Issues with starfish 0.2.1 installation

Hey guys!

The new starfish was just recently issued and I seem to be already having a problem installing it…

Despite the really nice instruction for starfish installation given here https://spacetx-starfish.readthedocs.io/en/latest/installation/, I have a persistent problem installing it on my Mac. I have tried creating virtual environments with venv and with conda and also installing numpy before installing actual starfish (with pip install), but i always run into the same problem – the installation seems to run smoothly, but I cannot import starfish module. Trying to uninstall it with conda also tells me, that there is not such a package in the environment, which is another indication, that it does not get installed properly, right?

On the contrary, installing starfish 0.2.0 from bioconda works without problems. However, this one has an issue with napari - when I am trying to use any display() functions, i get an error message import error:
ImportError:
Could not load requested Qt binding. Please ensure that
PyQt4 >= 4.7, PyQt5, PySide >= 1.0.3 or PySide2 is available,
and only one is imported per session.
And PySide2, as well as entire napari has been installed in the environment prior to starfish. I tried reinstalling napari (both with conda and pip) and PyQt, but it did not solve the issue, unfortunately.

Below I am attaching the error messages I get when I am trying to import starfish (from python console or from Jupyter notebook).

Could you help me please? Thank you in advance!

Kate.

import starfish

Traceback (most recent call last):

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/numpy/core/init.py”, line 22, in

from . import multiarray

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/numpy/core/multiarray.py”, line 12, in

from . import overrides

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/numpy/core/overrides.py”, line 7, in

from numpy.core._multiarray_umath import (

ImportError: dlopen(/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Library not loaded: /usr/local/gfortran/lib/libquadmath.0.dylib

Referenced from: /Users/ekaterina/tcoffee/Version_11.00.8cbe486/gfortran/libgfortran.3.dylib

Reason: image not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “”, line 1, in

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/starfish/init.py”, line 1, in

from . import (

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/starfish/image.py”, line 1, in

from starfish.core.image import (  # noqa: F401

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/starfish/core/image/init.py”, line 1, in

from ._registration import ApplyTransform

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/starfish/core/image/_registration/ApplyTransform/init.py”, line 1, in

from ._base import ApplyTransformAlgorithm

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/starfish/core/image/_registration/ApplyTransform/_base.py”, line 4, in

from starfish.core.imagestack.imagestack import ImageStack

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/starfish/core/imagestack/imagestack.py”, line 29, in

import numpy as np

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/numpy/init.py”, line 140, in

from . import core

File “/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/numpy/core/init.py”, line 48, in

raise ImportError(msg)

ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for

many reasons, often due to issues with your setup or how NumPy was

installed.

We have compiled some common reasons and troubleshooting tips at:

https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  • The Python version is: Python3.7 from “/opt/anaconda3/envs/starfish_env/bin/python”

  • The NumPy version is: “1.19.0”

and make sure that they are the versions you expect.

Please carefully study the documentation linked above for further help.

Original error was: dlopen(/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Library not loaded: /usr/local/gfortran/lib/libquadmath.0.dylib

Referenced from: /Users/ekaterina/tcoffee/Version_11.00.8cbe486/gfortran/libgfortran.3.dylib

Reason: image not found

Hi @kate_lupar! Thanks for reaching out :smiley:

I just tried to install starfish 0.2.1 on my Mac, using Anaconda, in a fresh conda environment with pip and I had no problems.

The lines in your traceback that I’m most curious about are these:

ImportError: dlopen(/opt/anaconda3/envs/starfish_env/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Library not loaded: /usr/local/gfortran/lib/libquadmath.0.dylib

Referenced from: /Users/ekaterina/tcoffee/Version_11.00.8cbe486/gfortran/libgfortran.3.dylib

Reason: image not found

It looks like numpy may be trying to import Fortran libraries from tcoffee instead of their normal location? I’ve never seen anything like this.

