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MolecularAI
How to run notebooks correctly
Thanks for your repo where I can learn how to use Reinvent. First of all, which notebook should I try first in terms of learning Reinvent? Do you have any proper orders? Secondly, I don't understand what you mean these """"1.5 Run REINVENT
Now it is time to execute REINVENT locally. Note, that depending on the number of epochs (steps) and the execution time of the scoring function components, this might take a while. As we have only specified a low number of epochs and all components should be fairly quick, this should not take too long in our case though.
The command-line execution looks like this:
activate envionment
conda activate reinvent_shared.v2.1
execute REINVENT
python <your_path>/input.py
Do you mean that I run REINVENT at the terminal instead of in the notebook? If that is the case, why did you have the !python **** cell after. I think I can run it in the notebook.
I tried Complete_Use-Case-DRD2_Demo.ipynb, everything was going well until I started to run REINVENT.
I got error messages as followings:
Traceback (most recent call last):
File "../../Reinvent/input.py", line 6, in
I ran it at the terminal reinvent.v3.0 conda env, I got different errors like these:
Traceback (most recent call last):
File "../../Reinvent/input.py", line 6, in
I am looking forward to getting your help. Many thanks
Hi, thanks for your interest in using our repo.
You can either run REINVENT from terminal or from the notebook. The notebook is simply to get you onboard and if you follow it through it should be possible to execute all the steps of the tutorials only through the notebook.
We have recently updated to REINVENT v.3.0 and the reinvent_shared.v2.1 is relevant for the previous version.
The correct environment name is 'reinvent.v3.0'.
Please, make sure you have got the latest state of the main branch and that you are using the reinvent.v3.0 environment.
Do let us know if you still encounter issues as there is a chance we may have left some pointers to the old state of the code.
Thank you so much for your reply.
First of all, I pasted the wrong error messages when I ran it at the terminal. The right error messages are:
(reinvent.v3.0) xzhang@R1124G1:~/projects/Reinvent$ python input.py REINVENT_Use-Case-DRD2_demo/DRD2_config.json
Traceback (most recent call last):
File "input.py", line 20, in
Secondly, I have made some changes to cell #1 reinvent_dir = os.path.expanduser("/home/xzhang/projects/Reinvent") reinvent_env = os.path.expanduser("~/miniconda3/envs/reinvent.v3.0") output_dir = os.path.expanduser("/home/xzhang/projects/Reinvent/REINVENT_Use-Case-DRD2_demo") and cell #8 configuration = { "version": 3, "run_type": "reinforcement_learning", "parameters": { "scoring_function": scoring_function } }
Thirdly, When I tried Reinforcement_Learning_Demo.ipynb, similarly, I got the same error messages:
Traceback (most recent call last):
File "../../Reinvent/input.py", line 6, in
It is true that I can't find reinvent_scoring.py file
Apologies for the slow response rate. Could you please check which version of reinvent-scoring library you have in your environment? It should be the same as in the reinvent.yml file.
My reinvent.yml is like this: name: reinvent.v3.0 channels:
- rdkit
- pytorch
- openeye
- conda-forge
- anaconda
- defaults dependencies:
- _libgcc_mutex=0.1
- _pytorch_select=0.1
- _tflow_select=2.3.0
- aiohttp=3.6.2
