cytomining / profiling-recipe

Image-based Profiling Recipe
BSD 3-Clause "New" or "Revised" License
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Conda env out of date #35

Open bethac07 opened 2 years ago

bethac07 commented 2 years ago

Trying to create today, I got the following stack trace. Since other conda-forge stuff is not listed as missing, I'm guessing it's that those versions of conda and pip are no longer supported. Will make a PR with a working version but wondering if there may be reasons for these particular pins. May also be due to being on an M1.

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

ResolvePackageNotFound: 
  - plotly::python-kaleido=0.0.3
  - conda-forge::pip=19.2.2
  - conda-forge::python=3.7.1
bethac07 commented 2 years ago

I could not get a conda environment to build correctly, I tried a whole bunch of things, but it kept saying there were dependency conflicts. These are the versions of packages I ran in my local, brew-installed python, does someone on a non-M1 (and who is better at conda than me, because I'm not good at it at all) want to try these to see if it's an M1 issue or something else?

name: profiling
dependencies:
- conda-forge::python=3.8.13
- conda-forge::pandas=1.4.3
- conda-forge::pyyaml=6.0
- conda-forge::plotly=5.10.0
- conda-forge::dvc-s3=2.19.0
- conda-forge::python-kaleido=0.2.1
- pip
- pip:
  - git+https://github.com/cytomining/pycytominer@0a0ff1543af9a2d4d0e823dfe75ca437572d3894
Console output from attempted build ``` bcimini@wm4f8-761 % conda --version conda 4.14.0 bcimini@wm4f8-761 % conda env create environment.yml 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 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 libiconv conflicts for: conda-forge::python-kaleido=0.2.1 -> python[version='>=3.5'] -> libiconv[version='>=1.16,<2.0a0'] conda-forge::plotly=5.10.0 -> python[version='>=3.6'] -> libiconv[version='>=1.16,<2.0a0'] pip -> python[version='>=3.9,<3.10.0a0'] -> libiconv[version='>=1.16,<2.0a0'] conda-forge::pyyaml=6.0 -> python[version='>=3.9,<3.10.0a0'] -> libiconv[version='>=1.16,<2.0a0'] conda-forge::dvc-s3=2.19.0 -> python[version='>=3.8'] -> libiconv[version='>=1.16,<2.0a0'] conda-forge::pandas=1.4.3 -> python[version='>=3.9,<3.10.0a0'] -> libiconv[version='>=1.16,<2.0a0'] Package pip conflicts for: conda-forge::plotly=5.10.0 -> python[version='>=3.6'] -> pip conda-forge::pandas=1.4.3 -> python[version='>=3.8,<3.9.0a0'] -> pip conda-forge::pyyaml=6.0 -> python[version='>=3.8,<3.9.0a0'] -> pip conda-forge::dvc-s3=2.19.0 -> python[version='>=3.8'] -> pip conda-forge::python-kaleido=0.2.1 -> python[version='>=3.5'] -> pip conda-forge::python=3.8.13 -> pip Package wheel conflicts for: pip -> wheel conda-forge::python=3.8.13 -> pip -> wheel Package python_abi conflicts for: conda-forge::pyyaml=6.0 -> python_abi[version='3.10.*|3.8.*|3.9.*',build='*_cp39|*_cp38|*_cp310'] conda-forge::pandas=1.4.3 -> python_abi[version='3.10.*|3.8.*|3.9.*',build='*_cp39|*_cp38|*_cp310'] pip -> setuptools -> python_abi[version='3.10.*|3.8.*|3.9.*',build='*_cp39|*_cp38|*_cp310'] Package six conflicts for: conda-forge::plotly=5.10.0 -> tenacity[version='>=6.2.0'] -> six[version='>=1.9.0'] conda-forge::pandas=1.4.3 -> python-dateutil[version='>=2.8.1'] -> six[version='>=1.5']The following specifications were found to be incompatible with your system: - feature:/osx-arm64::__osx==12.5.1=0 - feature:|@/osx-arm64::__osx==12.5.1=0 - conda-forge::python-kaleido=0.2.1 -> kaleido-core=0.2.1 -> __osx[version='>=10.11'] Your installed version is: 12.5.1 ```
ashdederich commented 1 year ago

I'm having the same issue. I tried pulling from the most recent git commit (hash afac3ea16818ad25f37318ecd5c5090c0eff5806). Creates dependency issues (particularly with cmake, where the fail originates from). Has this issue been solved? Is there an updated environment.yml file available?