pip install error #15
Description
When pip installing empanada-napari into a clean environment, it fails because numpy is not installed.
We tried this on an M1 Mac at the hackathon, it seems the installation of imagecodecs might be the package causing the error?
Details:
(base) genevieb@Admins-MacBook-Pro ~ % conda create -n napari-empanada python=3.9 pip ipython
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 4.13.0
Please update conda by running
$ conda update -n base conda
## Package Plan ##
environment location: /Users/genevieb/mambaforge/envs/napari-empanada
added / updated specs:
- ipython
- pip
- python=3.9
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-3.9.13 |h96fcbfb_0_cpython 12.2 MB conda-forge
python_abi-3.9 | 2_cp39 4 KB conda-forge
------------------------------------------------------------
Total: 12.2 MB
The following NEW packages will be INSTALLED:
appnope conda-forge/noarch::appnope-0.1.3-pyhd8ed1ab_0
asttokens conda-forge/noarch::asttokens-2.0.5-pyhd8ed1ab_0
backcall conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
backports conda-forge/noarch::backports-1.0-py_2
backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h3422bc3_4
ca-certificates conda-forge/osx-arm64::ca-certificates-2022.5.18.1-h4653dfc_0
decorator conda-forge/noarch::decorator-5.1.1-pyhd8ed1ab_0
executing conda-forge/noarch::executing-0.8.3-pyhd8ed1ab_0
ipython conda-forge/osx-arm64::ipython-8.4.0-py39h2804cbe_0
jedi conda-forge/osx-arm64::jedi-0.18.1-py39h2804cbe_1
libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
libzlib conda-forge/osx-arm64::libzlib-1.2.12-h90dfc92_0
matplotlib-inline conda-forge/noarch::matplotlib-inline-0.1.3-pyhd8ed1ab_0
ncurses conda-forge/osx-arm64::ncurses-6.3-h07bb92c_1
openssl conda-forge/osx-arm64::openssl-3.0.3-ha287fd2_0
parso conda-forge/noarch::parso-0.8.3-pyhd8ed1ab_0
pexpect conda-forge/noarch::pexpect-4.8.0-pyh9f0ad1d_2
pickleshare conda-forge/noarch::pickleshare-0.7.5-py_1003
pip conda-forge/noarch::pip-22.1.2-pyhd8ed1ab_0
prompt-toolkit conda-forge/noarch::prompt-toolkit-3.0.29-pyha770c72_0
ptyprocess conda-forge/noarch::ptyprocess-0.7.0-pyhd3deb0d_0
pure_eval conda-forge/noarch::pure_eval-0.2.2-pyhd8ed1ab_0
pygments conda-forge/noarch::pygments-2.12.0-pyhd8ed1ab_0
python conda-forge/osx-arm64::python-3.9.13-h96fcbfb_0_cpython
python_abi conda-forge/osx-arm64::python_abi-3.9-2_cp39
readline conda-forge/osx-arm64::readline-8.1-hedafd6a_0
setuptools conda-forge/osx-arm64::setuptools-62.3.2-py39h2804cbe_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
sqlite conda-forge/osx-arm64::sqlite-3.38.5-h40dfcc0_0
stack_data conda-forge/noarch::stack_data-0.2.0-pyhd8ed1ab_0
tk conda-forge/osx-arm64::tk-8.6.12-he1e0b03_0
traitlets conda-forge/noarch::traitlets-5.2.2.post1-pyhd8ed1ab_0
tzdata conda-forge/noarch::tzdata-2022a-h191b570_0
wcwidth conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_2
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-arm64::xz-5.2.5-h642e427_1
zlib conda-forge/osx-arm64::zlib-1.2.12-h90dfc92_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
python_abi-3.9 | 4 KB | ############################################################################### | 100%
python-3.9.13 | 12.2 MB | ############################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate napari-empanada
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) genevieb@Admins-MacBook-Pro ~ % conda activate napari-empanada
(napari-empanada) genevieb@Admins-MacBook-Pro ~ % conda install -c andfoy pyqt
