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I had just installed Anaconda from anaconda.com. The installation proceeded smoothly. After that, I was trying to create a new environment from this environment.yml file. (nbdev.yml)


name: nbdev
channels:
  - fastai
  - defaults
  - conda-forge
dependencies:
  - _r-mutex
  - _tflow_select
  - absl-py
  - alabaster
  - asn1crypto
  - astor
  - astroid
  - attrs
  - babel
  - backcall
  - backports
  - backports.functools_lru_cache
  - blas
  - bleach
  - bwidget
  - bzip2
  - c-ares
  - ca-certificates
  - cairo
  - certifi
  - cffi
  - chardet
  - cloudpickle
  - compiler-rt
  - constantly
  - cryptography
  - curl
  - cycler
  - cython
  - dbus
  - decorator
  - defusedxml
  - docutils
  - entrypoints
  - expat
  - fastcache
  - flake8
  - fontconfig
  - freetype
  - fribidi
  - gast
  - gettext
  - glib
  - gmp
  - gmpy2
  - graphite2
  - grpcio
  - gsl
  - h5py
  - harfbuzz
  - hdf5
  - html5lib
  - icu
  - idna
  - imagesize
  - intel-openmp
  - ipykernel
  - ipython
  - ipython_genutils
  - isort
  - jbig
  - jedi
  - jinja2
  - jpeg
  - jsonschema
  - jupyter_client
  - jupyter_contrib_core
  - jupyter_contrib_nbextensions
  - jupyter_core
  - jupyter_highlight_selected_word
  - jupyter_latex_envs
  - jupyter_nbextensions_configurator
  - keras-applications
  - keras-preprocessing
  - keyring
  - krb5
  - lazy-object-proxy
  - libcurl
  - libcxx
  - libcxxabi
  - libedit
  - libffi
  - libgcc
  - libgfortran
  - libiconv
  - libopenblas
  - libpng
  - libprotobuf
  - libsodium
  - libssh2
  - libtiff
  - libxml2
  - libxslt
  - llvm
  - llvm-openmp
  - lxml
  - make
  - markdown
  - markupsafe
  - matplotlib
  - mccabe
  - mistune
  - mkl
  - mkl_fft
  - mkl_random
  - mock
  - mpc
  - mpfr
  - mpmath
  - nbconvert
  - nbformat
  - ncurses
  - nomkl
  - notebook
  - numpy
  - numpy-base
  - numpydoc
  - olefile
  - openblas
  - openblas-devel
  - openssl
  - packaging
  - pandas
  - pandoc
  - pandocfilters
  - pango
  - pari
  - parso
  - patsy
  - pbr
  - pcre
  - perl
  - pexpect
  - pickleshare
  - pillow
  - pip
  - pixman
  - prometheus_client
  - prompt_toolkit
  - protobuf
  - psutil
  - ptyprocess
  - pycodestyle
  - pycparser
  - pyflakes
  - pygments
  - pylint
  - pyopenssl
  - pyparsing
  - pyqt
  - pyrsistent
  - pysocks
  - python
  - python-dateutil
  - python-symengine
  - pytz
  - pyyaml
  - pyzmq
  - qt
  - qtawesome
  - qtconsole
  - qtpy
  - qutip
  - r-base
  - r-clisymbols
  - readline
  - reportlab
  - requests
  - rope
  - scikit-learn
  - scipy
  - send2trash
  - setuptools
  - simplegeneric
  - sip
  - six
  - snowballstemmer
  - sphinx
  - sphinxcontrib
  - sphinxcontrib-applehelp
  - sphinxcontrib-devhelp
  - sphinxcontrib-htmlhelp
  - sphinxcontrib-jsmath
  - sphinxcontrib-qthelp
  - sphinxcontrib-serializinghtml
  - sphinxcontrib-websupport
  - spyder
  - spyder-kernels
  - sqlite
  - symengine
  - symmetrica
  - sympow
  - sympy
  - tensorboard
  - tensorflow
  - tensorflow-base
  - tensorflow-estimator
  - termcolor
  - terminado
  - testpath
  - tk
  - tktable
  - tornado
  - traitlets
  - typed-ast
  - typing
  - urllib3
  - wcwidth
  - webencodings
  - werkzeug
  - wheel
  - wrapt
  - wurlitzer
  - xz
  - yaml
  - zeromq
  - tqdm
  - zlib
  - zstd
  - pytest
  - numba
  - hypothesis
  - pytest-cov
  - mypy
  - pytest-xdist
  - watchdog
  - pytest-runner
  - coveralls
  - doctr
  - gitpython
  - pre-commit
  - tox
  - cookiecutter
  - pdbpp
  - sphinx-autobuild
  - sphinx-autodoc-typehints
  - sphinx_rtd_theme
  - travis-encrypt
  - twine
  - nbval
  - nbsphinx
  - watermark
  - ipyparallel
  - unittest2pytest
  - pytest-benchmark
  - pytest-repeat
  - pytest-subtests
  - fastcore
  - fastscript
  - asttokens
  - cached-property
  - crayons
  - executing
  - flask
  - humanize
  - ipywidgets
  - itsdangerous
  - jsonpickle
  - jupyter
  - littleutils
  - nbconvert
  - outdated
  - portpicker
  - sqlalchemy
  - widgetsnbextension
  - nbdime
  - rich
  - mayavi
  - pip:
    - birdseye
    - icecream
    - nbdev==1.1.12
    - snoop
    - git-remote-dropbox
    - odeintw
    - cyberbrain
    - cheap-repr
    - jupyter-console
    - get-port
    - flask-humanize
    - msgpack
    - jupyterlab-widgets
    - varname
    - blacktex

prefix: /anaconda3/envs/nbdev

I tried conda env create -f nbdev.yml But it just got stuck on solving the environment. Then I learned that mamba is a fast drop-in replacement for conda. So I typed in mamba env create -f nbdev.yml and mamba stuck on packages.

1 Answer 1

4

After a lot of research, I stumbled on to Mamba doesn't find a solution when mixing conda forge defaults and not specifying Python explicitly 1102. So I just edited nbdev.yml from

name: nbdev
channels:
  - fastai
  - defaults
  - conda-forge
dependencies:
  - _r-mutex
  - _tflow_select
  - absl-py
  - alabaster

to

name: nbdev
channels:
  - fastai
  - defaults
  - conda-forge
dependencies:
  - python
  - _r-mutex
  - _tflow_select
  - absl-py
  - alabaster

This fixed the problem.

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1 Comment

Thanks a ton! This worked for me when I was having the same issue when running through the snakemake-tutorial.

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