<jupyter_start><jupyter_text>**Installation**

This tutorial shows the details of installation on Google Golaboratory. **Step 1**

For changing version. (Edit: 2021/3/11)<jupyter_code>!pip3 uninstall -y imgaug && pip3 uninstall -y albumentations && pip3 install git+https://github.com/aleju/imgaug.git
!pip3 install pymatgen==2020.10.20
import pymatgen
print(pymatgen.__version__)
!pip3 install -U xenonpy==0.5.0
import xenonpy
print(xenonpy.__version__)
!pip3 install scikit-learn==0.23.2
import sklearn
print(sklearn.__version__)<jupyter_output>Collecting scikit-learn==0.23.2
[?25l  Downloading https://files.pythonhosted.org/packages/5c/a1/273def87037a7fb010512bbc5901c31cfddfca8080bc63b42b26e3cc55b3/scikit_learn-0.23.2-cp36-cp36m-manylinux1_x86_64.whl (6.8MB)
[K     |████████████████████████████████| 6.8MB 18.6MB/s 
[?25hRequirement already satisfied: scipy>=0.19.1 in /usr/local/lib/python3.6/dist-packages (from scikit-learn==0.23.2) (1.4.1)
Requirement already satisfied: joblib>=0.11 in /usr/local/lib/python3.6/dist-packages (from scikit-learn==0.23.2) (1.0.0)
Requirement already satisfied: numpy>=1.13.3 in /usr/local/lib/python3.6/dist-packages (from scikit-learn==0.23.2) (1.19.5)
Collecting threadpoolctl>=2.0.0
  Downloading https://files.pythonhosted.org/packages/f7/12/ec3f2e203afa394a149911729357aa48affc59c20e2c1c8297a60f33f133/threadpoolctl-2.1.0-py3-none-any.whl
Installing collected packages: threadpoolctl, scikit-learn
  Found existing installation: scikit-learn 0.22.2.post1
    Uninstalling scikit-learn-0.22.2.pos[...]<jupyter_text>**Step 2**

Install Anaconda and set PATH<jupyter_code>!wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
!bash Miniconda3-latest-Linux-x86_64.sh -b -f -p /usr/local
import sys
sys.path.append('/usr/local/lib/python3.6/site-packages/')<jupyter_output>--2021-01-29 10:19:03--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 192.168.3.11, 192.168.127.12, fc00:e968:6179::de52:7100:c84f, ...
Connecting to repo.continuum.io (repo.continuum.io)|192.168.3.11|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [following]
--2021-01-29 10:19:03--  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.anaconda.com (repo.anaconda.com)... 172.16.17.32, 172.16.17.32, fc00:db20:35b:7399::5:8203, ...
Connecting to repo.anaconda.com (repo.anaconda.com)|172.16.17.32|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 94235922 (90M) [application/x-sh]
Saving to: ‘Miniconda3-latest-Linux-x86_64.sh’

Miniconda3-latest-L 100%[===================>]  89.87M   208MB/s    in 0.4s    

2021-01-29 10:19:04 (208 MB/s) - ‘Miniconda3-latest-Linux[...]<jupyter_text>**step 3**

Install RDKit and check version.<jupyter_code>!conda install -q -y -c rdkit rdkit=2020.3 python=3.6
import rdkit
print(rdkit.__version__)<jupyter_output>Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /usr/local

  added / updated specs:
    - python=3.6
    - rdkit=2020.3


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    blas-1.0                   |              mkl           6 KB
    brotlipy-0.7.0             |py36h27cfd23_1003         320 KB
    bzip2-1.0.8                |       h7b6447c_0          78 KB
    ca-certificates-2021.1.19  |       h06a4308_0         121 KB
    cairo-1.14.12              |       h8948797_3         906 KB
    certifi-20[...]<jupyter_text>**step 4**

Install PyTorch and check version.<jupyter_code>!conda install -y pytorch==1.7.0 torchvision==0.8.0 torchaudio==0.7.0 cudatoolkit=10.1 -c pytorch
import torch
print(torch.__version__)<jupyter_output>Collecting package metadata (current_repodata.json): - \ | / - \ | / - \ | / - \ | / - \ done
Solving environment: / - \ | / - \ | / - \ | / - \ | / - \ done

## Package Plan ##

  environment location: /usr/local

  added / updated specs:
    - cudatoolkit=10.1
    - pytorch
    - torchaudio
    - torchvision


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    cudatoolkit-10.1.243       |       h6bb024c_0       347.4 MB
    dataclasses-0.7            |           py36_0          30 KB
    libuv-1.40.0               |       h7b6447c_0         736 KB
    ninja-1.10.2               |   py36hff7bd54_0         1.4 MB
    pytorch-1.7.1              |py3.6_cuda10.1.243_cudnn7.6.3_0       553.7 MB  pytorch
    torchaudio-0.7.2           |             py36         9.8 MB  pytorch
    torchvision-0.8.2          |       py36_cu[...]<jupyter_text>**step 5**

Install XenonPy and check version.<jupyter_code>!wget https://raw.githubusercontent.com/by-student-2017/xenonpy-gcolab/main/0.5.0/conda_env/cuda101.yml
!conda create --yes -n xenonpy python=3.6
!conda env update -n xenonpy -f cuda101.yml
!source activate xenonpy<jupyter_output>--2021-01-29 10:24:56--  https://raw.githubusercontent.com/by-student-2017/xenonpy-gcolab/main/0.5.0/conda_env/cuda101.yml
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 192.168.127.12, 192.168.3.11, 172.16.58.3, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|192.168.127.12|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 520 [text/plain]
Saving to: ‘cuda101.yml’

cuda101.yml         100%[===================>]     520  --.-KB/s    in 0s      

2021-01-29 10:24:56 (29.8 MB/s) - ‘cuda101.yml’ saved [520/520]

