Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

cannot install from main branch with python > 3.10 #305

Open
kushalkolar opened this issue Feb 7, 2025 · 4 comments
Open

cannot install from main branch with python > 3.10 #305

kushalkolar opened this issue Feb 7, 2025 · 4 comments

Comments

@kushalkolar
Copy link

Just posting here in case it helps someone else, took me a while to figure out. I tried installing using the current main branch on python3.11 on Fedora 41 and was getting cmake errors, probably related to building the cythonized code?

Using python3.10 instead worked.

Note that I was able to install the current pypi release on python3.11 but all the deeptime.data datasets only produced a single state, as seen in #303.

You may want to consider adding an upper version pin in the meantime.

pip error log when installing from python3.11:

(deeptime) kushal@fedora:~/repos/deeptime (main)
└─ $ ▶ pip install .
Processing /home/kushal/repos/deeptime
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numpy (from deeptime==0.4.4+11.g5f85b3e)
  Using cached numpy-2.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Collecting scipy>=1.9.0 (from deeptime==0.4.4+11.g5f85b3e)
  Using cached scipy-1.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting scikit-learn>=1.5.0 (from deeptime==0.4.4+11.g5f85b3e)
  Using cached scikit_learn-1.6.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Collecting threadpoolctl>=3.1.0 (from deeptime==0.4.4+11.g5f85b3e)
  Using cached threadpoolctl-3.5.0-py3-none-any.whl.metadata (13 kB)
Collecting joblib>=1.2.0 (from scikit-learn>=1.5.0->deeptime==0.4.4+11.g5f85b3e)
  Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Using cached scikit_learn-1.6.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.5 MB)
Using cached numpy-2.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.4 MB)
Using cached scipy-1.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (40.6 MB)
Using cached threadpoolctl-3.5.0-py3-none-any.whl (18 kB)
Using cached joblib-1.4.2-py3-none-any.whl (301 kB)
Building wheels for collected packages: deeptime
  Building wheel for deeptime (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for deeptime (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [103 lines of output]
      
      
      --------------------------------------------------------------------------------
      -- Trying 'Ninja' generator
      --------------------------------
      ---------------------------
      ----------------------
      -----------------
      ------------
      -------
      --
      CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
        Compatibility with CMake < 3.10 will be removed from a future version of
        CMake.
      
        Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
        to tell CMake that the project requires at least <min> but has been updated
        to work with policies introduced by <max> or earlier.
      
      Not searching for unused variables given on the command line.
      
      -- The C compiler identification is GNU 14.2.1
      -- Detecting C compiler ABI info
      -- Detecting C compiler ABI info - done
      -- Check for working C compiler: /usr/lib64/ccache/cc - skipped
      -- Detecting C compile features
      -- Detecting C compile features - done
      -- The CXX compiler identification is GNU 14.2.1
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Check for working CXX compiler: /usr/lib64/ccache/c++ - skipped
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      -- Configuring done (0.3s)
      -- Generating done (0.0s)
      -- Build files have been written to: /home/kushal/repos/deeptime/_cmake_test_compile/build
      --
      -------
      ------------
      -----------------
      ----------------------
      ---------------------------
      --------------------------------
      -- Trying 'Ninja' generator - success
      --------------------------------------------------------------------------------
      
      Configuring Project
        Working directory:
          /home/kushal/repos/deeptime/_skbuild/linux-x86_64-3.11/cmake-build
        Command:
          /tmp/pip-build-env-kj663eby/overlay/lib64/python3.11/site-packages/cmake/data/bin/cmake /home/kushal/repos/deeptime -G Ninja -DCMAKE_MAKE_PROGRAM:FILEPATH=ninja --no-warn-unused-cli -DCMAKE_INSTALL_PREFIX:PATH=/home/kushal/repos/deeptime/_skbuild/linux-x86_64-3.11/cmake-install/deeptime -DPYTHON_VERSION_STRING:STRING=3.11.11 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-kj663eby/overlay/lib/python3.11/site-packages/skbuild/resources/cmake -DPYTHON_EXECUTABLE:PATH=/home/kushal/venvs/deeptime/bin/python3.11 -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.11 -DPYTHON_LIBRARY:PATH=/usr/lib64/libpython3.11.so -DPython_EXECUTABLE:PATH=/home/kushal/venvs/deeptime/bin/python3.11 -DPython_ROOT_DIR:PATH=/home/kushal/venvs/deeptime -DPython_FIND_REGISTRY:STRING=NEVER -DPython_INCLUDE_DIR:PATH=/usr/include/python3.11 -DPython_NumPy_INCLUDE_DIRS:PATH=/tmp/pip-build-env-kj663eby/overlay/lib64/python3.11/site-packages/numpy/_core/include -DPython3_EXECUTABLE:PATH=/home/kushal/venvs/deeptime/bin/python3.11 -DPython3_ROOT_DIR:PATH=/home/kushal/venvs/deeptime -DPython3_FIND_REGISTRY:STRING=NEVER -DPython3_INCLUDE_DIR:PATH=/usr/include/python3.11 -DPython3_NumPy_INCLUDE_DIRS:PATH=/tmp/pip-build-env-kj663eby/overlay/lib64/python3.11/site-packages/numpy/_core/include -DCMAKE_MAKE_PROGRAM:FILEPATH=ninja -DDEEPTIME_VERSION=0.4.4 -DDEEPTIME_VERSION_INFO=0.4.4+11.g5f85b3e -DCMAKE_BUILD_TYPE:STRING=Release
      
