Package install seems to be broken

[mvinet99]

Hello,

I have tried installing the Pyradiomics package using pip, conda, and from source, and none of the options work for installing. I have tried installing on different python versions and with all previous pyraiodimics package versions and nothing has built correctly. Is anyone else having difficulties with installing? Has anyone else been able to recently install correctly? Thanks in advance for the help.

[meghutch]

conda and pip also have not worked for me. These steps work for me in order to get the current GitHub repo/package working on my local machine.

Note, I performed these steps in the terminal.

# create new environment
conda create -n pyrad-env python=3.13.5

# activate env
conda activate pyrad-env

# clone the current git repo
git clone https://github.com/AIM-Harvard/pyradiomics.git

# go into new pyradiomics folder
cd pyradiomics

# run following to install the package directly from repo
pip install -e .

# open python from terminal (but this should work if to connect env to notebook - I can provide steps for this if helpful)
python

# import package
import radiomics

[ttbek]

Trying from Pip was giving me the problem described here: #244 But obviously I didn't have a setup.py doing it from Pip... so I tried from source and wasn't seeing a setup.py... so the official way seems broken. So I found this issue, but

This isn't working for me either.

Obtaining file:///usr/local/pyradiomics/pyradiomics
Installing build dependencies ... done
Checking if build backend supports build_editable ... done
Getting requirements to build editable ... done
Installing backend dependencies ... done
Preparing editable metadata (pyproject.toml) ... done
Collecting numpy>=2.0
Using cached numpy-2.2.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB)
Collecting SimpleITK>=2.4.0
Using cached simpleitk-2.5.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (52.6 MB)
Collecting pykwalify>=1.6.0
Using cached pykwalify-1.8.0-py2.py3-none-any.whl (24 kB)
Collecting PyWavelets>=1.6.0
Using cached pywavelets-1.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.5 MB)
Collecting python-dateutil>=2.8.0
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Collecting ruamel.yaml>=0.16.0
Using cached ruamel.yaml-0.18.15-py3-none-any.whl (119 kB)
Collecting docopt>=0.6.2
Using cached docopt-0.6.2-py2.py3-none-any.whl
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.8.0->pykwalify>=1.6.0->pyradiomics==3.1.1.dev111+g8ed579383) (1.16.0)
Collecting ruamel.yaml.clib>=0.2.7
Using cached ruamel.yaml.clib-0.2.14-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (721 kB)
Building wheels for collected packages: pyradiomics
Building editable for pyradiomics (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building editable for pyradiomics (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [34 lines of output]
*** scikit-build-core 0.11.6 using CMake 3.22.1 (editable)
*** Configuring CMake...
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in
main()
File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 283, in build_editable
return hook(wheel_directory, config_settings, metadata_directory)
File "/tmp/pip-build-env-e_q_yl23/overlay/local/lib/python3.10/dist-packages/scikit_build_core/build/init.py", line 57, in build_editable
return _build_wheel_impl(
File "/tmp/pip-build-env-e_q_yl23/overlay/local/lib/python3.10/dist-packages/scikit_build_core/build/wheel.py", line 176, in _build_wheel_impl
return _build_wheel_impl_impl(
File "/tmp/pip-build-env-e_q_yl23/overlay/local/lib/python3.10/dist-packages/scikit_build_core/build/wheel.py", line 429, in _build_wheel_impl_impl
builder.configure(
File "/tmp/pip-build-env-e_q_yl23/overlay/local/lib/python3.10/dist-packages/scikit_build_core/builder/builder.py", line 191, in configure
local_def = set_environment_for_gen(
File "/tmp/pip-build-env-e_q_yl23/overlay/local/lib/python3.10/dist-packages/scikit_build_core/builder/generator.py", line 121, in set_environment_for_gen
ninja = best_program(get_ninja_programs(), version=ninja_settings.version)
File "/tmp/pip-build-env-e_q_yl23/overlay/local/lib/python3.10/dist-packages/scikit_build_core/program_search.py", line 233, in best_program
for program in programs:
File "/tmp/pip-build-env-e_q_yl23/overlay/local/lib/python3.10/dist-packages/scikit_build_core/program_search.py", line 194, in get_ninja_programs
result = Run(timeout=compute_timeout(ninja_path)).capture(
File "/tmp/pip-build-env-e_q_yl23/overlay/local/lib/python3.10/dist-packages/scikit_build_core/_shutil.py", line 42, in capture
return self._run(args, capture=True)
File "/tmp/pip-build-env-e_q_yl23/overlay/local/lib/python3.10/dist-packages/scikit_build_core/_shutil.py", line 70, in _run
return subprocess.run(
File "/usr/lib/python3.10/subprocess.py", line 503, in run
with Popen(*popenargs, **kwargs) as process:
File "/usr/lib/python3.10/subprocess.py", line 971, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib/python3.10/subprocess.py", line 1863, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'ninja'
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building editable for pyradiomics
Failed to build pyradiomics
ERROR: Could not build wheels for pyradiomics, which is required to install pyproject.toml-based projects

And the official documentation said to do: python -m pip install -r requirements.txt
But there is no requirements.txt

[ttbek]

It seems like the problem is that the installation guide should NOT tell people to clone the git repo, it seems that some other things go into an installable build. I downloaded the last tagged stable (non-alpha) build from https://github.com/AIM-Harvard/pyradiomics/releases/tag/v3.1.0 And there it has requirements.txt and setup.py and the instructions seem to work.

I can now run python and import radiomics, but the documentation says it can be run directly from the commandline via a pyradiomics entrypoint... that doesn't seem to be working. There doesn't seem to be any file by that name and grepping the files shows mostly just references to the website and an output message or two... nothing that I'm recognizing as an entrypoint... but I'm not really a Python person...