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Update README.md
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kushalkolar authored Sep 20, 2022
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Expand Up @@ -49,14 +49,18 @@ https://user-images.githubusercontent.com/9403332/191207883-2393664d-b5e1-49a5-8

### This is all possible within jupyter notebooks using `fastplotlib`!

# Examples

**See `notebooks/mcorr_cnmf.ipynb` for detailed examples.** Note that running the demo requires [`fastplotlib`](https://github.com/kushalkolar/fastplotlib) for visualizations.

# Installation

## For development

### conda

```bash
# create an env, can be same env you use for mesmerize-napari or another viz tool like fastplotlib
# create an env
conda create --item_name mesmerize-core python=3.10

# install mamba
Expand All @@ -73,9 +77,6 @@ cd mesmerize-core
# update env with environment file
mamba env update -n mesmerize-core --file environment.yml

# temporary until pandas v1.5.0 is released
pip install git+https://github.com/pandas-dev/pandas.git

# install caimanmanager
caimanmanager.py install

Expand All @@ -89,7 +90,8 @@ MESMERIZE_KEEP_TEST_DATA=1 DOWNLOAD_GROUND_TRUTHS=1 pytest -s .

### python venvs
```bash
# create a new env, can be the same env that you use for mesmerize-napari or another viz tool like fastplotlib
# create a new env
# tested on python3.9 and 3.10
python3.10 -m venv ~/python-venvs/mesmerize-core
source ~/python-venvs/mesmerize-core/bin/activate

Expand All @@ -106,25 +108,12 @@ pip install -r requirements.txt
pip install .
caimanmanager.py install

# clone this repo
# clone this repo and install mesmerize-core
cd ..
git clone https://github.com/nel-lab/mesmerize-core.git
cd mesmerize-core

# get dependencies
pip install -r requirements.txt

# temporary until pandas v1.5.0 is released
pip install git+https://github.com/pandas-dev/pandas.git

# install mesmerize-core
pip install -e .

# install pytest and run tests
pip install pytest
# run tests to make sure everything works
MESMERIZE_KEEP_TEST_DATA=1 DOWNLOAD_GROUND_TRUTHS=1 pytest -s .
```

# Examples

**See `notebooks/mcorr_cnmf.ipynb` for detailed examples.** Note that running the demo requires [`fastplotlib`](https://github.com/kushalkolar/fastplotlib) for visualizations.

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