Pip installation problems M1 macOS
steinjohannes opened this issue · comments
- Picasso version: 76a1ead
- Python version: 3.8
- Operating System: M1 macOS Monterey
Description
Following the pip installation guide and after apparent succesful installation, I receive the following error code when calling a picasso module (e.g. localize): ModuleNotFoundError: No module named 'picasso.ext'
What I Did
- conda create —name picasso_sr python=3.8
- conda activate picasso_sr
- conda install -c anaconda pyqt
- pip install picassosr
- picasso localize
(base) wyssuser@wyss12422 ~ % conda create --name picasso_sr python=3.8
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/wyssuser/opt/anaconda3/envs/picasso_sr
added / updated specs:
- python=3.8
The following NEW packages will be INSTALLED:
ca-certificates pkgs/main/osx-64::ca-certificates-2022.4.26-hecd8cb5_0
certifi pkgs/main/osx-64::certifi-2022.6.15-py38hecd8cb5_0
libcxx pkgs/main/osx-64::libcxx-12.0.0-h2f01273_0
libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2
ncurses pkgs/main/osx-64::ncurses-6.3-hca72f7f_3
openssl pkgs/main/osx-64::openssl-1.1.1q-hca72f7f_0
pip pkgs/main/osx-64::pip-22.1.2-py38hecd8cb5_0
python pkgs/main/osx-64::python-3.8.13-hdfd78df_0
readline pkgs/main/osx-64::readline-8.1.2-hca72f7f_1
setuptools pkgs/main/osx-64::setuptools-61.2.0-py38hecd8cb5_0
sqlite pkgs/main/osx-64::sqlite-3.38.5-h707629a_0
tk pkgs/main/osx-64::tk-8.6.12-h5d9f67b_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/osx-64::xz-5.2.5-hca72f7f_1
zlib pkgs/main/osx-64::zlib-1.2.12-h4dc903c_2
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate picasso_sr
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) wyssuser@wyss12422 ~ % conda activate picasso_sr
(picasso_sr) wyssuser@wyss12422 ~ % conda install -c anaconda pyqt
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/wyssuser/opt/anaconda3/envs/picasso_sr
added / updated specs:
- pyqt
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2022.4.26 | hecd8cb5_0 132 KB anaconda
certifi-2022.6.15 | py38hecd8cb5_0 157 KB anaconda
dbus-1.13.18 | h18a8e69_0 550 KB anaconda
expat-2.4.4 | he9d5cce_0 145 KB anaconda
gettext-0.21.0 | h7535e17_0 3.4 MB anaconda
glib-2.69.1 | h8346a28_1 3.3 MB anaconda
icu-58.2 | h0a44026_3 22.6 MB anaconda
jpeg-9e | hca72f7f_0 266 KB anaconda
libiconv-1.16 | hca72f7f_2 1.3 MB anaconda
libpng-1.6.37 | ha441bb4_0 325 KB anaconda
libxml2-2.9.14 | hbf8cd5e_0 686 KB anaconda
llvm-openmp-12.0.0 | h0dcd299_1 300 KB anaconda
openssl-1.1.1o | hca72f7f_0 3.5 MB anaconda
pcre-8.45 | h23ab428_0 221 KB anaconda
pyqt-5.9.2 | py38h655552a_2 4.4 MB anaconda
qt-5.9.7 | h468cd18_1 76.8 MB anaconda
sip-4.19.8 | py38h0a44026_0 253 KB anaconda
------------------------------------------------------------
Total: 118.3 MB
The following NEW packages will be INSTALLED:
dbus anaconda/osx-64::dbus-1.13.18-h18a8e69_0
expat anaconda/osx-64::expat-2.4.4-he9d5cce_0
gettext anaconda/osx-64::gettext-0.21.0-h7535e17_0
glib anaconda/osx-64::glib-2.69.1-h8346a28_1
icu anaconda/osx-64::icu-58.2-h0a44026_3
jpeg anaconda/osx-64::jpeg-9e-hca72f7f_0
libiconv anaconda/osx-64::libiconv-1.16-hca72f7f_2
libpng anaconda/osx-64::libpng-1.6.37-ha441bb4_0
libxml2 anaconda/osx-64::libxml2-2.9.14-hbf8cd5e_0
llvm-openmp anaconda/osx-64::llvm-openmp-12.0.0-h0dcd299_1
pcre anaconda/osx-64::pcre-8.45-h23ab428_0
pyqt anaconda/osx-64::pyqt-5.9.2-py38h655552a_2
qt anaconda/osx-64::qt-5.9.7-h468cd18_1
sip anaconda/osx-64::sip-4.19.8-py38h0a44026_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main --> anaconda
certifi pkgs/main --> anaconda
openssl pkgs/main::openssl-1.1.1q-hca72f7f_0 --> anaconda::openssl-1.1.1o-hca72f7f_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
ca-certificates-2022 | 132 KB | ##################################### | 100%
dbus-1.13.18 | 550 KB | ##################################### | 100%
jpeg-9e | 266 KB | ##################################### | 100%
certifi-2022.6.15 | 157 KB | ##################################### | 100%
gettext-0.21.0 | 3.4 MB | ##################################### | 100%
pyqt-5.9.2 | 4.4 MB | ##################################### | 100%
sip-4.19.8 | 253 KB | ##################################### | 100%
openssl-1.1.1o | 3.5 MB | ##################################### | 100%
libiconv-1.16 | 1.3 MB | ##################################### | 100%