To help us debug, can you run the following in a python script or terminal in that starfish_env environment?

import platform; print(platform.platform())
import sys; print("Python", sys.version)
import numpy; print("NumPy", numpy.__version__)
import scipy; print("SciPy", scipy.__version__)
import skimage; print("scikit-image", skimage.__version__)
import pandas; print("pandas", pandas.__version__)
import sklearn; print("sklearn", sklearn.__version__)
import xarray; print("xarray", xarray.__version__)
import sympy; print("sympy", sympy.__version__)

Regarding bioconda, it looks like there’s a problem with the build for 0.2.1. I’ve reached out to @joshmoore for help there. Since bioconda works for you on 0.2.0 (except for the PyQT issues with napari), getting that build to work might let you install 0.2.1.

Thank you so much for your reply, Justin!

I have tried to run the diagnostic script you have proposed in my starfish_pip_env environment. It gets locked on numpy again (I get the same error message when trying to import numpy, scipy, skimage, pandas, sklearn or xarray):

import platform; print(platform.platform())
Darwin-15.6.0-x86_64-i386-64bit

import sys; print(“Python”, sys.version)
Python 3.7.6 | packaged by conda-forge | (default, Jun 1 2020, 18:33:30)
[Clang 9.0.1 ]

import sympy; print(“sympy”, sympy.version)
sympy 1.6.1

import scipy; print(“SciPy”, scipy.version)
Traceback (most recent call last):
File “/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/numpy/core/init.py”, line 22, in
from . import multiarray
File “/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/numpy/core/multiarray.py”, line 12, in
from . import overrides
File “/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/numpy/core/overrides.py”, line 7, in
from numpy.core._multiarray_umath import (
ImportError: dlopen(/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Library not loaded: /usr/local/gfortran/lib/libquadmath.0.dylib
Referenced from: /Users/ekaterina/tcoffee/Version_11.00.8cbe486/gfortran/libgfortran.3.dylib
Reason: image not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “”, line 1, in
File “/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/scipy/init.py”, line 61, in
from numpy import show_config as show_numpy_config
File “/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/numpy/init.py”, line 140, in
from . import core
File “/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/numpy/core/init.py”, line 48, in
raise ImportError(msg)
ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  • The Python version is: Python3.7 from “/opt/anaconda3/envs/starfish_pip_env/bin/python”
  • The NumPy version is: “1.19.0”

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: dlopen(/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Library not loaded: /usr/local/gfortran/lib/libquadmath.0.dylib
Referenced from: /Users/ekaterina/tcoffee/Version_11.00.8cbe486/gfortran/libgfortran.3.dylib
Reason: image not found

I am also surprised that it tries to get libraries from tcoffee folder… I can try to uninstall tcoffee and delete it from my computer to see, whether it solves the problem…

Also many thanks for looking into a conda solution! I hope either way we will get it to work!

OK, this confirms that it’s not a starfish problem per se, but rather a problem with your environment.

I can try to uninstall tcoffee and delete it from my computer to see, whether it solves the problem…

Yeah, I think you should try that. It looks like at least one Qiime2 user had a very similar problem and deleting tcoffee did the trick.

Alternatively, it looks like there might be an environment variable set in your .bash_profile that you can unset?

Hi again :slight_smile:
I have uninstalled tcoffee and it indeed solved a problem I had before. But now I am running into the same problem with napari, as I have when I am installing starfish from bioconda. This is the error message which I get, when I am trying to import starfish:
ModuleNotFoundError Traceback (most recent call last)
/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/qtpy/init.py in
203 try:
–> 204 from PySide import version as PYSIDE_VERSION # analysis:ignore
205 from PySide.QtCore import version as QT_VERSION # analysis:ignore

ModuleNotFoundError: No module named ‘PySide’

During handling of the above exception, another exception occurred:

PythonQtError Traceback (most recent call last)
/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/napari/init.py in
10 try:
—> 11 from qtpy import API_NAME
12 except Exception as e:

/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/qtpy/init.py in
209 except ImportError:
–> 210 raise PythonQtError(‘No Qt bindings could be found’)
211

