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pprint dependency prevents conda env create

Open kevbrick opened this issue 4 years ago • 8 comments

Hi,

I get the error below when trying to create the conda env for bpnet. I get a similar error using either method in the git README. I can install the dependencies manually, then install bpnet with pip --no-deps but will I be missing something?

> conda env create -f conda-env.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound: 
  - pprint

kevbrick avatar Apr 15 '21 14:04 kevbrick

Hey! This is weird. pprint should be part of the standard data library. Do you know if there a way to check which of the dependencies transitively require the pprint package?

Which conda version are you using? It works fine for me with 4.7.10.

Could you try running conda env create -f conda-env.yml with the following environment file:

name: bpnet
channels:
  - pytorch
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1
  - _openmp_mutex=4.5
  - argon2-cffi=20.1.0
  - async_generator=1.10
  - attrs=20.3.0
  - backcall=0.2.0
  - backports=1.0
  - backports.functools_lru_cache=1.6.1
  - bcftools=1.6
  - bcolz=1.2.1
  - bedtools=2.27.1
  - blas=2.20
  - bleach=1.4.2
  - blosc=1.21.0
  - bokeh=2.3.0
  - bzip2=1.0.8
  - ca-certificates=2020.12.5
  - certifi=2020.12.5
  - cffi=1.14.5
  - click=7.1.2
  - cloudpickle=1.6.0
  - contextvars=2.4
  - cudatoolkit=10.2.89
  - curl=7.71.1
  - cython=0.29.22
  - cytoolz=0.11.0
  - dask=2021.3.0
  - dask-core=2021.3.0
  - dataclasses=0.8
  - decorator=4.4.2
  - defusedxml=0.7.1
  - distributed=2021.3.0
  - entrypoints=0.3
  - fastparquet=0.4.0
  - freetype=2.10.4
  - fsspec=0.8.7
  - genomelake=0.1.4
  - h5py=2.9.0
  - hdf5=1.10.5
  - heapdict=1.0.1
  - html5lib=1.1
  - htslib=1.7
  - immutables=0.15
  - importlib-metadata=3.7.2
  - ipykernel=5.5.0
  - ipython=7.16.1
  - ipython_genutils=0.2.0
  - jedi=0.17.2
  - jinja2=2.11.3
  - jpeg=9d
  - jsonschema=3.2.0
  - jupyter_client=6.1.12
  - jupyter_core=4.7.1
  - jupyterlab_pygments=0.1.2
  - krb5=1.17.2
  - lcms2=2.12
  - ld_impl_linux-64=2.35.1
  - libblas=3.8.0
  - libcblas=3.8.0
  - libcurl=7.71.1
  - libedit=3.1.20191231
  - libffi=3.3
  - libgcc=7.2.0
  - libgcc-ng=9.3.0
  - libgfortran-ng=7.5.0
  - libgfortran4=7.5.0
  - liblapack=3.8.0
  - liblapacke=3.8.0
  - libllvm10=10.0.1
  - libpng=1.6.37
  - libsodium=1.0.18
  - libssh2=1.9.0
  - libstdcxx-ng=9.3.0
  - libtiff=4.2.0
  - libuv=1.41.0
  - libwebp-base=1.2.0
  - llvm-openmp=11.0.1
  - llvmlite=0.36.0
  - locket=0.2.0
  - lz4-c=1.9.3
  - lzo=2.10
  - markupsafe=1.1.1
  - mistune=0.8.4
  - mkl=2020.4
  - mock=4.0.3
  - msgpack-python=1.0.2
  - nb_conda=2.2.1
  - nb_conda_kernels=2.3.1
  - nbclient=0.5.3
  - nbconvert=6.0.7
  - nbformat=5.1.2
  - ncurses=6.2
  - nest-asyncio=1.4.3
  - ninja=1.10.2
  - notebook=6.2.0
  - numba=0.53.0
  - numexpr=2.7.3
  - numpy=1.18.5
  - olefile=0.46
  - openssl=1.1.1j
  - packaging=20.9
  - pandoc=2.12
  - pandocfilters=1.4.2
  - parso=0.7.1
  - partd=1.1.0
  - patsy=0.5.1
  - pexpect=4.8.0
  - pickleshare=0.7.5
  - pillow=8.1.2
  - pip=21.0.1
  - prometheus_client=0.9.0
  - prompt-toolkit=3.0.17
  - psutil=5.8.0
  - ptyprocess=0.7.0
  - pybedtools=0.7.10
  - pybigwig=0.3.17
  - pycparser=2.20
  - pygments=2.8.1
  - pyparsing=2.4.7
  - pyrsistent=0.17.3
  - pysam=0.14.0
  - pytables=3.6.1
  - python=3.6.13
  - python-dateutil=2.8.1
  - python-snappy=0.5.4
  - python_abi=3.6
  - pytorch=1.7.1
  - pytz=2021.1
  - pyyaml=5.4.1
  - pyzmq=22.0.3
  - readline=8.0
  - samtools=1.7
  - scipy=1.4.1
  - send2trash=1.5.0
  - setuptools=49.6.0
  - six=1.15.0
  - snappy=1.1.8
  - sortedcontainers=2.3.0
  - sqlite=3.34.0
  - statsmodels=0.11.1
  - tblib=1.6.0
  - terminado=0.9.2
  - testpath=0.4.4
  - thrift=0.11.0
  - tk=8.6.10
  - toolz=0.11.1
  - tornado=6.1
  - tqdm=4.46.1
  - traitlets=4.3.3
  - typing_extensions=3.7.4.3
  - wcwidth=0.2.5
  - webencodings=0.5.1
  - wheel=0.36.2
  - xz=5.2.5
  - yaml=0.2.5
  - zeromq=4.3.4
  - zict=2.0.0
  - zipp=3.4.1
  - zlib=1.2.11
  - zstd=1.4.9
  - pip:
    - absl-py==0.12.0
    - ansiwrap==0.8.4
    - appdirs==1.4.4
    - argcomplete==1.12.2
    - argh==0.26.2
    - arrow==1.0.3
    - astor==0.8.1
    - attr==0.3.1
    - binaryornot==0.4.4
    - black==20.8b1
    - bpnet==0.0.23
    - chardet==4.0.0
    - colorlog==4.7.2
    - comet-ml==3.5.0
    - concise==0.6.7
    - configobj==5.0.6
    - configparser==5.0.2
    - cookiecutter==1.7.2
    - coverage==5.5
    - cycler==0.10.0
    - deepexplain==0.1
    - deprecation==2.1.0
    - descartes==1.1.0
    - distlib==0.3.1
    - docker-pycreds==0.4.0
    - dulwich==0.20.20
    - everett==1.0.3
    - filelock==3.0.12
    - future==0.18.2
    - gast==0.4.0
    - gdown==3.12.2
    - gffutils==0.10.1
    - gin-config==0.4.0
    - gitdb==4.0.5
    - gitpython==3.1.14
    - google-pasta==0.2.0
    - grpcio==1.36.1
    - gtfparse==1.2.1
    - hyperopt==0.2.5
    - idna==2.10
    - imageio==2.9.0
    - importlib-resources==5.1.2
    - iniconfig==1.1.1
    - ipywidgets==7.6.3
    - jinja2-time==0.2.0
    - joblib==0.15.1
    - jupyterlab-widgets==1.0.0
    - keras==2.2.4
    - keras-applications==1.0.8
    - keras-preprocessing==1.1.2
    - kipoi==0.6.25
    - kipoi-conda==0.2.2
    - kipoi-utils==0.3.8
    - kipoiseq==0.3.4
    - kiwisolver==1.3.1
    - markdown==3.3.4
    - matplotlib==3.3.4
    - mizani==0.7.2
    - modisco==0.5.3.0
    - mypy-extensions==0.4.3
    - networkx==2.5
    - nvidia-ml-py3==7.352.0
    - palettable==3.3.0
    - pandas==1.1.5
    - papermill==2.3.3
    - pathspec==0.8.1
    - pathtools==0.1.2
    - plotnine==0.7.1
    - pluggy==0.13.1
    - poyo==0.5.0
    - promise==2.3
    - protobuf==3.15.6
    - py==1.10.0
    - pyfaidx==0.5.9.5
    - pysocks==1.7.1
    - pytest==6.2.2
    - pytest-cov==2.11.1
    - python-slugify==4.0.1
    - pywavelets==1.1.1
    - regex==2020.11.13
    - related==0.7.2
    - requests==2.25.1
    - requests-toolbelt==0.9.1
    - scikit-image==0.17.2
    - scikit-learn==0.21.3
    - seaborn==0.11.1
    - sentry-sdk==1.0.0
    - shapely==1.7.1
    - shortuuid==1.0.1
    - simplejson==3.17.2
    - smmap==3.0.5
    - subprocess32==3.5.4
    - tenacity==7.0.0
    - tensorboard==1.14.0
    - tensorflow==1.14.0
    - tensorflow-estimator==1.14.0
    - termcolor==1.1.0
    - text-unidecode==1.3
    - textwrap3==0.9.2
    - threadpoolctl==2.1.0
    - tifffile==2020.9.3
    - tinydb==4.4.0
    - toml==0.10.2
    - typed-ast==1.4.2
    - urllib3==1.26.3
    - vdom==0.6
    - virtualenv==20.4.2
    - wandb==0.10.22
    - websocket-client==0.58.0
    - werkzeug==1.0.1
    - widgetsnbextension==3.5.1
    - wrapt==1.12.1
    - wurlitzer==2.0.1

