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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?
(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 ~ %
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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:
The text was updated successfully, but these errors were encountered: