Installation (Python 3.13, Mac)

[arokem]

@neurolabusc reports:

Neither the stable nor development version of pyAFQ installs on my Apple Silicon MacOS computer. I followed these instructions:
https://urldefense.com/v3/__https://yeatmanlab.github.io/pyAFQ/howto/installation_guide.html__;!!K-Hz7m0Vt54!lJ9cegaronGZ4M_8QKqv4XmRQbWICntNGKSK0c-A4cCXHruYhzJPy0M1girhHxy_FHRGKWoTAbkLLocPnd0$
Should I post a Github issue, or is there a known work around(if the latter, it would be nice to update the docs)?

I am not a Python packaging expert, but it looks like pyAFQ demands numpy==1.23.5 (released 19 Nov 2022) while the current stable version is 2.2.3.

% python --version
Python 3.13.2

% python -c "import numpy; print(numpy.__version__)"
2.1.3

% pip install pyAFQ
Collecting pyAFQ
  Using cached pyAFQ-1.3.6-py3-none-any.whl.metadata (5.3 kB)
Requirement already satisfied: scikit-image>=0.14.2 in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ) (0.25.1)
Collecting dipy<1.9.0,>=1.8.0 (from pyAFQ)
  Using cached dipy-1.8.0.tar.gz (6.5 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: pandas in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ) (2.2.3)
Collecting pybids>=0.16.2 (from pyAFQ)
  Using cached pybids-0.18.1-py3-none-any.whl.metadata (8.0 kB)
Collecting templateflow>=0.8 (from pyAFQ)
  Using cached templateflow-24.2.2-py3-none-any.whl.metadata (20 kB)
Collecting pimms (from pyAFQ)
  Using cached pimms-0.3.25.tar.gz (67 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pydra (from pyAFQ)
  Using cached pydra-0.25-py3-none-any.whl.metadata (5.8 kB)
Requirement already satisfied: joblib>=1.3.2 in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ) (1.4.2)
Requirement already satisfied: dask>=1.1 in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ) (2025.1.0)
Collecting s3bids>=0.1.7 (from pyAFQ)
  Using cached s3bids-0.1.7-py3-none-any.whl.metadata (727 bytes)
Requirement already satisfied: trx-python in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ) (0.3)
INFO: pip is looking at multiple versions of pyafq to determine which version is compatible with other requirements. This could take a while.
Collecting pyAFQ
  Using cached pyAFQ-1.3.5-py3-none-any.whl.metadata (5.5 kB)
Collecting boto3>=1.14.0 (from pyAFQ)
  Using cached boto3-1.36.26-py3-none-any.whl.metadata (6.7 kB)
Collecting s3fs~=0.4.2 (from pyAFQ)
  Using cached s3fs-0.4.2-py3-none-any.whl.metadata (1.3 kB)
Collecting toml>=0.10.0 (from pyAFQ)
  Using cached toml-0.10.2-py2.py3-none-any.whl.metadata (7.1 kB)
Collecting setuptools-scm<5.1.0,>=3.4.0 (from setuptools-scm[toml]<5.1.0,>=3.4.0->pyAFQ)
  Using cached setuptools_scm-5.0.2-py2.py3-none-any.whl.metadata (21 kB)
Collecting funcargparse>=0.2.0 (from pyAFQ)
  Using cached funcargparse-0.2.5.tar.gz (33 kB)
  Preparing metadata (setup.py) ... done
Collecting popylar==0.2.* (from pyAFQ)
  Using cached popylar-0.2.tar.gz (3.7 kB)
  Preparing metadata (setup.py) ... done
Collecting plotly==5.3.0 (from pyAFQ)
  Using cached plotly-5.3.0-py2.py3-none-any.whl.metadata (7.4 kB)
Collecting kaleido==0.2.1 (from pyAFQ)
  Using cached kaleido-0.2.1-py2.py3-none-macosx_11_0_arm64.whl.metadata (15 kB)
Requirement already satisfied: imageio>=2.0.0 in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ) (2.37.0)
Requirement already satisfied: Pillow in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ) (11.1.0)
Requirement already satisfied: matplotlib in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ) (3.10.0)
Collecting numpy==1.23.5 (from pyAFQ)
  Using cached numpy-1.23.5.tar.gz (10.7 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
     × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [32 lines of output]
      Traceback (most recent call last):
        File "/Users/chris/py3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
          ~~~~^^
        File "/Users/chris/py3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/chris/py3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 137, in get_requires_for_build_wheel
          backend = _build_backend()
        File "/Users/chris/py3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 70, in _build_backend
          obj = import_module(mod_path)
        File "/opt/homebrew/Cellar/python@3.13/3.13.2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/importlib/__init__.py", line 88, in import_module
          return _bootstrap._gcd_import(name[level:], package, level)
                 ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
        File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1310, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
        File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
        File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
        File "<frozen importlib._bootstrap_external>", line 1026, in exec_module
        File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
        File "/private/var/folders/29/hmj3qsmn51b_zyrnnck_y2rw0000gn/T/pip-build-env-337g3aeo/overlay/lib/python3.13/site-packages/setuptools/__init__.py", line 16, in <module>
          import setuptools.version
        File "/private/var/folders/29/hmj3qsmn51b_zyrnnck_y2rw0000gn/T/pip-build-env-337g3aeo/overlay/lib/python3.13/site-packages/setuptools/version.py", line 1, in <module>
          import pkg_resources
        File "/private/var/folders/29/hmj3qsmn51b_zyrnnck_y2rw0000gn/T/pip-build-env-337g3aeo/overlay/lib/python3.13/site-packages/pkg_resources/__init__.py", line 2172, in <module>
          register_finder(pkgutil.ImpImporter, find_on_path)
                          ^^^^^^^^^^^^^^^^^^^
      AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
      [end of output]
     note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.