PythonQtError: No Qt bindings could be found

The above exception was the direct cause of the following exception:

PythonQtError Traceback (most recent call last)
in
----> 1 import starfish

/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/starfish/init.py in
12 )
13 # display images and spots
—> 14 from .core._display import display
15 # top-level objects
16 from .core.codebook.codebook import Codebook

/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/starfish/core/_display.py in
14
15 try:
—> 16 from napari import Viewer
17 except ImportError:
18 Viewer = None

/opt/anaconda3/envs/starfish_pip_env/lib/python3.7/site-packages/napari/init.py in
18 '\nYou may also use “pip install napari[pyside2]” for Pyside2, ’
19 ‘or “pip install napari[pyqt5]” for PyQt5’
—> 20 ) from e
21 raise
22

PythonQtError: No Qt bindings could be found.

napari requires either PyQt5 or PySide2 to be installed in the environment.
To install the default backend (currently PyQt5), run “pip install napari[all]”
You may also use “pip install napari[pyside2]” for Pyside2, or “pip install napari[pyqt5]” for PyQt5

And of course PySide2 and PyQt5 are both installed in the environment, as you can see:
$ conda list

packages in environment at /opt/anaconda3/envs/starfish_pip_env:

Name Version Build Channel

alabaster 0.7.12 py_0 conda-forge
appnope 0.1.0 py37hc8dfbb8_1001 conda-forge
asciitree 0.3.3 py_2 conda-forge
attrs 19.3.0 pypi_0 pypi
babel 2.8.0 py_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
bleach 3.1.5 pypi_0 pypi
blosc 1.19.0 h4a8c4bd_0 conda-forge
bokeh 2.1.1 py37hc8dfbb8_0 conda-forge
boto3 1.14.21 pypi_0 pypi
botocore 1.17.21 pypi_0 pypi
brotli 1.0.7 h4a8c4bd_1004 conda-forge
brotlipy 0.7.0 py37h9bfed18_1000 conda-forge
brunsli 0.1 h4a8c4bd_0 conda-forge
bzip2 1.0.8 h0b31af3_2 conda-forge
ca-certificates 2020.6.20 hecda079_0 conda-forge
cachey 0.2.1 pyh9f0ad1d_0 conda-forge
certifi 2020.6.20 py37hc8dfbb8_0 conda-forge
cffi 1.14.0 py37h356ff06_0 conda-forge
chardet 3.0.4 py37hc8dfbb8_1006 conda-forge
charls 2.1.0 h4a8c4bd_2 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
cloudpickle 1.5.0 py_0 conda-forge
cryptography 2.9.2 py37he655712_0 conda-forge
cycler 0.10.0 py_2 conda-forge
cytoolz 0.10.1 py37h0b31af3_0 conda-forge
dask 2.20.0 py_0 conda-forge
dask-core 2.20.0 py_0 conda-forge
dataclasses 0.6 pypi_0 pypi
dbus 1.13.6 h2f22bb5_0 conda-forge
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 pypi_0 pypi
diskcache 4.1.0 pypi_0 pypi
distributed 2.20.0 py37hc8dfbb8_0 conda-forge
docutils 0.15.2 pypi_0 pypi
entrypoints 0.3 pypi_0 pypi
expat 2.2.9 h4a8c4bd_2 conda-forge
fasteners 0.14.1 py_3 conda-forge
fontconfig 2.13.1 h6b1039f_1001 conda-forge
freetype 2.10.2 h8da9a1a_0 conda-forge
freetype-py 2.2.0 pyh9f0ad1d_0 conda-forge
fsspec 0.7.4 py_0 conda-forge
gettext 0.19.8.1 h46ab8bc_1002 conda-forge
giflib 5.2.1 h0b31af3_2 conda-forge
