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Setup on non-intel Mac #16

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hannesbecher opened this issue Dec 13, 2023 · 2 comments
Closed

Setup on non-intel Mac #16

hannesbecher opened this issue Dec 13, 2023 · 2 comments

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@hannesbecher
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Hi there,

Exciting-looking software! I am struggling to set up the dependencies on my M2 MacBook Air :( Looks like some of these dependencies may not exist as conda envs for my CPU architecture? I appreciate this is not your fault. But I expect there will be an increasing number of people using this kind of Mac in the future.

Running:

$ conda create -n shadie pandas numpy toyplot toytree altair msprime pyslim tskit loguru IPython -c conda-forge -c bioconda

Gives me:

Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                                  /

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package pyrsistent conflicts for:
tskit -> jsonschema -> pyrsistent[version='!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0|>=0.14.0|>=0.14.0,!=0.17.0,!=0.17.1,!=0.17.2']
altair -> jsonschema[version='>=3.0'] -> pyrsistent[version='!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0|>=0.14.0|>=0.14.0,!=0.17.0,!=0.17.1,!=0.17.2']

Package python-dateutil conflicts for:
altair -> pandas[version='>=0.25'] -> python-dateutil[version='>=2.7.3|>=2.8.1|>=2.8.2']
pandas -> python-dateutil[version='>=2.7.3|>=2.8.1|>=2.8.2']
toyplot -> arrow -> python-dateutil[version='>=2.7.0']

Package packaging conflicts for:
ipython -> black -> packaging[version='>=22.0']
altair -> packaging
pandas -> numexpr[version='>=2.8.0'] -> packaging

Package _python_rc conflicts for:
altair -> python[version='>=3.8'] -> _python_rc
ipython -> python[version='>=3.9'] -> _python_rc
toyplot -> python[version='>=3.6'] -> _python_rc
pyslim -> python[version='>=3.6'] -> _python_rc
toytree -> python -> _python_rc
loguru -> python[version='>=3.12.0rc3,<3.13.0a0'] -> _python_rc
pandas -> python[version='>=3.12.0rc3,<3.13.0a0'] -> _python_rc
numpy -> python[version='>=3.12.0rc3,<3.13.0a0'] -> _python_rc

Package pygments conflicts for:
ipython -> pygments[version='>=2.4.0']
loguru -> better_exceptions_fork[version='>=0.2.1.post6'] -> pygments[version='>=2.2.0']
altair -> ipython -> pygments[version='>=2.4.0']

Package libcxx conflicts for:
pandas -> libcxx[version='>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=14.0.6|>=15.0.7|>=16.0.6|>=12.0.0']
numpy -> libcxx[version='>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=14.0.6|>=15.0.7|>=16.0.6|>=12.0.0']
tskit -> numpy[version='>=1.22.4,<2.0a0'] -> libcxx[version='>=11.0.0.rc1|>=11.0.0|>=11.0.1|>=12.0.0|>=13.0.1|>=14.0.4|>=14.0.6|>=15.0.7|>=16.0.6|>=11.1.0|>=12.0.1']
pandas -> python[version='>=3.9,<3.10.0a0'] -> libcxx[version='>=11.0.0.rc1']
msprime -> numpy[version='>=1.22.4,<2.0a0'] -> libcxx[version='>=11.0.0.rc1|>=11.0.0|>=11.0.1|>=12.0.0|>=13.0.1|>=14.0.4|>=14.0.6|>=15.0.7|>=16.0.6|>=11.1.0|>=12.0.1']
altair -> numpy -> libcxx[version='>=11.0.0.rc1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=14.0.6|>=15.0.7|>=16.0.6|>=12.0.0']
numpy -> python[version='>=3.9,<3.10.0a0'] -> libcxx[version='>=11.0.0.rc1|>=11.0.0|>=11.0.1']
toytree -> numpy[version='>=1.10'] -> libcxx[version='>=11.0.0.rc1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=14.0.6|>=15.0.7|>=16.0.6|>=12.0.0']
loguru -> python[version='>=3.8,<3.9.0a0'] -> libcxx[version='>=11.0.0.rc1|>=11.0.0|>=11.0.1|>=11.1.0|>=14.0.6|>=12.0.0']
toyplot -> numpy[version='>=1.8.0'] -> libcxx[version='>=11.0.0.rc1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=14.0.6|>=15.0.7|>=16.0.6|>=12.0.0']
ipython -> python[version='>=3.9'] -> libcxx[version='>=11.0.0.rc1|>=11.0.0|>=11.0.1|>=14.0.6|>=12.0.0|>=11.1.0']
pyslim -> numpy -> libcxx[version='>=11.0.0.rc1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=14.0.6|>=15.0.7|>=16.0.6|>=12.0.0']