- argon2-cffi=20.1.0
- astunparse=1.6.3
- async-timeout=3.0.1
- async_generator=1.10
- attrs=19.3.0
- backcall=0.2.0
- blas=1.0
- bleach=3.2.1
- blinker=1.4
- brotlipy=0.7.0
- bzip2=1.0.8
- c-ares=1.17.1
- ca-certificates=2021.4.13
- cachetools=4.2.2
- cairo=1.14.12
- certifi=2020.12.5
- cffi=1.14.3
- chardet=3.0.4
- click=8.0.0
- cmarkgfm=0.4.2
- colorama=0.4.4
- coverage=5.5
- cryptography=3.2.1
- cudatoolkit=10.2.89
- cycler=0.10.0
- cython=0.29.23
- dacite=1.5.1
- dataclasses=0.7
- dbus=1.13.12
- decorator=5.0.7
- defusedxml=0.7.1
- dill=0.3.1.1
- docutils=0.16
- entrypoints=0.3
- expat=2.2.9
- fontconfig=2.13.0
- freetype=2.9.1
- glib=2.63.1
- google-auth=1.28.0
- google-auth-oauthlib=0.4.1
- google-pasta=0.2.0
- gst-plugins-base=1.14.0
- gstreamer=1.14.0
- h5py=2.10.0
- hdf5=1.10.6
- icu=58.2
- idna=2.10
- importlib-metadata=3.10.0
- importlib_metadata=1.5.0
- intel-openmp=2020.0
- ipykernel=5.3.4
- ipython=7.22.0
- ipython_genutils=0.2.0
- ipywidgets=7.6.3
- jedi=0.17.0
- jeepney=0.6.0
- jinja2=2.11.3
- joblib=0.15.1
- jpeg=9b
- jsonschema=3.2.0
- jupyter=1.0.0
- jupyter_client=6.1.12
- jupyter_console=6.4.0
- jupyter_core=4.7.1
- jupyterlab_pygments=0.1.2
- jupyterlab_widgets=1.0.0
- keras-preprocessing=1.1.2
- keyring=21.5.0
- kiwisolver=1.1.0
- ld_impl_linux-64=2.33.1
- libboost=1.67.0
- libedit=3.1.20181209
- libffi=3.2.1
- libgcc-ng=9.1.0
- libgfortran-ng=7.3.0
- libpng=1.6.37
- libprotobuf=3.14.0
- libsodium=1.0.18
- libstdcxx-ng=9.1.0
- libtiff=4.1.0
- libuuid=1.0.3
- libuv=1.40.0
- libxcb=1.13
- libxml2=2.9.9
- markupsafe=1.1.1
- matplotlib=3.1.3
- matplotlib-base=3.1.3
- mistune=0.8.4
- mkl=2020.0
- mkl-service=2.3.0
- mkl_fft=1.0.15
- mkl_random=1.1.0
- more-itertools=8.2.0
- multidict=4.7.3
- multiprocess=0.70.9
- nbclient=0.5.3
- nbconvert=6.0.7
- nbformat=5.1.3
- ncurses=6.2
- nest-asyncio=1.5.1
- ninja=1.9.0
- notebook=6.3.0
- numpy=1.18.1
- numpy-base=1.18.1
- oauthlib=3.1.0
- olefile=0.46
- openeye-toolkits=2020.2.2
- openssl=1.1.1k
- packaging=20.3
- pandas=1.0.3
- pandoc=2.12
- pandocfilters=1.4.3
- parso=0.8.2
- pathos=0.2.5
- pcre=8.43
- pexpect=4.8.0
- pickleshare=0.7.5
- pillow=7.0.0
- pip=20.0.2
- pixman=0.38.0
- pkginfo=1.6.1
- pluggy=0.13.1
- pox=0.2.7
- ppft=1.6.6.1
- prometheus_client=0.10.1
- prompt-toolkit=3.0.17
- prompt_toolkit=3.0.17
- ptyprocess=0.7.0
- py=1.8.1
- py-boost=1.67.0
- py4j=0.10.7
- pyasn1=0.4.8
- pyasn1-modules=0.2.8
- pycparser=2.20
- pydantic=1.8.2
- pygments=2.7.2
- pyjwt=1.7.1
- pyopenssl=19.1.0
- pyparsing=2.4.6
- pyqt=5.9.2
- pyrsistent=0.17.3
- pysocks=1.7.1
- pytest=5.4.1
- python=3.7.7
- python-dateutil=2.8.1
- python_abi=3.7
- pytorch=1.7.1
- pytz=2019.3
- pyzmq=20.0.0
- qt=5.9.7
- qtconsole=5.0.3
- qtpy=1.9.0
- rdkit=2020.03.3.0
- readline=8.0
- readme_renderer=27.0
- requests=2.25.0
- requests-oauthlib=1.3.0
- requests-toolbelt=0.9.1
- rfc3986=1.4.0
- rsa=4.7.2
- scikit-learn=0.21.3
- scipy=1.4.1
- secretstorage=3.2.0
- send2trash=1.5.0
- setuptools=46.1.1
- sip=4.19.8
- six=1.14.0
- sqlite=3.31.1
- tensorboard-plugin-wit=1.6.0
- termcolor=1.1.0
- terminado=0.9.4
- testpath=0.4.4
- tk=8.6.8
- tornado=6.0.4
- tqdm=4.43.0
- traitlets=5.0.5
- twine=3.2.0
- typing_extensions=3.7.4.3
- urllib3=1.25.11
- wcwidth=0.1.9
- webencodings=0.5.1
- wheel=0.34.2
- widgetsnbextension=3.5.1
- wrapt=1.12.1
- xz=5.2.4
- yarl=1.4.2
- zeromq=4.3.4
- zipp=2.2.0
- zlib=1.2.11
- zstd=1.3.7
- pip:
- absl-py==0.9.0
- astor==0.8.1
- future==0.18.2
- gast==0.2.2
- grpcio==1.27.2