glib 2.65.0 h577aef8_0 conda-forge
h5py 2.10.0 pypi_0 pypi
heapdict 1.0.1 py_0 conda-forge
icu 64.2 h6de7cb9_1 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
imagecodecs 2020.5.30 py37h64a549b_2 conda-forge
imageio 2.9.0 py_0 conda-forge
imagesize 1.2.0 py_0 conda-forge
importlib-metadata 1.7.0 py37hc8dfbb8_0 conda-forge
importlib_metadata 1.7.0 0 conda-forge
ipykernel 5.3.2 py37h43977f1_0 conda-forge
ipython 7.16.1 py37h43977f1_0 conda-forge
ipython-genutils 0.2.0 pypi_0 pypi
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 pypi_0 pypi
jedi 0.17.1 py37hc8dfbb8_0 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
jmespath 0.10.0 pypi_0 pypi
joblib 0.16.0 pypi_0 pypi
jpeg 9d h0b31af3_0 conda-forge
jsonschema 3.2.0 pypi_0 pypi
jupyter_client 6.1.6 py_0 conda-forge
jupyter_core 4.6.3 py37hc8dfbb8_1 conda-forge
jxrlib 1.1 h0b31af3_2 conda-forge
kiwisolver 1.2.0 py37ha1cc60f_0 conda-forge
krb5 1.17.1 h14dd6a4_1 conda-forge
lcms2 2.11 h174193d_0 conda-forge
lerc 2.2 h4a8c4bd_0 conda-forge
libaec 1.0.4 h4a8c4bd_1 conda-forge
libblas 3.8.0 17_openblas conda-forge
libcblas 3.8.0 17_openblas conda-forge
libclang 9.0.1 default_hf57f61e_0 conda-forge
libcxx 10.0.0 h1af66ff_2 conda-forge
libedit 3.1.20191231 hed1e85f_1 conda-forge
libffi 3.2.1 h4a8c4bd_1007 conda-forge
libgfortran 4.0.0 2 conda-forge
libiconv 1.15 h0b31af3_1006 conda-forge
liblapack 3.8.0 17_openblas conda-forge
libllvm9 9.0.1 h7475705_1 conda-forge
libopenblas 0.3.10 openmp_h63d9170_2 conda-forge
libpng 1.6.37 hbbe82c9_1 conda-forge
libpq 12.3 h489d428_0 conda-forge
libsodium 1.0.17 h01d97ff_0 conda-forge
libtiff 4.1.0 h2ae36a8_6 conda-forge
libwebp-base 1.1.0 h0b31af3_3 conda-forge
libxml2 2.9.10 h53d96d6_0 conda-forge
libxslt 1.1.33 h320ff13_0 conda-forge
libzopfli 1.0.3 h4a8c4bd_0 conda-forge
llvm-openmp 10.0.0 h28b9765_0 conda-forge
locket 0.2.0 py_2 conda-forge
lz4-c 1.9.2 h4a8c4bd_1 conda-forge
markupsafe 1.1.1 py37h9bfed18_1 conda-forge
matplotlib-base 3.2.2 py37hddda452_1 conda-forge
mistune 0.8.4 pypi_0 pypi
monotonic 1.5 py_0 conda-forge
mpmath 1.1.0 pypi_0 pypi
msgpack-python 1.0.0 py37ha1cc60f_1 conda-forge
napari 0.3.5 pypi_0 pypi
napari-plugin-engine 0.1.6 py_0 conda-forge
napari-svg 0.1.3 py_0 conda-forge
nbconvert 5.6.1 pypi_0 pypi
nbformat 5.0.7 pypi_0 pypi
ncurses 6.2 hb1e8313_1 conda-forge
networkx 2.4 py_1 conda-forge
notebook 6.0.3 pypi_0 pypi
nspr 4.20 h0a44026_1000 conda-forge
nss 3.47 hc0980d9_0 conda-forge
numcodecs 0.6.4 py37h4a8c4bd_0 conda-forge
numpy 1.19.0 pypi_0 pypi
numpydoc 1.1.0 pyh9f0ad1d_0 conda-forge
olefile 0.46 py_0 conda-forge
openjpeg 2.3.1 h254dc36_3 conda-forge
openssl 1.1.1g h0b31af3_0 conda-forge
packaging 20.4 pyh9f0ad1d_0 conda-forge
pandas 1.0.5 py37h94625e5_0 conda-forge
pandocfilters 1.4.2 pypi_0 pypi
parso 0.7.0 pyh9f0ad1d_0 conda-forge
partd 1.1.0 py_0 conda-forge
pcre 8.44 h4a8c4bd_0 conda-forge
