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biocore / q2-greengenes2

A QIIME 2 plugin for interaction with the Greengenes2 database
BSD 3-Clause "New" or "Revised" License
26 stars 3 forks source link

ModuleNotFoundError: No module named 'numpy' #19

Closed flopflip closed 1 year ago

flopflip commented 1 year ago

Hello,

on OS X Ventura the installation throws error ModuleNotFoundError: No module named 'numpy' even though it is already install

this was tried for all versions of qiime2, both with and without qiime2 activated

full log below:

python -mpip install q2-greengenes2 Collecting q2-greengenes2 Using cached q2-greengenes2-2023.3.tar.gz (38 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: biom-format in ./.pyenv/versions/3.9.1/lib/python3.9/site-packages (from q2-greengenes2) (2.1.14) Collecting iow (from q2-greengenes2) Using cached iow-1.0.6.tar.gz (941 kB) Installing build dependencies ... done Getting requirements to build wheel ... error error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [17 lines of output] Traceback (most recent call last): File "/Users/ergo/.pyenv/versions/3.9.1/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in main() File "/Users/ergo/.pyenv/versions/3.9.1/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/Users/ergo.pyenv/versions/3.9.1/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/private/var/folders/5m/3yj_f6vx3rxgqplmzcq4bt_h0000gn/T/pip-build-env-2u2j3ocl/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/private/var/folders/5m/3yj_f6vx3rxgqplmzcq4bt_h0000gn/T/pip-build-env-2u2j3ocl/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/private/var/folders/5m/3yj_f6vx3rxgqplmzcq4bt_h0000gn/T/pip-build-env-2u2j3ocl/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 487, in run_setup super(_BuildMetaLegacyBackend, File "/private/var/folders/5m/3yj_f6vx3rxgqplmzcq4bt_h0000gn/T/pip-build-env-2u2j3ocl/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "", line 18, in ModuleNotFoundError: No module named 'numpy' [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output.

pip install numpy
Requirement already satisfied: numpy in ./.pyenv/versions/3.9.1/lib/python3.9/site-packages (1.25.2)

wasade commented 1 year ago

Hi @flopflip, thank you for opening the issue. I'm puzzled by this as QIIME 2 environments already have numpy, and a version which is compatible with the q2-greengenes2 dependencies.

I suspect there may be a more general issue going on, rather than being specific to q2-greengenes2. Would you be able to open a thread on the QIIME 2 forum with this detail? Please tag me on there with @wasade

I'll leave this issue open for the time being just incase

flopflip commented 1 year ago

Hi there,

I think your plugin installation happens in some kind of temporary “private” directory where the install script does not see what is installed system-wide - is there a chance you can bundle the libraries like dumpy or at least add a script line to download them via pip in that private directory instead of throwing an error?

Thank you in advance for considering this request.

BTW, your install worked fine on my linux computer, but it gags on OS X.

Oh, and I am not holding my breath on the qiime people fixing this.

Cheers,

Mr. Flip

On 8 Aug 2023, at 18:39, Daniel McDonald @.***> wrote:

Hi @flopfliphttps://github.com/flopflip, thank you for opening the issue. I'm puzzled by this as QIIME 2 environments already have numpy, and a version which is compatible with the q2-greengenes2 dependencies.

I suspect there may be a more general issue going on, rather than being specific to q2-greengenes2. Would you be able to open a thread on the QIIME 2 forum<x-msg://1/forum.qiime2.org/> with this detail? Please tag me on there with @wasadehttps://github.com/wasade

I'll leave this issue open for the time being just incase

— Reply to this email directly, view it on GitHubhttps://github.com/biocore/q2-greengenes2/issues/19#issuecomment-1669823796, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACHWNJOVGBY365E6COUBLG3XUJKINANCNFSM6AAAAAA3H4UQOY. You are receiving this because you were mentioned.Message ID: @.***>

wasade commented 1 year ago

q2-greengenes2 installs without issue into a vanilla QIIME 2 2023.5 environment on my local OSX system. That doesn't definitively rule out the issue being isolated to this plugin, or OSX. However, it does work with QIIME 2 on OSX on some systems, and I'm unaware of anything about this plugin which would lead to differences across OSX systems.

As this is a simple plugin by QIIME 2 standards, it very likely is a more general problem with your environment or some other type of edge case related to the QIIME 2 framework.

What happens if you do pip install q2-fragment-insertion?

