Unable to compile/install

[raacampbell]

Moving this problem from https://github.com/openjournals/joss-reviews/issues/7125 to an Issue.

The install.bat install method failed with miniconda for me. I made an environment and tried to install in that. After double-clicking on the icon I get an error window stating that the Cython modules can not be found. If I try to compile this happens:

(venv) (brighteyes) C:\Users\shopp\Downloads\BrightEyes-MCS-main\BrightEyes-MCS-main>python setup.py build_ext -inplace
No parent package detected, impossible to derive `name`
running build_ext
error: --plat-name must be one of ('win32', 'win-amd64', 'win-arm32', 'win-arm64')

The response from @mattia-donato was:

I suppose you are not using Visual Studio compiler but msys2. In this case, python setup.py build_ext -inplace is not enough. You need to run from a terminal (with venv or conda activated) the compile_cython_msys2.bat which set some env variables and parameter to the compilation.

compile_cython_msys2.bat:

@REM VERSION WITH MSYS2
@ECHO This is the script to compile the Cython part of the code
@ECHO "msys2" must be installed on your system in the default folder (C:\msys64)
@ECHO you can download it from https://www.msys2.org/
@ECHO and inside msys2 environment gcc must be installed
@ECHO (you can install it inside msys2 environment with the
@ECHO command 'pacman -S mingw-w64-ucrt-x86_64-gcc' inside msys2 env)

SET PATH=%PATH%;C:\msys64\usr\bin;C:\msys64\ucrt64\bin
python setup.py build_ext --inplace --force --compiler=mingw32 -DMS_WIN64

I installed MSYS2 then in the window that came up ran pacman -S mingw-w64-ucrt-x86_64-gcc as instructed. After this, the compile script (compile_cython_msys2.bat) seems to do something but ends with many errors.

brighteyes_mcs/libs/cython/fastconverter.c: In function '__Pyx_ImportType_3_0_11':
brighteyes_mcs/libs/cython/fastconverter.c:30252:13: warning: unknown conversion type character 'z' in format [-Wformat=]
30252 |             "%s.%s size changed, may indicate binary incompatibility. "
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
brighteyes_mcs/libs/cython/fastconverter.c:30253:24: note: format string is defined here
30253 |             "Expected %zd from C header, got %zd from PyObject",
      |                        ^
brighteyes_mcs/libs/cython/fastconverter.c:30252:13: warning: unknown conversion type character 'z' in format [-Wformat=]
30252 |             "%s.%s size changed, may indicate binary incompatibility. "
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
brighteyes_mcs/libs/cython/fastconverter.c:30253:47: note: format string is defined here
30253 |             "Expected %zd from C header, got %zd from PyObject",
      |                                               ^
brighteyes_mcs/libs/cython/fastconverter.c:30252:13: warning: too many arguments for format [-Wformat-extra-args]
30252 |             "%s.%s size changed, may indicate binary incompatibility. "
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
error: command 'C:\\msys64\\ucrt64\\bin\\gcc.exe' failed with exit code 1

(venv) (brighteyes) C:\Users\shopp\Downloads\BrightEyes-MCS-main\BrightEyes-MCS-main>

I suggest much more detailed and hand-holding install instructions, as the steps are not trivial.

[mattia-donato]

@raacampbell Thanks for your feedback!

I read that you use conda. Did you test the installation inside a conda env or in directly the system? t should be the same, but I worried that some packages are different. Actually the installation I used was using a "pure" Python and creating a venv from scratch without conda.

Could you please attach here the "pip freeze" (or the equivalent for conda) in the current env? Which version of Python are you using?

