From 7d26eb2056f598de29b9592c114694f57b4ed850 Mon Sep 17 00:00:00 2001 From: Samuel Sledzieski Date: Tue, 17 Nov 2020 09:13:18 -0500 Subject: [PATCH] updated conda environment --- conda-env.yml | 139 ------------------------------------------ docs/Makefile | 3 - docs/requirements.txt | 4 -- environment.yml | 17 ++++++ 4 files changed, 17 insertions(+), 146 deletions(-) delete mode 100644 conda-env.yml create mode 100644 environment.yml diff --git a/conda-env.yml b/conda-env.yml deleted file mode 100644 index 70073cc..0000000 --- a/conda-env.yml +++ /dev/null @@ -1,139 +0,0 @@ -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: linux-64 -_libgcc_mutex=0.1=conda_forge -_openmp_mutex=4.5=1_llvm -_pytorch_select=0.2=gpu_0 -argon2-cffi=20.1.0=py37h8f50634_1 -async_generator=1.10=py_0 -attrs=20.2.0=pyh9f0ad1d_0 -backcall=0.2.0=pyh9f0ad1d_0 -backports=1.0=py_2 -backports.functools_lru_cache=1.6.1=py_0 -blas=1.0=mkl -bleach=3.2.1=pyh9f0ad1d_0 -ca-certificates=2020.6.20=hecda079_0 -certifi=2020.6.20=py37hc8dfbb8_0 -cffi=1.14.1=py37h2b28604_0 -cudatoolkit=10.0.130=0 -cudnn=7.6.5=cuda10.0_0 -cycler=0.10.0=py_2 -dbus=1.13.6=he372182_0 -decorator=4.4.2=py_0 -defusedxml=0.6.0=py_0 -entrypoints=0.3=py37hc8dfbb8_1001 -expat=2.2.9=he1b5a44_2 -fontconfig=2.13.1=h86ecdb6_1001 -freetype=2.10.2=he06d7ca_0 -gettext=0.19.8.1=hc5be6a0_1002 -glib=2.66.0=h0dae87d_0 -gst-plugins-base=1.14.5=h0935bb2_2 -gstreamer=1.14.5=h36ae1b5_2 -h5py=2.10.0=nompi_py37h90cd8ad_104 -hdf5=1.10.6=nompi_h3c11f04_101 -icu=64.2=he1b5a44_1 -importlib-metadata=1.7.0=py37hc8dfbb8_0 -importlib_metadata=1.7.0=0 -ipykernel=5.3.4=py37h43977f1_0 -ipython=7.18.1=py37hc6149b9_0 -ipython_genutils=0.2.0=py_1 -ipywidgets=7.5.1=pyh9f0ad1d_1 -jedi=0.15.2=py37_0 -jinja2=2.11.2=pyh9f0ad1d_0 -joblib=0.16.0=py_0 -jpeg=9d=h516909a_0 -json5=0.9.4=pyh9f0ad1d_0 -jsonschema=3.2.0=py37hc8dfbb8_1 -jupyter=1.0.0=py_2 -jupyter_client=6.1.7=py_0 -jupyter_console=6.2.0=py_0 -jupyter_core=4.6.3=py37hc8dfbb8_1 -jupyterlab_pygments=0.1.1=pyh9f0ad1d_0 -kiwisolver=1.2.0=py37h99015e2_0 -ld_impl_linux-64=2.35=h769bd43_9 -libblas=3.8.0=16_mkl -libcblas=3.8.0=16_mkl -libffi=3.2.1=he1b5a44_1007 -libgcc-ng=9.3.0=h24d8f2e_16 -libgfortran-ng=7.5.0=hdf63c60_16 -libiconv=1.16=h516909a_0 -liblapack=3.8.0=16_mkl -libpng=1.6.37=hed695b0_2 -libsodium=1.0.18=h516909a_0 -libstdcxx-ng=9.3.0=hdf63c60_16 -libuuid=2.32.1=h14c3975_1000 -libxcb=1.13=h14c3975_1002 -libxml2=2.9.10=hee79883_0 -llvm-openmp=10.0.1=hc9558a2_0 -markupsafe=1.1.1=py37h8f50634_1 -matplotlib=3.1.3=py37_0 -matplotlib-base=3.1.3=py37h250f245_0 -mistune=0.8.4=py37h8f50634_1001 -mkl=2020.2=256 -mkl-service=2.3.0=py37h8f50634_1 -nbclient=0.5.0=py_0 -nbconvert=6.0.5=py37hc8dfbb8_0 -nbformat=5.0.7=py_0 -ncurses=6.2=he1b5a44_1 -nest-asyncio=1.4.0=py_1 -networkx=2.4=py_1 -ninja=1.10.1=hc9558a2_1 -notebook=6.1.4=py37hc8dfbb8_0 -numpy=1.18.5=py37h8960a57_0 -openssl=1.1.1g=h516909a_1 -packaging=20.4=pyh9f0ad1d_0 -pandas=1.0.5=py37h0da4684_0 -pandoc=2.10.1=h516909a_0 -pandocfilters=1.4.2=py_1 -parso=0.5.2=py_0 -patsy=0.5.1=py_0 -pcre=8.44=he1b5a44_0 -pexpect=4.8.0=py37hc8dfbb8_1 -pickleshare=0.7.5=py37hc8dfbb8_1001 -pip=20.2.3=py_0 -prometheus_client=0.8.0=pyh9f0ad1d_0 -prompt-toolkit=3.0.7=py_0 -prompt_toolkit=3.0.7=0 -pthread-stubs=0.4=h14c3975_1001 -ptyprocess=0.6.0=py_1001 -pycparser=2.20=pyh9f0ad1d_2 -pygments=2.7.1=py_0 -pyparsing=2.4.7=pyh9f0ad1d_0 -pyqt=5.9.2=py37hcca6a23_4 -pyrsistent=0.17.3=py37h8f50634_0 -python=3.7.8=h6f2ec95_1_cpython -python-dateutil=2.8.1=py_0 -python_abi=3.7=1_cp37m -pytorch=1.2.0=cuda100py37h938c94c_0 -pytz=2020.1=pyh9f0ad1d_0 -pyzmq=19.0.2=py37hac76be4_0 -qt=5.9.7=h0c104cb_3 -qtconsole=4.7.7=pyh9f0ad1d_0 -qtpy=1.9.0=py_0 -readline=8.0=he28a2e2_2 -scikit-learn=0.22.2.post1=py37hcdab131_0 -scipy=1.4.1=py37ha3d9a3c_3 -seaborn=0.10.1=1 -seaborn-base=0.10.1=py_1 -send2trash=1.5.0=py_0 -setuptools=49.6.0=py37hc8dfbb8_0 -sip=4.19.8=py37hf484d3e_1000 -six=1.15.0=pyh9f0ad1d_0 -sqlite=3.33.0=h4cf870e_0 -statsmodels=0.12.0=py37h8f50634_0 -terminado=0.9.1=py37hc8dfbb8_0 -testpath=0.4.4=py_0 -tk=8.6.10=hed695b0_0 -tornado=6.0.4=py37h8f50634_1 -tqdm=4.42.1=py_0 -traitlets=5.0.4=py_0 -wcwidth=0.2.5=pyh9f0ad1d_1 -webencodings=0.5.1=py_1 -wheel=0.35.1=pyh9f0ad1d_0 -widgetsnbextension=3.5.1=py37hc8dfbb8_1 -xorg-libxau=1.0.9=h14c3975_0 -xorg-libxdmcp=1.1.3=h516909a_0 -xz=5.2.5=h516909a_1 -zeromq=4.3.2=he1b5a44_3 -zipp=3.1.0=py_0 -zlib=1.2.11=h516909a_1009 diff --git a/docs/Makefile b/docs/Makefile index 5851c22..d0c3cbf 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -14,9 +14,6 @@ help: .PHONY: help Makefile -modules: - sphinx-apidoc -d 2 -f --tocfile index -H API -o source/api ../dscript - # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile diff --git a/docs/requirements.txt b/docs/requirements.txt index 05607c3..ed2f129 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,9 +1,5 @@ -biopython h5py -json5 -jsonschema==3.2.0 matplotlib==3.1.3 -networkx==2.4 numpy pandas scikit-learn==0.22.2.post1 diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..615029f --- /dev/null +++ b/environment.yml @@ -0,0 +1,17 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +cudatoolkit=10.0.130=0 +cudnn=7.6.5=cuda10.0_0 +h5py=2.10.0=nompi_py37h90cd8ad_104 +matplotlib=3.1.3=py37_0 +numpy=1.18.5=py37h8960a57_0 +pandas=1.0.5=py37h0da4684_0 +pip=20.2.3=py_0 +python=3.7.8=h6f2ec95_1_cpython +pytorch=1.2.0=cuda100py37h938c94c_0 +scikit-learn=0.22.2.post1=py37hcdab131_0 +scipy=1.4.1=py37ha3d9a3c_3 +seaborn=0.10.1=1 +setuptools=49.6.0=py37hc8dfbb8_0 +tqdm=4.42.1=py_0