<commit_before>:: Install additional python dependecies.
conda install -y numpy matplotlib pytables pandas gitpython pyqt \
	h5py scipy scikit-learn scikit-image seaborn xlrd cython statsmodels
conda install -y -c conda-forge tensorflow keras

conda install --channel https://conda.anaconda.org/ver228 opencv3
:: conda config --add channels menpo
:: conda build --no-anaconda-upload installation/menpo_conda-opencv3
:: conda install -y --use-local opencv3

:: Install packages
cd ..\..\open-worm-analysis-toolbox
python setup.py develop
rename .\open_worm_analysis_toolbox\user_config_example.txt user_config.py
cd ..\tierpsy-tracker
python setup.py develop

:: Test installation
python -c "import cv2; import h5py; import MWTracker; import open_worm_analysis_toolbox"<commit_msg>update installation<commit_after>set MW_MAIN_DIR=%~dp0%..\
set OPENWORM_DIR=%MW_MAIN_DIR%..\open-worm-analysis-toolbox

if "%1" == "link_desktop" GOTO link_desktop

: conda_depedencies
:: Install additional python dependecies.
:: Currently only python 3.5 works for tensorflow
conda install -y python=3.5 
conda install -y numpy matplotlib pytables pandas gitpython pyqt h5py scipy scikit-learn scikit-image seaborn xlrd cython statsmodels
conda install -y -c conda-forge tensorflow keras


: install_opencv
:: conda install --channel https://conda.anaconda.org/ver228 opencv3
conda install -y anaconda-client conda-build 
conda config --add channels menpo
conda build --no-anaconda-upload installation/menpo_conda-opencv3
conda install -y --use-local opencv3

: install_openworm_toolbox
git clone https://github.com/openworm/open-worm-analysis-toolbox %OPENWORM_DIR%

cd %OPENWORM_DIR%
git pull
python setup.py develop
copy %OPENWORM_DIR%\open_worm_analysis_toolbox\user_config_example.txt %OPENWORM_DIR%\open_worm_analysis_toolbox\user_config.py

: install_tierpsy
cd %MW_MAIN_DIR%
python setup.py develop

: test
python -c "import cv2; import h5py; import tierpsy; import open_worm_analysis_toolbox"

: link_desktop
echo python %MW_MAIN_DIR%cmd_scripts\TierpsyTrackerConsole.py > %HOMEPATH%\Desktop\TierpsyTracker.bat
{'fraction_non_alphanumeric': 0.08761904761904762, 'fraction_numerical': 0.011428571428571429, 'mean_word_length': 5.386018237082067, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 4, 'https://': 3, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5433000', 'n_tokens_mistral': 743, 'n_tokens_neox': 701, 'n_words': 186}