The QIIME 2 team is incredibly responsive, and I strongly recommend considering their assistance.

flopflip commented 1 year ago

So, to test other plugins I was able to install in qiime2023.5: pip install redbiom

which successfully pulled all its dependencies and installed them, then compiled, etc.

Is there any chance to include a hook in your scrip to pull numpy for the greengenes2, as it does not see the one that is already installed?

wasade commented 1 year ago

redbiom is not a QIIME 2 plugin. Was an install for q2-fragment-insertion within a vanilla QIIME 2 environment successful?

I just created a new environment on OSX, followed by pip install q2-greengenes2. Pip reports the numpy requirement is already satisfied. This is expected as Numpy is both part of the standard QIIME 2 installation, and is a requirement implicitly through its direct dependencies install_requires as they all use and require numpy. Adding numpy as another install_requires is unlikely to lead to a change on your system. There is nothing particularly special about the pip installation for q2-greengenes2, hence the request to open an issue on a more general forum.

While I cannot recreate your issue, which complicates a definitive resolution, it is the case that we are not exercising CI in OSX, and the CI steps themselves do not mirror user action, so I'll be issuing a PR to address that momentarily.

Could you provide the following output in full so that I can better understand your environment?

$ conda activate qiime2-2023.5
$ which conda
$ which pip
$ conda list
$ pip freeze
$ uname -a
wasade commented 1 year ago

@flopflip, for reference, CI passes on OS X as well and reports numpy is already satisfied. The commands used to install QIIME 2 are here, and the command used to install q2-greengenes2 is here

flopflip commented 1 year ago

Hello again and thank you for looking into this!

The other plug-in seems to be unavailable? :

(qiime2-2023.5) ergo@ergos-MacBook-Pro Downloads % pip install q2-fragment-insertion ERROR: Could not find a version that satisfies the requirement q2-fragment-insertion (from versions: none) ERROR: No matching distribution found for q2-fragment-insertion

The same error happens for previous versions of qiime2.

Next, the output of the commands you listed:

(base) ergo@ergos-MacBook-Pro Downloads % conda activate qiime2-2023.5 (qiime2-2023.5) ergo@ergos-MacBook-Pro Downloads % which conda conda () { \local cmd="${1-missing}" case "$cmd" in (activate | deactivate) conda_activate "$@" ;; (install | update | upgrade | remove | uninstall) __conda_exe "$@" || \return conda_reactivate ;; (*) __conda_exe "$@" ;; esac } (qiime2-2023.5) ergo@ergos-MacBook-Pro Downloads % which pip /Users/ergo/.pyenv/shims/pip (qiime2-2023.5) ergo@ergos-MacBook-Pro Downloads % conda list

packages in environment at /Users/ergo/miniconda3/envs/qiime2-2023.5:

#

Name Version Build Channel

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r42h4c50009_1 bioconda bioconductor-matrixgenerics 1.10.0 r42hdfd78af_0 bioconda bioconductor-mia 1.6.0 r42hdfd78af_0 bioconda bioconductor-multiassayexperiment 1.24.0 r42hdfd78af_0 bioconda bioconductor-multtest 2.54.0 r42h4c50009_1 bioconda bioconductor-phyloseq 1.42.0 r42hdfd78af_0 bioconda bioconductor-rhdf5 2.42.0 r42hfab559d_2 bioconda bioconductor-rhdf5filters 1.10.0 r42hc0ef7c4_1 bioconda bioconductor-rhdf5lib 1.20.0 r42h4c50009_2 bioconda bioconductor-rhtslib 2.0.0 r42h4c50009_1 bioconda bioconductor-rsamtools 2.14.0 r42hc0ef7c4_1 bioconda bioconductor-s4vectors 0.36.0 r42h4c50009_1 bioconda bioconductor-scaledmatrix 1.6.0 r42hdfd78af_0 bioconda bioconductor-scater 1.26.0 r42hdfd78af_0 bioconda bioconductor-scuttle 1.8.0 r42hc0ef7c4_1 bioconda bioconductor-shortread 1.56.0 r42hc0ef7c4_1 bioconda bioconductor-singlecellexperiment 1.20.0 r42hdfd78af_0 bioconda bioconductor-sparsematrixstats 1.10.0 r42hc0ef7c4_1 bioconda bioconductor-summarizedexperiment 1.28.0 r42hdfd78af_0 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conda-forge gfortran_osx-64 11.3.0 h18f7dce_1 conda-forge globus-sdk 3.19.0 pyhd8ed1ab_0 conda-forge glpk 5.0 h3cb5acd_0 conda-forge gmp 6.2.1 h2e338ed_0 conda-forge gneiss 0.4.6 py_0 bioconda graphite2 1.3.13 h2e338ed_1001 conda-forge graphlib-backport 1.0.3 pyhd8ed1ab_0 conda-forge gsl 2.7 h93259b0_0 conda-forge h5py 2.10.0 nompi_py38h9a16e60_106 conda-forge harfbuzz 7.3.0 h413ba03_0 conda-forge hdf5 1.10.6 h10fe05b_1
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conda-forge r-viridislite 0.4.1 r42hc72bb7e_1 conda-forge r-vroom 1.6.3 r42hac7d2d5_1 conda-forge r-withr 2.5.0 r42hc72bb7e_2 conda-forge r-xfun 0.39 r42hac7d2d5_1 conda-forge r-xml2 1.3.4 r42hcf629ed_0 conda-forge r-xtable 1.8_4 r42hc72bb7e_5 conda-forge r-yaml 2.3.7 r42h6dc245f_1 conda-forge r-yulab.utils 0.0.6 r42hc72bb7e_1 conda-forge raxml 8.2.12 h2413b67_6 bioconda readline 8.2 h9e318b2_1 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge samtools 1.17 h25dfcfb_1 bioconda scikit-bio 0.5.7 py38hbe852b5_0 conda-forge scikit-learn 0.24.1 py38hfd19401_0 conda-forge scipy 1.8.1 py38hfb8b963_3 conda-forge seaborn 0.12.2 hd8ed1ab_0 conda-forge seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge send2trash 1.8.2 pyhd1c38e8_0 conda-forge sepp 4.3.10 py38h3252c3a_2 bioconda setproctitle 1.3.2 py38hef030d1_1 conda-forge setuptools 67.7.2 pyhd8ed1ab_0 conda-forge sigtool 0.1.3 h88f4db0_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sniffio 1.3.0 pyhd8ed1ab_0 conda-forge sortmerna 2.0 h5c9b4e4_4 bioconda soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge statsmodels 0.14.0 py38hd2faf92_1 conda-forge tapi 1100.0.11 h9ce4665_0 conda-forge tbb 2021.9.0 hb8565cd_0 conda-forge tblib 1.7.0 pyhd8ed1ab_0 conda-forge terminado 0.17.1 pyhd1c38e8_0 conda-forge threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge tk 8.6.12 h5dbffcc_0 conda-forge tktable 2.10 h49f0cf7_3 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tomlkit 0.11.8 pyha770c72_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tornado 6.3.2 py38hcafd530_0 conda-forge tqdm 4.65.0 pyhd8ed1ab_1 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge typeguard 2.13.3 pyhd8ed1ab_0 conda-forge types-cryptography 3.3.23.2 pyhd8ed1ab_0 conda-forge types-enum34 1.1.8 pyhd8ed1ab_0 conda-forge types-ipaddress 1.0.8 pyhd8ed1ab_0 conda-forge types-paramiko 3.0.0.10 pyhd8ed1ab_0 conda-forge types-requests 2.31.0.1 pyhd8ed1ab_0 conda-forge types-six 1.16.21.8 pyhd8ed1ab_0 conda-forge types-urllib3 1.26.25.13 pyhd8ed1ab_0 conda-forge typing-extensions 4.6.2 hd8ed1ab_0 conda-forge typing_extensions 4.6.2 pyha770c72_0 conda-forge typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge tzlocal 2.1 pyh9f0ad1d_0 conda-forge umap-learn 0.5.3 py38h50d1736_1 conda-forge unicodedata2 15.0.0 py38hef030d1_0 conda-forge unifrac 1.1.1 py38h6da613f_0 bioconda unifrac-binaries 1.1.1 h8c74715_4 bioconda uri-template 1.3.0 pyhd8ed1ab_0 conda-forge urllib3 2.0.2 pyhd8ed1ab_0 conda-forge vsearch 2.22.1 hc4bba69_2 bioconda wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge webcolors 1.13 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 py_1 conda-forge websocket-client 1.5.2 pyhd8ed1ab_0 conda-forge wget 1.20.3 hd3787cc_1 conda-forge wheel 0.40.0 pyhd8ed1ab_1 conda-forge widgetsnbextension 4.0.7 pyhd8ed1ab_0 conda-forge wrapt 1.15.0 py38hef030d1_0 conda-forge xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge xopen 1.7.0 py38h50d1736_2 conda-forge xorg-libxau 1.0.11 h0dc2134_0 conda-forge xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge xyzservices 2023.5.0 pyhd8ed1ab_1 conda-forge xz 5.2.6 h775f41a_0 conda-forge yaml 0.2.5 h0d85af4_2 conda-forge yq 3.2.2 pyhd8ed1ab_0 conda-forge zeromq 4.3.4 he49afe7_1 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h8a1eda9_5 conda-forge zstandard 0.19.0 py38hd8fc1c9_2 conda-forge zstd 1.5.2 h829000d_7 conda-forge (qiime2-2023.5) ergo@ergos-MacBook-Pro Downloads % pip freeze appnope==0.1.3 asttokens==2.2.1 backcall==0.2.0 biom-format==2.1.14 certifi==2023.7.22 cffi==1.15.1 charset-normalizer==3.2.0 click==8.1.3 contourpy==1.1.0 cycler==0.11.0 Cython==0.29.33 decorator==5.1.1 executing==1.2.0 fonttools==4.42.0 h5py==3.8.0 hdmedians==0.14.2 idna==3.4 importlib-resources==6.0.1 ipython==8.14.0 jedi==0.19.0 joblib==1.2.0 kiwisolver==1.4.4 matplotlib==3.7.2 matplotlib-inline==0.1.6 msgpack==1.0.5 natsort==8.4.0 nltk==3.8.1 numpy==1.25.2 packaging==23.1 pandas==1.5.3 parso==0.8.3 pexpect==4.8.0 pickleshare==0.7.5