- keras-applications==1.0.8
- markdown==3.2.1
- opt-einsum==3.2.0
- protobuf==3.11.3
- reinvent-chemistry==0.0.38
- reinvent-models==0.0.3
- reinvent-scoring==0.0.41
- tensorboard==1.15.0
- tensorflow==1.15.2
- tensorflow-estimator==1.15.1
- termcolor==1.1.0
- werkzeug==1.0.0
I used this file to create my reinvent.v3.0. Then I used conda list to check the version
packages in environment at /home/xzhang/miniconda3/envs/reinvent.v3.0:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
_pytorch_select 0.1 cpu_0 anaconda
_tflow_select 2.3.0 mkl anaconda
absl-py 0.9.0 pypi_0 pypi
aiohttp 3.6.2 py37h8f50634_1 conda-forge
argon2-cffi 20.1.0 py37h4abf009_2 conda-forge
astor 0.8.1 pypi_0 pypi
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-timeout 3.0.1 py_1000 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 19.3.0 py_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
blas 1.0 mkl conda-forge
bleach 3.2.1 pyh9f0ad1d_0 conda-forge
blinker 1.4 py_1 conda-forge
brotlipy 0.7.0 py37hb5d75c8_1001 conda-forge
bzip2 1.0.8 h516909a_3 conda-forge
c-ares 1.17.1 h36c2ea0_0 conda-forge
ca-certificates 2021.4.13 h06a4308_1
cachetools 4.2.2 pyhd8ed1ab_0 conda-forge
cairo 1.14.12 h8948797_3
certifi 2020.12.5 py37h89c1867_1 conda-forge
cffi 1.14.3 py37h00ebd2e_1 conda-forge
chardet 3.0.4 py37he5f6b98_1008 conda-forge
click 8.0.0 py37h89c1867_0 conda-forge
cmarkgfm 0.4.2 py37h4abf009_4 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
coverage 5.5 py37h27cfd23_2
cryptography 3.2.1 py37hc72a4ac_0 conda-forge
cudatoolkit 10.2.89 hfd86e86_1 anaconda
cycler 0.10.0 py_2 conda-forge
cython 0.29.23 py37h2531618_0
dacite 1.5.1 pyh9f0ad1d_0 conda-forge
dataclasses 0.7 pyhb2cacf7_7 conda-forge
dbus 1.13.12 h746ee38_0
decorator 5.0.7 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dill 0.3.1.1 py37hc8dfbb8_1 conda-forge
docutils 0.16 py37h89c1867_3 conda-forge
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
fontconfig 2.13.0 h9420a91_0 anaconda
freetype 2.9.1 he983fc9_1006 conda-forge
future 0.18.2 pypi_0 pypi
gast 0.2.2 pypi_0 pypi
glib 2.63.1 h5a9c865_0 anaconda
google-auth 1.28.0 pyhd3eb1b0_0
google-auth-oauthlib 0.4.1 py_2 conda-forge
google-pasta 0.2.0 pyh8c360ce_0 conda-forge
grpcio 1.27.2 pypi_0 pypi
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
h5py 2.10.0 nompi_py37h1e651dc_105 conda-forge
hdf5 1.10.6 nompi_h3c11f04_101 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
importlib-metadata 3.10.0 py37h89c1867_0 conda-forge
importlib_metadata 1.5.0 py37_0 conda-forge
intel-openmp 2020.0 166 anaconda
ipykernel 5.3.4 py37h888b3d9_1 conda-forge
ipython 7.22.0 py37h085eea5_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.6.3 pyhd3deb0d_0 conda-forge
jedi 0.17.0 py37_0 anaconda
jeepney 0.6.0 pyhd8ed1ab_0 conda-forge
jinja2 2.11.3 pyh44b312d_0 conda-forge
joblib 0.15.1 py_0 conda-forge
jpeg 9b habf39ab_1 anaconda
jsonschema 3.2.0 pyhd8ed1ab_3 conda-forge
jupyter 1.0.0 py37h89c1867_6 conda-forge
jupyter_client 6.1.12 pyhd8ed1ab_0 conda-forge
jupyter_console 6.4.0 pyhd8ed1ab_0 conda-forge
jupyter_core 4.7.1 py37h89c1867_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge
keras-applications 1.0.8 pypi_0 pypi
keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge
keyring 21.5.0 py37h89c1867_0 conda-forge
kiwisolver 1.1.0 py37h99015e2_1 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_8 conda-forge
libblas 3.8.0 21_mkl conda-forge
libboost 1.67.0 h46d08c1_4 anaconda
libcblas 3.8.0 21_mkl conda-forge