pexpect 4.8.0 py37hc8dfbb8_1 conda-forge
pickleshare 0.7.5 py37hc8dfbb8_1001 conda-forge
pillow 7.2.0 py37hfd78ece_1 conda-forge
pip 20.1.1 py_1 conda-forge
pluggy 0.13.1 py37hc8dfbb8_2 conda-forge
prometheus-client 0.8.0 pypi_0 pypi
prompt-toolkit 3.0.5 py_1 conda-forge
psutil 5.7.2 py37h60d8a13_0 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pygments 2.6.1 py_0 conda-forge
pyopengl 3.1.5 py_0 conda-forge
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.12.3 py37ha62fc16_3 conda-forge
pyqt5 5.14.2 pypi_0 pypi
pyqt5-sip 12.8.0 pypi_0 pypi
pyqtchart 5.12 pypi_0 pypi
pyqtwebengine 5.12.1 pypi_0 pypi
pyrsistent 0.16.0 pypi_0 pypi
pyside2 5.13.2 py37ha8f7116_2 conda-forge
pysocks 1.7.1 py37hc8dfbb8_1 conda-forge
python 3.7.6 cpython_h1fd5dd1_6 conda-forge
python-dateutil 2.8.0 pypi_0 pypi
python_abi 3.7 1_cp37m conda-forge
pytz 2020.1 pyh9f0ad1d_0 conda-forge
pywavelets 1.1.1 py37h10e2902_1 conda-forge
pyyaml 5.3.1 pypi_0 pypi
pyzmq 19.0.1 pypi_0 pypi
qt 5.12.5 h514805e_3 conda-forge
qtconsole 4.7.5 pyh9f0ad1d_0 conda-forge
qtpy 1.9.0 py_0 conda-forge
read-roi 1.6.0 pypi_0 pypi
readline 8.0 h0678c8f_2 conda-forge
regional 1.1.2 pypi_0 pypi
requests 2.24.0 pyh9f0ad1d_0 conda-forge
s3transfer 0.3.3 pypi_0 pypi
scikit-image 0.15.0 pypi_0 pypi
scikit-learn 0.23.1 pypi_0 pypi
scipy 1.5.1 pypi_0 pypi
semantic-version 2.8.5 pypi_0 pypi
send2trash 1.5.0 pypi_0 pypi
setuptools 49.2.0 py37hc8dfbb8_0 conda-forge
showit 1.1.4 pypi_0 pypi
six 1.15.0 pyh9f0ad1d_0 conda-forge
slicedimage 4.1.1 pypi_0 pypi
snappy 1.1.8 h4a8c4bd_3 conda-forge
snowballstemmer 2.0.0 py_0 conda-forge
sortedcontainers 2.2.2 pyh9f0ad1d_0 conda-forge
sphinx 3.1.2 py_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 1.0.3 py_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.4 py_0 conda-forge
sqlite 3.32.3 h93121df_1 conda-forge
starfish 0.2.1 pypi_0 pypi
sympy 1.6.1 pypi_0 pypi
tblib 1.6.0 py_0 conda-forge
terminado 0.8.3 pypi_0 pypi
testpath 0.4.4 pypi_0 pypi
threadpoolctl 2.1.0 pypi_0 pypi
tifffile 2020.7.4 py_0 conda-forge
tk 8.6.10 hbbe82c9_0 conda-forge
toolz 0.10.0 py_0 conda-forge
tornado 6.0.4 py37h9bfed18_1 conda-forge
tqdm 4.47.0 pypi_0 pypi
trackpy 0.4.2 pypi_0 pypi
traitlets 4.3.3 py37hc8dfbb8_1 conda-forge
typing_extensions 3.7.4.2 py_0 conda-forge
urllib3 1.25.9 py_0 conda-forge
validators 0.15.0 pypi_0 pypi
vispy 0.6.4 py37h1defe42_1 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_0 conda-forge
webencodings 0.5.1 pypi_0 pypi
wheel 0.34.2 py_1 conda-forge
widgetsnbextension 3.5.1 pypi_0 pypi
wrapt 1.12.1 py37h9bfed18_1 conda-forge
xarray 0.16.0 pypi_0 pypi
xz 5.2.5 h0b31af3_1 conda-forge
yaml 0.2.5 h0b31af3_0 conda-forge
zarr 2.4.0 py_0 conda-forge
zeromq 4.3.2 h6de7cb9_2 conda-forge
zfp 0.5.5 h4a8c4bd_1 conda-forge
zict 2.0.0 py_0 conda-forge
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h0b31af3_1006 conda-forge
zstd 1.4.4 h4b3e974_3 conda-forge

