Updated README and Conda environment configuration file

.gitignore

@@ -165,5 +165,6 @@ cython_debug/
 data/uniprot2embedding.h5
 data/PROTAC-DB.csv
 data/PROTAC-Pedia.csv
+data/cellosaurus.txt
 logs/
 notebooks/per-protein*

README.md

@@ -1,22 +1,19 @@
-<!-- ![Maturity level-0](https://img.shields.io/badge/Maturity%20Level-ML--0-red)
+![Maturity level-0](https://img.shields.io/badge/Maturity%20Level-ML--0-red)
+<a href="https://colab.research.google.com/github/ribesstefano/PROTAC-Degradation-Predictor/blob/main/notebooks/protac_degradation_predictor_tutorial.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
 
-# PROTAC-Degradation-Predictor -->
 
-<p align="center">
-  <img src="https://img.shields.io/badge/Maturity%20Level-ML--0-red" alt="Maturity level-0">
-</p>
+# PROTAC-Degradation-Predictor
 
-<h1 align="center">PROTAC-Degradation-Predictor</h1>
-
-<p align="center">
-  A machine learning-based tool for predicting PROTAC protein degradation activity.
-</p>
+A machine learning-based tool for predicting PROTAC protein degradation activity.
 
 ## 📚 Table of Contents
 
 - [Data Curation](#-data-curation)
 - [Installation](#-installation)
 - [Usage](#-usage)
+- [Training](#-training)
+- [Citation](#-citation)
+- [License](#-license)
 
 ## 📝 Data Curation
 
@@ -36,12 +33,14 @@ The package has been developed on a Linux machine with Python 3.10.8. It is reco
 
