open-reaction-database / ord-schema

Schema for the Open Reaction Database
https://open-reaction-database.org
Apache License 2.0
92 stars 26 forks source link

Prioblem running Jupyter Notebook #680

Closed stuchalk closed 1 year ago

stuchalk commented 1 year ago

Describe the bug I tried to run the Jupyter notebook linked via the readme file the notebook crashed in Binder.

To Reproduce Steps to reproduce the behavior:

  1. ORD-schema readme file
  2. Click on 'Launch Binder' button under 'Examples'
  3. Error shows at the end of the binder processing

Expected behavior The Jupyter Notebook was correctly loaded and I was able to run the cells in the notebook.

Screenshots Screen Shot 2023-06-01 at 3 03 26 PM

Desktop (please complete the following information):

Additional context NA

connorcoley commented 1 year ago

Can reproduce. Full log copied below since it takes >15 minutes to run...

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockeretjql14k'...
HEAD is now at bf662fd Bump version: 0.3.52 → 0.3.53 [skip actions]
Python version unspecified, using current default Python version 3.10. This will change in the future.Building conda environment for python=3.10
Using CondaBuildPack builder
Step 1/52 : FROM buildpack-deps:bionic
 ---> 3f42bc7df665
Step 2/52 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 647d94ffe129
Step 3/52 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 27bdb3854134
Step 4/52 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> e42a6460bbf6
Step 5/52 : ENV LC_ALL=en_US.UTF-8     LANG=en_US.UTF-8     LANGUAGE=en_US.UTF-8
 ---> Using cache
 ---> 384dabd588c4
Step 6/52 : ENV SHELL=/bin/bash
 ---> Using cache
 ---> 150613f4b929
Step 7/52 : ARG NB_USER
 ---> Using cache
 ---> 14dfe30505a2
Step 8/52 : ARG NB_UID
 ---> Using cache
 ---> 3309ef5f5992
Step 9/52 : ENV USER=${NB_USER}     HOME=/home/${NB_USER}
 ---> Using cache
 ---> 9260cab8ad7f
Step 10/52 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 44091361e844
Step 11/52 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 904fad8c1cde
Step 12/52 : EXPOSE 8888
 ---> Using cache
 ---> bd3588304a43
Step 13/52 : ENV APP_BASE=/srv
 ---> Using cache
 ---> fdb843af1eff
Step 14/52 : ENV CONDA_DIR=${APP_BASE}/conda
 ---> Using cache
 ---> e112768d1169
Step 15/52 : ENV NB_PYTHON_PREFIX=${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> cfa59f3721ae
Step 16/52 : ENV NPM_DIR=${APP_BASE}/npm
 ---> Using cache
 ---> 4164be65bad3
Step 17/52 : ENV NPM_CONFIG_GLOBALCONFIG=${NPM_DIR}/npmrc
 ---> Using cache
 ---> 5b02c0f508b8
Step 18/52 : ENV NB_ENVIRONMENT_FILE=/tmp/env/environment.lock
 ---> Using cache
 ---> 710b8711f752
Step 19/52 : ENV MAMBA_ROOT_PREFIX=${CONDA_DIR}
 ---> Using cache
 ---> 5030ce1a267c
Step 20/52 : ENV MAMBA_EXE=${CONDA_DIR}/bin/mamba
 ---> Using cache
 ---> a7615a46de8d
Step 21/52 : ENV CONDA_PLATFORM=linux-64
 ---> Using cache
 ---> c8bc5adb3cbc
Step 22/52 : ENV KERNEL_PYTHON_PREFIX=${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 7bf3d1b6a6db
Step 23/52 : ENV PATH=${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> f729859acce0
Step 24/52 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e10-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-44e764 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> d96606106a01
Step 25/52 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e10-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e10-2dlinux-2d64-2elock-388e0b /tmp/env/environment.lock
 ---> Using cache
 ---> c383960275bb
Step 26/52 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e10-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dbase-2denv-2ebash-e5509f /tmp/install-base-env.bash
 ---> Using cache
 ---> 69e4301a7578
Step 27/52 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-base-env.bash' && rm -rf /tmp/install-base-env.bash /tmp/env
 ---> Using cache
 ---> cb35a6b95c60
Step 28/52 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 490f61de4b9f
Step 29/52 : USER root
 ---> Using cache
 ---> 752b09bfd671
Step 30/52 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> f9dcd3b5510e
Step 31/52 : ENV REPO_DIR=${REPO_DIR}
 ---> Using cache
 ---> b984155b9432
Step 32/52 : RUN if [ ! -d "${REPO_DIR}" ]; then         /usr/bin/install -o ${NB_USER} -g ${NB_USER} -d "${REPO_DIR}";     fi
 ---> Using cache
 ---> 89c98b0b295f
Step 33/52 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 48ca1ef2bca5
Step 34/52 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> a7c86ee8445e
Step 35/52 : ENV PATH=${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> a88714022cc0
Step 36/52 : ENV CONDA_DEFAULT_ENV=${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 25c49864bfba
Step 37/52 : COPY --chown=1000:1000 src/environment.yml ${REPO_DIR}/environment.yml
 ---> 1725b08e9a97
Step 38/52 : USER ${NB_USER}
 ---> Running in ad1f0109f4be
Removing intermediate container ad1f0109f4be
 ---> 600303015dd9
Step 39/52 : RUN TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '
 ---> Running in e60b4d83ecb2

Looking for: ['python', 'rdkit', 'pip']

Transaction

  Prefix: /srv/conda/envs/notebook

  Updating specs:

   - rdkit
   - python
   - pip

  Package                              Version  Build               Channel                   Size
────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────────────────────────