icu-58.2 | 22.6 MB | ##################################### | 100%
libpng-1.6.37 | 325 KB | ##################################### | 100%
llvm-openmp-12.0.0 | 300 KB | ##################################### | 100%
libxml2-2.9.14 | 686 KB | ##################################### | 100%
expat-2.4.4 | 145 KB | ##################################### | 100%
glib-2.69.1 | 3.3 MB | ##################################### | 100%
qt-5.9.7 | 76.8 MB | ##################################### | 100%
pcre-8.45 | 221 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(picasso_sr) wyssuser@wyss12422 ~ % pip install picassosr
Collecting picassosr
Downloading picassosr-0.4.6-py3-none-any.whl (551 kB)
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Collecting scikit-learn==0.23.2
Using cached scikit_learn-0.23.2-cp38-cp38-macosx_10_9_x86_64.whl (7.2 MB)
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Collecting h5py>=2.10.0
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Collecting matplotlib==3.3.2
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Collecting scipy>=1.5.3
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Collecting colorama==0.4.4
Using cached colorama-0.4.4-py2.py3-none-any.whl (16 kB)
Collecting protobuf==3.20
Downloading protobuf-3.20.0-cp38-cp38-macosx_10_9_x86_64.whl (962 kB)
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Collecting watchdog==2.1.4
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Collecting numba>=0.51.2
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Collecting plotly-express==0.4.1
Downloading plotly_express-0.4.1-py2.py3-none-any.whl (2.9 kB)
Collecting streamlit==1.10.0
Downloading streamlit-1.10.0-py2.py3-none-any.whl (9.1 MB)
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Collecting lmfit==1.0.1
Using cached lmfit-1.0.1-py3-none-any.whl
Collecting pyyaml==5.3.1
Using cached PyYAML-5.3.1-cp38-cp38-macosx_10_9_x86_64.whl
Collecting tqdm==4.50.2
Using cached tqdm-4.50.2-py2.py3-none-any.whl (70 kB)
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Collecting uncertainties>=3.0.1
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Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3
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Collecting cycler>=0.10
Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)
Requirement already satisfied: certifi>=2020.06.20 in ./opt/anaconda3/envs/picasso_sr/lib/python3.8/site-packages (from matplotlib==3.3.2->picassosr) (2022.6.15)
Collecting kiwisolver>=1.0.1
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Collecting pillow>=6.2.0
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Collecting python-dateutil>=2.1
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Collecting statsmodels>=0.9.0
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Collecting pandas>=0.20.0
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Collecting pyarrow
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Requirement already satisfied: setuptools in ./opt/anaconda3/envs/picasso_sr/lib/python3.8/site-packages (from numba>=0.51.2->picassosr) (61.2.0)
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Building wheels for collected packages: validators
Building wheel for validators (setup.py) ... done
Created wheel for validators: filename=validators-0.20.0-py3-none-any.whl size=19582 sha256=fc43eb5d36343489997de6fc86d8704d96744034d3d59c54940c337c73eba633
Stored in directory: /Users/wyssuser/Library/Caches/pip/wheels/19/09/72/3eb74d236bb48bd0f3c6c3c83e4e0c5bbfcbcad7c6c3539db8
Successfully built validators
Installing collected packages: webencodings, wcwidth, Send2Trash, pytz, PyQt5-Qt5, pure-eval, ptyprocess, pickleshare, mistune, ipython-genutils, fastjsonschema, executing, commonmark, backcall, appnope, zipp, watchdog, urllib3, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, toml, tinycss2, threadpoolctl, tenacity, soupsieve, smmap, six, semver, pyzmq, pyyaml, pyrsistent, PyQt5-sip, pyparsing, pympler, pygments, pycparser, psutil, protobuf, prompt-toolkit, prometheus-client, pillow, pexpect, parso, pandocfilters, numpy, nest-asyncio, MarkupSafe, llvmlite, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, joblib, idna, greenlet, future, entrypoints, defusedxml, decorator, debugpy, cycler, colorama, click, charset-normalizer, cachetools, blinker, backports.zoneinfo, attrs, asteval, validators, uncertainties, terminado, sqlalchemy, scipy, rich, requests, pytz-deprecation-shim, python-dateutil, PyQt5, pyarrow, plotly, patsy, packaging, numba, matplotlib-inline, jupyter-core, jinja2, jedi, importlib-resources, importlib-metadata, h5py, gitdb, cffi, bleach, beautifulsoup4, asttokens, tzlocal, stack-data, scikit-learn, pandas, matplotlib, lmfit, jupyter-client, jsonschema, gitpython, argon2-cffi-bindings, statsmodels, nbformat, ipython, argon2-cffi, altair, plotly-express, nbclient, ipykernel, nbconvert, notebook, widgetsnbextension, ipywidgets, pydeck, streamlit, picassosr