 ## 🎯 Usage
 
+For a thorough explanation on how to use the package, please refer to the tutorial notebook [`protac_degradation_tutorial.ipynb`](notebooks/protac_degradation_tutorial.ipynb).
+
 After installing the package, you can use it as follows:
 
 ```python
 import protac_degradation_predictor as pdp
 
-protac_smiles = 'CC(C)(C)OC(=O)N1CCN(CC1)C2=CC(=C(C=C2)C(=O)NC3=CC(=C(C=C3)F)Cl)C(=O)NC4=CC=C(C=C4)F'
+protac_smiles = 'Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)[C@@H](NC(=O)COCCCCCCCCCOCC(=O)Nc2ccc(C(=O)Nc3ccc(F)cc3N)cc2)C(C)(C)C)cc1'
 e3_ligase = 'VHL'
 target_uniprot = 'P04637'
 cell_line = 'HeLa'
@@ -51,8 +50,6 @@ active_protac = pdp.is_protac_active(
     e3_ligase,
     target_uniprot,
     cell_line,
-    device='cuda', # Default to 'cpu'
-    proba_threshold=0.5, # Default value
 )
 
 print(f'The given PROTAC is: {"active" if active_protac else "inactive"}')
@@ -62,12 +59,26 @@ This example demonstrates how to predict the activity of a PROTAC molecule. The
 
 The function supports batch computation by passing lists of SMILES strings, E3 ligases, UniProt IDs, and cell lines. In this case, it returns a list of booleans indicating the activity of each PROTAC.
 
+## 📈 Training
 
 
+Before running the experiments, here are some required steps to follow (assuming one is in the repository directory already):
+1. Download the data from the [Cellosaurus database](https://web.expasy.org/cellosaurus/) and save it in the `data` directory:
+```bash
+wget https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt data/
+```
+2. Make a copy of the Uniprot embeddings to be placed in the `data` directory:
+```bash
+cp protac_degradation_predictor/data/uniprot2embedding.h5 data/
+```
+3. Create a virtual environment and install the required packages by running the following commands:
+```bash
+conda env create -f environment.yaml
+conda activate protac-degradation-predictor
+```
+4. The code for training the model can be found in the file [`run_experiments.py`](src/run_experiments.py).
 
-## 📈 Training
-
-The code for training the model can be found in the file [`run_experiments.py`](src/run_experiments.py).
+(Don't forget to adjust the `PYTHONPATH` environment variable to include the repository directory: `export PYTHONPATH=$PYTHONPATH:/path/to/PROTAC-Degradation-Predictor`)
 
 ## 📄 Citation
 

environment.yml

@@ -0,0 +1,399 @@
+name: env-protac-degradation-predictor
+channels:
+  - pyg
+  - anaconda
+  - pytorch
+  - huggingface
+  - nvidia
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - _py-xgboost-mutex=2.0=cpu_0
+  - abseil-cpp=20211102.0=h27087fc_1
+  - absl-py=1.4.0=pyhd8ed1ab_0
+  - accelerate=0.21.0=pyhd8ed1ab_0
+  - aiohttp=3.8.3=py310h5eee18b_0
+  - aiosignal=1.2.0=pyhd8ed1ab_0
+  - alembic=1.12.0=pyhd8ed1ab_0
+  - anyio=3.7.1=pyhd8ed1ab_0
+  - arrow=1.2.3=pyhd8ed1ab_0
+  - arrow-cpp=11.0.0=py310h7516544_0
+  - async-timeout=4.0.2=pyhd8ed1ab_0
+  - aws-c-common=0.4.57=he1b5a44_1
+  - aws-c-event-stream=0.1.6=h72b8ae1_3