I obtained that environment by installing the bpnet environment and then exporting it with conda env export --no-builds > environment.yml as suggested here:

Avsecz avatar May 09 '21 21:05 Avsecz

Hey,

Sadly I'm receiving the same error message. I also tried setting up the environment with the environment.yml you posted, but the problem persists. Is there any workaround for this problem?

Note that using your environment.yml it first stated that ERROR: Cannot install bpnet... Conflict is caused by: bpnet depends on deepexplain. So i installed deepexplain from their github repo. Then again the installation of bpnet fails due to pprint dependecy.

Conda version: 4.10.1

nicolasgoedert97 avatar Jun 07 '21 17:06 nicolasgoedert97

Hm. This is really weird because pprint is a standard library https://docs.python.org/3/library/pprint.html.

Can you create the conda environment from my environment.yml above, but replace deepexplain==0.1 with git+https://github.com/kundajelab/DeepExplain.git?

Avsecz avatar Oct 07 '21 23:10 Avsecz

Hi,

Unfortunately, installation of bpnet (via the yml file above, and deepexplain==0.1 replaced with git+https://github.com/kundajelab/DeepExplain.git ) also fails for me due to the same error concerning pprint. Do you have any ideas on how to solve this?

Thanks in advance!

HNeikes avatar Nov 19 '21 14:11 HNeikes

Hm. The pypi version of BPNet is out-of-date and it might be including pprint as a dependency. One should be installing bpnet from github. Therefore, I would suggest replacing bpnet==0.0.23 with git+https://github.com/kundajelab/bpnet.git. Let me know if that works for you.

Avsecz avatar Jan 02 '22 19:01 Avsecz

Hm. The pypi version of BPNet is out-of-date and it might be including pprint as a dependency. One should be installing bpnet from github. Therefore, I would suggest replacing bpnet==0.0.23 with git+https://github.com/kundajelab/bpnet.git. Let me know if that works for you.

I tried to install bpnet from github. It works. Thanks!

JokerOuO avatar Jan 03 '22 15:01 JokerOuO

pip install pprint -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com can solve this problem

wangdepin avatar Mar 28 '22 06:03 wangdepin

I had a similar issue and can confirm that the solution given by @wangdepin worked for me -- thank you.

pip install pprint -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com can solve this problem

~running on macOS Big Sur 11.3.1

evanseitz avatar Apr 18 '22 17:04 evanseitz