[BUG] antspyx installation error when using Python3.13 (conda) environment #104
Description
when I install in a Python 3.13 env I get the following installation error because of antspyx.
Not sure if this is something we could fix easily, or whether we should add some documentation?
Using cached urllib3-2.3.0-py3-none-any.whl (128 kB)
Building wheels for collected packages: antspyx
Building wheel for antspyx (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [178 lines of output]
running bdist_wheel
running build
running build_py
running build_ext
Configuring ITK
No local ITK installation found... Building ITK now...
Cloning into 'itksource'...
Updating files: 85% (13119/15272)
Updating files: 86% (13134/15272)
Updating files: 87% (13287/15272)
Updating files: 88% (13440/15272)
Updating files: 89% (13593/15272)
Updating files: 90% (13745/15272)
Updating files: 91% (13898/15272)
Updating files: 92% (14051/15272)
Updating files: 93% (14203/15272)
Updating files: 94% (14356/15272)
Updating files: 95% (14509/15272)
Updating files: 96% (14662/15272)
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Updating files: 99% (15120/15272)
Updating files: 100% (15272/15272)
Updating files: 100% (15272/15272), done.
Already on 'master'
Your branch is up to date with 'origin/master'.
Note: switching to 'ce57f309f4f4142b80367fd89a88f8dac9d6943a'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at ce57f309f4 STYLE: Remove obsolete `__GNUC__` macro checks for GCC version 4
./scripts/configure_ITK.sh: line 48: cmake: command not found
make: *** No targets specified and no makefile found. Stop.
Configuring ANTs core
Cloning into 'pybind11'...
Cloning into 'antsrepo'...
Already on 'master'
Your branch is up to date with 'origin/master'.
Already up to date.
Note: switching to 'dfd9e6664f2fc5f0dbd05c6c23d5e4895e82abee'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at dfd9e666 BUG: forget EOL
Configuring ANTsPy library
Traceback (most recent call last):
File "/tmp/pip-install-t8rc6bix/antspyx_90a56fa513014e218b44d07328f95ead/setup.py", line 101, in run
out = subprocess.check_output(["cmake", "--version"])
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/subprocess.py", line 474, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**kwargs).stdout
^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/subprocess.py", line 556, in run
with Popen(*popenargs, **kwargs) as process:
~~~~~^^^^^^^^^^^^^^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/subprocess.py", line 1038, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pass_fds, cwd, env,
^^^^^^^^^^^^^^^^^^^
...<5 lines>...
gid, gids, uid, umask,
^^^^^^^^^^^^^^^^^^^^^^
start_new_session, process_group)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/subprocess.py", line 1974, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'cmake'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 2, in <module>
exec(compile('''
~~~~^^^^^^^^^^^^
# This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
...<31 lines>...
exec(compile(setup_py_code, filename, "exec"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
''' % ('/tmp/pip-install-t8rc6bix/antspyx_90a56fa513014e218b44d07328f95ead/setup.py',), "<pip-setuptools-caller>", "exec"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<pip-setuptools-caller>", line 34, in <module>
File "/tmp/pip-install-t8rc6bix/antspyx_90a56fa513014e218b44d07328f95ead/setup.py", line 174, in <module>
setup(
~~~~~^
name="antspyx",
^^^^^^^^^^^^^^^
...<41 lines>...
classifiers=["Programming Language :: Python :: 3.9"],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/__init__.py", line 117, in setup
return distutils.core.setup(**attrs)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 186, in setup
return run_commands(dist)
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
dist.run_commands()
~~~~~~~~~~~~~~~~~^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 983, in run_commands
self.run_command(cmd)
~~~~~~~~~~~~~~~~^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/command/bdist_wheel.py", line 379, in run
self.run_command("build")
~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
self.distribution.run_command(command)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/command/build.py", line 136, in run
self.run_command(cmd_name)
~~~~~~~~~~~~~~~~^^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
self.distribution.run_command(command)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/tmp/pip-install-t8rc6bix/antspyx_90a56fa513014e218b44d07328f95ead/setup.py", line 39, in run
self.run_command("build_ext")
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
self.distribution.run_command(command)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/florian/miniconda3/envs/zudepy13/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/tmp/pip-install-t8rc6bix/antspyx_90a56fa513014e218b44d07328f95ead/setup.py", line 103, in run
raise RuntimeError(
...<2 lines>...
)
RuntimeError: CMake must be installed to build the following extensions: ants
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for antspyx
Running setup.py clean for antspyx
Failed to build antspyx
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (antspyx)