+  - aws-checksums=0.1.9=h346380f_0
+  - aws-sdk-cpp=1.8.185=hce553d0_0
+  - backports=1.0=pyhd8ed1ab_3
+  - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0
+  - beautifulsoup4=4.12.2=pyha770c72_0
+  - binaryornot=0.4.4=py_1
+  - blas=1.0=mkl
+  - blessed=1.19.1=pyhe4f9e05_2
+  - blinker=1.6.2=pyhd8ed1ab_0
+  - boltons=23.0.0=pyhd8ed1ab_0
+  - boost-cpp=1.73.0=h7f8727e_12
+  - bottleneck=1.3.5=py310ha9d4c09_0
+  - brotlipy=0.7.0=py310h5764c6d_1004
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.19.0=h5eee18b_0
+  - ca-certificates=2023.08.22=h06a4308_0
+  - cachecontrol=0.12.14=pyhd8ed1ab_0
+  - certifi=2023.7.22=py310h06a4308_0
+  - cffi=1.15.1=py310h5eee18b_3
+  - chardet=5.1.0=py310hff52083_0
+  - charset-normalizer=2.0.4=pyhd8ed1ab_0
+  - cleo=2.0.1=pyhd8ed1ab_0
+  - click=8.0.4=py310hff52083_0
+  - cmaes=0.10.0=pyhd8ed1ab_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - colorlog=6.7.0=py310hff52083_1
+  - conda=23.7.4=py310hff52083_0
+  - conda-content-trust=0.1.3=pyhd8ed1ab_0
+  - conda-package-handling=1.9.0=py310h5eee18b_1
+  - cookiecutter=2.3.0=pyh1a96a4e_0
+  - crashtest=0.4.1=pyhd8ed1ab_0
+  - croniter=1.3.15=pyhd8ed1ab_0
+  - cryptography=38.0.1=py310h9ce1e76_0
+  - cuda-cudart=11.8.89=0
+  - cuda-cupti=11.8.87=0
+  - cuda-libraries=11.8.0=0
+  - cuda-nvrtc=11.8.89=0
+  - cuda-nvtx=11.8.86=0
+  - cuda-runtime=11.8.0=0
+  - dataclasses=0.8=pyhc8e2a94_3
+  - datasets=2.14.4=py_0
+  - dateutils=0.6.12=py_0
+  - dbus=1.13.0=h4e0c4b3_1000
+  - deepdiff=6.2.2=pyhd8ed1ab_0
+  - dill=0.3.6=pyhd8ed1ab_1
+  - distlib=0.3.7=pyhd8ed1ab_0
+  - dulwich=0.21.3=py310h5eee18b_0
+  - evaluate=0.2.2=pyhd8ed1ab_0
+  - exceptiongroup=1.1.3=pyhd8ed1ab_0
+  - expat=2.4.8=h27087fc_0
+  - fastapi=0.103.1=pyhd8ed1ab_0
+  - ffmpeg=4.3=hf484d3e_0
+  - filelock=3.9.0=pyhd8ed1ab_0
+  - freetype=2.12.1=h4a9f257_0
+  - frozenlist=1.3.3=py310h5eee18b_0
+  - fsspec=2023.4.0=pyh1a96a4e_0
+  - gflags=2.2.2=he1b5a44_1004
+  - giflib=5.2.1=h36c2ea0_2
+  - glog=0.5.0=h48cff8f_0
+  - gmp=6.2.1=h58526e2_0
+  - gmpy2=2.1.2=py310heeb90bb_0
+  - gnutls=3.6.15=he1e5248_0
+  - google-auth-oauthlib=0.4.1=py_2
+  - greenlet=1.1.2=py310hd8f1fbe_2
+  - grpc-cpp=1.46.1=h33aed49_1
+  - grpcio=1.42.0=py310hce63b2e_0
+  - h11=0.14.0=pyhd8ed1ab_0
+  - html5lib=1.1=pyh9f0ad1d_0
+  - huggingface_hub=0.16.4=py_0
+  - icu=58.2=hf484d3e_1000
+  - idna=3.4=pyhd8ed1ab_0
+  - importlib-metadata=6.8.0=pyha770c72_0
+  - importlib_metadata=6.8.0=hd8ed1ab_0
+  - importlib_resources=6.0.1=pyhd8ed1ab_0
+  - inquirer=3.1.3=pyhd8ed1ab_0
+  - intel-openmp=2023.1.0=hdb19cb5_46305
+  - itsdangerous=2.1.2=pyhd8ed1ab_0
+  - jaraco.classes=3.3.0=pyhd8ed1ab_0
+  - jeepney=0.8.0=pyhd8ed1ab_0
+  - jinja2=3.1.2=pyhd8ed1ab_1
+  - joblib=1.2.0=pyhd8ed1ab_0
+  - jpeg=9e=h166bdaf_1
+  - jsonpatch=1.32=pyhd8ed1ab_0
+  - jsonpointer=2.1=pyhd3eb1b0_0
+  - keyring=23.13.1=py310hff52083_0
+  - krb5=1.20.1=h568e23c_1
+  - lame=3.100=h7f98852_1001
+  - lcms2=2.12=h3be6417_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - lerc=3.0=h9c3ff4c_0