(py3) pyScripts % pip install git+https://github.com/yeatmanlab/pyAFQ.git
Collecting git+https://github.com/yeatmanlab/pyAFQ.git
  Cloning https://urldefense.com/v3/__https://github.com/yeatmanlab/pyAFQ.git__;!!K-Hz7m0Vt54!lJ9cegaronGZ4M_8QKqv4XmRQbWICntNGKSK0c-A4cCXHruYhzJPy0M1girhHxy_FHRGKWoTAbkL8bGYuP0$  to /private/var/folders/29/hmj3qsmn51b_zyrnnck_y2rw0000gn/T/pip-req-build-ojtx7sp9
  Running command git clone --filter=blob:none --quiet https://urldefense.com/v3/__https://github.com/yeatmanlab/pyAFQ.git__;!!K-Hz7m0Vt54!lJ9cegaronGZ4M_8QKqv4XmRQbWICntNGKSK0c-A4cCXHruYhzJPy0M1girhHxy_FHRGKWoTAbkL8bGYuP0$  /private/var/folders/29/hmj3qsmn51b_zyrnnck_y2rw0000gn/T/pip-req-build-ojtx7sp9
  Resolved https://urldefense.com/v3/__https://github.com/yeatmanlab/pyAFQ.git__;!!K-Hz7m0Vt54!lJ9cegaronGZ4M_8QKqv4XmRQbWICntNGKSK0c-A4cCXHruYhzJPy0M1girhHxy_FHRGKWoTAbkL8bGYuP0$  to commit 79368ed4aaefd9820e1e2f91f91bdf4a7282cc43
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: scikit_image>=0.14.2 in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ==1.3.4.dev2679368434) (0.25.1)
Collecting dipy<1.9.0,>=1.8.0 (from pyAFQ==1.3.4.dev2679368434)
  Using cached dipy-1.8.0.tar.gz (6.5 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: pandas in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ==1.3.4.dev2679368434) (2.2.3)
Collecting pybids>=0.16.2 (from pyAFQ==1.3.4.dev2679368434)
  Using cached pybids-0.18.1-py3-none-any.whl.metadata (8.0 kB)
Collecting templateflow>=0.8 (from pyAFQ==1.3.4.dev2679368434)
  Using cached templateflow-24.2.2-py3-none-any.whl.metadata (20 kB)
Collecting pimms (from pyAFQ==1.3.4.dev2679368434)
  Using cached pimms-0.3.25.tar.gz (67 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pydra (from pyAFQ==1.3.4.dev2679368434)
  Using cached pydra-0.25-py3-none-any.whl.metadata (5.8 kB)
Requirement already satisfied: joblib>=1.3.2 in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ==1.3.4.dev2679368434) (1.4.2)
Requirement already satisfied: dask>=1.1 in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ==1.3.4.dev2679368434) (2025.1.0)
Collecting s3bids>=0.1.7 (from pyAFQ==1.3.4.dev2679368434)
  Using cached s3bids-0.1.7-py3-none-any.whl.metadata (727 bytes)
Collecting boto3>=1.14.0 (from pyAFQ==1.3.4.dev2679368434)
  Using cached boto3-1.36.26-py3-none-any.whl.metadata (6.7 kB)
Collecting s3fs~=0.4.2 (from pyAFQ==1.3.4.dev2679368434)
  Using cached s3fs-0.4.2-py3-none-any.whl.metadata (1.3 kB)
Collecting toml>=0.10.0 (from pyAFQ==1.3.4.dev2679368434)
  Using cached toml-0.10.2-py2.py3-none-any.whl.metadata (7.1 kB)
Collecting setuptools_scm<5.1.0,>=3.4.0 (from setuptools_scm[toml]<5.1.0,>=3.4.0->pyAFQ==1.3.4.dev2679368434)
  Using cached setuptools_scm-5.0.2-py2.py3-none-any.whl.metadata (21 kB)
Collecting funcargparse>=0.2.0 (from pyAFQ==1.3.4.dev2679368434)
  Using cached funcargparse-0.2.5.tar.gz (33 kB)
  Preparing metadata (setup.py) ... done
Collecting popylar==0.2.* (from pyAFQ==1.3.4.dev2679368434)
  Using cached popylar-0.2.tar.gz (3.7 kB)
  Preparing metadata (setup.py) ... done
Collecting plotly==5.3.0 (from pyAFQ==1.3.4.dev2679368434)
  Using cached plotly-5.3.0-py2.py3-none-any.whl.metadata (7.4 kB)
Collecting kaleido==0.2.1 (from pyAFQ==1.3.4.dev2679368434)
  Using cached kaleido-0.2.1-py2.py3-none-macosx_11_0_arm64.whl.metadata (15 kB)
