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elissasoroj / shadie

GNU General Public License v3.0
11 stars 4 forks source link

Setup on non-intel Mac #16

Closed hannesbecher closed 11 months ago

hannesbecher commented 11 months ago

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 commented 11 months ago

Hello!

Thank you for letting me know! I am not sure exactly what the issue is for your M2, but I do think that I can help you get to the bottom of it, or else make some changes to the dependencies to avoid any issues with the new macs. Do you mind telling me what version of Python you have installed?

I am actually right in the middle of testing some possible bugs introduced into shadie by the newest update to SLiM 4.1 and also updating all the models to be more efficient and work with the SLiM4 release, so I would suggest holding off using shadie until those changes are implemented anyways. Should just be a week or so.

I will finish updating the software then do some trouble-shooting on the dependencies. I have an M1 Mac and no issues, so I am fairly confident that we can get it working.

Thanks for the interest - I'll be in touch again soon.

~Elissa

Elissa Sorojsrisom PhD Candidate Columbia University | E3B Department New York Botanical Garden @.***

On Dec 13, 2023, at 12:14 PM, Hannes Becher @.***> wrote:

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']

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hannesbecher commented 11 months ago

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.