Closed stuchalk closed 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)
â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â” 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)
â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â” 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)
â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â” 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)
â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â” 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)
â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â” 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)
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Collecting xlrd<2.0.0
Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
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Collecting xlwt>=1.3.0
Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
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Collecting joblib>=1.0.0
Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
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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)
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Collecting Werkzeug>=2.2.2
Downloading Werkzeug-2.2.3-py3-none-any.whl (233 kB)
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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)
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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)
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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)
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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
[91mtime: 321.280
[0mWill remove 1 package cache(s).
[91mtime: 8.331
[0m# 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
[91m+ pip install -e '.[examples]'
[0mObtaining 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)
â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â” 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)
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Collecting tensorflow>=2.4.1
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Downloading tensorflow-2.8.4-cp37-cp37m-manylinux2010_x86_64.whl (497.9 MB)
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Collecting pygithub>=1.51
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Collecting protobuf<3.20,>=3.13.0
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Collecting pandas>=1.0.4
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[91mERROR: Package 'ord-schema' requires a different Python: 3.7.16 not in '>=3.10'
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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
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)
Thanks @stuchalk, I'll take a look at this.
@stuchalk can you try again?
Good to go! Thanks!
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:
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](https://github.com/open-reaction-database/ord-schema/assets/540150/7ca54420-bb63-4f6a-af44-c2aece03d412)
Desktop (please complete the following information):
Additional context NA