Requirement already satisfied: imageio>=2.0.0 in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ==1.3.4.dev2679368434) (2.37.0)
Requirement already satisfied: Pillow in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ==1.3.4.dev2679368434) (11.1.0)
Requirement already satisfied: matplotlib in /Users/chris/py3/lib/python3.13/site-packages (from pyAFQ==1.3.4.dev2679368434) (3.10.0)
Collecting numpy==1.23.5 (from pyAFQ==1.3.4.dev2679368434)
  Using cached numpy-1.23.5.tar.gz (10.7 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
     × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [32 lines of output]
      Traceback (most recent call last):
        File "/Users/chris/py3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
          ~~~~^^
        File "/Users/chris/py3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/chris/py3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 137, in get_requires_for_build_wheel
          backend = _build_backend()
        File "/Users/chris/py3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 70, in _build_backend
          obj = import_module(mod_path)
        File "/opt/homebrew/Cellar/python@3.13/3.13.2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/importlib/__init__.py", line 88, in import_module
          return _bootstrap._gcd_import(name[level:], package, level)
                 ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
        File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1310, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
        File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
        File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
        File "<frozen importlib._bootstrap_external>", line 1026, in exec_module
        File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
        File "/private/var/folders/29/hmj3qsmn51b_zyrnnck_y2rw0000gn/T/pip-build-env-qu8onlgd/overlay/lib/python3.13/site-packages/setuptools/__init__.py", line 16, in <module>
          import setuptools.version
        File "/private/var/folders/29/hmj3qsmn51b_zyrnnck_y2rw0000gn/T/pip-build-env-qu8onlgd/overlay/lib/python3.13/site-packages/setuptools/version.py", line 1, in <module>
          import pkg_resources
        File "/private/var/folders/29/hmj3qsmn51b_zyrnnck_y2rw0000gn/T/pip-build-env-qu8onlgd/overlay/lib/python3.13/site-packages/pkg_resources/__init__.py", line 2172, in <module>
          register_finder(pkgutil.ImpImporter, find_on_path)
                          ^^^^^^^^^^^^^^^^^^^
      AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
      [end of output]
     note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[arokem]

We have not tried installing on Python 3.13 yet, so I bet this is somehow related to Python 3.13, and not a Mac issue per se. I'll start by adding Python 3.13 to our ci and see what gives.

[arokem]

Based on https://scientific-python.org/specs/spec-0000/#support-window, looks like we might consider dropping Python 3.10 if that becomes challenging.

[arokem]

@neurolabusc: Does the installation work fine for you if you try it on Python 3.12? We're working on 3.13 support (#65) but that might take a while.

[neurolabusc]

I did get it to work with Python 3.11

$ python3.11 -m venv ~/py311
$ source ~/py311/bin/activate
$ python --version
    Python 3.11.11
(py311) ~ % pip install pyAFQ