Commit beeef2d6 authored by Carlos GO's avatar Carlos GO
Browse files

YML

parent 742d35a6
......@@ -29,8 +29,12 @@ See README in each folder for details on how to use each component.
* tqdm
* networkx >= 2.1
See `requirements.txt` for detailed list of versions.
You can automatically install all the dependencies with Anaconda using the following command:
```
conda env create -f environment.yml
```
## Usage
......
name: rnamigos_minimal
channels:
- pytorch
- dglteam
- conda-forge
- defaults
dependencies:
- absl-py=0.9.0=py36_0
- biopython=1.76=py36h0b31af3_0
- blas=1.0=mkl
- blinker=1.4=py_1
- brotlipy=0.7.0=py36h37b9a7d_1000
- c-ares=1.15.0=h01d97ff_1001
- ca-certificates=2020.1.1=0
- cachetools=4.1.0=py_1
- cairo=1.16.0=ha8983da_1004
- certifi=2020.6.20=py36_0
- cffi=1.14.0=py36h356ff06_0
- chardet=3.0.4=py36h9f0ad1d_1006
- click=7.1.2=pyh9f0ad1d_0
- cryptography=2.9.2=py36hc9d8292_0
- cycler=0.10.0=py36hfc81398_0
- decorator=4.4.2=py_0
- dgl=0.4.3post2=py36_0
- fontconfig=2.13.1=h79c0d67_1002
- freetype=2.10.2=h8da9a1a_0
- gettext=0.19.8.1=h46ab8bc_1002
- glib=2.64.3=h577aef8_0
- google-auth=1.17.2=py_0
- google-auth-oauthlib=0.4.1=py_2
- grpcio=1.27.2=py36h7c1f37e_0
- icu=67.1=h4a8c4bd_0
- idna=2.9=py_1
- importlib-metadata=1.6.1=py36h9f0ad1d_0
- intel-openmp=2019.4=233
- kiwisolver=1.2.0=py36h04f5b5a_0
- libcxx=10.0.0=1
- libedit=3.1.20191231=haf1e3a3_0
- libffi=3.2.1=h4a8c4bd_1007
- libgfortran=3.0.1=h93005f0_2
- libiconv=1.15=h0b31af3_1006
- libpng=1.6.37=hbbe82c9_1
- libprotobuf=3.12.3=hd174df1_0
- libxml2=2.9.10=hc06c4ae_1
- markdown=3.2.2=py_0
- matplotlib=3.2.1=0
- matplotlib-base=3.2.1=py36h5670ca0_0
- mkl=2019.4=233
- mkl-service=2.3.0=py36hfbe908c_0
- mkl_fft=1.1.0=py36hc64f4ea_0
- mkl_random=1.1.1=py36h959d312_0
- ncurses=6.2=h0a44026_1
- networkx=2.4=py_0
- ninja=1.9.0=py36h04f5b5a_0
- numpy=1.18.5=py36h1da2735_0
- numpy-base=1.18.5=py36h3304bdc_0
- oauthlib=3.0.1=py_0
- openbabel=3.1.1=py36h715b1f7_0
- openssl=1.1.1g=h1de35cc_0
- pandas=1.0.5=py36h959d312_0
- pcre=8.44=h4a8c4bd_0
- pip=20.1.1=py36_1
- pixman=0.38.0=h01d97ff_1003
- protobuf=3.12.3=py36h0130604_0
- pyasn1=0.4.8=py_0
- pyasn1-modules=0.2.7=py_0
- pycparser=2.20=py_0
- pyjwt=1.7.1=py_0
- pyopenssl=19.1.0=py_1
- pyparsing=2.4.7=py_0
- pysocks=1.7.1=py36h9f0ad1d_1
- python=3.6.10=hc70fcce_1
- python-dateutil=2.8.1=py_0
- python_abi=3.6=1_cp36m
- pytorch=1.5.1=py3.6_0
- pytz=2020.1=py_0
- readline=8.0=h1de35cc_0
- requests=2.24.0=pyh9f0ad1d_0
- requests-oauthlib=1.2.0=py_0
- rsa=4.6=pyh9f0ad1d_0
- scipy=1.4.1=py36h9fa6033_0
- seaborn=0.10.1=py_0
- setuptools=47.3.1=py36_0
- six=1.15.0=py_0
- sqlite=3.32.2=hffcf06c_0
- tensorboard=2.2.2=py_0
- tensorboard-plugin-wit=1.6.0=pyh9f0ad1d_0
- tk=8.6.10=hb0a8c7a_0
- tornado=6.0.4=py36h1de35cc_1
- tqdm=4.46.1=py_0
- urllib3=1.25.9=py_0
- werkzeug=1.0.1=pyh9f0ad1d_0
- wheel=0.34.2=py36_0
- xz=5.2.5=h1de35cc_0
- zipp=3.1.0=py_0
- zlib=1.2.11=h1de35cc_3
......@@ -161,7 +161,7 @@ class Loader():
sim_function="R_1",
shuffle=False,
seed=0,
get_sim_mat=False,
get_sim_mat=True,
nucs=True,
depth=3):
"""
......@@ -191,7 +191,7 @@ class Loader():
def get_data(self, k_fold=0):
n = len(self.dataset)
indices = list(range(n))
collate_block = collate_wrapper(self.dataset.node_sim_func)
collate_block = collate_wrapper(self.dataset.node_sim_func, self.dataset.get_sim_mat)
if k_fold > 1:
from sklearn.model_selection import KFold
......
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