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francescameneghello / RIMS_tool

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python3.12 distutils deprecation #1

Open topongo opened 2 weeks ago

topongo commented 2 weeks ago

Hi, probably it could be helpful to disclose a warning for python>=3.12 that the default installation guide won't work for them. This is due to distutils being deprecated since 3.12 according to PEP0632.

steps to reproduce:

python3.12

docker run --rm -it --entrypoint pip python:3.12 install scikit-learn==1.2.1 scipy==1.11.2 simpy==4.0.1 pm4py==2.7.5.2 statsmodels==0.14.0 pandas==1.5.3 Output:

Collecting scikit-learn==1.2.1
  Downloading scikit-learn-1.2.1.tar.gz (7.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 39.5 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done

[notice] A new release of pip is available: 24.2 -> 24.3.1
[notice] To update, run: pip install --upgrade pip
ERROR: Exception:
Traceback (most recent call last):
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper
    status = _inner_run()
             ^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run
    return self.run(options, args)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper
    return func(self, options, args)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 379, in run
    requirement_set = resolver.resolve(
                      ^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 95, in resolve
    result = self._result = resolver.resolve(
                            ^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve
    state = resolution.resolve(requirements, max_rounds=max_rounds)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_vendor/resolvelib/resolvers.py", line 397, in resolve
    self._add_to_criteria(self.state.criteria, r, parent=None)
  File "/usr/local/lib/python3.12/site-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria
    if not criterion.candidates:
           ^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_vendor/resolvelib/structs.py", line 156, in __bool__
    return bool(self._sequence)
           ^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 174, in __bool__
    return any(self)
           ^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 162, in <genexpr>
    return (c for c in iterator if id(c) not in self._incompatible_ids)
                       ^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 53, in _iter_built
    candidate = func()
                ^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 186, in _make_candidate_from_link
    base: Optional[BaseCandidate] = self._make_base_candidate_from_link(
                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 232, in _make_base_candidate_from_link
    self._link_candidate_cache[link] = LinkCandidate(
                                       ^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 303, in __init__
    super().__init__(
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 158, in __init__
    self.dist = self._prepare()
                ^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 235, in _prepare
    dist = self._prepare_distribution()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 314, in _prepare_distribution
    return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 527, in prepare_linked_requirement
    return self._prepare_linked_requirement(req, parallel_builds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 642, in _prepare_linked_requirement
    dist = _get_prepared_distribution(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 72, in _get_prepared_distribution
    abstract_dist.prepare_distribution_metadata(
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 56, in prepare_distribution_metadata
    self._install_build_reqs(finder)
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 126, in _install_build_reqs
    build_reqs = self._get_build_requires_wheel()
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 103, in _get_build_requires_wheel
    return backend.get_requires_for_build_wheel()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 706, in get_requires_for_build_wheel
    return super().get_requires_for_build_wheel(config_settings=cs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 166, in get_requires_for_build_wheel
    return self._call_hook('get_requires_for_build_wheel', {
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 321, in _call_hook
    raise BackendUnavailable(data.get('traceback', ''))
pip._vendor.pyproject_hooks._impl.BackendUnavailable: Traceback (most recent call last):
  File "/usr/local/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 77, in _build_backend
    obj = import_module(mod_path)
          ^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/importlib/__init__.py", line 90, 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 995, in exec_module
  File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
  File "/tmp/pip-build-env-frs36kmk/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 10, in <module>
    import distutils.core
ModuleNotFoundError: No module named 'distutils'

python3.11

docker run --rm -it --entrypoint pip python:3.11 install scikit-learn==1.2.1 scipy==1.11.2 simpy==4.0.1 pm4py==2.7.5.2 statsmodels==0.14.0 pandas==1.5.3

