diff --git a/README.md b/README.md index 2d82b73..e59dd2d 100644 --- a/README.md +++ b/README.md @@ -49,6 +49,10 @@ 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 @@ -56,7 +60,7 @@ https://user-images.githubusercontent.com/9403332/191207883-2393664d-b5e1-49a5-8 ### 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 @@ -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 @@ -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 @@ -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.