libedit 3.1.20181209 hc058e9b_0 anaconda
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 9.1.0 hdf63c60_0 anaconda
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.8.0 21_mkl conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libprotobuf 3.14.0 h8c45485_0
libsodium 1.0.18 h36c2ea0_1 conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0 anaconda
libtiff 4.1.0 h2733197_0 anaconda
libuuid 1.0.3 h1bed415_2 anaconda
libuv 1.40.0 hd18ef5c_0 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.9 h13577e0_2 conda-forge
llvm-openmp 12.0.1 h4bd325d_1 conda-forge
lz4 3.1.1 py37h96bc0eb_0 conda-forge
lz4-c 1.9.2 he1b5a44_3 conda-forge
markdown 3.2.1 pypi_0 pypi
markupsafe 1.1.1 py37hb5d75c8_2 conda-forge
matplotlib 3.1.3 py37_0 anaconda
matplotlib-base 3.1.3 py37hef1b27d_0 anaconda
mistune 0.8.4 py37h4abf009_1002 conda-forge
mkl 2020.0 166 conda-forge
mkl-service 2.3.0 py37he8ac12f_0
mkl_fft 1.0.15 py37ha843d7b_0
mkl_random 1.1.0 py37hd6b4f25_0
more-itertools 8.2.0 py_1 conda-forge
multidict 4.7.3 py37h516909a_0 conda-forge
multiprocess 0.70.9 py37h8f50634_1 conda-forge
nbclient 0.5.3 pyhd8ed1ab_0 conda-forge
nbconvert 6.0.7 py37h89c1867_3 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge
ninja 1.9.0 hc9558a2_1 conda-forge
notebook 6.3.0 py37h06a4308_0
numpy 1.18.1 py37h8960a57_1 conda-forge
numpy-base 1.18.1 py37hde5b4d6_1
oauthlib 3.1.0 pyhd8ed1ab_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openeye-toolkits 2020.2.2 py37_0 openeye
openssl 1.1.1k h27cfd23_0
opt-einsum 3.2.0 pypi_0 pypi
packaging 20.3 py_0 anaconda
pandas 1.0.3 py37h0da4684_1 conda-forge
pandoc 2.12 h7f98852_0 conda-forge
pandocfilters 1.4.3 py37h06a4308_1
parso 0.8.2 pyhd8ed1ab_0 conda-forge
pathos 0.2.5 py_0 conda-forge
pcre 8.43 he1b5a44_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 7.0.0 py37hb39fc2d_0 anaconda
pip 21.2.4 pypi_0 pypi
pixman 0.38.0 h516909a_1003 conda-forge
pkginfo 1.6.1 pyh9f0ad1d_0 conda-forge
pluggy 0.13.1 py37h89c1867_4 conda-forge
pox 0.2.7 py_0 conda-forge
ppft 1.6.6.1 py37hc8dfbb8_1 conda-forge
prometheus_client 0.10.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.17 pyha770c72_0 conda-forge
prompt_toolkit 3.0.17 hd8ed1ab_0 conda-forge
protobuf 3.11.3 pypi_0 pypi
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
py 1.8.1 py_0 conda-forge
py-boost 1.67.0 py37h04863e7_4 anaconda
py4j 0.10.7 py_1 conda-forge
pyasn1 0.4.8 py_0 conda-forge
pyasn1-modules 0.2.8 py_0 anaconda
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pydantic 1.8.2 py37h27cfd23_0
pygments 2.7.2 py_0 conda-forge
pyjwt 1.7.1 py_0 conda-forge
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.6 py_0 conda-forge
pyqt 5.9.2 py37hcca6a23_4 conda-forge
pyrsistent 0.17.3 py37h4abf009_1 conda-forge
pysocks 1.7.1 py37h89c1867_3 conda-forge
pytest 5.4.1 py37hc8dfbb8_0 conda-forge
python 3.7.7 hcf32534_0_cpython anaconda
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.7 2_cp37m conda-forge
pytz 2019.3 py_0 conda-forge
pyzmq 20.0.0 py37h5a562af_1 conda-forge
qt 5.9.7 h5867ecd_1
qtconsole 5.0.3 pyhd8ed1ab_0 conda-forge
qtpy 1.9.0 py_0 conda-forge
rdkit 2020.03.3.0 py37hc20afe1_1 rdkit
readline 8.0 he28a2e2_2 conda-forge
readme_renderer 27.0 pyh9f0ad1d_0 conda-forge
reinvent-chemistry 0.0.38 pypi_0 pypi
reinvent-models 0.0.3 pypi_0 pypi
reinvent-scoring 0.0.41 pypi_0 pypi
requests 2.25.0 pyhd3deb0d_0 conda-forge
requests-oauthlib 1.3.0 pyh9f0ad1d_0 conda-forge
requests-toolbelt 0.9.1 py_0 conda-forge