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 4.13.0
Please update conda by running
$ conda update -n base conda
## Package Plan ##
environment location: /Users/genevieb/mambaforge/envs/napari-empanada
added / updated specs:
- pyqt
The following packages will be downloaded:
package | build
---------------------------|-----------------
libclang-14.0.4 |default_h81a5282_0 127 KB conda-forge
mysql-libs-8.0.29 | h0a1dba2_1 1.9 MB conda-forge
pyqt-5.15.4 | py39hdf13c20_1 18 KB andfoy
------------------------------------------------------------
Total: 2.1 MB
The following NEW packages will be INSTALLED:
gettext conda-forge/osx-arm64::gettext-0.19.8.1-h049c9fb_1008
giflib conda-forge/osx-arm64::giflib-5.2.1-h27ca646_2
gst-plugins-base conda-forge/osx-arm64::gst-plugins-base-1.20.2-hbf05cfb_1
gstreamer conda-forge/osx-arm64::gstreamer-1.20.2-h3d5cedb_1
icu conda-forge/osx-arm64::icu-70.1-h6b3803e_0
jpeg conda-forge/osx-arm64::jpeg-9e-h1c322ee_1
krb5 conda-forge/osx-arm64::krb5-1.19.3-hf9b2bbe_0
lerc conda-forge/osx-arm64::lerc-3.0-hbdafb3b_0
libclang conda-forge/osx-arm64::libclang-14.0.4-default_h81a5282_0
libclang13 conda-forge/osx-arm64::libclang13-14.0.4-default_he70ec0d_0
libcxx conda-forge/osx-arm64::libcxx-14.0.4-h6a5c8ee_0
libdeflate conda-forge/osx-arm64::libdeflate-1.10-h3422bc3_0
libedit conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2
libglib conda-forge/osx-arm64::libglib-2.70.2-h67e64d8_4
libiconv conda-forge/osx-arm64::libiconv-1.16-h642e427_0
libllvm14 conda-forge/osx-arm64::libllvm14-14.0.4-h37c5ba8_0
libogg conda-forge/osx-arm64::libogg-1.3.4-h27ca646_1
libopus conda-forge/osx-arm64::libopus-1.3.1-h27ca646_1
libpng conda-forge/osx-arm64::libpng-1.6.37-hf7e6567_2
libpq conda-forge/osx-arm64::libpq-14.3-h8ab49ba_0
libtiff conda-forge/osx-arm64::libtiff-4.4.0-h2810ee2_0
libvorbis conda-forge/osx-arm64::libvorbis-1.3.7-h9f76cd9_0
libwebp conda-forge/osx-arm64::libwebp-1.2.2-h0d20362_0
libwebp-base conda-forge/osx-arm64::libwebp-base-1.2.2-h3422bc3_1
lz4-c conda-forge/osx-arm64::lz4-c-1.9.3-hbdafb3b_1
mysql-common conda-forge/osx-arm64::mysql-common-8.0.29-haa90c7b_1
mysql-libs conda-forge/osx-arm64::mysql-libs-8.0.29-h0a1dba2_1
nspr conda-forge/osx-arm64::nspr-4.32-hbdafb3b_1
nss conda-forge/osx-arm64::nss-3.78-h1483a63_0
packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
pcre conda-forge/osx-arm64::pcre-8.45-hbdafb3b_0
pyparsing conda-forge/noarch::pyparsing-3.0.9-pyhd8ed1ab_0
pyqt andfoy/osx-arm64::pyqt-5.15.4-py39hdf13c20_1
pyqt-impl andfoy/osx-arm64::pyqt-impl-5.15.4-py39h259b073_1
pyqt5-sip andfoy/osx-arm64::pyqt5-sip-12.9.0-py39h259b073_1
pyqtchart andfoy/osx-arm64::pyqtchart-5.15.4-py39h259b073_1
pyqtwebengine andfoy/osx-arm64::pyqtwebengine-5.15.4-py39h259b073_1
qt-main conda-forge/osx-arm64::qt-main-5.15.3-haf604a7_2
qt-webengine conda-forge/osx-arm64::qt-webengine-5.15.4-h43c6231_3
sip conda-forge/osx-arm64::sip-6.5.1-py39hfb83b0d_2
toml conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0
zstd conda-forge/osx-arm64::zstd-1.5.2-hd705a24_1
The following packages will be DOWNGRADED:
openssl 3.0.3-ha287fd2_0 --> 1.1.1o-ha287fd2_0
python 3.9.13-h96fcbfb_0_cpython --> 3.9.13-hc596b02_0_cpython
Proceed ([y]/n)? y
Downloading and Extracting Packages
mysql-libs-8.0.29 | 1.9 MB | ############################################################################### | 100%
pyqt-5.15.4 | 18 KB | ############################################################################### | 100%