Package tskit conflicts for:
msprime -> tskit[version='>=0.3.5|>=0.4']
pyslim -> msprime[version='>=0.7.0'] -> tskit[version='>=0.3.5|>=0.4']
tskit
pyslim -> tskit

Package python conflicts for:
tskit -> python[version='>=3.10,<3.11.0a0|>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.11,<3.12.0a0|>=3.9,<3.10.0a0|>=3.12,<3.13.0a0|>=3.12,<3.13.0a0|>=3.8,<3.9.0a0|>=3.8,<3.9.0a0',build=*_cpython]
tskit -> jsonschema -> python[version='3.10.*|3.11.*|3.9.*|>=3.12.0rc3,<3.13.0a0|>=3.12.0rc3,<3.13.0a0|>=3.6|>=3.7|>=3.8|3.8.*',build=*_cpython]

Package setuptools conflicts for:
pandas -> numexpr[version='>=2.8.0'] -> setuptools
tskit -> jsonschema -> setuptools
ipython -> setuptools[version='>=18.5']
ipython -> pygments[version='>=2.4.0'] -> setuptools
altair -> jinja2 -> setuptools[version='<60.0.0|>=18.5']
pandas -> setuptools[version='<60.0.0']

Package numpy conflicts for:
numpy
toytree -> toyplot[version='>=0.17.0'] -> numpy[version='>=1.8.0']
msprime -> tskit[version='>=0.3.5'] -> numpy[version='>=1.21.3,<2.0a0']
toytree -> numpy[version='>=1.10']
pandas -> numpy[version='>=1.19.2,<2.0a0|>=1.19.4,<2.0a0|>=1.19.5,<2.0a0|>=1.20.3,<2.0a0|>=1.21.6,<2.0a0|>=1.22.4,<2.0a0|>=1.23.5,<2.0a0|>=1.26.2,<2.0a0|>=1.26.0,<2.0a0|>=1.23.4,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0|>=1.23,<2.0a0|>=1.21,<2.0a0|>=1.21.2,<2.0a0']
pyslim -> msprime[version='>=0.7.0'] -> numpy[version='>=1.19.5,<2.0a0|>=1.20.3,<2.0a0|>=1.22.4,<2.0a0|>=1.26.0,<2.0a0|>=1.23.5,<2.0a0|>=1.23.4,<2.0a0|>=1.21.6,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0|>=1.21.3,<2.0a0']
pandas -> bottleneck[version='>=1.3.4'] -> numpy[version='>=1.21.3,<2.0a0|>=1.22.3,<2.0a0']
pyslim -> numpy
altair -> numpy[version='>=0.18']
toyplot -> numpy[version='>=1.8.0']
altair -> pandas[version='>=0.25'] -> numpy[version='>=1.19.2,<2.0a0|>=1.19.4,<2.0a0|>=1.19.5,<2.0a0|>=1.20.3,<2.0a0|>=1.21.6,<2.0a0|>=1.22.4,<2.0a0|>=1.23.5,<2.0a0|>=1.26.2,<2.0a0|>=1.26.0,<2.0a0|>=1.23.4,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0|>=1.23,<2.0a0|>=1.21,<2.0a0|>=1.21.2,<2.0a0']
msprime -> numpy[version='>=1.19.5,<2.0a0|>=1.20.3,<2.0a0|>=1.22.4,<2.0a0|>=1.26.0,<2.0a0|>=1.23.5,<2.0a0|>=1.23.4,<2.0a0|>=1.21.6,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0']

Package jsonschema conflicts for:
altair -> jsonschema[version='<4.17|>=3.0,<4.17|>=3.0|>=3.0,!=4.18.1']
msprime -> tskit[version='>=0.4'] -> jsonschema
tskit -> jsonschema
pyslim -> tskit -> jsonschema

Package typing_extensions conflicts for:
toyplot -> arrow -> typing_extensions
ipython -> black -> typing_extensions[version='>=3.10,!=3.10.0.1|>=3.10|>=4.0.1|>=3.7.4|>=3.10.0.0']
altair -> importlib-metadata -> typing_extensions[version='4.0.1|4.1.1|4.2.0|4.2.0|4.3.0|4.4.0|4.5.0|4.6.0|4.6.1|4.6.2|4.6.3|4.7.0|4.7.1|4.8.0|4.9.0|>=3.6.4|4.7.1|4.7.1|4.7.1|4.7.1|4.7.1|4.6.3|4.6.3|4.6.3|4.6.3|4.5.0|4.5.0|4.5.0|4.5.0|4.4.0|4.4.0|4.4.0|4.4.0|4.3.0|4.3.0|4.3.0|4.1.1',build='py39hca03da5_0|py39hca03da5_0|py39hca03da5_0|py39hca03da5_0|py312hca03da5_0|pyha770c72_1|pyha770c72_0|pyha770c72_0|pyha770c72_0|pyha770c72_0|py38hca03da5_0|py310hca03da5_0|py311hca03da5_0|py38hca03da5_0|py311hca03da5_0|py310hca03da5_0|py38hca03da5_0|py310hca03da5_0|py39hca03da5_0|py311hca03da5_0|py311hca03da5_0|py38hca03da5_0|py310hca03da5_0|py38hca03da5_0|py310hca03da5_0|pyh06a4308_0']
ipython -> typing_extensions
tskit -> jsonschema -> typing_extensions