  + blas                                   1.0  openblas            pkgs/main/linux-64        47kB
  + bottleneck                           1.3.5  py37h7deecbd_0      pkgs/main/linux-64       118kB
  + cairo                               1.16.0  hb05425b_4          pkgs/main/linux-64         1MB
  + fontconfig                          2.14.1  hef1e5e3_0          pkgs/main/linux-64       291kB
  + freetype                            2.12.1  h4a9f257_0          pkgs/main/linux-64       641kB
  + giflib                               5.2.1  h5eee18b_3          pkgs/main/linux-64        82kB
  + glib                                2.69.1  he621ea3_2          pkgs/main/linux-64         2MB
  + jpeg                                    9e  h5eee18b_1          pkgs/main/linux-64       268kB
  + lcms2                                 2.12  h3be6417_0          pkgs/main/linux-64       319kB
  + lerc                                   3.0  h295c915_0          pkgs/main/linux-64       201kB
  + libboost                            1.73.0  h28710b8_12         pkgs/main/linux-64        14MB
  + libdeflate                            1.17  h5eee18b_0          pkgs/main/linux-64        71kB
  + libgfortran-ng                      11.2.0  h00389a5_1          pkgs/main/linux-64        20kB
  + libgfortran5                        11.2.0  h1234567_1          pkgs/main/linux-64         2MB
  + libopenblas                         0.3.21  h043d6bf_0          pkgs/main/linux-64         6MB
  + libpng                              1.6.39  h5eee18b_0          pkgs/main/linux-64       311kB
  + libtiff                              4.5.0  h6a678d5_2          pkgs/main/linux-64       491kB
  + libwebp                              1.2.4  h11a3e52_1          pkgs/main/linux-64        88kB
  + libwebp-base                         1.2.4  h5eee18b_1          pkgs/main/linux-64       385kB
  + libxcb                                1.15  h7f8727e_0          pkgs/main/linux-64       518kB
  + libxml2                             2.9.14  h74e7548_0          pkgs/main/linux-64       735kB
  + lz4-c                                1.9.4  h6a678d5_0          pkgs/main/linux-64       158kB
  + numexpr                              2.8.4  py37hd2a5715_0      pkgs/main/linux-64       136kB
  + numpy                               1.21.5  py37hf838250_3      pkgs/main/linux-64        10kB
  + numpy-base                          1.21.5  py37h1e6e340_3      pkgs/main/linux-64         5MB
  + pandas                               1.3.5  py37h8c16a72_0      pkgs/main/linux-64        10MB
  + pcre                                  8.45  h295c915_0          pkgs/main/linux-64       212kB
  + pillow                               9.4.0  py37h6a678d5_0      pkgs/main/linux-64       739kB
  + pixman                              0.40.0  h7f8727e_1          pkgs/main/linux-64       382kB
  + py-boost                            1.73.0  py37h51133e4_12     pkgs/main/linux-64       199kB
  + rdkit                          2020.09.1.0  py37hd50e099_1      rdkit/linux-64            27MB
  + sqlite                              3.40.1  h5082296_0          pkgs/main/linux-64         1MB
  + zstd                                 1.5.5  hc292b87_0          pkgs/main/linux-64       663kB

  Change:
────────────────────────────────────────────────────────────────────────────────────────────────────

  - argon2-cffi-bindings                21.2.0  py310h5764c6d_3     conda-forge                   
  + argon2-cffi-bindings                21.2.0  py37h7f8727e_0      pkgs/main/linux-64        33kB
  - attrs                               22.2.0  pyh71513ae_0        conda-forge                   
  + attrs                               22.2.0  pyh71513ae_0        conda-forge/noarch        54kB
  - brotlipy                             0.7.0  py310h5764c6d_1005  conda-forge                   
  + brotlipy                             0.7.0  py37h27cfd23_1003   pkgs/main/linux-64       328kB
  - cffi                                1.15.1  py310h255011f_3     conda-forge                   
  + cffi                                1.15.1  py37h5eee18b_3      pkgs/main/linux-64       245kB
  - nodejs                             18.15.0  h8d033a5_0          conda-forge                   
  + nodejs                             18.15.0  ha637b67_0          pkgs/main/linux-64        16MB
  - pycparser                             2.21  pyhd8ed1ab_0        conda-forge                   
  + pycparser                             2.21  pyhd8ed1ab_0        conda-forge/noarch       103kB
  - pysocks                              1.7.1  pyha2e5f31_6        conda-forge                   
  + pysocks                              1.7.1  py37_1              pkgs/main/linux-64        28kB
  - ruamel.yaml                        0.17.21  py310h1fa729e_3     conda-forge                   
  + ruamel.yaml                        0.17.21  py37h5eee18b_0      pkgs/main/linux-64       181kB
  - tornado                                6.2  py310h5764c6d_1     conda-forge                   
  + tornado                                6.2  py37h5eee18b_0      pkgs/main/linux-64       598kB

  Reinstall:
────────────────────────────────────────────────────────────────────────────────────────────────────

