Bad Install due opencv-python

Hi There,

I followed the install instructions and I encountered the following error on Ubuntu 22.04.1 LTS:

After this:

cd chromeister && make all -C src/ && python3 -m venv chromeisterenv && source chromeisterenv/bin/activate && pip install -r src/requirements.txt

I have the following error:

  /tmp/pip-build-env-uj14l2ll/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:242:9: error: 'PyTuple_GET_SIZE' was not declared in this scope
       if (PyTuple_GET_SIZE(value) != 3) {
           ^~~~~~~~~~~~~~~~
  /tmp/pip-build-env-uj14l2ll/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:242:9: note: suggested alternative: 'PyTuple_GetSlice'
       if (PyTuple_GET_SIZE(value) != 3) {
           ^~~~~~~~~~~~~~~~
           PyTuple_GetSlice
  /tmp/pip-build-env-uj14l2ll/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:245:13: error: 'PyTuple_GET_ITEM' was not declared in this scope
       title = PyTuple_GET_ITEM(value, 2);
               ^~~~~~~~~~~~~~~~
  /tmp/pip-build-env-uj14l2ll/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:245:13: note: suggested alternative: 'PyArray_GETITEM'
       title = PyTuple_GET_ITEM(value, 2);
               ^~~~~~~~~~~~~~~~
               PyArray_GETITEM
  gmake[2]: *** [modules/python3/CMakeFiles/opencv_python3.dir/build.make:76: modules/python3/CMakeFiles/opencv_python3.dir/__/src2/cv2.cpp.o] Error 1
  gmake[1]: *** [CMakeFiles/Makefile2:2077: modules/python3/CMakeFiles/opencv_python3.dir/all] Error 2
  gmake: *** [Makefile:166: all] Error 2
  Traceback (most recent call last):
    File "/tmp/pip-build-env-uj14l2ll/overlay/lib/python3.7/site-packages/skbuild/setuptools_wrap.py", line 640, in setup
      cmkr.make(make_args, install_target=cmake_install_target, env=env)
    File "/tmp/pip-build-env-uj14l2ll/overlay/lib/python3.7/site-packages/skbuild/cmaker.py", line 672, in make
      self.make_impl(clargs=clargs, config=config, source_dir=source_dir, install_target=install_target, env=env)
    File "/tmp/pip-build-env-uj14l2ll/overlay/lib/python3.7/site-packages/skbuild/cmaker.py", line 704, in make_impl
      "An error occurred while building with CMake.\n"

  An error occurred while building with CMake.
    Command:
      cmake --build . --target install --config Release --
    Install target:
      install
    Source directory:
      /tmp/pip-install-pjy3pvde/opencv-python
    Working directory:
      /tmp/pip-install-pjy3pvde/opencv-python/_skbuild/linux-x86_64-3.7/cmake-build
  Please check the install target is valid and see CMake's output for more information.
  ----------------------------------------
  ERROR: Failed building wheel for opencv-python
  Running setup.py clean for opencv-python
Failed to build opencv-python
ERROR: Could not build wheels for opencv-python which use PEP 517 and cannot be installed directly

I checked the requirements for the program and I workaround the following conda recipe for Ubuntu 22.04:

cd --
git clone https://github.com/estebanpw/chromeister.git
cd chromeister
make all -C src/

conda create --name chromeister python=3.6.13         # create environment
conda activate chromeister                            # load environment

# Install packages
conda install -c bioconda -y scikit-build
conda install -c anaconda -y cycler
conda install -c anaconda -y kiwisolver
conda install -c bioconda -y numpy
pip install opencv-python
conda install -c bioconda -y Pillow
conda install -c bioconda -y pyparsing
conda install -c bioconda -y python-dateutil
conda install -c bioconda -y six

In this manner, as an example, I can call chromeister as follows:

conda activate chromeister
/home/carlos/chromeister/bin/CHROMEISTER -query GRCm39.genome.fa -db Mus_musculus.GRCm39.dna.toplevel.fa -out dotplot.mat && Rscript /home/carlos/chromeister/bin/compute_score.R dotplot.mat 1000

and the program is working as follows:

[INFO] Generating a 1000x1000 matrix
[INFO] Loading database
99%...[INFO] Database loaded and of length 2728222451.
[INFO] Ratios: Q [2.728222e+06] D [2.728222e+06]. Lenghts: Q [2728222451] D [2728222451]
[INFO] Pixel size: Q [3.665390e-07] D [3.665390e-07].
[INFO] Computing absolute hit numbers.
19%...
79%...
99%...Scanning hits table.
99%...
[INFO] Query length 2728222451.
[INFO] Writing matrix.
[INFO] Found 2234272 unique hits for z = 4.
0

My question is, can I just use the program in this way, or I do need to work on the python-opencv error?

Cheers,

Carlos

estebanpw / chromeister

Bad Install due opencv-python #30