rfc3986 1.4.0 pyh9f0ad1d_0 conda-forge
rsa 4.7.2 pyh44b312d_0 conda-forge
scikit-learn 0.21.3 py37hcdab131_0 conda-forge
scipy 1.4.1 py37ha3d9a3c_3 conda-forge
secretstorage 3.2.0 py37h89c1867_0 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 46.1.1 py37hc8dfbb8_0 conda-forge
sip 4.19.8 py37hf484d3e_1000 conda-forge
six 1.14.0 py_1 conda-forge
sqlite 3.31.1 h62c20be_1 anaconda
tensorboard 1.15.0 pypi_0 pypi
tensorboard-plugin-wit 1.6.0 pyh9f0ad1d_0 conda-forge
tensorflow 1.15.2 pypi_0 pypi
tensorflow-estimator 1.15.1 pypi_0 pypi
termcolor 1.1.0 py_2 conda-forge
terminado 0.9.4 py37h89c1867_0 conda-forge
testpath 0.4.4 py_0 conda-forge
tk 8.6.8 h84994c4_1000 conda-forge
torch 1.9.0+cu111 pypi_0 pypi
torchaudio 0.9.0 pypi_0 pypi
torchvision 0.10.0+cu111 pypi_0 pypi
tornado 6.0.4 py37h8f50634_2 conda-forge
tqdm 4.43.0 py_0 conda-forge
traitlets 5.0.5 py_0 conda-forge
twine 3.2.0 py37hc8dfbb8_1 conda-forge
typing-extensions 3.7.4.3 0 conda-forge
typing_extensions 3.7.4.3 py_0 conda-forge
urllib3 1.25.11 py_0 conda-forge
wcwidth 0.1.9 pyh9f0ad1d_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
werkzeug 1.0.0 pypi_0 pypi
wheel 0.34.2 py_1 conda-forge
widgetsnbextension 3.5.1 py37h89c1867_4 conda-forge
wrapt 1.12.1 py37h4abf009_2 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xz 5.2.4 h516909a_1002 conda-forge
yarl 1.4.2 py37h7b6447c_0 anaconda
zeromq 4.3.4 h2531618_0
zipp 2.2.0 py_0 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.3.7 h0a35d5f_1001 conda-forge
I checked they are the same.
Could you please try upgrading to reinvent-scoring==0.0.42 and the verify whether the same error message occurs?
First of all, I pasted the wrong error messages when I ran it at the terminal. The right error messages are: (reinvent.v3.0) xzhang@R1124G1:~/projects/Reinvent$ python input.py REINVENT_Use-Case-DRD2_demo/DRD2_config.json Traceback (most recent call last): File "input.py", line 20, in manager = Manager(configuration) File "/home/xzhang/projects/Reinvent/running_modes/manager.py", line 13, in init self._load_environmental_variables() File "/home/xzhang/projects/Reinvent/running_modes/manager.py", line 22, in _load_environmental_variables with open(os.path.join(project_root, '../configs/config.json'), 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/xzhang/projects/Reinvent/running_modes/../configs/config.json'
Now reading again this part of your previously reported issue I realized that you are missing the config.json which should be placed in the folder that corresponds to: https://github.com/MolecularAI/Reinvent/tree/master/configs
Please, see that you have this file as explained in REINVENT`s readme - section "Tests".
@patronov Thank you for your reply.
I still got the same error messages even I upgraded to reinvent-scoring==0.0.42.
Traceback (most recent call last):
File "../../Reinvent/input.py", line 6, in
Im not sure for the exact cause of the issue especially since you have the library installed. We are currently amidst some breaking changes and we are preparing updated tutorials and several new features. Perhaps with the new release these issues will be resolved for you. Sorry for your troubles.
@patronov Thank you for your reply. Please let me know when you have the new release.
Hi @xuzhang5788,
I have just pushed changes to both the reinvent repository and reinvent community repository. The changes correspond to the release of REINVENT 3.0. Would you be able to try the notebooks again?