Collecting package metadata (current_repodata.json): - \ | / done
Solving environment: \ done

## Package Plan ##

  environment location: /usr/local/envs/xenonpy

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    readline-8.1               |       h27cfd23_0  [...]<jupyter_text>**step 6**

Install XenonPy samples<jupyter_code>!git clone https://github.com/by-student-2017/xenonpy-gcolab.git
%cd xenonpy-gcolab/0.5.0/samples
!wget https://github.com/yoshida-lab/XenonPy/releases/download/v0.4.1/iQSPR_sample_data.csv
!ls<jupyter_output>Cloning into 'xenonpy-gcolab'...
remote: Enumerating objects: 234, done.[K
remote: Counting objects: 100% (234/234), done.[K
remote: Compressing objects: 100% (130/130), done.[K
remote: Total 234 (delta 106), reused 217 (delta 92), pack-reused 0[K
Receiving objects: 100% (234/234), 5.46 MiB | 29.92 MiB/s, done.
Resolving deltas: 100% (106/106), done.
/content/xenonpy-gcolab/0.4.4/samples
--2021-01-29 10:29:37--  https://github.com/yoshida-lab/XenonPy/releases/download/v0.4.1/iQSPR_sample_data.csv
Resolving github.com (github.com)... 172.16.58.3
Connecting to github.com (github.com)|172.16.58.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-releases.githubusercontent.com/117819602/14925c00-e455-11e9-9065-7d987b463251?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210129%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210129T102937Z&X-Amz-Expires=300&X-Amz-Signature=1de4689adf3ec8ffe06b5b90ad59bafd958bffa19d116[...]<jupyter_text>**step 7**

Install Gaussian process<jupyter_code>!pip3 install GPy==1.9.9<jupyter_output>Collecting GPy==1.9.9
  Downloading GPy-1.9.9.tar.gz (995 kB)
[K     |████████████████████████████████| 995 kB 16.6 MB/s 
[?25hRequirement already satisfied: numpy>=1.7 in /usr/local/lib/python3.6/site-packages (from GPy==1.9.9) (1.19.2)
Requirement already satisfied: scipy>=0.16 in /usr/local/lib/python3.6/site-packages (from GPy==1.9.9) (1.5.2)
Requirement already satisfied: six in /usr/local/lib/python3.6/site-packages (from GPy==1.9.9) (1.15.0)
Collecting paramz>=0.9.0
  Downloading paramz-0.9.5.tar.gz (71 kB)
[K     |████████████████████████████████| 71 kB 11.6 MB/s 
[?25hRequirement already satisfied: decorator>=4.0.10 in /usr/local/lib/python3.6/site-packages (from paramz>=0.9.0->GPy==1.9.9) (4.4.2)
Building wheels for collected packages: GPy, paramz
  Building wheel for GPy (setup.py) ... [?25l[?25hdone
  Created wheel for GPy: filename=GPy-1.9.9-cp36-cp36m-linux_x86_64.whl size=2633495 sha256=9bb14035d6cddab60f5ce501f7818091cc8cd16776a37f2c35cd5b35fcb56b11
  Stored in di[...]<jupyter_text>**step 8**

Install OpenNMT-py<jupyter_code>!pip3 install OpenNMT-py==1.2.0<jupyter_output>Collecting OpenNMT-py==1.2.0
  Downloading OpenNMT_py-1.2.0-py3-none-any.whl (195 kB)
[K     |████████████████████████████████| 195 kB 16.9 MB/s 
[?25hRequirement already satisfied: future in /usr/local/lib/python3.6/site-packages (from OpenNMT-py==1.2.0) (0.18.2)
Requirement already satisfied: tqdm in /usr/local/lib/python3.6/site-packages (from OpenNMT-py==1.2.0) (4.51.0)
Requirement already satisfied: pyyaml in /usr/local/lib/python3.6/site-packages (from OpenNMT-py==1.2.0) (5.3.1)
Requirement already satisfied: torch>=1.6.0 in /usr/local/lib/python3.6/site-packages (from OpenNMT-py==1.2.0) (1.7.1)
Requirement already satisfied: flask in /usr/local/lib/python3.6/site-packages (from OpenNMT-py==1.2.0) (1.1.2)
Requirement already satisfied: six in /usr/local/lib/python3.6/site-packages (from OpenNMT-py==1.2.0) (1.15.0)
Collecting pyonmttok==1.*
  Downloading pyonmttok-1.23.0-cp36-cp36m-manylinux1_x86_64.whl (2.5 MB)
[K     |████████████████████████████████| 2.5 MB 45.2 MB/s 
[?25h[...]<jupyter_text>**step 9**

Check versions one more.
(For some reason pytorch is displayed as 1.8.0+cu101)<jupyter_code>import pymatgen
print(pymatgen.__version__)
import xenonpy
print(xenonpy.__version__)
import sklearn
print(sklearn.__version__)
import rdkit
print(rdkit.__version__)
import torch
print(torch.__version__)<jupyter_output>0.23.2
2020.03.3
1.7.0+cu101
2020.10.20
0.5.0
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