  o alembic                             1.10.3  pyhd8ed1ab_0        conda-forge                   
  o anyio                                3.6.2  pyhd8ed1ab_0        conda-forge                   
  o argon2-cffi                         21.3.0  pyhd8ed1ab_0        conda-forge                   
  o asttokens                            2.2.1  pyhd8ed1ab_0        conda-forge                   
  o async_generator                       1.10  py_0                conda-forge                   
  o babel                               2.12.1  pyhd8ed1ab_1        conda-forge                   
  o backcall                             0.2.0  pyh9f0ad1d_0        conda-forge                   
  o backports                              1.0  pyhd8ed1ab_3        conda-forge                   
  o backports.functools_lru_cache        1.6.4  pyhd8ed1ab_0        conda-forge                   
  o beautifulsoup4                      4.12.2  pyha770c72_0        conda-forge                   
  o bleach                               6.0.0  pyhd8ed1ab_0        conda-forge                   
  o blinker                                1.6  pyhd8ed1ab_0        conda-forge                   
  o certifi                          2022.12.7  pyhd8ed1ab_0        conda-forge                   
  o certipy                              0.1.3  py_0                conda-forge                   
  o charset-normalizer                   3.1.0  pyhd8ed1ab_0        conda-forge                   
  o comm                                 0.1.3  pyhd8ed1ab_0        conda-forge                   
  o decorator                            5.1.1  pyhd8ed1ab_0        conda-forge                   
  o defusedxml                           0.7.1  pyhd8ed1ab_0        conda-forge                   
  o entrypoints                            0.4  pyhd8ed1ab_0        conda-forge                   
  o executing                            1.2.0  pyhd8ed1ab_0        conda-forge                   
  o flit-core                            3.8.0  pyhd8ed1ab_0        conda-forge                   
  o idna                                   3.4  pyhd8ed1ab_0        conda-forge                   
  o importlib_resources                 5.12.0  pyhd8ed1ab_0        conda-forge                   
  o ipython_genutils                     0.2.0  py_1                conda-forge                   
  o ipywidgets                           8.0.2  pyhd8ed1ab_1        conda-forge                   
  o jedi                                0.18.2  pyhd8ed1ab_0        conda-forge                   
  o jinja2                               3.1.2  pyhd8ed1ab_1        conda-forge                   
  o json5                                0.9.5  pyh9f0ad1d_0        conda-forge                   
  o jsonschema                          4.17.3  pyhd8ed1ab_0        conda-forge                   
  o jupyter-offlinenotebook              0.2.2  pyh1d7be83_0        conda-forge                   
  o jupyter-resource-usage               0.7.0  pyhd8ed1ab_0        conda-forge                   
  o jupyter_telemetry                    0.1.0  pyhd8ed1ab_1        conda-forge                   
  o jupyterhub-base                      3.1.1  pyh2a2186d_0        conda-forge                   
  o jupyterhub-singleuser                3.1.1  pyh2a2186d_0        conda-forge                   
  o jupyterlab                           3.4.8  pyhd8ed1ab_0        conda-forge                   
  o jupyterlab_pygments                  0.2.2  pyhd8ed1ab_0        conda-forge                   
  o jupyterlab_server                   2.22.0  pyhd8ed1ab_0        conda-forge                   
  o jupyterlab_widgets                   3.0.7  pyhd8ed1ab_0        conda-forge                   
  o mako                                 1.2.4  pyhd8ed1ab_0        conda-forge                   
  o matplotlib-inline                    0.1.6  pyhd8ed1ab_0        conda-forge                   
  o mistune                              2.0.5  pyhd8ed1ab_0        conda-forge                   
  o nbclassic                            0.5.5  pyhb4ecaf3_1        conda-forge                   
  o nbconvert                            7.3.0  pyhd8ed1ab_2        conda-forge                   
  o nbconvert-core                       7.3.0  pyhd8ed1ab_2        conda-forge                   
  o nbconvert-pandoc                     7.3.0  pyhd8ed1ab_2        conda-forge                   
  o nbformat                             5.8.0  pyhd8ed1ab_0        conda-forge                   
  o nest-asyncio                         1.5.6  pyhd8ed1ab_0        conda-forge                   
  o notebook                            6.4.12  pyha770c72_0        conda-forge                   
  o notebook-shim                        0.2.2  pyhd8ed1ab_0        conda-forge                   
  o oauthlib                             3.2.2  pyhd8ed1ab_0        conda-forge                   
  o packaging                             23.0  pyhd8ed1ab_0        conda-forge                   
  o pamela                               1.0.0  py_0                conda-forge                   
  o pandocfilters                        1.5.0  pyhd8ed1ab_0        conda-forge                   
  o parso                                0.8.3  pyhd8ed1ab_0        conda-forge                   
  o pexpect                              4.8.0  pyh1a96a4e_2        conda-forge                   
  o pickleshare                          0.7.5  py_1003             conda-forge                   
  o pip                                 23.0.1  pyhd8ed1ab_0        conda-forge                   
  o pkgutil-resolve-name                1.3.10  pyhd8ed1ab_0        conda-forge                   
  o platformdirs                         3.2.0  pyhd8ed1ab_0        conda-forge                   
  o prometheus_client                   0.16.0  pyhd8ed1ab_0        conda-forge                   
  o prompt-toolkit                      3.0.38  pyha770c72_0        conda-forge                   
  o ptyprocess                           0.7.0  pyhd3deb0d_0        conda-forge                   
  o pure_eval                            0.2.2  pyhd8ed1ab_0        conda-forge                   
  o pygments                            2.14.0  pyhd8ed1ab_0        conda-forge                   
  o pyjwt                                2.6.0  pyhd8ed1ab_0        conda-forge                   
  o pyopenssl                           23.1.1  pyhd8ed1ab_0        conda-forge                   
  o python-dateutil                      2.8.2  pyhd8ed1ab_0        conda-forge                   
  o python-fastjsonschema               2.16.3  pyhd8ed1ab_0        conda-forge                   
  o python-json-logger                   2.0.7  pyhd8ed1ab_0        conda-forge                   
  o pytz                                2023.3  pyhd8ed1ab_0        conda-forge                   
  o requests                            2.28.2  pyhd8ed1ab_1        conda-forge                   
  o send2trash                           1.8.0  pyhd8ed1ab_0        conda-forge                   
  o setuptools                          67.6.1  pyhd8ed1ab_0        conda-forge                   
  o six                                 1.16.0  pyh6c4a22f_0        conda-forge                   
  o sniffio                              1.3.0  pyhd8ed1ab_0        conda-forge                   
  o soupsieve                      2.3.2.post1  pyhd8ed1ab_0        conda-forge                   
  o stack_data                           0.6.2  pyhd8ed1ab_0        conda-forge                   
  o terminado                           0.17.1  pyh41d4057_0        conda-forge                   
  o tinycss2                             1.2.1  pyhd8ed1ab_0        conda-forge                   
  o tomli                                2.0.1  pyhd8ed1ab_0        conda-forge                   
  o traitlets                            5.9.0  pyhd8ed1ab_0        conda-forge                   
  o typing-extensions                    4.5.0  hd8ed1ab_0          conda-forge                   
  o typing_extensions                    4.5.0  pyha770c72_0        conda-forge                   
  o urllib3                            1.26.15  pyhd8ed1ab_0        conda-forge                   
  o wcwidth                              0.2.6  pyhd8ed1ab_0        conda-forge                   
  o webencodings                         0.5.1  py_1                conda-forge                   
  o websocket-client                     1.5.1  pyhd8ed1ab_0        conda-forge                   
  o wheel                               0.40.0  pyhd8ed1ab_0        conda-forge                   
  o widgetsnbextension                   4.0.7  pyhd8ed1ab_0        conda-forge                   
  o zipp                                3.15.0  pyhd8ed1ab_0        conda-forge                   

  Upgrade:
────────────────────────────────────────────────────────────────────────────────────────────────────

  - xz                                   5.2.6  h166bdaf_0          conda-forge                   
  + xz                                   5.4.2  h5eee18b_0          pkgs/main/linux-64       657kB

  Downgrade:
────────────────────────────────────────────────────────────────────────────────────────────────────

  - cryptography                        40.0.1  py310h34c0648_0     conda-forge                   
  + cryptography                        39.0.1  py37h9ce1e76_0      pkgs/main/linux-64         1MB
  - debugpy                              1.6.7  py310heca2aa9_0     conda-forge                   
  + debugpy                              1.5.1  py37h295c915_0      pkgs/main/linux-64         2MB
  - greenlet                             2.0.2  py310heca2aa9_0     conda-forge                   
  + greenlet                             2.0.1  py37h6a678d5_0      pkgs/main/linux-64       196kB
  - icu                                   70.1  h27087fc_0          conda-forge                   
  + icu                                   58.2  he6710b0_3          pkgs/main/linux-64        11MB
  - importlib-metadata                   6.2.0  pyha770c72_0        conda-forge                   
  + importlib-metadata                  4.11.3  py37h06a4308_0      pkgs/main/linux-64        41kB
  - importlib_metadata                   6.2.0  hd8ed1ab_0          conda-forge                   
  + importlib_metadata                  4.11.3  hd3eb1b0_0          pkgs/main/noarch          13kB
  - ipykernel                           6.22.0  pyh210e3f2_0        conda-forge                   
  + ipykernel                           6.15.2  py37h06a4308_0      pkgs/main/linux-64       194kB
  - ipython                             8.12.0  pyh41d4057_0        conda-forge                   
  + ipython                             7.31.1  py37h06a4308_1      pkgs/main/linux-64         1MB
  - jupyter_client                       8.1.0  pyhd8ed1ab_0        conda-forge                   
  + jupyter_client                       7.4.9  py37h06a4308_0      pkgs/main/linux-64       209kB
  - jupyter_core                         5.3.0  py310hff52083_0     conda-forge                   
  + jupyter_core                        4.11.2  py37h06a4308_0      pkgs/main/linux-64        82kB
  - jupyter_server                      1.23.6  pyhd8ed1ab_0        conda-forge                   
  + jupyter_server                      1.23.4  py37h06a4308_0      pkgs/main/linux-64       391kB
  - markupsafe                           2.1.2  py310h1fa729e_0     conda-forge                   
  + markupsafe                           2.1.1  py37h7f8727e_0      pkgs/main/linux-64        22kB
  - nbclient                             0.7.3  pyhd8ed1ab_0        conda-forge                   
  + nbclient                            0.5.13  py37h06a4308_0      pkgs/main/linux-64        93kB
  - openssl                              3.1.0  h0b41bf4_0          conda-forge                   
  + openssl                             1.1.1t  h7f8727e_0          pkgs/main/linux-64         4MB
  - psutil                               5.9.4  py310h5764c6d_0     conda-forge                   
  + psutil                               5.9.0  py37h5eee18b_0      pkgs/main/linux-64       336kB
  - pyrsistent                          0.19.3  py310h1fa729e_0     conda-forge                   
  + pyrsistent                          0.18.0  py37heee7806_0      pkgs/main/linux-64        97kB
  - python                             3.10.10  he550d4f_0_cpython  conda-forge                   
  + python                              3.7.16  h7a1cb2a_0          pkgs/main/linux-64        47MB
  - python_abi                            3.10  3_cp310             conda-forge                   
  + python_abi                             3.7  2_cp37m             conda-forge/linux-64       4kB
  - pyzmq                               25.0.2  py310h059b190_0     conda-forge                   
  + pyzmq                               23.2.0  py37h6a678d5_0      pkgs/main/linux-64       448kB
  - ruamel.yaml.clib                     0.2.7  py310h1fa729e_1     conda-forge                   
  + ruamel.yaml.clib                     0.2.6  py37h5eee18b_1      pkgs/main/linux-64       144kB
  - sqlalchemy                           2.0.9  py310h1fa729e_0     conda-forge                   
  + sqlalchemy                          1.4.39  py37h5eee18b_0      pkgs/main/linux-64         2MB

