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nel-lab / mesmerize-core

High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn
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Unable to install mesmerize_core #219

Closed zhouyi0812 closed 1 year ago

zhouyi0812 commented 1 year ago

Hi,

I was unable to use mesmerize for reconstruct the movie by following the installation from the instruction of the installation with mamba.

(caiman) yizhou@DN51s0e6 ~ % mamba activate mescore Run 'mamba init' to be able to run mamba activate/deactivate and start a new shell session. Or use conda to activate/deactivate.

----> 1 import mesmerize_core

ModuleNotFoundError: No module named 'mesmerize_core'

In [2]: mesmerize_core.version

kushalkolar commented 1 year ago

It looks like you're not in the right environment, assuming you installed mesmerize-core in a separate environment:

Run 'mamba init' to be able to run mamba activate/deactivate and start a new shell session. Or use conda to activate/deactivate.

zhouyi0812 commented 1 year ago

I tried 'mamba init' and then restart my terminal. Then tried "mamba activate memerize_core", it return: (base) yizhou@DN51s0e6 ~ % mamba activate mesmerize_core Traceback (most recent call last): File "/Users/yizhou/miniconda3/bin/mamba", line 7, in from mamba.mamba import main File "/Users/yizhou/miniconda3/lib/python3.10/site-packages/mamba/mamba.py", line 49, in import libmambapy as api File "/Users/yizhou/miniconda3/lib/python3.10/site-packages/libmambapy/init.py", line 7, in raise e File "/Users/yizhou/miniconda3/lib/python3.10/site-packages/libmambapy/init.py", line 4, in from libmambapy.bindings import * # noqa: F401,F403 ImportError: dlopen(/Users/yizhou/miniconda3/lib/python3.10/site-packages/libmambapy/bindings.cpython-310-darwin.so, 2): Library not loaded: @rpath/libarchive.13.dylib Referenced from: /Users/yizhou/miniconda3/lib/libmamba.2.0.0.dylib Reason: image not found

I think I install mesmerize_core in caiman........

kushalkolar commented 1 year ago

Are you able to import it in your caiman environment if you installed it in that env?

How did you install caiman? Was it not using mamba?

zhouyi0812 commented 1 year ago

what do you mean with import it in caiman? if I enter 'mamba' in caiman envior:

(caiman) yizhou@DN51s0e6 ~ % mamba usage: mamba [-h] [-V] command ...

conda is a tool for managing and deploying applications, environments and packages.

Options:

positional arguments: command clean Remove unused packages and caches. compare Compare packages between conda environments. config Modify configuration values in .condarc. This is modeled after the git config command. Writes to the user .condarc file (/Users/yizhou/.condarc) by default. Use the --show-sources flag to display all identified configuration locations on your computer.

I can't remember how I install caiman, and I use Mac, probably mamba is not required for it.

kushalkolar commented 1 year ago

I asked Pat, you have to activate with conda even if you used mamba to install it.

Use: conda activate env-name

(replace env-name with the name of the environment that has mesmerize-core)

On Thu, Jul 20, 2023, 23:17 Yi Zhou @.***> wrote:

what do you mean with import it in caiman? if I enter 'mamba' in caiman envior:

(caiman) @.*** ~ % mamba usage: mamba [-h] [-V] command ...

conda is a tool for managing and deploying applications, environments and packages.

Options:

positional arguments: command clean Remove unused packages and caches. compare Compare packages between conda environments. config Modify configuration values in .condarc. This is modeled after the git config command. Writes to the user .condarc file (/Users/yizhou/.condarc) by default. Use the --show-sources flag to display all identified configuration locations on your computer.

I can't remember how I install caiman, and I use Mac, probably mamba is not required for it.

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zhouyi0812 commented 1 year ago

Thank you!

I checked my conda environment and found I install mesmerize_core in caiman, and I: conda activate caiman; and check in ipython: pip install mesmerize_core; and mesmerize_core.__version, and it return: .

10/site-packages (from stack-data->ipython>=7.23.1->ipykernel->jupyterlab->mesmerize_core) (0.2.2) Requirement already satisfied: pycparser in ./miniconda3/envs/caiman/lib/python3.10/site-packages (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi->jupyter-server<3,>=2.4.0->jupyterlab->mesmerize_core) (2.21) Requirement already satisfied: arrow>=0.15.0 in ./miniconda3/envs/caiman/lib/python3.10/site-packages (from isoduration->jsonschema>=4.17.3->jupyterlab-server<3,>=2.19.0->jupyterlab->mesmerize_core) (1.2.3)

In [2]: mesmerize_core.version

NameError Traceback (most recent call last) Cell In[2], line 1 ----> 1 mesmerize_core.version

NameError: name 'mesmerize_core' is not defined

                     /Users/yizhou/Library/r-miniconda
                     /Users/yizhou/Library/r-miniconda/envs/r-reticulate

base * /Users/yizhou/miniconda3 caiman /Users/yizhou/miniconda3/envs/caiman /Users/yizhou/miniconda3/envs/caiman/envs/mescore caiman_env /Users/yizhou/miniconda3/envs/caiman_env opencv /Users/yizhou/miniconda3/envs/opencv py39 /Users/yizhou/miniconda3/envs/py39 snakes /Users/yizhou/miniconda3/envs/snakes snowflakes /Users/yizhou/miniconda3/envs/snowflakes /Users/yizhou/opt/anaconda3

kushalkolar commented 1 year ago

Don't use pip to install mesmerize-core in a conda environment. If you've installed mesmerize-core you can import it in ipython, jupyter etc.

On Fri, Jul 21, 2023, 01:45 Yi Zhou @.***> wrote:

Thank you!

I checked my conda environment and found I install mesmerize_core in caiman, and I: conda activate caiman; and check in ipython: pip install mesmerize_core; and mesmerize_core.__version, and it return: .

10/site-packages (from stack-data->ipython>=7.23.1->ipykernel->jupyterlab->mesmerize_core) (0.2.2) Requirement already satisfied: pycparser in ./miniconda3/envs/caiman/lib/python3.10/site-packages (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi->jupyter-server<3,>=2.4.0->jupyterlab->mesmerize_core) (2.21) Requirement already satisfied: arrow>=0.15.0 in ./miniconda3/envs/caiman/lib/python3.10/site-packages (from isoduration->jsonschema>=4.17.3->jupyterlab-server<3,>=2.19.0->jupyterlab->mesmerize_core) (1.2.3) In [2]: mesmerize_core.version

NameError Traceback (most recent call last) Cell In[2], line 1 ----> 1 mesmerize_core.version

NameError: name 'mesmerize_core' is not defined

                 /Users/yizhou/Library/r-miniconda
                 /Users/yizhou/Library/r-miniconda/envs/r-reticulate

base * /Users/yizhou/miniconda3 caiman /Users/yizhou/miniconda3/envs/caiman /Users/yizhou/miniconda3/envs/caiman/envs/mescore caiman_env /Users/yizhou/miniconda3/envs/caiman_env opencv /Users/yizhou/miniconda3/envs/opencv py39 /Users/yizhou/miniconda3/envs/py39 snakes /Users/yizhou/miniconda3/envs/snakes snowflakes /Users/yizhou/miniconda3/envs/snowflakes /Users/yizhou/opt/anaconda3

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