239 -0.06e-3 │ │ bkg │ 0.21e-3 1.55e-3 -0.06e-3 0.000234 │ └──────┴─────────────────────────────────────┘ Best fit chi-squared: 120.679 for 100 bins and 96 d.o.f Reduced chi-squared: 1.25707 Fitting test passed, output written to file test_plot_fit.pdf Saving model image test passed, test image written to test_outmod.fits PSF calculation test passed WARNING: VerifyWarning: Keyword name 'ROT_ANGLE' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card] WARNING: VerifyWarning: Keyword name 'ELL_RATIO' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card] Output profile saving test passed, file written to test_sb.fits Determining X-ray peak Coordinates of surface-brightness peak: 272.0 281.0 Corresponding FK5 coordinates: 55.72147733144434 -53.628226297404545 Running PyMC3 reconstruction JAX not found, using default sampler Running MCMC... |█████████████| 100.00% [360/360 00:00<00:00 logp = -637.88, ||grad|| = 1.5661] Only 100 samples in chain. Auto-assigning NUTS sampler... Initializing NUTS using jitter+adapt_diag... Multiprocess sampling (4 chains in 4 jobs) NUTS: [coefs, bkg] Sampling 4 chains for 500 tune and 100 draw iterations (2_000 + 400 draws total) took 135 seconds. The rhat statistic is larger than 1.01 for some parameters. This indicates problems during sampling. See https://arxiv.org/abs/1903.08008 for details The effective sample size per chain is smaller than 100 for some parameters. A higher number is needed for reliable rhat and ess computation. See https://arxiv.org/abs/1903.08008 for details There were 40 divergences after tuning. Increase target_accept or reparameterize. Chain 0 reached the maximum tree depth. Increase max_treedepth, increase target_accept or reparameterize. Chain 1 reached the maximum tree depth. Increase max_treedepth, increase target_accept or reparameterize. Chain 2 reached the maximum tree depth. Increase max_treedepth, increase target_accept or reparameterize. Chain 3 reached the maximum tree depth. Increase max_treedepth, increase target_accept or reparameterize. Done. Total computing time is: 2.420164668560028 minutes /home/gabriel/astrosoft/pyproffit-master/validation/test_script.py:147: RuntimeWarning: invalid value encountered in divide check_pymc3_sb=np.nan_to_num(ref_pymc3[:,0]/depr.sb) Possible issue with PyMC3 reconstruction, check plots Possible issue with gas density calculation, check plots Possible issue with Mgas calculation, check plots Density profile outputted to test_density.pdf Mgas profile outputted to test_mgas.pdf Reconstruction test passed, results written to file test_save_all.fits Running Onion Peeling test Running Stan reconstruction Traceback (most recent call last): File "/home/gabriel/astrosoft/pyproffit-master/validation/test_script.py", line 261, in run() File "/home/gabriel/astrosoft/pyproffit-master/validation/test_script.py", line 231, in run depr_stan.Multiscale(backend='stan', nmcmc=1000, bkglim=25.) File "/home/gabriel/miniconda3/lib/python3.10/site-packages/pyproffit/deproject.py", line 948, in Multiscale Deproject_Multiscale_Stan(self,bkglim=bkglim,back=back,nmcmc=nmcmc,samplefile=samplefile,nrc=nrc,nbetas=nbetas,depth=depth,min_beta=min_beta) File "/home/gabriel/miniconda3/lib/python3.10/site-packages/pyproffit/deproject.py", line 477, in Deproject_Multiscale_Stan import stan_utility as su File "/home/gabriel/miniconda3/lib/python3.10/site-packages/stan_utility/init.py", line 1, in from stan_utility.utils import compile_model, check_all_diagnostics File "/home/gabriel/miniconda3/lib/python3.10/site-packages/stan_utility/utils.py", line 1, in import pystan ModuleNotFoundError: No module named 'pystan' gabriel@gabriel-Aspire-A515-51G:~/astrosoft/pyproffit-master/validation$ python Python 3.10.11 (main, May 16 2023, 00:28:57) [GCC 11.2.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import stan import pystan Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'pystan' exit()

[domeckert]

Seems like a duplicate from this issue:

https://github.com/domeckert/pyproffit/issues/21

Try the following:

pip install pystan<3.0

[gabriel-fontinele]

the command doesn't work, it said nonexistent file or directory

[domeckert]

Add quotes

pip install "pystan<3.0"

[ktrehaeven]

Hi. I'm getting a similar error. Any work-arounds @gabriel-fontinele ?