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sollan / alma

Fully automated (rodent) limb motion analysis toolbox for behavioral analysis with bodypart coordinate data, building upon markerless pose estimation.
GNU General Public License v3.0
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Installation error #40

Open tedeschisunlab opened 5 months ago

tedeschisunlab commented 5 months ago

Hi, We installed Python 3.10 and Miniconda3 as instructed. We used the following code: conda env create -f conda_env_python_3_10.yml conda activate venv_python_3_10

Then we tried to run pip install -r requirements.txt

We got the following error message:

Using cached numpy-1.19.0.zip (7.3 MB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... error error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [88 lines of output] Running from numpy source directory.

:460: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates /private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py:73: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. required_version = LooseVersion('0.29.14') /private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py:75: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if LooseVersion(cython_version) < required_version: performance hint: _common.pyx:275:19: Exception check after calling 'random_func' will always require the GIL to be acquired. Declare 'random_func' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:299:19: Exception check after calling 'random_func' will always require the GIL to be acquired. Declare 'random_func' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:322:50: Exception check after calling 'random_func' will always require the GIL to be acquired. Declare 'random_func' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:426:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:465:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:509:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:592:36: Exception check after calling 'f0' will always require the GIL to be acquired. Declare 'f0' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:596:36: Exception check after calling 'f1' will always require the GIL to be acquired. Declare 'f1' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:600:36: Exception check after calling 'f2' will always require the GIL to be acquired. Declare 'f2' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:604:36: Exception check after calling 'f3' will always require the GIL to be acquired. Declare 'f3' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:638:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:675:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:712:63: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:754:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:785:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:903:40: Exception check after calling 'f0' will always require the GIL to be acquired. Declare 'f0' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:907:40: Exception check after calling 'fd' will always require the GIL to be acquired. Declare 'fd' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:911:41: Exception check after calling 'fdd' will always require the GIL to be acquired. Declare 'fdd' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:916:40: Exception check after calling 'fi' will always require the GIL to be acquired. Declare 'fi' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:920:41: Exception check after calling 'fdi' will always require the GIL to be acquired. Declare 'fdi' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:924:38: Exception check after calling 'fiii' will always require the GIL to be acquired. Declare 'fiii' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:960:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _common.pyx:1002:32: Exception check after calling 'f1' will always require the GIL to be acquired. Declare 'f1' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: _generator.pyx:706:41: Exception check after calling '_shuffle_int' will always require the GIL to be acquired. Possible solutions: 1. Declare '_shuffle_int' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_shuffle_int' to allow an error code to be returned. performance hint: _generator.pyx:735:45: Exception check after calling '_shuffle_int' will always require the GIL to be acquired. Possible solutions: 1. Declare '_shuffle_int' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_shuffle_int' to allow an error code to be returned. Error compiling Cython file: ------------------------------------------------------------ ... for i in range(1, RK_STATE_LEN): self.rng_state.key[i] = val[i] self.rng_state.pos = i self._bitgen.state = &self.rng_state self._bitgen.next_uint64 = &mt19937_uint64 ^ ------------------------------------------------------------ _mt19937.pyx:138:35: Cannot assign type 'uint64_t (*)(void *) except? -1 nogil' to 'uint64_t (*)(void *) noexcept nogil'. Exception values are incompatible. Suggest adding 'noexcept' to the type of the value being assigned. Processing numpy/random/_bounded_integers.pxd.in Processing numpy/random/_bounded_integers.pyx.in Processing numpy/random/_common.pyx Processing numpy/random/_generator.pyx Processing numpy/random/_mt19937.pyx Traceback (most recent call last): File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 235, in main() File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 231, in main find_process_files(root_dir) File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 222, in find_process_files process(root_dir, fromfile, tofile, function, hash_db) File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 188, in process processor_function(fromfile, tofile) File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 77, in process_pyx subprocess.check_call( File "/Users/tedeschia/miniconda3/envs/venv_python_3_10/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/Users/tedeschia/miniconda3/envs/venv_python_3_10/bin/python3.10', '-m', 'cython', '-3', '--fast-fail', '-o', '_mt19937.c', '_mt19937.pyx']' returned non-zero exit status 1. Cythonizing sources Traceback (most recent call last): File "/Users/tedeschia/miniconda3/envs/venv_python_3_10/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in main() File "/Users/tedeschia/miniconda3/envs/venv_python_3_10/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/Users/tedeschia/miniconda3/envs/venv_python_3_10/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel return hook(metadata_directory, config_settings) File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-build-env-914leq5a/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 366, in prepare_metadata_for_build_wheel self.run_setup() File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-build-env-914leq5a/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 487, in run_setup super().run_setup(setup_script=setup_script) File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-build-env-914leq5a/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 311, in run_setup exec(code, locals()) File "", line 489, in File "", line 469, in setup_package File "", line 274, in generate_cython RuntimeError: Running cythonize failed! [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. Our mac operating system is macOS Sierra version 10.12.6 with 16 GB memory. Any help will be greatly appreciated. Thanks,
josh-oloro commented 3 months ago

Hi, I got the same error. Was this ever solved?

sollan commented 3 months ago

Hi, if you've installed the libraries with Conda, there should be no need to run pip install.

You could simply run

conda env create -f conda_env_python_3_10.yml
conda activate venv_python_3_10
pythonw ./alma.py

And the program should start.

Can you let me know if that works?

Best, Annette