  Summary:

  Install: 33 packages
  Change: 9 packages
  Reinstall: 90 packages
  Upgrade: 1 packages
  Downgrade: 21 packages

  Total download: 165MB

────────────────────────────────────────────────────────────────────────────────────────────────────

Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Installing pip dependencies: ...working... Ran pip subprocess with arguments:
['/srv/conda/envs/notebook/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/jovyan/condaenv.ytqn_c7k.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting flask>=1.1.2
  Downloading Flask-2.2.5-py3-none-any.whl (101 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 101.8/101.8 kB 4.4 MB/s eta 0:00:00
Requirement already satisfied: numpy>=1.18.1 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 2)) (1.21.5)
Collecting numpy>=1.18.1
  Downloading numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 30.8 MB/s eta 0:00:00
Collecting openpyxl>=3.0.5
  Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 33.5 MB/s eta 0:00:00
Requirement already satisfied: pandas>=1.0.4 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 4)) (1.3.5)
Collecting protobuf>=3.13.0
  Downloading protobuf-4.23.2-cp37-abi3-manylinux2014_x86_64.whl (304 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 304.5/304.5 kB 37.2 MB/s eta 0:00:00
Collecting protoc-wheel-0>=3.14.0
  Downloading protoc_wheel_0-22.0-py2.py3-none-manylinux1_x86_64.whl (2.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 36.5 MB/s eta 0:00:00
Collecting pygithub>=1.51
  Downloading PyGithub-1.58.2-py3-none-any.whl (312 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 312.5/312.5 kB 35.0 MB/s eta 0:00:00
Requirement already satisfied: python-dateutil>=1.10.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 8)) (2.8.2)
Requirement already satisfied: jinja2>=2.0.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 9)) (3.1.2)
Collecting xlrd<2.0.0
  Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.3/103.3 kB 21.1 MB/s eta 0:00:00
Collecting xlwt>=1.3.0
  Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 23.8 MB/s eta 0:00:00
Collecting joblib>=1.0.0
  Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 298.0/298.0 kB 41.4 MB/s eta 0:00:00
Requirement already satisfied: importlib-metadata>=3.6.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from flask>=1.1.2->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 1)) (4.11.3)
Collecting itsdangerous>=2.0
  Downloading itsdangerous-2.1.2-py3-none-any.whl (15 kB)
Collecting click>=8.0
  Downloading click-8.1.3-py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.6/96.6 kB 21.6 MB/s eta 0:00:00
Collecting Werkzeug>=2.2.2
  Downloading Werkzeug-2.2.3-py3-none-any.whl (233 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.6/233.6 kB 45.2 MB/s eta 0:00:00
Collecting et-xmlfile
  Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)
Requirement already satisfied: pytz>=2017.3 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pandas>=1.0.4->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 4)) (2023.3)
Collecting deprecated
  Downloading Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB)
Requirement already satisfied: pyjwt[crypto]>=2.4.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pygithub>=1.51->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 7)) (2.6.0)
Collecting pynacl>=1.4.0
  Downloading PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 856.7/856.7 kB 22.0 MB/s eta 0:00:00
Requirement already satisfied: requests>=2.14.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pygithub>=1.51->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 7)) (2.28.2)
Requirement already satisfied: six>=1.5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from python-dateutil>=1.10.0->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 8)) (1.16.0)
Requirement already satisfied: MarkupSafe>=2.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jinja2>=2.0.0->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 9)) (2.1.1)
Requirement already satisfied: zipp>=0.5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from importlib-metadata>=3.6.0->flask>=1.1.2->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 1)) (3.15.0)
Requirement already satisfied: typing-extensions>=3.6.4 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from importlib-metadata>=3.6.0->flask>=1.1.2->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 1)) (4.5.0)
Requirement already satisfied: cryptography>=3.4.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pyjwt[crypto]>=2.4.0->pygithub>=1.51->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 7)) (39.0.1)
Requirement already satisfied: cffi>=1.4.1 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pynacl>=1.4.0->pygithub>=1.51->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 7)) (1.15.1)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from requests>=2.14.0->pygithub>=1.51->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 7)) (1.26.15)
Requirement already satisfied: idna<4,>=2.5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from requests>=2.14.0->pygithub>=1.51->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 7)) (3.4)
Requirement already satisfied: charset-normalizer<4,>=2 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from requests>=2.14.0->pygithub>=1.51->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 7)) (3.1.0)
Requirement already satisfied: certifi>=2017.4.17 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from requests>=2.14.0->pygithub>=1.51->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 7)) (2022.12.7)
Collecting wrapt<2,>=1.10
  Downloading wrapt-1.15.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (75 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 75.7/75.7 kB 14.0 MB/s eta 0:00:00
Requirement already satisfied: pycparser in /srv/conda/envs/notebook/lib/python3.7/site-packages (from cffi>=1.4.1->pynacl>=1.4.0->pygithub>=1.51->-r /home/jovyan/condaenv.ytqn_c7k.requirements.txt (line 7)) (2.21)
Installing collected packages: xlwt, protoc-wheel-0, xlrd, wrapt, Werkzeug, protobuf, numpy, joblib, itsdangerous, et-xmlfile, pynacl, openpyxl, deprecated, click, flask, pygithub
  Attempting uninstall: numpy
    Found existing installation: numpy 1.21.5
    Uninstalling numpy-1.21.5:
      Successfully uninstalled numpy-1.21.5
Successfully installed Werkzeug-2.2.3 click-8.1.3 deprecated-1.2.14 et-xmlfile-1.1.0 flask-2.2.5 itsdangerous-2.1.2 joblib-1.2.0 numpy-1.21.6 openpyxl-3.1.2 protobuf-4.23.2 protoc-wheel-0-22.0 pygithub-1.58.2 pynacl-1.5.0 wrapt-1.15.0 xlrd-1.2.0 xlwt-1.3.0

done
#
# To activate this environment, use
#
#     $ conda activate /srv/conda/envs/notebook
#
# To deactivate an active environment, use
#
#     $ conda deactivate