      Not searching for unused variables given on the command line.
      -- Got deeptime version 0.4.4
      -- Got deeptime full version 0.4.4+11.g5f85b3e
      -- Building tests: OFF
      '/home/kushal/venvs/deeptime/bin/python3.11' '-c' 'import pybind11; print(pybind11.get_cmake_dir())'
      -- Found Python: /usr/include/python3.11 (found version "3.11.11") found components: Development NumPy Interpreter Development.Module Development.Embed
      -- Found pybind11: /tmp/pip-build-env-kj663eby/overlay/lib/python3.11/site-packages/pybind11/include (found version "2.13.6")
      CMake Error at /tmp/pip-build-env-kj663eby/overlay/lib/python3.11/site-packages/skbuild/resources/cmake/FindCython.cmake:71 (message):
        Command "/tmp/pip-build-env-1__0fcw1/overlay/bin/cython;--version" failed
        with output:
      
      Call Stack (most recent call first):
        deeptime/numeric/CMakeLists.txt:6 (find_package)
      
      
      CMake Warning (dev) at /tmp/pip-build-env-kj663eby/overlay/lib/python3.11/site-packages/skbuild/resources/cmake/FindPythonExtensions.cmake:245 (find_package):
        Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
        are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
        the cmake_policy command to set the policy and suppress this warning.
      
      Call Stack (most recent call first):
        deeptime/numeric/CMakeLists.txt:8 (find_package)
      This warning is for project developers.  Use -Wno-dev to suppress it.
      
      CMake Warning (dev) at /tmp/pip-build-env-kj663eby/overlay/lib/python3.11/site-packages/skbuild/resources/cmake/FindPythonExtensions.cmake:252 (find_package):
        Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
        are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
        the cmake_policy command to set the policy and suppress this warning.
      
      Call Stack (most recent call first):
        deeptime/numeric/CMakeLists.txt:8 (find_package)
      This warning is for project developers.  Use -Wno-dev to suppress it.
      
      _modinit_prefix:PyInit_
      -- Configuring incomplete, errors occurred!
      Traceback (most recent call last):
        File "/tmp/pip-build-env-kj663eby/overlay/lib/python3.11/site-packages/skbuild/setuptools_wrap.py", line 660, in setup
          env = cmkr.configure(
                ^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-kj663eby/overlay/lib/python3.11/site-packages/skbuild/cmaker.py", line 354, in configure
          raise SKBuildError(msg)
      
      An error occurred while configuring with CMake.
        Command:
          /tmp/pip-build-env-kj663eby/overlay/lib64/python3.11/site-packages/cmake/data/bin/cmake /home/kushal/repos/deeptime -G Ninja -DCMAKE_MAKE_PROGRAM:FILEPATH=ninja --no-warn-unused-cli -DCMAKE_INSTALL_PREFIX:PATH=/home/kushal/repos/deeptime/_skbuild/linux-x86_64-3.11/cmake-install/deeptime -DPYTHON_VERSION_STRING:STRING=3.11.11 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-kj663eby/overlay/lib/python3.11/site-packages/skbuild/resources/cmake -DPYTHON_EXECUTABLE:PATH=/home/kushal/venvs/deeptime/bin/python3.11 -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.11 -DPYTHON_LIBRARY:PATH=/usr/lib64/libpython3.11.so -DPython_EXECUTABLE:PATH=/home/kushal/venvs/deeptime/bin/python3.11 -DPython_ROOT_DIR:PATH=/home/kushal/venvs/deeptime -DPython_FIND_REGISTRY:STRING=NEVER -DPython_INCLUDE_DIR:PATH=/usr/include/python3.11 -DPython_NumPy_INCLUDE_DIRS:PATH=/tmp/pip-build-env-kj663eby/overlay/lib64/python3.11/site-packages/numpy/_core/include -DPython3_EXECUTABLE:PATH=/home/kushal/venvs/deeptime/bin/python3.11 -DPython3_ROOT_DIR:PATH=/home/kushal/venvs/deeptime -DPython3_FIND_REGISTRY:STRING=NEVER -DPython3_INCLUDE_DIR:PATH=/usr/include/python3.11 -DPython3_NumPy_INCLUDE_DIRS:PATH=/tmp/pip-build-env-kj663eby/overlay/lib64/python3.11/site-packages/numpy/_core/include -DCMAKE_MAKE_PROGRAM:FILEPATH=ninja -DDEEPTIME_VERSION=0.4.4 -DDEEPTIME_VERSION_INFO=0.4.4+11.g5f85b3e -DCMAKE_BUILD_TYPE:STRING=Release
        Source directory:
          /home/kushal/repos/deeptime
        Working directory:
          /home/kushal/repos/deeptime/_skbuild/linux-x86_64-3.11/cmake-build
      Please see CMake's output for more information.
      
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for deeptime
Failed to build deeptime
ERROR: Failed to build installable wheels for some pyproject.toml based projects (deeptime)
@kushalkolar
Copy link
Author

Got it installed, needed this: #251 (comment)

@clonker
Copy link
Member

clonker commented Feb 26, 2025

That's interesting, this should have no effect unless you were trying to make an editable install...

@kushalkolar
Copy link
Author

I'm not alone, from the person's above comment: #251 (comment):

Furthermore, installing on my other (Linux) machine fails both with and without the -e flag, with the same ModuleNotFoundError error. I am attaching both the output of pip install . -v and pip install -e . -v from this machine.

Thanks for your help! 😄

@Zheka17
Copy link

Zheka17 commented Feb 26, 2025 •
edited
Loading

Having the exact same issue (with skbuild not finding Cython), trying to install with
uv add "deeptime @ git+https://github.com/deeptime-ml/deeptime.git@main"

export SETUPTOOLS_ENABLE_FEATURES="legacy-editable" didn't help, neither did downgrading cmake to 3.25.

Python is 3.13; i haven't tried with 3.10 as the error seems unrelated.

UPD: installs under 3.12...how/why is this related?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@clonker @kushalkolar @Zheka17