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| This folder defines the conda package build for Linux and Windows. There are runners for both Linux and Windows on GitHub Actions, but it is faster to experiment with builds locally first. | ||
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| To build, first go to the base repo directory and install the build environment: | ||
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| ``` | ||
| conda env create -f environment_build.yml -n sleap_build && conda activate sleap_build | ||
| ``` | ||
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| And finally, run the build command pointing to this directory: | ||
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| ``` | ||
| conda build .conda --output-folder build -c conda-forge -c nvidia -c https://conda.anaconda.org/sleap/ -c anaconda | ||
| ``` | ||
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| To install the local package: | ||
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| ``` | ||
| conda create -n sleap_0 -c conda-forge -c nvidia -c ./build -c https://conda.anaconda.org/sleap/ -c anaconda sleap=x.x.x | ||
| ``` | ||
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| replacing x.x.x with the version of SLEAP that you just built. |
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| @echo off | ||
| @REM Install anything that didn't get conda installed via pip. | ||
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| rem # Install anything that didn't get conda installed via pip. | ||
| rem # We need to turn pip index back on because Anaconda turns | ||
| rem # it off for some reason. Just pip install -r requirements.txt | ||
| rem # doesn't seem to work, tensorflow-gpu, jsonpickle, networkx, | ||
| rem # all get installed twice if we do this. pip doesn't see the | ||
| rem # conda install of the packages. | ||
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| rem # Install the pip dependencies and their dependencies. Conda turns of | ||
| rem # pip index and dependencies by default so re-enable them. Had to figure | ||
| rem # this out myself, ughhh. | ||
| @REM We need to turn pip index back on because Anaconda turns it off for some reason. | ||
| set PIP_NO_INDEX=False | ||
| set PIP_NO_DEPENDENCIES=False | ||
| set PIP_IGNORE_INSTALLED=False | ||
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| pip install numpy==1.19.5 | ||
| pip install six==1.15.0 | ||
| pip install imageio==2.15.0 | ||
| pip install attrs==21.2.0 | ||
| pip install cattrs==1.1.1 | ||
| pip install jsonpickle==1.2 | ||
| pip install networkx | ||
| pip install nixio>=1.5.3 | ||
| @REM pip install tensorflow>=2.6.3,<=2.7.1 | ||
| @REM pip install h5py>=3.1.0,<=3.6.0 | ||
| pip install python-rapidjson | ||
| @REM pip install opencv-python-headless>=4.2.0.34,<=4.5.5.62 | ||
| @REM pip install opencv-python @ git+https://github.com/talmolab/wrap_opencv-python-headless.git@ede49f6a23a73033216339f29515e59d594ba921 | ||
| @REM pip install pandas | ||
| pip install psutil | ||
| @REM pip install PySide2>=5.13.2,<=5.14.1 | ||
| pip install pyzmq | ||
| pip install pyyaml | ||
| pip install imgaug==0.4.0 | ||
| @REM pip install scipy>=1.4.1,<=1.7.3 | ||
| pip install scikit-image | ||
| pip install scikit-learn==1.0.* | ||
| pip install scikit-video | ||
| pip install tensorflow-hub | ||
| pip install imgstore==0.2.9 | ||
| pip install qimage2ndarray==1.9.0 | ||
| pip install jsmin | ||
| pip install seaborn | ||
| pip install pykalman==0.9.5 | ||
| pip install segmentation-models==1.0.1 | ||
| pip install rich==10.16.1 | ||
| pip install certifi==2021.10.8 | ||
| pip install pynwb | ||
| pip install ndx-pose | ||
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| rem # Use and update environment.yml call to install pip dependencies. This is slick. | ||
| rem # While environment.yml contains the non pip dependencies, the only thing left | ||
| rem # uninstalled should be the pip stuff because that is left out of meta.yml | ||
| rem conda env update -f=environment.yml | ||
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| rem # Install requires setuptools-scm | ||
| pip install setuptools-scm | ||
| @REM Install the pip dependencies. Note: Using urls to wheels might be better: | ||
| @REM https://docs.conda.io/projects/conda-build/en/stable/user-guide/wheel-files.html) | ||
| pip install --no-cache-dir -r .\requirements.txt | ||