time: 321.280
Will remove 1 package cache(s).
time: 8.331
# packages in environment at /srv/conda/envs/notebook:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
alembic                   1.10.3             pyhd8ed1ab_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py37h7f8727e_0    defaults
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
async_generator           1.10                       py_0    defaults
attrs                     22.2.0             pyh71513ae_0    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
blas                      1.0                    openblas    defaults
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blinker                   1.6                pyhd8ed1ab_0    conda-forge
bottleneck                1.3.5            py37h7deecbd_0    defaults
brotlipy                  0.7.0           py37h27cfd23_1003    defaults
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cairo                     1.16.0               hb05425b_4    defaults
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
certipy                   0.1.3                      py_0    defaults
cffi                      1.15.1           py37h5eee18b_3    defaults
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
click                     8.1.3                    pypi_0    pypi
comm                      0.1.3              pyhd8ed1ab_0    conda-forge
cryptography              39.0.1           py37h9ce1e76_0    defaults
debugpy                   1.5.1            py37h295c915_0    defaults
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecated                1.2.14                   pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
et-xmlfile                1.1.0                    pypi_0    pypi
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
flask                     2.2.5                    pypi_0    pypi
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
fontconfig                2.14.1               hef1e5e3_0    defaults
freetype                  2.12.1               h4a9f257_0    defaults
giflib                    5.2.1                h5eee18b_3    defaults
glib                      2.69.1               he621ea3_2    defaults
greenlet                  2.0.1            py37h6a678d5_0    defaults
icu                       58.2                 he6710b0_3    defaults
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.3           py37h06a4308_0    defaults
importlib_metadata        4.11.3               hd3eb1b0_0    defaults
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.15.2           py37h06a4308_0    defaults
ipython                   7.31.1           py37h06a4308_1    defaults
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.2              pyhd8ed1ab_1    conda-forge
itsdangerous              2.1.2                    pypi_0    pypi
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.2.0                    pypi_0    pypi
jpeg                      9e                   h5eee18b_1    defaults
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter-offlinenotebook   0.2.2              pyh1d7be83_0    conda-forge
jupyter-resource-usage    0.7.0              pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.9            py37h06a4308_0    defaults
jupyter_core              4.11.2           py37h06a4308_0    defaults
jupyter_server            1.23.4           py37h06a4308_0    defaults
jupyter_telemetry         0.1.0              pyhd8ed1ab_1    conda-forge
jupyterhub-base           3.1.1              pyh2a2186d_0    conda-forge
jupyterhub-singleuser     3.1.1              pyh2a2186d_0    conda-forge
jupyterlab                3.4.8              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.22.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.7              pyhd8ed1ab_0    conda-forge
lcms2                     2.12                 h3be6417_0    defaults
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      3.0                  h295c915_0    defaults
libboost                  1.73.0              h28710b8_12    defaults
libdeflate                1.17                 h5eee18b_0    defaults
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            11.2.0               h00389a5_1    defaults
libgfortran5              11.2.0               h1234567_1    defaults
libgomp                   12.2.0              h65d4601_19    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21               h043d6bf_0    defaults
libpng                    1.6.39               h5eee18b_0    defaults
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.40.0               h753d276_0    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtiff                   4.5.0                h6a678d5_2    defaults
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.44.2               h166bdaf_0    conda-forge
libwebp                   1.2.4                h11a3e52_1    defaults
libwebp-base              1.2.4                h5eee18b_1    defaults
libxcb                    1.15                 h7f8727e_0    defaults
libxml2                   2.9.14               h74e7548_0    defaults
libzlib                   1.2.13               h166bdaf_4    conda-forge
lz4-c                     1.9.4                h6a678d5_0    defaults
mako                      1.2.4              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.1            py37h7f8727e_0    defaults
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
nbclassic                 0.5.5              pyhb4ecaf3_1    conda-forge
nbclient                  0.5.13           py37h06a4308_0    defaults
nbconvert                 7.3.0              pyhd8ed1ab_2    conda-forge
nbconvert-core            7.3.0              pyhd8ed1ab_2    conda-forge
nbconvert-pandoc          7.3.0              pyhd8ed1ab_2    conda-forge
nbformat                  5.8.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
nodejs                    18.15.0              ha637b67_0    defaults
notebook                  6.4.12             pyha770c72_0    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
numexpr                   2.8.4            py37hd2a5715_0    defaults
numpy                     1.21.6                   pypi_0    pypi
oauthlib                  3.2.2              pyhd8ed1ab_0    conda-forge
openpyxl                  3.1.2                    pypi_0    pypi
openssl                   1.1.1t               h7f8727e_0    defaults
packaging                 23.0               pyhd8ed1ab_0    conda-forge
pamela                    1.0.0                      py_0    defaults
pandas                    1.3.5            py37h8c16a72_0    defaults
pandoc                    2.19.2               h32600fe_2    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h295c915_0    defaults
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0            py37h6a678d5_0    defaults
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h7f8727e_1    defaults
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.2.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
protobuf                  4.23.2                   pypi_0    pypi
protoc-wheel-0            22.0                     pypi_0    pypi
psutil                    5.9.0            py37h5eee18b_0    defaults
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py-boost                  1.73.0          py37h51133e4_12    defaults
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygithub                  1.58.2                   pypi_0    pypi
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.6.0              pyhd8ed1ab_0    conda-forge
pynacl                    1.5.0                    pypi_0    pypi
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyrsistent                0.18.0           py37heee7806_0    defaults
pysocks                   1.7.1                    py37_1    defaults
python                    3.7.16               h7a1cb2a_0    defaults
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.7                     2_cp37m    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pyzmq                     23.2.0           py37h6a678d5_0    defaults
rdkit                     2020.09.1.0      py37hd50e099_1    rdkit
readline                  8.2                  h8228510_1    conda-forge
requests                  2.28.2             pyhd8ed1ab_1    conda-forge
ruamel.yaml               0.17.21          py37h5eee18b_0    defaults
ruamel.yaml.clib          0.2.6            py37h5eee18b_1    defaults
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                67.6.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlalchemy                1.4.39           py37h5eee18b_0    defaults
