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Revise dependencies (LorenFrankLab#822)
* Change dependencies. See details. Across `pyproject.toml` and both `environment.yml`: - Alphabetical sort to allow for easier comparison across toml/yaml files. - Remove dependencies required by other dependencies to reduce build time. - Move `black` to `test` dependencies. Could be `dev` instead? - Move `click` to `test` dependencies. CLI should be its own package. - Add ruff config to `pyproject.toml`. Flake8 replacement to allow removal of `setup.cfg`. - Remove `tqdm`, as it is required by `datajoint` Standard environment: - Add comments for all dependencies specific to position environment to allow for easier comparison across yaml files. - Remove `dask`, as it is required by `ghostipy` - Remove `hdmf`, as it is required by `pynwb` - Remove `pymysql`, as it is required by `datajoint` - Remove `pyyaml`, as it is required by `sortingview` - Remove `pydotplus` from `pip` section, as it is already in `conda` section Position environment: - Rename `_position` or `-position` to `_dlc` or `-dlc` to be more precise. - Remove `ipython`, `numba`, and `tensorflow`, as they are all required by `deeplabcut` - Add items present in standard environment but not in position environment. * Add pybind11 for std env.yml * Change dependencies. See details. - `trajectory_analysis_tools` and `replay_trajectory_classification` are superceded by `non_local_detector`. - `dask-cuda` not in use, per @edeno * Fixes for running notebooks up to 41 * Further dependency adjustments following PR review @edeno * Depedencies for panel * LorenFrankLab#810
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# 1. Install a conda distribution. | ||
# https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html | ||
# 2. Run: `mamba env create -f environment.yml` | ||
# 3. Activate: `conda activate spyglass` | ||
# | ||
# (lines intentionally left blank) | ||
# | ||
# | ||
name: spyglass | ||
channels: | ||
- conda-forge | ||
- defaults | ||
# - pytorch # dlc-only | ||
- franklab | ||
- edeno | ||
dependencies: | ||
- python>=3.9,<3.10 | ||
- bottleneck | ||
# - cudatoolkit=11.3 # dlc-only | ||
# - ffmpeg # dlc-only | ||
- ipympl | ||
- jupyterlab>=3.* | ||
- pydotplus | ||
- dask | ||
# - libgcc # dlc-only | ||
- matplotlib | ||
- non_local_detector | ||
- numpy<1.24 | ||
- pip | ||
- position_tools | ||
- numpy<1.24 | ||
- track_linearization>=2.3 | ||
- pybind11 # req by mountainsort4 -> isosplit5 | ||
- pydotplus | ||
- pyfftw<=0.12.0 # ghostipy req. install from conda-forge for Mac ARM | ||
- python>=3.9,<3.10 | ||
- pytorch<1.12.0 | ||
- ripple_detection | ||
- non_local_detector | ||
- matplotlib | ||
- seaborn | ||
- bottleneck | ||
- ipympl | ||
- tqdm | ||
- pyfftw<=0.12.0 # used by ghostipy. install from conda-forge so that it works on Mac ARM processors | ||
# - torchaudio # dlc-only | ||
# - torchvision # dlc-only | ||
- track_linearization>=2.3 | ||
- pip: | ||
- pubnub<6.4.0 | ||
- spikeinterface>=0.98.2,<0.99 | ||
- pynwb>=2.2.0,<3 | ||
- hdmf>=3.4.6 | ||
- "black[jupyter]" | ||
- datajoint>=0.13.6 | ||
- ghostipy | ||
- pymysql | ||
# - deeplabcut<2.3.0 # dlc-only | ||
- ghostipy # for common_filter | ||
- ndx-franklab-novela>=0.1.0 | ||
- mountainsort4 | ||
- panel<=1.3.5 # See panel #6325 | ||
- pubnub<=6.4.0 | ||
- pynwb>=2.2.0,<3 | ||
- sortingview>=0.11 | ||
- figurl-jupyter | ||
- git+https://github.com/LorenFrankLab/ndx-franklab-novela.git | ||
- pyyaml | ||
- click | ||
- "black[jupyter]" | ||
- spikeinterface>=0.98.2,<0.99 | ||
- . |
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# 1. INSTALL CORRECT DRIVER for your GPU-equipped machine. | ||
# see https://stackoverflow.com/questions/30820513/what-is-the-correct-version-of-cuda-for-my-nvidia-driver/30820690 | ||
# 2. install: mamba env create -f environment_dlc.yml | ||
# update existing install: mamba env update -f environment_dlc.yml | ||
# 2. After installing... | ||
# run: conda activate spyglass-dlc | ||
# run: mamba env config vars set LD_LIBRARY_PATH=~/path/to/<anaconda3 or mambaforge>/envs/spyglass-position/lib/ | ||
# run: mamba install -c conda-forge wxpython | ||
name: spyglass-dlc | ||
channels: | ||
- conda-forge | ||
- defaults | ||
- pytorch # dlc-only | ||
- franklab | ||
- edeno | ||
dependencies: | ||
- bottleneck | ||
- cudatoolkit=11.3 # dlc-only | ||
- ffmpeg # dlc-only | ||
- ipympl | ||
- jupyterlab>=3.* | ||
- libgcc # dlc-only | ||
- matplotlib | ||
- non_local_detector | ||
- numpy<1.24 | ||
- pip>=20.2.* | ||
- position_tools | ||
- pybind11 # req by mountainsort4 -> isosplit5 | ||
- pydotplus>=2.0.* | ||
- pyfftw<=0.12.0 # ghostipy req. install from conda-forge for Mac ARM | ||
- python>=3.9,<3.10 | ||
- pytorch<1.12.0 | ||
- ripple_detection | ||
- seaborn | ||
- torchaudio # dlc-only | ||
- torchvision # dlc-only | ||
- track_linearization>=2.3 | ||
- pip: | ||
- "black[jupyter]" | ||
- datajoint>=0.13.6 | ||
- deeplabcut<2.3.0 # dlc-only | ||
- ghostipy # for common_filter | ||
- ndx-franklab-novela>=0.1.0 | ||
- mountainsort4 | ||
- panel<=1.3.5 # See panel #6325 | ||
- pubnub<=6.4.0 | ||
- pynwb>=2.2.0,<3 | ||
- sortingview>=0.11 | ||
- spikeinterface>=0.98.2,<0.99 | ||
- .[dlc] |
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