+  - libboost=1.73.0=h28710b8_12
+  - libbrotlicommon=1.0.9=h166bdaf_7
+  - libbrotlidec=1.0.9=h166bdaf_7
+  - libbrotlienc=1.0.9=h166bdaf_7
+  - libcublas=11.11.3.6=0
+  - libcufft=10.9.0.58=0
+  - libcufile=1.7.1.12=0
+  - libcurand=10.3.3.129=0
+  - libcurl=8.1.1=h91b91d3_2
+  - libcusolver=11.4.1.48=0
+  - libcusparse=11.7.5.86=0
+  - libdeflate=1.8=h7f98852_0
+  - libedit=3.1.20221030=h5eee18b_0
+  - libev=4.33=h516909a_1
+  - libevent=2.1.12=h8f2d780_0
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgfortran-ng=11.2.0=h00389a5_1
+  - libgfortran5=11.2.0=h1234567_1
+  - libgomp=11.2.0=h1234567_1
+  - libiconv=1.16=h516909a_0
+  - libidn2=2.3.4=h5eee18b_0
+  - libnghttp2=1.52.0=ha637b67_1
+  - libnpp=11.8.0.86=0
+  - libnvjpeg=11.9.0.86=0
+  - libpng=1.6.39=h5eee18b_0
+  - libprotobuf=3.20.3=he621ea3_0
+  - libssh2=1.10.0=ha56f1ee_2
+  - libstdcxx-ng=11.2.0=he4da1e4_16
+  - libtasn1=4.19.0=h5eee18b_0
+  - libthrift=0.15.0=h0d84882_2
+  - libtiff=4.5.0=hecacb30_0
+  - libunistring=0.9.10=h7f98852_0
+  - libuuid=1.41.5=h5eee18b_0
+  - libwebp=1.2.4=h11a3e52_1
+  - libwebp-base=1.2.4=h5eee18b_1
+  - libxgboost=1.5.1=cpu_h3d145d1_2
+  - lightning=2.0.4=pyhd8ed1ab_0
+  - lightning-cloud=0.5.38=pyhd8ed1ab_0
+  - lightning-utilities=0.9.0=pyhd8ed1ab_0
+  - lockfile=0.12.2=py_1
+  - lz4-c=1.9.4=h6a678d5_0
+  - mako=1.2.4=pyhd8ed1ab_0
+  - markdown=3.4.4=pyhd8ed1ab_0
+  - markdown-it-py=3.0.0=pyhd8ed1ab_0
+  - markupsafe=2.1.1=py310h5764c6d_1
+  - mdurl=0.1.0=pyhd8ed1ab_0
+  - mkl=2023.1.0=h213fc3f_46343
+  - mkl-service=2.4.0=py310h5eee18b_1
+  - mkl_fft=1.3.6=py310h1128e8f_1
+  - mkl_random=1.2.2=py310h1128e8f_1
+  - more-itertools=10.1.0=pyhd8ed1ab_0
+  - mpc=1.1.0=h04dde30_1009
+  - mpfr=4.0.2=he80fd80_1
+  - mpmath=1.3.0=pyhd8ed1ab_0
+  - msgpack-python=1.0.3=py310hbf28c38_1
+  - multidict=6.0.2=py310h5764c6d_1
+  - multiprocess=0.70.14=py310h06a4308_0
+  - ncurses=6.3=h27087fc_1
+  - nettle=3.7.3=hbbd107a_1
+  - networkx=3.1=pyhd8ed1ab_0
+  - numexpr=2.8.4=py310h85018f9_1
+  - numpy=1.25.2=py310h5f9d8c6_0
+  - numpy-base=1.25.2=py310hb5e798b_0
+  - oauthlib=3.2.2=pyhd8ed1ab_0
+  - openh264=2.1.1=h780b84a_0
+  - openssl=1.1.1w=h7f8727e_0
+  - optuna=3.3.0=pyhd8ed1ab_0
+  - orc=1.7.4=hb3bc3d3_1
+  - ordered-set=4.1.0=pyhd8ed1ab_0
+  - packaging=23.0=pyhd8ed1ab_0
+  - pandas=1.5.3=py310h1128e8f_0
+  - pexpect=4.8.0=pyh1a96a4e_2
+  - pillow=9.4.0=py310h6a678d5_0
+  - pip=22.3.1=pyhd8ed1ab_0
+  - pkginfo=1.9.6=pyhd8ed1ab_0
+  - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
+  - platformdirs=2.6.2=pyhd8ed1ab_0
+  - poetry=1.4.2=linux_pyhd8ed1ab_0
+  - poetry-core=1.5.2=pyhd8ed1ab_0
+  - poetry-plugin-export=1.3.1=pyhd8ed1ab_0
+  - protobuf=3.20.3=py310h6a678d5_0
+  - psutil=5.9.0=py310h5764c6d_1
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - py-xgboost=1.5.1=cpu_py310hd1aba9c_2
+  - pyarrow=11.0.0=py310h468efa6_0
+  - pyasn1=0.4.8=py_0
+  - pyasn1-modules=0.2.7=py_0
+  - pycosat=0.6.4=py310h5eee18b_0