Package pandas conflicts for:
altair -> pandas[version='>=0.18|>=0.25']
pandas

Package six conflicts for:
altair -> six
toyplot -> six
toytree -> toyplot[version='>=0.17.0'] -> six
ipython -> prompt-toolkit[version='>3.0.1,<3.1.0'] -> six[version='>=1.9.0']
altair -> jsonschema[version='>=3.0'] -> six[version='>=1.11.0']
tskit -> jsonschema -> six[version='>=1.11.0']
pandas -> python-dateutil[version='>=2.8.1'] -> six[version='>=1.5']

Package ipython conflicts for:
ipython
altair -> ipython

Package toyplot conflicts for:
toyplot
toytree -> toyplot[version='>=0.17.0']

Package colorama conflicts for:
loguru -> colorama[version='>=0.3.4']
loguru -> ansimarkup[version='>=1.4.0'] -> colorama

Package attrs conflicts for:
ipython -> black -> attrs[version='>=17.4.0|>=18.1.0']
msprime -> demes[version='>=0.2'] -> attrs[version='>=20.3']
altair -> jsonschema[version='>=3.0'] -> attrs[version='>=17.4.0|>=22.2.0']
pyslim -> attrs
tskit -> jsonschema -> attrs[version='>=17.4.0|>=22.2.0']

Package msprime conflicts for:
pyslim -> msprime[version='>=0.7.0']
msprime

Package certifi conflicts for:
toytree -> requests -> certifi[version='>=2017.4.17']
ipython -> setuptools[version='>=18.5'] -> certifi[version='>=2016.9.26']
pandas -> setuptools[version='<60.0.0'] -> certifi[version='>=2016.9.26']The following specifications were found to be incompatible with your system:

  - feature:/osx-arm64::__osx==13.6.1=0
  - feature:/osx-arm64::__unix==0=0
  - feature:|@/osx-arm64::__osx==13.6.1=0
  - feature:|@/osx-arm64::__unix==0=0
  - altair -> ipython -> __unix
  - altair -> numpy -> __osx[version='>=10.9']
  - ipython -> __osx
  - ipython -> __unix
  - msprime -> numpy[version='>=1.22.4,<2.0a0'] -> __osx[version='>=10.9']
  - numpy -> __osx[version='>=10.9']
  - pandas -> __osx[version='>=10.9']
  - pyslim -> numpy -> __osx[version='>=10.9']
  - toyplot -> numpy[version='>=1.8.0'] -> __osx[version='>=10.9']
  - toytree -> numpy[version='>=1.10'] -> __osx[version='>=10.9']

Your installed version is: 13.6.1
@elissasoroj
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elissasoroj commented Dec 13, 2023 via email

@hannesbecher
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Hi Elissa,

Thank you for your quick response! First of all, my python version should not matter as I am setting up shadie in a separate conda environment (conda create -n <envName>). So, anaconda should pick the right version of python.

That said, I have now updated my anaconda version and I am getting a clearer error message.

Could not solve for environment specs
The following package could not be installed
└─ pyslim is not installable because it requires
   └─ kastore, which does not exist (perhaps a missing channel).

So, kasatore may not be available via anaconda for M2? I've opened an issue here. I should add that this all works on my Linux machine which is why I think it may be an M2 issue.

Now, I managed to set up everything on my M2 (I think) by omitting pyslim at first and then setting it up via pip:

conda create -n shadie pandas numpy toyplot toytree altair msprime tskit loguru IPython  -c conda-forge
conda activate shadie
python -m pip install kastore
python -m pip install pyslim
# prepare for running in Jupyter:
conda install ipykernel

So this very much looks like a kastore/conda recipe issue and not one with shadie/your instructions. So, feel free to close this issue...

Unfortunately I now get errors running shadie on Jupyter. Going to open a separate issue about this.

@hannesbecher hannesbecher mentioned this issue Dec 14, 2023
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@hannesbecher @elissasoroj