Editable install with no version control (PICRUSt2==2.5.1)

-e /Users/ergo/Downloads/picrust2-2.5.1 Pillow==10.0.0 prompt-toolkit==3.0.36 ptyprocess==0.7.0 pure-eval==0.2.2 pycparser==2.21 Pygments==2.13.0 pyparsing==3.0.9 python-dateutil==2.8.2 pytz==2022.7.1 radian==0.6.4 rchitect==0.3.39 redbiom==0.3.9 regex==2023.8.8 requests==2.31.0 scikit-bio==0.5.9 scikit-learn==1.3.0 scipy==1.10.0 six==1.16.0 stack-data==0.6.2 threadpoolctl==3.2.0 tqdm==4.65.2 traitlets==5.9.0 typing_extensions==4.7.1 urllib3==2.0.4 wcwidth==0.2.5 zipp==3.16.2 (qiime2-2023.5) ergo@ergos-MacBook-Pro Downloads % uname -a Darwin ergos-MacBook-Pro.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:22:05 PDT 2023; root:xnu-8898.141.3~6/RELEASE_ARM64_T6000 arm64

wasade commented 1 year ago

Thanks! So from this, it looks like the wrong pip is being used. It is correct that q2-fragment-insertion is not in pypi (blanked on that...), however pip should detect it in the environment as it is part of the QIIME 2 2023.5 install. Here's what I see:

$ pip install q2-fragment-insertion                                                                                                                    
Requirement already satisfied: q2-fragment-insertion in /Users/dtmcdonald/micromamba/envs/qiime2-2023.5-test/lib/python3.8/site-packages (2023.5.0)
$ pip freeze | grep frag                                                                                                                               
q2-fragment-insertion==2023.5.0

The reported path for pip on your system is /Users/ergo/.pyenv/shims/pip. Instead, the environment needs to use the installation of pip that came with conda, e.g. pip 23.1.2 pyhd8ed1ab_0 conda-forge in the output above. On my environment, the specific path corresponds to /Users/dtmcdonald/micromamba/envs/qiime2-2023.5-test/bin/pip.

It looks like there are multiple Python environment managers being used, pyenv and conda. These almost certainly are not interacting properly. My best guess is that your PATH environment variable, set in ~/.bashrc or ~/.bash_profile if using bash, is setting a precedence for your pyenv shims over binaries for conda.

Are you able to remove pyenv, or modify your PATH so pyenv is not used with conda?

At this stage, this issue is definitively general and not specific to this plugin. I really recommend moving this to the forum as the developers there have substantially more experience with varied QIIME 2 installation issues, and I think it's been a decade since I've used pyenv

flopflip commented 1 year ago

Thank you for the help! as per you suggestion, this fixed it:

rm -rf $(pyenv root)
brew uninstall pyenv

This can be closed

wasade commented 1 year ago

Great!!