updated conda environment

conda-env.yml

@@ -1,139 +0,0 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this 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

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

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

environment.yml

@@ -0,0 +1,17 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this 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