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pydantic=1.9.1=py310h5764c6d_0
+  - pyg=2.3.1=py310_torch_2.0.0_cu118
+  - pygments=2.16.1=pyhd8ed1ab_0
+  - pyjwt=2.8.0=pyhd8ed1ab_0
+  - pyopenssl=22.0.0=pyhd8ed1ab_1
+  - pyparsing=3.0.9=py310h06a4308_0
+  - pyproject_hooks=1.0.0=pyhd8ed1ab_0
+  - pyrsistent=0.18.1=py310h5764c6d_1
+  - pysocks=1.7.1=pyha2e5f31_6
+  - python=3.10.8=h7a1cb2a_1
+  - python-build=0.10.0=pyhd8ed1ab_1
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-editor=1.0.4=py_0
+  - python-installer=0.7.0=pyhd8ed1ab_0
+  - python-multipart=0.0.6=pyhd8ed1ab_0
+  - python-slugify=8.0.1=pyhd8ed1ab_0
+  - python-xxhash=2.0.2=py310h6acc77f_1
+  - python_abi=3.10=2_cp310
+  - pytorch=2.0.1=py3.10_cuda11.8_cudnn8.7.0_0
+  - pytorch-cuda=11.8=h7e8668a_5
+  - pytorch-lightning=2.0.9=pyhd8ed1ab_0
+  - pytorch-mutex=1.0=cuda
+  - pytz=2022.7.1=pyhd8ed1ab_0
+  - pyu2f=0.1.5=pyhd8ed1ab_0
+  - pyyaml=6.0=py310h5764c6d_4
+  - rapidfuzz=2.13.7=py310h1128e8f_0
+  - re2=2022.04.01=h27087fc_0
+  - readchar=4.0.5=pyhd8ed1ab_0
+  - readline=8.2=h5eee18b_0
+  - regex=2022.7.9=py310h5eee18b_0
+  - requests-oauthlib=1.3.1=pyhd8ed1ab_0
+  - requests-toolbelt=0.10.1=pyhd8ed1ab_0
+  - responses=0.18.0=pyhd8ed1ab_0
+  - rich=13.5.1=pyhd8ed1ab_0
+  - rsa=4.9=pyhd8ed1ab_0
+  - ruamel.yaml=0.17.21=py310h5764c6d_1
+  - ruamel.yaml.clib=0.2.6=py310h5764c6d_1
+  - sacremoses=master=py_0
+  - scikit-learn=1.2.0=py310h6a678d5_1
+  - scipy=1.9.3=py310h5f9d8c6_2
+  - secretstorage=3.3.3=py310hff52083_1
+  - setuptools=65.5.0=pyhd8ed1ab_0
+  - shellingham=1.5.3=pyhd8ed1ab_0
+  - six=1.16.0=pyh6c4a22f_0
+  - snappy=1.1.9=hbd366e4_1
+  - sniffio=1.3.0=pyhd8ed1ab_0
+  - soupsieve=2.5=pyhd8ed1ab_1
+  - sqlalchemy=1.4.36=py310h5764c6d_0
+  - sqlite=3.40.0=h5082296_0
+  - starlette=0.27.0=pyhd8ed1ab_0
+  - starsessions=1.3.0=pyhd8ed1ab_0
+  - sympy=1.11.1=pyh04b8f61_3
+  - tabulate=0.9.0=pyhd8ed1ab_1
+  - tbb=2021.8.0=hdb19cb5_0
+  - tensorboard=2.6.0=py_0
+  - tensorboard-plugin-wit=1.8.1=pyhd8ed1ab_0
+  - text-unidecode=1.3=py_0
+  - threadpoolctl=2.2.0=pyh0d69192_0
+  - tk=8.6.12=h1ccaba5_0
+  - tokenizers=0.13.2=py310he7d60b5_1
+  - tomli=2.0.1=pyhd8ed1ab_0
+  - tomlkit=0.12.1=pyha770c72_0
+  - toolz=0.12.0=pyhd8ed1ab_0
+  - torchaudio=2.0.2=py310_cu118
+  - torchmetrics=1.1.2=pyhd8ed1ab_0
+  - torchtriton=2.0.0=py310
+  - torchvision=0.15.2=py310_cu118
+  - tqdm=4.64.1=pyhd8ed1ab_0
+  - transformers=4.29.2=pyhd8ed1ab_0
+  - trove-classifiers=2023.8.7=pyhd8ed1ab_0
+  - typing-extensions=4.7.1=hd8ed1ab_0
+  - typing_extensions=4.7.1=pyha770c72_0
+  - tzdata=2022g=h191b570_0
+  - unidecode=1.3.6=pyhd8ed1ab_0
+  - urllib3=1.26.13=pyhd8ed1ab_0
+  - utf8proc=2.6.1=h27cfd23_0
+  - uvicorn=0.23.2=py310hff52083_0
+  - virtualenv=20.21.1=pyhd8ed1ab_0
+  - wcwidth=0.2.6=pyhd8ed1ab_0
+  - webencodings=0.5.1=pyhd8ed1ab_2
+  - websockets=10.3=py310h5764c6d_0
+  - werkzeug=2.3.6=pyhd8ed1ab_0
+  - wheel=0.37.1=pyhd8ed1ab_0
+  - xxhash=0.8.0=h7f98852_3
+  - xz=5.2.8=h5eee18b_0