sqlite                    3.40.1               h5082296_0    defaults
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.2              py37h5eee18b_0    defaults
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
werkzeug                  2.2.3                    pypi_0    pypi
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.7              pyhd8ed1ab_0    conda-forge
wrapt                     1.15.0                   pypi_0    pypi
xlrd                      1.2.0                    pypi_0    pypi
xlwt                      1.3.0                    pypi_0    pypi
xz                        5.4.2                h5eee18b_0    defaults
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.5                hc292b87_0    defaults
Removing intermediate container e60b4d83ecb2
 ---> d61434e0401a
Step 40/52 : USER root
 ---> Running in 119ed6553cfa
Removing intermediate container 119ed6553cfa
 ---> 72ae81829820
Step 41/52 : COPY --chown=1000:1000 src/ ${REPO_DIR}/
 ---> 22340e738c00
Step 42/52 : LABEL repo2docker.ref="bf662fd60f4e8c6775a3256de91359589bb860ae"
 ---> Running in defd848d6cb4
Removing intermediate container defd848d6cb4
 ---> 4847970df7a5
Step 43/52 : LABEL repo2docker.repo="https://github.com/open-reaction-database/ord-schema"
 ---> Running in 6aa36af86e8d
Removing intermediate container 6aa36af86e8d
 ---> b024861e68dd
Step 44/52 : LABEL repo2docker.version="2022.10.0+169.g6250c06"
 ---> Running in 49968f912a67
Removing intermediate container 49968f912a67
 ---> 7c9bf31f928e
Step 45/52 : USER ${NB_USER}
 ---> Running in 7dbd813809ff
Removing intermediate container 7dbd813809ff
 ---> 2949ef61ad6e
Step 46/52 : RUN chmod +x postBuild
 ---> Running in 62edf92c89d6
Removing intermediate container 62edf92c89d6
 ---> 3fed75806c49
Step 47/52 : RUN ./postBuild
 ---> Running in e342427093cc
+ pip install -e '.[examples]'
Obtaining file:///home/jovyan
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Checking if build backend supports build_editable: started
  Checking if build backend supports build_editable: finished with status 'done'
  Getting requirements to build editable: started
  Getting requirements to build editable: finished with status 'done'
  Preparing editable metadata (pyproject.toml): started
  Preparing editable metadata (pyproject.toml): finished with status 'done'
Collecting psycopg2>=2.8.5
  Downloading psycopg2-2.9.6.tar.gz (383 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 384.0/384.0 kB 1.4 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting inflection>=0.5.1
  Downloading inflection-0.5.1-py2.py3-none-any.whl (9.5 kB)
Collecting docopt>=0.6.2
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: joblib>=1.0.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ord-schema==0.3.53) (1.2.0)
Requirement already satisfied: openpyxl>=3.0.5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ord-schema==0.3.53) (3.1.2)
Requirement already satisfied: pygithub>=1.51 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ord-schema==0.3.53) (1.58.2)
Collecting rdkit>=2021.9.5
  Downloading rdkit-2023.3.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (29.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 29.5/29.5 MB 23.3 MB/s eta 0:00:00
Requirement already satisfied: jinja2>=2.0.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ord-schema==0.3.53) (3.1.2)
Requirement already satisfied: pandas>=1.0.4 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ord-schema==0.3.53) (1.3.5)
Requirement already satisfied: sqlalchemy>=1.4.39 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ord-schema==0.3.53) (1.4.39)
Collecting protobuf<3.20,>=3.13.0
  Downloading protobuf-3.19.6-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 29.7 MB/s eta 0:00:00
Requirement already satisfied: flask>=1.1.2 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ord-schema==0.3.53) (2.2.5)
Requirement already satisfied: python-dateutil>=1.10.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ord-schema==0.3.53) (2.8.2)
Requirement already satisfied: numpy>=1.18.1 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ord-schema==0.3.53) (1.21.6)
Collecting wget>=3.2
  Downloading wget-3.2.zip (10 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting glob2>=0.7
  Downloading glob2-0.7.tar.gz (10 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting tqdm>=4.61.2
  Downloading tqdm-4.65.0-py3-none-any.whl (77 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.1/77.1 kB 6.9 MB/s eta 0:00:00
Collecting tensorflow>=2.4.1
  Downloading tensorflow-2.11.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (588.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 588.3/588.3 MB 1.1 MB/s eta 0:00:00
Collecting scikit-learn>=0.24.1
  Downloading scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 24.8/24.8 MB 19.6 MB/s eta 0:00:00
Collecting matplotlib>=3.3.4
  Downloading matplotlib-3.5.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.2/11.2 MB 14.0 MB/s eta 0:00:00
Requirement already satisfied: click>=8.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from flask>=1.1.2->ord-schema==0.3.53) (8.1.3)
Requirement already satisfied: itsdangerous>=2.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from flask>=1.1.2->ord-schema==0.3.53) (2.1.2)
Requirement already satisfied: importlib-metadata>=3.6.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from flask>=1.1.2->ord-schema==0.3.53) (4.11.3)
Requirement already satisfied: Werkzeug>=2.2.2 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from flask>=1.1.2->ord-schema==0.3.53) (2.2.3)
Requirement already satisfied: MarkupSafe>=2.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jinja2>=2.0.0->ord-schema==0.3.53) (2.1.1)
Requirement already satisfied: pillow>=6.2.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from matplotlib>=3.3.4->ord-schema==0.3.53) (9.4.0)
Requirement already satisfied: packaging>=20.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from matplotlib>=3.3.4->ord-schema==0.3.53) (23.0)
Collecting cycler>=0.10
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.4.4-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 25.4 MB/s eta 0:00:00
Collecting pyparsing>=2.2.1
  Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 13.2 MB/s eta 0:00:00
Collecting fonttools>=4.22.0
  Downloading fonttools-4.38.0-py3-none-any.whl (965 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 965.4/965.4 kB 25.7 MB/s eta 0:00:00
Requirement already satisfied: et-xmlfile in /srv/conda/envs/notebook/lib/python3.7/site-packages (from openpyxl>=3.0.5->ord-schema==0.3.53) (1.1.0)
Requirement already satisfied: pytz>=2017.3 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pandas>=1.0.4->ord-schema==0.3.53) (2023.3)
Requirement already satisfied: requests>=2.14.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pygithub>=1.51->ord-schema==0.3.53) (2.28.2)
Requirement already satisfied: pyjwt[crypto]>=2.4.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pygithub>=1.51->ord-schema==0.3.53) (2.6.0)
Requirement already satisfied: deprecated in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pygithub>=1.51->ord-schema==0.3.53) (1.2.14)
Requirement already satisfied: pynacl>=1.4.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pygithub>=1.51->ord-schema==0.3.53) (1.5.0)
Requirement already satisfied: six>=1.5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from python-dateutil>=1.10.0->ord-schema==0.3.53) (1.16.0)
Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Collecting scipy>=1.1.0
  Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.1/38.1 MB 19.5 MB/s eta 0:00:00
Requirement already satisfied: greenlet!=0.4.17 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from sqlalchemy>=1.4.39->ord-schema==0.3.53) (2.0.1)
Collecting tensorboard<2.12,>=2.11
  Downloading tensorboard-2.11.2-py3-none-any.whl (6.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.0/6.0 MB 17.7 MB/s eta 0:00:00
Collecting h5py>=2.9.0
  Downloading h5py-3.8.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.3/4.3 MB 10.7 MB/s eta 0:00:00
Collecting flatbuffers>=2.0
  Downloading flatbuffers-23.5.26-py2.py3-none-any.whl (26 kB)
Collecting astunparse>=1.6.0
  Downloading astunparse-1.6.3-py2.py3-none-any.whl (12 kB)
Collecting tensorflow-io-gcs-filesystem>=0.23.1
  Downloading tensorflow_io_gcs_filesystem-0.32.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (2.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.4/2.4 MB 10.9 MB/s eta 0:00:00
Collecting opt-einsum>=2.3.2
