deeptime cannot be installed on Mac computers with Apple Silicon and Python 3.12.0.

[GuangchenJ]

deeptime cannot be installed on Mac computers with Apple Silicon and Python 3.12.0.

[GuangchenJ]

and the gfortran shows that

$ gfortran -Wl,--version
collect2 version 13.2.0
/usr/bin/ld -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/ -dynamic -arch arm64 -platform_version macos 14.0.0 0.0 -o a.out -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13 -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13/../../.. --version -lemutls_w -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current
ld: unknown options: --version 
collect2: error: ld returned 1 exit status

[clonker]

Can you try building the package from source? Ie just call pip install . on a clone. FWIW deeptime is available on conda-forge and already updated to python 3.12, which puzzles me a bit (see conda-forge/deeptime-feedstock/pull/24). In any case, I will look into it shortly.

[GuangchenJ]

I can't build it from the source, it's fine for linux, but for my Mac, it goes wrong. I can't find the version for arm64 Python3.12 on conda-forge.
when I build it, my Mac shows that

$ pip install .

Processing /Users/guangchenj/PythonProjects/deeptime
  Installing build dependencies ... error
  error: subprocess-exited-with-error
  
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [71 lines of output]
      Ignoring tomli: markers 'python_version < "3.11"' don't match your environment
      Collecting setuptools>=42
        Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB)
      Collecting wheel
        Using cached wheel-0.41.2-py3-none-any.whl.metadata (2.2 kB)
      Collecting scikit-build>=0.16
        Using cached scikit_build-0.17.6-py3-none-any.whl.metadata (14 kB)
      Collecting cython>=0.29.30
        Using cached Cython-3.0.4-py2.py3-none-any.whl.metadata (3.2 kB)
      Collecting pybind11>=2.10.1
        Using cached pybind11-2.11.1-py3-none-any.whl.metadata (9.5 kB)
      Collecting numpy>=1.20
        Using cached numpy-1.26.1-cp312-cp312-macosx_11_0_arm64.whl.metadata (61 kB)
      Collecting cmake>=3.24
        Using cached cmake-3.27.7-py2.py3-none-macosx_10_10_universal2.macosx_10_10_x86_64.macosx_11_0_arm64.macosx_11_0_universal2.whl.metadata (6.7 kB)
      Collecting scipy==1.9.3
        Using cached scipy-1.9.3.tar.gz (42.1 MB)
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Installing backend dependencies: started
        Installing backend dependencies: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'error'
        error: subprocess-exited-with-error
      
        × Preparing metadata (pyproject.toml) did not run successfully.
        │ exit code: 1
        ╰─> [31 lines of output]
            + meson setup /private/var/folders/00/hgdnr2413c1fhm721v97yq4r0000gn/T/pip-install-ckph9gnu/scipy_b648fb437a9d4b1ea5d178c4aa280fef /private/var/folders/00/hgdnr2413c1fhm721v97yq4r0000gn/T/pip-install-ckph9gnu/scipy_b648fb437a9d4b1ea5d178c4aa280fef/.mesonpy-3b31abbp -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/private/var/folders/00/hgdnr2413c1fhm721v97yq4r0000gn/T/pip-install-ckph9gnu/scipy_b648fb437a9d4b1ea5d178c4aa280fef/.mesonpy-3b31abbp/meson-python-native-file.ini
            The Meson build system
            Version: 1.2.3
            Source dir: /private/var/folders/00/hgdnr2413c1fhm721v97yq4r0000gn/T/pip-install-ckph9gnu/scipy_b648fb437a9d4b1ea5d178c4aa280fef
            Build dir: /private/var/folders/00/hgdnr2413c1fhm721v97yq4r0000gn/T/pip-install-ckph9gnu/scipy_b648fb437a9d4b1ea5d178c4aa280fef/.mesonpy-3b31abbp
            Build type: native build
            Project name: SciPy
            Project version: 1.9.3
            C compiler for the host machine: cc (clang 15.0.0 "Apple clang version 15.0.0 (clang-1500.0.40.1)")
            C linker for the host machine: cc ld64 1015.7
            C++ compiler for the host machine: c++ (clang 15.0.0 "Apple clang version 15.0.0 (clang-1500.0.40.1)")
            C++ linker for the host machine: c++ ld64 1015.7
            Host machine cpu family: aarch64
            Host machine cpu: aarch64
            Compiler for C supports arguments -Wno-unused-but-set-variable: YES
            Compiler for C supports arguments -Wno-unused-but-set-variable: YES (cached)
            Compiler for C supports arguments -Wno-unused-function: YES
            Compiler for C supports arguments -Wno-conversion: YES
            Compiler for C supports arguments -Wno-misleading-indentation: YES
            Compiler for C supports arguments -Wno-incompatible-pointer-types: YES
            Library m found: YES
      