+  - yaml=0.2.5=h7f98852_2
+  - yarl=1.8.1=py310h5eee18b_0
+  - zipp=3.16.2=pyhd8ed1ab_0
+  - zlib=1.2.13=h5eee18b_0
+  - zstd=1.5.2=ha4553b6_0
+  - pip:
+      - appdirs==1.4.4
+      - argon2-cffi==23.1.0
+      - argon2-cffi-bindings==21.2.0
+      - asttokens==2.4.1
+      - async-lru==2.0.4
+      - attrs==23.2.0
+      - babel==2.14.0
+      - bleach==6.1.0
+      - cachetools==4.2.4
+      - comm==0.2.2
+      - contourpy==1.2.1
+      - cycler==0.12.1
+      - debugpy==1.8.1
+      - decorator==5.1.1
+      - defusedxml==0.7.1
+      - docker-pycreds==0.4.0
+      - docstring-parser==0.15
+      - executing==2.0.1
+      - fastjsonschema==2.19.1
+      - fonttools==4.51.0
+      - fqdn==1.5.1
+      - gitdb==4.0.11
+      - gitpython==3.1.42
+      - google-auth==1.35.0
+      - h5py==3.10.0
+      - httpcore==1.0.5
+      - httpx==0.27.0
+      - imbalanced-learn==0.12.0
+      - iniconfig==2.0.0
+      - ipykernel==6.29.4
+      - ipython==8.23.0
+      - ipywidgets==8.1.2
+      - isoduration==20.11.0
+      - jedi==0.19.1
+      - json5==0.9.25
+      - jsonargparse==4.23.1
+      - jsonschema==4.21.1
+      - jsonschema-specifications==2023.12.1
+      - jupyter==1.0.0
+      - jupyter-client==8.6.1
+      - jupyter-console==6.6.3
+      - jupyter-core==5.7.2
+      - jupyter-events==0.10.0
+      - jupyter-lsp==2.2.5
+      - jupyter-server==2.14.0
+      - jupyter-server-terminals==0.5.3
+      - jupyterlab==4.1.6
+      - jupyterlab-pygments==0.3.0
+      - jupyterlab-server==2.26.0
+      - jupyterlab-widgets==3.0.10
+      - kiwisolver==1.4.5
+      - llvmlite==0.42.0
+      - matplotlib==3.8.4
+      - matplotlib-inline==0.1.7
+      - mistune==3.0.2
+      - nbclient==0.10.0
+      - nbconvert==7.16.3
+      - nbformat==5.10.4
+      - nest-asyncio==1.6.0
+      - nltk==3.8.1
+      - notebook==7.1.3
+      - notebook-shim==0.2.4
+      - numba==0.59.1
+      - overrides==7.7.0
+      - pandocfilters==1.5.1
+      - parso==0.8.4
+      - pluggy==1.5.0
+      - prometheus-client==0.20.0
+      - prompt-toolkit==3.0.43
+      - pure-eval==0.2.2
+      - pynndescent==0.5.12
+      - pynvml==11.5.0
+      - pytest==8.1.1
+      - python-json-logger==2.0.7
+      - pyzmq==26.0.1
+      - qtconsole==5.5.1
+      - qtpy==2.4.1
+      - rdkit==2023.9.5
+      - rdkit-pypi==2022.9.5
+      - referencing==0.34.0
+      - requests==2.31.0
+      - rfc3339-validator==0.1.4
+      - rfc3986-validator==0.1.1
+      - rouge-score==0.1.2
+      - rpds-py==0.18.0
+      - seaborn==0.13.2
+      - send2trash==1.8.3
+      - sentry-sdk==1.41.0
+      - setproctitle==1.3.3
+      - smmap==5.0.1
+      - stack-data==0.6.3
+      - tensorboard-data-server==0.6.1
+      - terminado==0.18.1
+      - tinycss2==1.2.1
+      - tornado==6.4
+      - traitlets==5.14.3
+      - typeshed-client==2.3.0
+      - umap-learn==0.5.6
+      - uri-template==1.3.0
+      - wandb==0.16.4
+      - webcolors==1.13
+      - websocket-client==1.7.0
+      - widgetsnbextension==4.0.10