installing with pip in python/3.11 fails with this error.

[schloegl]

I'm trying to install tierspy-tracker on Debian12 with pip/venv. In order to do so, I updated the requirements file in this way

diff --git a/requirements.txt b/requirements.txt
index 922ee57..a94ff3c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,12 +1,12 @@
 cython
-keras=2.1.5
-opencv
+keras #==2.1.5
+opencv-python
 tensorflow
-numpy >=1.14
+numpy>=1.14
 matplotlib
-pytables
-pandas<1.0
-pyqt
+tables
+pandas #<1.0
+pyqt5
 scipy
 scikit-learn
 scikit-image

It fails with the following error

$ pip install -e .
Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com
Obtaining file:///nfs/scistore16/itgrp/schloegl/src/tierpsy-tracker
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [34 lines of output]
      /mnt/nfs/clustersw/Debian/bookworm/tierpsy-tracker/20250107/lib/python3.11/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /nfs/scistore16/itgrp/schloegl/src/tierpsy-tracker/tierpsy/analysis/ske_create/segWormPython/cython_files/cleanWorm_cython.pyx
        tree = Parsing.p_module(s, pxd, full_module_name)
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              int k;
              bint isExtrema;
              int numberOfPoints = x.size;
              int lastIndexChain = numberOfPoints - 1;
              np.ndarray[np.float_t, ndim=1]  peaks = np.zeros(numberOfPoints, dtype = np.float);
              np.ndarray[np.int_t, ndim=1] indices = np.zeros(numberOfPoints, dtype = np.int)
                            ^
      ------------------------------------------------------------
      
      tierpsy/analysis/ske_create/segWormPython/cython_files/cleanWorm_cython.pyx:68:22: Invalid type.
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/nfs/scistore16/itgrp/schloegl/src/tierpsy-tracker/setup.py", line 64, in <module>
          ext_modules = _get_ext_modules(),
                        ^^^^^^^^^^^^^^^^^^
        File "/nfs/scistore16/itgrp/schloegl/src/tierpsy-tracker/setup.py", line 38, in _get_ext_modules
          ext_modules = cythonize(os.path.join(cython_path, "*_cython.pyx"))
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/mnt/nfs/clustersw/Debian/bookworm/tierpsy-tracker/20250107/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
          cythonize_one(*args)
        File "/mnt/nfs/clustersw/Debian/bookworm/tierpsy-tracker/20250107/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: tierpsy/analysis/ske_create/segWormPython/cython_files/cleanWorm_cython.pyx
      Compiling tierpsy/analysis/ske_create/segWormPython/cython_files/cleanWorm_cython.pyx because it changed.
      Compiling tierpsy/analysis/ske_create/segWormPython/cython_files/linearSkeleton_cython.pyx because it changed.
      Compiling tierpsy/analysis/ske_create/segWormPython/cython_files/segWorm_cython.pyx because it changed.
      [1/3] Cythonizing tierpsy/analysis/ske_create/segWormPython/cython_files/cleanWorm_cython.pyx
      [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.

Do know how this could be fixed ?

[JavierRBe]

Hey there! Thanks for bringing this up. There is known compatibility issues with the newer versions of Cython. I would advice you to try downgrading Cython to cython==0.29.21 in the requirements file and try the installation again. Hope this sorts the issue. Have a nice day!.

[schloegl]

Unfortunately, that is not sufficient. After installing, Cython 0.29.21, running "pip install -e ." fails with the attached log file.

tierpsy-installer.log

When I impose also "numpy<2.0", it fails with

    tierpsy/analysis/ske_create/segWormPython/cython_files/cleanWorm_cython.c:209:12: fatal error: longintrepr.h: No such file or directory
      209 |   #include "longintrepr.h"
          |            ^~~~~~~~~~~~~~~
    compilation terminated.
    error: command '/usr/bin/gcc' failed with exit code 1
    [end of output]

So it seems there are more dependencies to consider.

[aexbrown]

This is from a user installing Tierpsy on Ubuntu 22.04 that may be helpful:

########################################

$ curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" bash

$ Miniforge3-$(uname)-$(uname -m).sh$ bash Miniforge3-$(uname)-$(uname -m).sh

$ source /home/lab/miniforge3/bin/activate

$ mamba create --name "tierpsy36" python=3.6

$ git clone https://github.com/Tierpsy/tierpsy-tracker

$ conda activate tierpsy36

comment out keras and tensorflow from requirements.txt and install them with pip, conda and mamba think this version combination is not possible

$ nano requirements.txt

$ mamba install --file requirements.txt

$ pip install tensorflow==1.14.0 keras==2.1.5

$ pip install torch==1.5.0+cu101 torchvision==0.6.0+cu101 -f https://download.pytorch.org/whl/torch_stable.html

$ pip install imgstore

$ pip install -e .

$ tierpsy_gui

[schloegl]

Python 3.6 - really ? its EOL since 2021 - https://devguide.python.org/versions/