            ../meson.build:57:0: ERROR: Unable to detect linker for compiler `gfortran -Wl,--version`
            stdout:
            stderr: collect2 version 13.2.0
            /usr/bin/ld -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/ -dynamic -arch arm64 -platform_version macos 14.0.0 0.0 -o a.out -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13 -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13/../../.. --version -lemutls_w -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current
            ld: unknown options: --version
            collect2: error: ld returned 1 exit status
      
      
            A full log can be found at /private/var/folders/00/hgdnr2413c1fhm721v97yq4r0000gn/T/pip-install-ckph9gnu/scipy_b648fb437a9d4b1ea5d178c4aa280fef/.mesonpy-3b31abbp/meson-logs/meson-log.txt
            [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.
      ╰─> See above for output.
      
      note: This is an issue with the package mentioned above, not pip.
      hint: See above for details.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

And I try to check the gfortran:

$ gfortran --version

GNU Fortran (Homebrew GCC 13.2.0) 13.2.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

and I check gfortran -Wl,--version, it shows that

$ gfortran -Wl,--version

collect2 version 13.2.0
/usr/bin/ld -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/ -dynamic -arch arm64 -platform_version macos 14.0.0 0.0 -o a.out -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13 -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13/../../.. --version -lemutls_w -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current
ld: unknown options: --version 
collect2: error: ld returned 1 exit status

And I try to modify the file pyproject.toml, remove the requirement python_version < '3.11' and change "scipy==1.9.3" to "scipy>=1.9.3"

[build-system]
requires = [
    "setuptools>=42",
    "wheel",
    "scikit-build>=0.16",
    "cython>=0.29.30",
    "pybind11>=2.10.1",
    "numpy>=1.20",
    "cmake>=3.24",
    "tomli",
    "scipy>=1.9.3",
    "ninja; platform_system!='Windows'",
    "versioneer[toml]==0.28"
]

and build it by calling pip install ., it shows that:

$ pip install .

Processing /Users/guangchenj/PythonProjects/deeptime
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numpy>=1.20 (from deeptime==0.4.4+6.ga6ac0b9.dirty)
  Using cached numpy-1.26.1-cp312-cp312-macosx_11_0_arm64.whl.metadata (61 kB)
Collecting scipy>=1.9.0 (from deeptime==0.4.4+6.ga6ac0b9.dirty)
  Using cached scipy-1.11.3-cp312-cp312-macosx_12_0_arm64.whl.metadata (217 kB)
Collecting scikit-learn>=1.1 (from deeptime==0.4.4+6.ga6ac0b9.dirty)
  Downloading scikit_learn-1.3.2-cp312-cp312-macosx_12_0_arm64.whl.metadata (11 kB)
Collecting threadpoolctl>=3.1.0 (from deeptime==0.4.4+6.ga6ac0b9.dirty)
  Using cached threadpoolctl-3.2.0-py3-none-any.whl.metadata (10.0 kB)
Collecting joblib>=1.1.1 (from scikit-learn>=1.1->deeptime==0.4.4+6.ga6ac0b9.dirty)
  Using cached joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Using cached numpy-1.26.1-cp312-cp312-macosx_11_0_arm64.whl (13.7 MB)
Downloading scikit_learn-1.3.2-cp312-cp312-macosx_12_0_arm64.whl (9.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.3/9.3 MB 5.2 MB/s eta 0:00:00
Using cached scipy-1.11.3-cp312-cp312-macosx_12_0_arm64.whl (29.6 MB)
Using cached threadpoolctl-3.2.0-py3-none-any.whl (15 kB)
Using cached joblib-1.3.2-py3-none-any.whl (302 kB)
Building wheels for collected packages: deeptime
  Building wheel for deeptime (pyproject.toml) ... done
  Created wheel for deeptime: filename=deeptime-0.4.4+6.ga6ac0b9.dirty-cp312-cp312-macosx_14_0_arm64.whl size=1529419 sha256=e3811008f50f66927d6b03495aa1098e420e418469a4ffc10e389a61f9facedb
  Stored in directory: /private/var/folders/00/hgdnr2413c1fhm721v97yq4r0000gn/T/pip-ephem-wheel-cache-wbqjr82m/wheels/42/aa/ae/137d294a8f2ca28c2cd247961e34d387f9be2f55f5525f6170
Successfully built deeptime
Installing collected packages: threadpoolctl, numpy, joblib, scipy, scikit-learn, deeptime
Successfully installed deeptime-0.4.4+6.ga6ac0b9.dirty joblib-1.3.2 numpy-1.26.1 scikit-learn-1.3.2 scipy-1.11.3 threadpoolctl-3.2.0

It looks like fine......
Please update the requirement in pyproject.toml.

[clonker]

Since conda-forge/deeptime-feedstock#25 is merged I expect conda support for this architecture