Collecting scikit-learn==1.2.1
  Downloading scikit_learn-1.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting scipy==1.11.2
  Downloading scipy-1.11.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (59 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 59.1/59.1 kB 1.2 MB/s eta 0:00:00
Collecting simpy==4.0.1
  Downloading simpy-4.0.1-py2.py3-none-any.whl.metadata (12 kB)
Collecting pm4py==2.7.5.2
  Downloading pm4py-2.7.5.2-py3-none-any.whl.metadata (3.4 kB)
Collecting statsmodels==0.14.0
  Downloading statsmodels-0.14.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.0 kB)
Collecting pandas==1.5.3
  Downloading pandas-1.5.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting numpy>=1.17.3 (from scikit-learn==1.2.1)
  Downloading numpy-2.1.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
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Collecting joblib>=1.1.1 (from scikit-learn==1.2.1)
  Downloading joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Collecting threadpoolctl>=2.0.0 (from scikit-learn==1.2.1)
  Downloading threadpoolctl-3.5.0-py3-none-any.whl.metadata (13 kB)
Collecting numpy>=1.17.3 (from scikit-learn==1.2.1)
  Downloading numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
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Collecting deprecation (from pm4py==2.7.5.2)
  Downloading deprecation-2.1.0-py2.py3-none-any.whl.metadata (4.6 kB)
Collecting graphviz (from pm4py==2.7.5.2)
  Downloading graphviz-0.20.3-py3-none-any.whl.metadata (12 kB)
Collecting intervaltree (from pm4py==2.7.5.2)
  Downloading intervaltree-3.1.0.tar.gz (32 kB)
  Preparing metadata (setup.py) ... done
Collecting lxml (from pm4py==2.7.5.2)
  Downloading lxml-5.3.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.8 kB)
Collecting matplotlib (from pm4py==2.7.5.2)
  Downloading matplotlib-3.9.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting networkx (from pm4py==2.7.5.2)
  Downloading networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting pydotplus (from pm4py==2.7.5.2)
  Downloading pydotplus-2.0.2.tar.gz (278 kB)
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  Preparing metadata (setup.py) ... done
Collecting pytz (from pm4py==2.7.5.2)
  Downloading pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting stringdist (from pm4py==2.7.5.2)
  Downloading StringDist-1.0.9.tar.gz (7.4 kB)
  Preparing metadata (setup.py) ... done
Collecting tqdm (from pm4py==2.7.5.2)
  Downloading tqdm-4.67.0-py3-none-any.whl.metadata (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 15.2 MB/s eta 0:00:00
Collecting cvxopt (from pm4py==2.7.5.2)
  Downloading cvxopt-1.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.3 kB)
Collecting patsy>=0.5.2 (from statsmodels==0.14.0)
  Downloading patsy-1.0.1-py2.py3-none-any.whl.metadata (3.3 kB)
Collecting packaging>=21.3 (from statsmodels==0.14.0)
  Downloading packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting python-dateutil>=2.8.1 (from pandas==1.5.3)
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.1->pandas==1.5.3)
  Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting sortedcontainers<3.0,>=2.0 (from intervaltree->pm4py==2.7.5.2)
  Downloading sortedcontainers-2.4.0-py2.py3-none-any.whl.metadata (10 kB)
Collecting contourpy>=1.0.1 (from matplotlib->pm4py==2.7.5.2)
  Downloading contourpy-1.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.4 kB)
Collecting cycler>=0.10 (from matplotlib->pm4py==2.7.5.2)
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->pm4py==2.7.5.2)
  Downloading fonttools-4.54.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (163 kB)
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Collecting kiwisolver>=1.3.1 (from matplotlib->pm4py==2.7.5.2)
  Downloading kiwisolver-1.4.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.3 kB)
Collecting pillow>=8 (from matplotlib->pm4py==2.7.5.2)
  Downloading pillow-11.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
Collecting pyparsing>=2.3.1 (from matplotlib->pm4py==2.7.5.2)
  Downloading pyparsing-3.2.0-py3-none-any.whl.metadata (5.0 kB)
Downloading scikit_learn-1.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.6 MB)
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Downloading scipy-1.11.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (36.3 MB)
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Downloading simpy-4.0.1-py2.py3-none-any.whl (29 kB)
Downloading pm4py-2.7.5.2-py3-none-any.whl (1.8 MB)
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Downloading statsmodels-0.14.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (10.1 MB)
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Downloading pandas-1.5.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.0 MB)
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Downloading joblib-1.4.2-py3-none-any.whl (301 kB)
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Downloading packaging-24.2-py3-none-any.whl (65 kB)
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Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
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Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB)
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Downloading matplotlib-3.9.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.3 MB)
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Downloading networkx-3.4.2-py3-none-any.whl (1.7 MB)
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Building wheels for collected packages: intervaltree, pydotplus, stringdist
  Building wheel for intervaltree (setup.py) ... done
  Created wheel for intervaltree: filename=intervaltree-3.1.0-py2.py3-none-any.whl size=26095 sha256=b4682da3f202d0dec9072f27eca6ad9bde1b25ae61026ad533a736478b147d55
  Stored in directory: /root/.cache/pip/wheels/31/d7/d9/eec6891f78cac19a693bd40ecb8365d2f4613318c145ec9816
  Building wheel for pydotplus (setup.py) ... done
  Created wheel for pydotplus: filename=pydotplus-2.0.2-py3-none-any.whl size=24551 sha256=bcc7e847c15e09cefcb951e63c54fb9ca04128a413842768a3d1f97c5069ca77
  Stored in directory: /root/.cache/pip/wheels/bd/ce/e8/ff9d9c699514922f57caa22fbd55b0a32761114b4c4acc9e03
  Building wheel for stringdist (setup.py) ... done
  Created wheel for stringdist: filename=StringDist-1.0.9-cp311-cp311-linux_x86_64.whl size=17109 sha256=faae4983a3dd7943608445b222a301ecefa87d9fd15b4d85f427e8e613fb0ac6
  Stored in directory: /root/.cache/pip/wheels/fd/d0/9b/188e72fe6cc1ad1ae96a71835adb85cd58b0622a3440b4acdf
Successfully built intervaltree pydotplus stringdist
Installing collected packages: stringdist, sortedcontainers, pytz, tqdm, threadpoolctl, six, simpy, pyparsing, pillow, packaging, numpy, networkx, lxml, kiwisolver, joblib, intervaltree, graphviz, fonttools, cycler, cvxopt, scipy, python-dateutil, pydotplus, patsy, deprecation, contourpy, scikit-learn, pandas, matplotlib, statsmodels, pm4py
Successfully installed contourpy-1.3.1 cvxopt-1.3.2 cycler-0.12.1 deprecation-2.1.0 fonttools-4.54.1 graphviz-0.20.3 intervaltree-3.1.0 joblib-1.4.2 kiwisolver-1.4.7 lxml-5.3.0 matplotlib-3.9.2 networkx-3.4.2 numpy-1.26.4 packaging-24.2 pandas-1.5.3 patsy-1.0.1 pillow-11.0.0 pm4py-2.7.5.2 pydotplus-2.0.2 pyparsing-3.2.0 python-dateutil-2.9.0.post0 pytz-2024.2 scikit-learn-1.2.1 scipy-1.11.2 simpy-4.0.1 six-1.16.0 sortedcontainers-2.4.0 statsmodels-0.14.0 stringdist-1.0.9 threadpoolctl-3.5.0 tqdm-4.67.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

[notice] A new release of pip is available: 24.0 -> 24.3.1
[notice] To update, run: pip install --upgrade pip
francescameneghello commented 1 week ago

Thank you for your comment. In the meantime, I have added the requirement to use Python version 3.10 to the README and documentation. In the future, I will ensure all packages and Python versions are updated and checked.