  Downloading opt_einsum-3.3.0-py3-none-any.whl (65 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.5/65.5 kB 477.3 kB/s eta 0:00:00
Requirement already satisfied: wrapt>=1.11.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from tensorflow>=2.4.1->ord-schema==0.3.53) (1.15.0)
Requirement already satisfied: typing-extensions>=3.6.6 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from tensorflow>=2.4.1->ord-schema==0.3.53) (4.5.0)
Collecting tensorflow-estimator<2.12,>=2.11.0
  Downloading tensorflow_estimator-2.11.0-py2.py3-none-any.whl (439 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 439.2/439.2 kB 5.2 MB/s eta 0:00:00
Collecting gast<=0.4.0,>=0.2.1
  Downloading gast-0.4.0-py3-none-any.whl (9.8 kB)
Collecting absl-py>=1.0.0
  Downloading absl_py-1.4.0-py3-none-any.whl (126 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.5/126.5 kB 970.4 kB/s eta 0:00:00
Collecting google-pasta>=0.1.1
  Downloading google_pasta-0.2.0-py3-none-any.whl (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.5/57.5 kB 243.9 kB/s eta 0:00:00
Requirement already satisfied: setuptools in /srv/conda/envs/notebook/lib/python3.7/site-packages (from tensorflow>=2.4.1->ord-schema==0.3.53) (67.6.1)
Collecting grpcio<2.0,>=1.24.3
  Downloading grpcio-1.54.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.1/5.1 MB 18.6 MB/s eta 0:00:00
Collecting keras<2.12,>=2.11.0
  Downloading keras-2.11.0-py2.py3-none-any.whl (1.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 9.7 MB/s eta 0:00:00
Collecting libclang>=13.0.0
  Downloading libclang-16.0.0-py2.py3-none-manylinux2010_x86_64.whl (22.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 22.9/22.9 MB 22.8 MB/s eta 0:00:00
Collecting termcolor>=1.1.0
  Downloading termcolor-2.3.0-py3-none-any.whl (6.9 kB)
INFO: pip is looking at multiple versions of wget to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of tqdm to determine which version is compatible with other requirements. This could take a while.
Collecting tqdm>=4.61.2
  Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 18.9 MB/s eta 0:00:00
  Downloading tqdm-4.64.0-py2.py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.4/78.4 kB 12.8 MB/s eta 0:00:00
  Downloading tqdm-4.63.2-py2.py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.6/76.6 kB 17.3 MB/s eta 0:00:00
  Downloading tqdm-4.63.1-py2.py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.6/76.6 kB 15.6 MB/s eta 0:00:00
  Downloading tqdm-4.63.0-py2.py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.6/76.6 kB 17.4 MB/s eta 0:00:00
  Downloading tqdm-4.62.3-py2.py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.2/76.2 kB 16.5 MB/s eta 0:00:00
  Downloading tqdm-4.62.2-py2.py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.2/76.2 kB 13.1 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of tqdm to determine which version is compatible with other requirements. This could take a while.
  Downloading tqdm-4.62.1-py2.py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.2/76.2 kB 12.2 MB/s eta 0:00:00
  Downloading tqdm-4.62.0-py2.py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.0/76.0 kB 16.8 MB/s eta 0:00:00
  Downloading tqdm-4.61.2-py2.py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.0/76.0 kB 7.2 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of tensorflow to determine which version is compatible with other requirements. This could take a while.
Collecting tensorflow>=2.4.1
  Downloading tensorflow-2.10.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (578.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 578.1/578.1 MB 1.1 MB/s eta 0:00:00
Collecting tensorboard<2.11,>=2.10
  Downloading tensorboard-2.10.1-py3-none-any.whl (5.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.9/5.9 MB 31.8 MB/s eta 0:00:00
Collecting keras-preprocessing>=1.1.1
  Downloading Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.6/42.6 kB 10.1 MB/s eta 0:00:00
Collecting keras<2.11,>=2.10.0
  Downloading keras-2.10.0-py2.py3-none-any.whl (1.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 30.0 MB/s eta 0:00:00
Collecting tensorflow-estimator<2.11,>=2.10.0
  Downloading tensorflow_estimator-2.10.0-py2.py3-none-any.whl (438 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 438.7/438.7 kB 36.5 MB/s eta 0:00:00
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C.
Collecting tensorflow>=2.4.1
  Downloading tensorflow-2.10.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (578.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 578.0/578.0 MB 891.3 kB/s eta 0:00:00
  Downloading tensorflow-2.9.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (511.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 511.8/511.8 MB 1.4 MB/s eta 0:00:00
Collecting flatbuffers<2,>=1.12
  Downloading flatbuffers-1.12-py2.py3-none-any.whl (15 kB)
Collecting tensorboard<2.10,>=2.9
  Downloading tensorboard-2.9.1-py3-none-any.whl (5.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.8/5.8 MB 30.1 MB/s eta 0:00:00
Collecting keras<2.10.0,>=2.9.0rc0
  Downloading keras-2.9.0-py2.py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 32.2 MB/s eta 0:00:00
Collecting tensorflow-estimator<2.10.0,>=2.9.0rc0
  Downloading tensorflow_estimator-2.9.0-py2.py3-none-any.whl (438 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 438.7/438.7 kB 30.2 MB/s eta 0:00:00
Collecting tensorflow>=2.4.1
  Downloading tensorflow-2.9.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (511.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 511.8/511.8 MB 1.6 MB/s eta 0:00:00
  Downloading tensorflow-2.9.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (511.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 511.7/511.7 MB 1.0 MB/s eta 0:00:00
  Downloading tensorflow-2.9.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (511.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 511.7/511.7 MB 1.0 MB/s eta 0:00:00
  Downloading tensorflow-2.8.4-cp37-cp37m-manylinux2010_x86_64.whl (497.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 497.9/497.9 MB 1.5 MB/s eta 0:00:00
Collecting tensorflow-estimator<2.9,>=2.8
  Downloading tensorflow_estimator-2.8.0-py2.py3-none-any.whl (462 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 462.3/462.3 kB 39.2 MB/s eta 0:00:00
Collecting gast>=0.2.1
  Downloading gast-0.5.4-py3-none-any.whl (19 kB)
Collecting tensorboard<2.9,>=2.8
  Downloading tensorboard-2.8.0-py3-none-any.whl (5.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.8/5.8 MB 34.1 MB/s eta 0:00:00
Collecting keras<2.9,>=2.8.0rc0
  Downloading keras-2.8.0-py2.py3-none-any.whl (1.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 38.8 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of tensorflow to determine which version is compatible with other requirements. This could take a while.
Collecting tensorflow>=2.4.1
  Downloading tensorflow-2.8.3-cp37-cp37m-manylinux2010_x86_64.whl (497.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 497.9/497.9 MB 1.2 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of sqlalchemy to determine which version is compatible with other requirements. This could take a while.
Collecting sqlalchemy>=1.4.39
  Downloading SQLAlchemy-2.0.15-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB 6.1 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of scikit-learn to determine which version is compatible with other requirements. This could take a while.
Collecting scikit-learn>=0.24.1
  Downloading scikit_learn-1.0.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (23.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 23.2/23.2 MB 9.6 MB/s eta 0:00:00
  Downloading scikit_learn-1.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (23.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 23.1/23.1 MB 18.5 MB/s eta 0:00:00
  Downloading scikit_learn-0.24.2-cp37-cp37m-manylinux2010_x86_64.whl (22.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 22.3/22.3 MB 27.4 MB/s eta 0:00:00
  Downloading scikit_learn-0.24.1-cp37-cp37m-manylinux2010_x86_64.whl (22.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 22.3/22.3 MB 8.0 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of rdkit to determine which version is compatible with other requirements. This could take a while.
Collecting rdkit>=2021.9.5
  Downloading rdkit-2022.9.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (29.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 29.2/29.2 MB 9.9 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of scikit-learn to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of python-dateutil to determine which version is compatible with other requirements. This could take a while.