Do you maybe have an idea, what else might be going wrong?.. Thank you so much!

Fantastic!

Oh no :frowning:

OK, am I right that you want to install the optional napari dependency? You’re trying to install locally and want to visualize the data, you’re not trying to install this on a cluster or remote server?

If that’s the case, we should ping some of the napari folks like @sofroniewn and @talley to help out… I know that pyqt/pyside can be a challenge.

As @neuromusic mentioned, this definitely looks like an environment problem… and though we could spend some time trying to figure out what went wrong with your starfish_pip_env environment, most of the time, these things are eventually solved by just creating a new environment. Have you definitely tried that? And if so, can you provide the steps you followed to create the environment?
Currently, you have not one but three different versions of Qt installed:

pyqt 5.12.3 py37ha62fc16_3 conda-forge
pyqt5 5.14.2 pypi_0 pypi
pyside2 5.13.2 py37ha8f7116_2 conda-forge

in particular: having pyqt5 from both conda and pip is almost always a recipe for disaster. If it were me would nuke the environment and start over.

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Thanks a lot for you help!
Indeed, I was trying to install starfish and napari locally to run some tests and visualize the data. The next plan is to install it on the remote server as well :slight_smile:

Hi @talley! I have indeed tried installing it in the brand new environment. Actually, this starfish_pip_env is created exclusively for this. Here are the steps I took:
conda create -n starfish_pip_env python=3.7
conda activate starfish_pip_env
pip install starfish
pip install starfish[napari]

Then I activate IPython and try to import starfish in the console. It gives me an error message, which I posted earlier, that it cannot find PySide2. I tried solving it by running
conda install pyside2

And after the problem persisted, i tried
conda install napari
(this I did, hoping that conda installation of napari would bring all the necessary dependencies)

That is why I have so many of Qt versions, but none of them seems to be identified properly by starfish…

I hope you can make sense of it all… Thank you in advance!

Hi @neuromusic and @talley!

I have now tried to install starfish in a new conda environment on the remote server, everything went fine this time, no complaints during installation or module import.
However, when I run display(), I get an warning message and kernel dies:
WARNING: Could not load the Qt platform plugin "xcb" in "" even though it was found.

Do you guys have an idea, what’s going on now?

I see, maybe the [napari] extra on starfish needs to be updated since we made some changes (and now don’t install a qt backend by default).

The xcb issue is a driver/Qt-plugin issue that will need to be solved by installing some more packages on your remote server… but I’ll warn you that the OpenGL/Gui aspect of napari has created a lot of challenges for running remotely. How were you planning on using it remotely, via X11 forwarding? Or just command line with no GUI?

The idea was to run jupyter notebook from the remote server and have the visual stuff displayed that way. But I can also do it via X11 forwarding. What do you think would be easier?

Unfortunately, neither is super easy at the moment. See issues like #1457, #799, #881 & #896

for a jupyter notebook approach you could try the experimental tips here (i haven’t tested):