problems on M1

[cmungall]

When running poetry run python -m unittest

I get

======================================================================
ERROR: tests.test_plugin (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: tests.test_plugin
Traceback (most recent call last):
  File "/Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
  File "/Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/unittest/loader.py", line 377, in _get_module_from_name
    __import__(name)
  File "/Users/cjm/repos/oakx-grape/tests/test_plugin.py", line 4, in <module>
    from oaklib.implementations import get_implementation_resolver
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/oakx-grape-pUaGkv-X-py3.9/lib/python3.9/site-packages/oaklib/__init__.py", line 9, in <module>
    from oaklib.selector import get_implementation_from_shorthand  # noqa:F401
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/oakx-grape-pUaGkv-X-py3.9/lib/python3.9/site-packages/oaklib/selector.py", line 8, in <module>
    from oaklib.implementations import GildaImplementation
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/oakx-grape-pUaGkv-X-py3.9/lib/python3.9/site-packages/oaklib/implementations/__init__.py", line 28, in <module>
    from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/oakx-grape-pUaGkv-X-py3.9/lib/python3.9/site-packages/oaklib/implementations/pronto/pronto_implementation.py", line 13, in <module>
    import pronto
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/oakx-grape-pUaGkv-X-py3.9/lib/python3.9/site-packages/pronto/__init__.py", line 24, in <module>
    from .definition import Definition
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/oakx-grape-pUaGkv-X-py3.9/lib/python3.9/site-packages/pronto/definition.py", line 5, in <module>
    from .xref import Xref
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/oakx-grape-pUaGkv-X-py3.9/lib/python3.9/site-packages/pronto/xref.py", line 6, in <module>
    import fastobo
ImportError: dlopen(/Users/cjm/Library/Caches/pypoetry/virtualenvs/oakx-grape-pUaGkv-X-py3.9/lib/python3.9/site-packages/fastobo.cpython-39-darwin.so, 0x0002): tried: '/Users/cjm/Library/Caches/pypoetry/virtualenvs/oakx-grape-pUaGkv-X-py3.9/lib/python3.9/site-packages/fastobo.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e)))

[cmungall]

also reported here: fastobo/fastobo-py#313

[cmungall]

If I do this

poetry export -f requirements.txt --output requirements.txt
pip install -r requirements.txt

then it builds the fastobo wheel rather than trying to use an existing (incorrect) one

[cmungall]

spoke to soon, still didn't solve it

✗ python
Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:01:00)
[Clang 13.0.1 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import fastobo
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: dlopen(/Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/site-packages/fastobo.cpython-39-darwin.so, 0x0002): tried: '/Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/site-packages/fastobo.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e)))
>>>

[cmungall]

✗ pip install fastobo
Collecting fastobo
  Using cached fastobo-0.12.1-cp39-cp39-macosx_12_0_arm64.whl
Installing collected packages: fastobo
Successfully installed fastobo-0.12.1
(oakx-grape-env) ➜  oakx-grape git:(main) ✗ ls /Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/site-packages/fastobo*
/Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/site-packages/fastobo.cpython-39-darwin.so

/Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/site-packages/fastobo-0.12.1.dist-info:
COPYING       INSTALLER     METADATA      RECORD        REQUESTED     WHEEL         top_level.txt

[cmungall]

(oakx-grape-env) ➜  oakx-grape git:(main) ✗ pip cache remove "*"
Files removed: 708
(oakx-grape-env) ➜  oakx-grape git:(main) ✗
(oakx-grape-env) ➜  oakx-grape git:(main) ✗
(oakx-grape-env) ➜  oakx-grape git:(main) ✗
(oakx-grape-env) ➜  oakx-grape git:(main) ✗ pip uninstall fastobo-py
WARNING: Skipping fastobo-py as it is not installed.
(oakx-grape-env) ➜  oakx-grape git:(main) ✗ pip uninstall fastobo
WARNING: Skipping fastobo as it is not installed.
(oakx-grape-env) ➜  oakx-grape git:(main) ✗ pip install fastobo
Collecting fastobo
  Downloading fastobo-0.12.1.tar.gz (20.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 20.1/20.1 MB 18.4 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: fastobo
  Building wheel for fastobo (pyproject.toml) ... done
  Created wheel for fastobo: filename=fastobo-0.12.1-cp39-cp39-macosx_12_0_arm64.whl size=1796933 sha256=f0a943c59bfeaaba11923aaab5ff861546809a0cd061eeff1e74c63cb2dfb8a3
  Stored in directory: /Users/cjm/Library/Caches/pip/wheels/54/ee/59/8ac6727dde642d9bbf7d66ad34bf234a2c5a8218a04365511f
Successfully built fastobo
Installing collected packages: fastobo
Successfully installed fastobo-0.12.1
(oakx-grape-env) ➜  oakx-grape git:(main) ✗
(oakx-grape-env) ➜  oakx-grape git:(main) ✗
(oakx-grape-env) ➜  oakx-grape git:(main) ✗
(oakx-grape-env) ➜  oakx-grape git:(main) ✗ !ls
(oakx-grape-env) ➜  oakx-grape git:(main) ✗ ls /Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/site-packages/fastobo*
/Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/site-packages/fastobo.cpython-39-darwin.so

[cmungall]

(oakx-grape-env) ➜  oakx-grape git:(main) ✗ conda install -c bioconda fastobo
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - fastobo

Current channels:

  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

[cmungall]

✗ file /Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/site-packages/fastobo.cpython-39-darwin.so
/Users/cjm/opt/anaconda3/envs/oakx-grape-env/lib/python3.9/site-packages/fastobo.cpython-39-darwin.so: Mach-O 64-bit dynamically linked shared library x86_64

[cmungall]

thanks to @hrshdhgd for help, still no further along

[cmungall]

@justaddcoffee shared his .so file, which looks like this:

✗ file ~/Downloads/fastobo.cpython-39-darwin.so
/Users/cjm/Downloads/fastobo.cpython-39-darwin.so: Mach-O 64-bit dynamically linked shared library arm64

I substituted that... and it works!

success... in some sense