[raacampbell]

I did it in Conda with Python version 10

alabaster==1.0.0
annotated-types==0.7.0
anyio==4.4.0
app-model==0.2.8
appdirs==1.4.4
asttokens==2.4.1
atomics==1.0.2
attrs==24.2.0
babel==2.16.0
build==1.2.2
cachey==0.2.1
certifi==2024.8.30
cffi==1.17.1
charset-normalizer==3.3.2
click==8.1.7
cloudpickle==3.0.0
colorama==0.4.6
comm==0.2.2
contourpy==1.3.0
cycler==0.12.1
Cython==0.29.37
darkdetect==0.7.1
dask==2024.9.0
debugpy==1.8.5
decorator==5.1.1
docstring_parser==0.16
docutils==0.21.2
exceptiongroup==1.2.2
executing==2.1.0
fastapi==0.114.2
flexcache==0.3
flexparser==0.3.1
fonttools==4.53.1
freetype-py==2.5.1
fsspec==2024.9.0
future==1.0.0
h5py==3.11.0
HeapDict==1.0.1
hsluv==5.0.4
idna==3.10
imageio==2.35.1
imagesize==1.4.1
importlib_metadata==8.5.0
in-n-out==0.2.1
ipykernel==6.29.5
ipython==8.27.0
jedi==0.19.1
Jinja2==3.1.4
jsonschema==4.23.0
jsonschema-specifications==2023.12.1
jupyter_client==8.6.2
jupyter_core==5.7.2
kiwisolver==1.4.7
lazy_loader==0.4
locket==1.0.0
magicgui==0.9.1
markdown-it-py==3.0.0
MarkupSafe==2.1.5
matplotlib==3.9.2
matplotlib-inline==0.1.7
mdurl==0.1.2
napari==0.5.3
napari-console==0.0.9
napari-plugin-engine==0.2.0
napari-svg==0.2.0
nest-asyncio==1.6.0
networkx==3.3
nifpga==20.0.0
nifpga-fast-fifo-recv==0.101.3
npe2==0.7.7
numpy==1.26.4
numpydoc==1.8.0
packaging==24.1
pandas==2.2.2
parso==0.8.4
partd==1.4.2
pillow==10.4.0
Pint==0.24.3
platformdirs==4.3.3
pooch==1.8.2
prompt_toolkit==3.0.47
psutil==6.0.0
psygnal==0.11.1
pure_eval==0.2.3
pyconify==0.1.6
pycparser==2.22
pydantic==2.9.1
pydantic-compat==0.1.2
pydantic_core==2.23.3
Pygments==2.18.0
PyOpenGL==3.1.7
pyparsing==3.1.4
pyproject_hooks==1.1.0
pyqtdarktheme==2.1.0
pyqtgraph==0.12.4
PySide2==5.15.2.1
python-dateutil==2.9.0.post0
pytz==2024.2
pywin32==306
PyYAML==6.0.2
pyzmq==26.2.0
qtconsole==5.6.0
QtPy==2.4.1
referencing==0.35.1
requests==2.32.3
rich==13.8.1
rpds-py==0.20.0
scikit-image==0.24.0
scipy==1.14.1
shellingham==1.5.4
shiboken2==5.15.2.1
six==1.16.0
sniffio==1.3.1
snowballstemmer==2.2.0
Sphinx==8.0.2
sphinxcontrib-applehelp==2.0.0
sphinxcontrib-devhelp==2.0.0
sphinxcontrib-htmlhelp==2.1.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==2.0.0
sphinxcontrib-serializinghtml==2.0.0
stack-data==0.6.3
starlette==0.38.5
superqt==0.6.7
tabulate==0.9.0
tifffile==2024.8.30
tomli==2.0.1
tomli_w==1.0.0
toolz==0.12.1
tornado==6.4.1
tqdm==4.66.5
traitlets==5.14.3
typer==0.12.5
typing_extensions==4.12.2
tzdata==2024.1
urllib3==2.2.3
vispy==0.14.3
wcwidth==0.2.13
wrapt==1.16.0
zipp==3.20.2

[mattia-donato]

Actually they looks like warnings and not errors, maybe the libraries actually are compiled.

Could please you try from that folder and in the venv the following command? python -c "import brighteyes_mcs.libs.cython.fastconverter as fc; print(fc.convertRawDataToCountsDirect.__name__)"

[raacampbell]

I will check on Monday, away now.

[raacampbell]

Sorry, I think I can't contribute more to finding a solution to this.

[mattia-donato]

Thank you for your feedback. I completly changed the installer script and finally now works also with conda. And I updated the README about the installation and the requirements.