cannot install from main branch with python > 3.10

[kushalkolar]

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)