Collecting python-dateutil>=1.10.0
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 12.9 MB/s eta 0:00:00
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C.
INFO: pip is looking at multiple versions of pygithub to determine which version is compatible with other requirements. This could take a while.
Collecting pygithub>=1.51
  Using cached PyGithub-1.58.2-py3-none-any.whl (312 kB)
INFO: pip is looking at multiple versions of psycopg2 to determine which version is compatible with other requirements. This could take a while.
Collecting psycopg2>=2.8.5
  Downloading psycopg2-2.9.5.tar.gz (384 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 384.3/384.3 kB 24.2 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
  Downloading psycopg2-2.9.4.tar.gz (384 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 384.0/384.0 kB 33.8 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
  Downloading psycopg2-2.9.3.tar.gz (380 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 380.6/380.6 kB 32.9 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
  Downloading psycopg2-2.9.2.tar.gz (380 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 380.3/380.3 kB 26.8 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
  Downloading psycopg2-2.9.1.tar.gz (379 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 380.0/380.0 kB 1.5 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
  Downloading psycopg2-2.9.tar.gz (379 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 379.8/379.8 kB 6.6 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
  Downloading psycopg2-2.8.6.tar.gz (383 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 383.8/383.8 kB 31.2 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
INFO: pip is looking at multiple versions of psycopg2 to determine which version is compatible with other requirements. This could take a while.
  Downloading psycopg2-2.8.5.tar.gz (380 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 380.9/380.9 kB 8.5 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
INFO: pip is looking at multiple versions of protobuf to determine which version is compatible with other requirements. This could take a while.
Collecting protobuf<3.20,>=3.13.0
  Downloading protobuf-3.19.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 38.2 MB/s eta 0:00:00
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C.
  Downloading protobuf-3.19.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 9.6 MB/s eta 0:00:00
  Downloading protobuf-3.19.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 37.6 MB/s eta 0:00:00
  Downloading protobuf-3.19.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 39.8 MB/s eta 0:00:00
  Downloading protobuf-3.19.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 38.5 MB/s eta 0:00:00
  Downloading protobuf-3.19.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 40.6 MB/s eta 0:00:00
  Downloading protobuf-3.18.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 35.6 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of protobuf to determine which version is compatible with other requirements. This could take a while.
  Downloading protobuf-3.18.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 34.7 MB/s eta 0:00:00
  Downloading protobuf-3.17.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 37.1 MB/s eta 0:00:00
  Downloading protobuf-3.17.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 3.6 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of pandas to determine which version is compatible with other requirements. This could take a while.
Collecting pandas>=1.0.4
  Downloading pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.3/11.3 MB 16.3 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of openpyxl to determine which version is compatible with other requirements. This could take a while.
Collecting openpyxl>=3.0.5
  Using cached openpyxl-3.1.2-py2.py3-none-any.whl (249 kB)
INFO: pip is looking at multiple versions of numpy to determine which version is compatible with other requirements. This could take a while.
Collecting numpy>=1.18.1
  Using cached numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
INFO: pip is looking at multiple versions of matplotlib to determine which version is compatible with other requirements. This could take a while.
Collecting matplotlib>=3.3.4
  Downloading matplotlib-3.5.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.2/11.2 MB 18.2 MB/s eta 0:00:00
  Downloading matplotlib-3.5.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.2/11.2 MB 11.6 MB/s eta 0:00:00
  Downloading matplotlib-3.5.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.2/11.2 MB 7.1 MB/s eta 0:00:00
Collecting setuptools-scm>=4
  Downloading setuptools_scm-7.1.0-py3-none-any.whl (43 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.8/43.8 kB 7.1 MB/s eta 0:00:00
Collecting matplotlib>=3.3.4
  Downloading matplotlib-3.4.3-cp37-cp37m-manylinux1_x86_64.whl (10.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.3/10.3 MB 8.6 MB/s eta 0:00:00
  Downloading matplotlib-3.4.2-cp37-cp37m-manylinux1_x86_64.whl (10.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.3/10.3 MB 11.5 MB/s eta 0:00:00
  Downloading matplotlib-3.4.1-cp37-cp37m-manylinux1_x86_64.whl (10.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.3/10.3 MB 13.9 MB/s eta 0:00:00
  Downloading matplotlib-3.4.0-cp37-cp37m-manylinux1_x86_64.whl (10.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.3/10.3 MB 15.7 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of matplotlib to determine which version is compatible with other requirements. This could take a while.
  Downloading matplotlib-3.3.4-cp37-cp37m-manylinux1_x86_64.whl (11.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.5/11.5 MB 9.1 MB/s eta 0:00:00
INFO: pip is looking at multiple versions of joblib to determine which version is compatible with other requirements. This could take a while.
Collecting joblib>=1.0.0
  Using cached joblib-1.2.0-py3-none-any.whl (297 kB)
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C.
INFO: pip is looking at multiple versions of jinja2 to determine which version is compatible with other requirements. This could take a while.
Collecting jinja2>=2.0.0
  Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 949.7 kB/s eta 0:00:00
INFO: pip is looking at multiple versions of <Python from Requires-Python> to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of inflection to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of glob2 to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of flask to determine which version is compatible with other requirements. This could take a while.
Collecting flask>=1.1.2
  Using cached Flask-2.2.5-py3-none-any.whl (101 kB)
ERROR: Package 'ord-schema' requires a different Python: 3.7.16 not in '>=3.10'
INFO: pip is looking at multiple versions of docopt to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of ord-schema[examples] to determine which version is compatible with other requirements. This could take a while.
Removing intermediate container e342427093cc
The command '/bin/sh -c ./postBuild' returned a non-zero code: 1
stuchalk commented 1 year ago

Conner

Thanks for this and the other email. Exactly what I need! And thank you for the quick reply.

One further comment that does not need an immediate response….

Has there been any discussion of adding an API endpoint to get the data from the web interface as yaml or json? While I can code in Python, handle the repo download and understand the process below, there are many in the community that are not so tech savvy. A URL based API to get access to the (currently) yaml data would make it more accessible to the community.

Cheers, Stuart

connorcoley commented 1 year ago

Steve has written a Client in Python to use the API that can be found in the ord-interface repo. By default, the target URL is the public open-reaction-database.org, but it can be used with a local database deployment: https://github.com/open-reaction-database/ord-interface/blob/main/ord_interface/client/ord_client.py

A simpler example showing how to fetch a dataset by ID can be found in message_helpers.py file as well, fetch_dataset (https://github.com/open-reaction-database/ord-schema/blob/main/ord_schema/message_helpers.py#L713)

skearnes commented 1 year ago

Thanks @stuchalk, I'll take a look at this.

skearnes commented 1 year ago

@stuchalk can you try again?

stuchalk commented 1 year ago

Good to go! Thanks!