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| rem # Install sleap itself. | ||
| rem # NOTE: This is the recommended way to install packages | ||
| @REM Install sleap itself. This does not install the requirements, but will list which | ||
| @REM requirements are missing (see "install_requires") when user attempts to install. | ||
| python setup.py install --single-version-externally-managed --record=record.txt |
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| #!/usr/bin/env bash | ||
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| # Install anything that didn't get conda installed via pip. | ||
| # We need to turn pip index back on because Anaconda turns | ||
| # it off for some reason. Just pip install -r requirements.txt | ||
| # doesn't seem to work, tensorflow-gpu, jsonpickle, networkx, | ||
| # all get installed twice if we do this. pip doesn't see the | ||
| # conda install of the packages. | ||
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| # We need to turn pip index back on because Anaconda turns it off for some reason. | ||
| export PIP_NO_INDEX=False | ||
| export PIP_NO_DEPENDENCIES=False | ||
| export PIP_IGNORE_INSTALLED=False | ||
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| pip install numpy==1.19.5 | ||
| pip install six==1.15.0 | ||
| pip install imageio==2.15.0 | ||
| pip install attrs==21.2.0 | ||
| pip install cattrs==1.1.1 | ||
| pip install jsonpickle==1.2 | ||
| pip install networkx | ||
| pip install nixio>=1.5.3 | ||
| # pip install tensorflow>=2.6.3,<=2.7.1 | ||
| # pip install h5py>=3.1.0,<=3.6.0 | ||
| pip install python-rapidjson | ||
| # pip install opencv-python-headless==4.5.5.62 | ||
| # pip install git+https://github.com/talmolab/wrap_opencv-python-headless.git@ede49f6a23a73033216339f29515e59d594ba921 | ||
| # pip install pandas | ||
| pip install psutil | ||
| # pip install PySide2>=5.13.2,<=5.14.1 | ||
| pip install pyzmq | ||
| pip install pyyaml | ||
| pip install imgaug==0.4.0 | ||
| # pip install scipy>=1.4.1,<=1.7.3 | ||
| pip install scikit-image | ||
| pip install scikit-learn==1.0.* | ||
| pip install scikit-video | ||
| pip install tensorflow-hub | ||
| pip install imgstore==0.2.9 | ||
| pip install qimage2ndarray==1.9.0 | ||
| pip install jsmin | ||
| pip install seaborn | ||
| pip install pykalman==0.9.5 | ||
| pip install segmentation-models==1.0.1 | ||
| pip install rich==10.16.1 | ||
| pip install certifi==2021.10.8 | ||
| pip install pynwb | ||
| pip install ndx-pose | ||
| # Install the pip dependencies. Note: Using urls to wheels might be better: | ||
| # https://docs.conda.io/projects/conda-build/en/stable/user-guide/wheel-files.html) | ||
| pip install --no-cache-dir -r ./requirements.txt | ||
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| pip install setuptools-scm | ||
| # Install sleap itself. This does not install the requirements, but will list which | ||
| # requirements are missing (see "install_requires") when user attempts to install. | ||
| python setup.py install --single-version-externally-managed --record=record.txt | ||
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| python setup.py install --single-version-externally-managed --record=record.txt | ||
| # Copy the activate scripts to $PREFIX/etc/conda/activate.d. | ||
| # This will allow them to be run on environment activation. | ||
| for CHANGE in "activate" "deactivate" | ||
| do | ||
| mkdir -p "${PREFIX}/etc/conda/${CHANGE}.d" | ||
| cp "${RECIPE_DIR}/${PKG_NAME}_${CHANGE}.sh" "${PREFIX}/etc/conda/${CHANGE}.d/${PKG_NAME}_${CHANGE}.sh" | ||
| done |
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| channels: | ||
| - conda-forge | ||
| - nvidia | ||
| - https://conda.anaconda.org/sleap/label/dev | ||
| - sleap | ||
| - anaconda |
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| #!/bin/sh | ||
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| # Remember the old library path for when we deactivate | ||
| export SLEAP_OLD_LD_LIBRARY_PATH=$LD_LIBRARY_PATH | ||
| # Help CUDA find GPUs! | ||
| export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH |
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| #!/bin/sh | ||
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| # Reset to the old library path for when deactivating the environment | ||
| export LD_LIBRARY_PATH=$SLEAP_OLD_LD_LIBRARY_PATH |
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