Successfully installed MarkupSafe-2.1.1 PyQt5-5.15.7 PyQt5-Qt5-5.15.2 PyQt5-sip-12.11.0 Send2Trash-1.8.0 altair-4.2.0 appnope-0.1.3 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 asteval-0.9.27 asttokens-2.0.5 attrs-21.4.0 backcall-0.2.0 backports.zoneinfo-0.2.1 beautifulsoup4-4.11.1 bleach-5.0.1 blinker-1.5 cachetools-5.2.0 cffi-1.15.1 charset-normalizer-2.1.0 click-8.1.3 colorama-0.4.4 commonmark-0.9.1 cycler-0.11.0 debugpy-1.6.2 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 executing-0.8.3 fastjsonschema-2.16.1 future-0.18.2 gitdb-4.0.9 gitpython-3.1.27 greenlet-1.1.2 h5py-3.7.0 idna-3.3 importlib-metadata-4.12.0 importlib-resources-5.8.0 ipykernel-6.15.1 ipython-8.4.0 ipython-genutils-0.2.0 ipywidgets-7.7.1 jedi-0.18.1 jinja2-3.1.2 joblib-1.1.0 jsonschema-4.7.2 jupyter-client-7.3.4 jupyter-core-4.11.1 jupyterlab-pygments-0.2.2 jupyterlab-widgets-1.1.1 kiwisolver-1.4.4 llvmlite-0.38.1 lmfit-1.0.1 matplotlib-3.3.2 matplotlib-inline-0.1.3 mistune-0.8.4 nbclient-0.6.6 nbconvert-6.5.0 nbformat-5.4.0 nest-asyncio-1.5.5 notebook-6.4.12 numba-0.55.2 numpy-1.22.4 packaging-21.3 pandas-1.4.3 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.2 pexpect-4.8.0 picassosr-0.4.6 pickleshare-0.7.5 pillow-9.2.0 plotly-5.9.0 plotly-express-0.4.1 prometheus-client-0.14.1 prompt-toolkit-3.0.30 protobuf-3.20.0 psutil-5.8.0 ptyprocess-0.7.0 pure-eval-0.2.2 pyarrow-8.0.0 pycparser-2.21 pydeck-0.7.1 pygments-2.12.0 pympler-1.0.1 pyparsing-3.0.9 pyrsistent-0.18.1 python-dateutil-2.8.2 pytz-2022.1 pytz-deprecation-shim-0.1.0.post0 pyyaml-5.3.1 pyzmq-23.2.0 requests-2.28.1 rich-12.5.1 scikit-learn-0.23.2 scipy-1.8.1 semver-2.13.0 six-1.16.0 smmap-5.0.0 soupsieve-2.3.2.post1 sqlalchemy-1.4.22 stack-data-0.3.0 statsmodels-0.13.2 streamlit-1.10.0 tenacity-8.0.1 terminado-0.15.0 threadpoolctl-3.1.0 tinycss2-1.1.1 toml-0.10.2 toolz-0.12.0 tornado-6.2 tqdm-4.50.2 traitlets-5.3.0 typing-extensions-4.3.0 tzdata-2022.1 tzlocal-4.2 uncertainties-3.1.7 urllib3-1.26.10 validators-0.20.0 watchdog-2.1.4 wcwidth-0.2.5 webencodings-0.5.1 widgetsnbextension-3.6.1 zipp-3.8.1
(picasso_sr) wyssuser@wyss12422 ~ % picasso localize
Traceback (most recent call last):
File "/Users/wyssuser/opt/anaconda3/envs/picasso_sr/bin/picasso", line 8, in <module>
sys.exit(main())
File "/Users/wyssuser/opt/anaconda3/envs/picasso_sr/lib/python3.8/site-packages/picasso/__main__.py", line 1530, in main
from picasso.gui import localize
File "/Users/wyssuser/opt/anaconda3/envs/picasso_sr/lib/python3.8/site-packages/picasso/gui/localize.py", line 19, in <module>
from .. import io, localize, gausslq, gaussmle, zfit, lib, CONFIG, avgroi
File "/Users/wyssuser/opt/anaconda3/envs/picasso_sr/lib/python3.8/site-packages/picasso/io.py", line 23, in <module>
from .ext.bitplane import IMSWRITER
ModuleNotFoundError: No module named 'picasso.ext'
Could you check if the error also occurs when you start picasso with python -m picasso localize?
In any case, I just pushed a new version to PyPi that should fix the underlying import error. Please comment in case this works/does not.
Hi Max,
thanks for your quick response. I still received the same error regardless of wether using python -m picasso localize or picasso localize. I checked the picasso package content /Users/wyssuser/opt/anaconda3/envs/picasso_sr/lib/python3.8/site-packages/picasso and found that indeed the folder 'ext' containing bitplane.py was missing. Copying it in from the current repo fixed the issue. I also checked at https://pypi.org/project/picassosr/, it's also missing here. I guess running the builder once more should fix that?
Hi,
I did publish an updated version to PyPi again. Could you try if it works (pip install picassor --upgrade) now?
Works, thanks Max!