libclang-14.0.4 | 127 KB | ############################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(napari-empanada) genevieb@Admins-MacBook-Pro ~ % pip install empanada-napari
Collecting empanada-napari
Using cached empanada_napari-0.2.0-py3-none-any.whl (68 kB)
Collecting napari-plugin-engine>=0.1.4
Using cached napari_plugin_engine-0.2.0-py3-none-any.whl (33 kB)
Collecting imagecodecs
Using cached imagecodecs-2022.2.22.tar.gz (11.4 MB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [44 lines of output]
running egg_info
creating /private/var/folders/82/phlx_f6j5518qtvpm4x0_0fm0000gq/T/pip-pip-egg-info-hapx6ltu/imagecodecs.egg-info
writing /private/var/folders/82/phlx_f6j5518qtvpm4x0_0fm0000gq/T/pip-pip-egg-info-hapx6ltu/imagecodecs.egg-info/PKG-INFO
writing dependency_links to /private/var/folders/82/phlx_f6j5518qtvpm4x0_0fm0000gq/T/pip-pip-egg-info-hapx6ltu/imagecodecs.egg-info/dependency_links.txt
writing entry points to /private/var/folders/82/phlx_f6j5518qtvpm4x0_0fm0000gq/T/pip-pip-egg-info-hapx6ltu/imagecodecs.egg-info/entry_points.txt
writing requirements to /private/var/folders/82/phlx_f6j5518qtvpm4x0_0fm0000gq/T/pip-pip-egg-info-hapx6ltu/imagecodecs.egg-info/requires.txt
writing top-level names to /private/var/folders/82/phlx_f6j5518qtvpm4x0_0fm0000gq/T/pip-pip-egg-info-hapx6ltu/imagecodecs.egg-info/top_level.txt
writing manifest file '/private/var/folders/82/phlx_f6j5518qtvpm4x0_0fm0000gq/T/pip-pip-egg-info-hapx6ltu/imagecodecs.egg-info/SOURCES.txt'
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/private/var/folders/82/phlx_f6j5518qtvpm4x0_0fm0000gq/T/pip-install-3n7ooxv9/imagecodecs_769fec73556e49f7a05fb2dbd5397692/setup.py", line 644, in <module>
setup(
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 148, in setup
return run_commands(dist)
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 163, in run_commands
dist.run_commands()
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 967, in run_commands
self.run_command(cmd)
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/dist.py", line 1229, in run_command
super().run_command(command)
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 308, in run
self.find_sources()
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 315, in find_sources
mm.run()
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 550, in run
self.add_defaults()
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 587, in add_defaults
sdist.add_defaults(self)
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/_distutils/command/sdist.py", line 228, in add_defaults
self._add_defaults_ext()
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/_distutils/command/sdist.py", line 311, in _add_defaults_ext
build_ext = self.get_finalized_command('build_ext')
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 299, in get_finalized_command
cmd_obj.ensure_finalized()
File "/Users/genevieb/mambaforge/envs/napari-empanada/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 107, in ensure_finalized
self.finalize_options()
File "/private/var/folders/82/phlx_f6j5518qtvpm4x0_0fm0000gq/T/pip-install-3n7ooxv9/imagecodecs_769fec73556e49f7a05fb2dbd5397692/setup.py", line 613, in finalize_options
import numpy
ModuleNotFoundError: No module named 'numpy'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
(napari-empanada) genevieb@Admins-MacBook-Pro ~ % conda list | grep numpy
(napari-empanada) genevieb@Admins-MacBook-Pro ~ %