Unsupported section type: 0 when reading in file

[IanQS]

Say I have an SWC file with the following two lines:

1 1 595156.06 205099.5 22046.521 3197 -1
2 0 454329.12 244148.88 118028.86 108 367

when I try to load it via:

import morphio
morph = morphio.Morphology("some_test.swc").as_mutable()

I receive

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
morphio._morphio.RawDataError:
some_test.swc:2:error
```

---

Looking at the specification docs

Description of how MorphIO sees morphologies. MorphIO supports .asc (Neurolucida), .h5 (H5 version 1) and .swc extensions

It seems like your library and the library that generated the SWC follow the neuronland convention, where "0 - undefined"?

[mgeplf]

Thanks for the clear report.

I agree that it's not accepting 0 as a type, however, I'm confused as to why that's the case - there's not a reason I can think of on the implementation side that would require this, but I will admit it's been a while since I've been in this codebase.

I have implemented the change to fix it here:
#15

I'm not sure when I will have a chance to release it, though, as I seem to remember our windows build is broken, and I haven't had the time to fix that.

[IanQS]

Ahh, sorry to bother you about this more. I tried installing the branch via: pip install "git+https://github.com/openbraininstitute/MorphIO@allow-swc-0-type"

but ran into a bunch of errors:

  error: subprocess-exited-with-error

  × Building wheel for morphio (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [85 lines of output]
      /tmp/pip-build-env-fx23fprr/normal/local/lib/python3.10/dist-packages/setuptools_scm/_integration/setuptools.py:24: RuntimeWarning:
      ERROR: setuptools==59.6.0 is used in combination with setuptools-scm>=8.x

      Your build configuration is incomplete and previously worked by accident!
      setuptools-scm requires setuptools>=61 (recommended: >=80)

      Suggested workaround if applicable:
       - migrating from the deprecated setup_requires mechanism to pep517/518
         and using a pyproject.toml to declare build dependencies
         which are reliably pre-installed before running the build tools

        warnings.warn(
      [08/28/25 09:59:11] WARNING  toml section missing Posix pyproject_reading.py:208
                                   Path('pyproject.toml')
                                   does not contain a
                                   tool.setuptools_scm
                                   section
                          WARNING  toml section missing Posix pyproject_reading.py:208
                                   Path('pyproject.toml')
                                   does not contain a
                                   tool.setuptools_scm
                                   section
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-3.10
      creating build/lib.linux-x86_64-3.10/morphio
      copying morphio/__init__.py -> build/lib.linux-x86_64-3.10/morphio
      creating build/lib.linux-x86_64-3.10/morphio/mut
      copying morphio/mut/__init__.py -> build/lib.linux-x86_64-3.10/morphio/mut
      creating build/lib.linux-x86_64-3.10/morphio/vasculature
      copying morphio/vasculature/__init__.py -> build/lib.linux-x86_64-3.10/morphio/vasculature
      running build_ext
      CMake Error: CMake was unable to find a build program corresponding to "Ninja".  CMAKE_MAKE_PROGRAM is not set.  You probably need to select a different build tool.
      CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
      CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
      -- Configuring incomplete, errors occurred!
      See also "/tmp/pip-req-build-710xzc7j/build/temp.linux-x86_64-3.10/CMakeFiles/CMakeOutput.log".
      Traceback (most recent call last):
        File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 261, in build_wheel
          return _build_backend().build_wheel(wheel_directory, config_settings,
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 230, in build_wheel
          return self._build_with_temp_dir(['bdist_wheel'], '.whl',
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 215, in _build_with_temp_dir
          self.run_setup()
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 267, in run_setup
          super(_BuildMetaLegacyBackend,
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 158, in run_setup
          exec(compile(code, __file__, 'exec'), locals())
        File "setup.py", line 72, in <module>
          setup(
        File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 153, in setup
          return distutils.core.setup(**attrs)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 148, in setup
          return run_commands(dist)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 163, in run_commands
          dist.run_commands()
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 967, in run_commands
          self.run_command(cmd)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command
          cmd_obj.run()
        File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 299, in run
          self.run_command('build')
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command
          cmd_obj.run()
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command
          cmd_obj.run()
        File "setup.py", line 28, in run
          self.build_extension(ext)
        File "setup.py", line 59, in build_extension
          subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp)
        File "/usr/lib/python3.10/subprocess.py", line 369, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-req-build-710xzc7j', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-req-build-710xzc7j/build/lib.linux-x86_64-3.10/morphio', '-DMORPHIO_VERSION_STRING=3.4.1.dev12+ga03a7bc71', '-DMORPHIO_TESTS=OFF', '-DPYTHON_EXECUTABLE=/usr/bin/python3', '-DHIGHFIVE_EXAMPLES=OFF', '-DHIGHFIVE_UNIT_TESTS=OFF', '-DCMAKE_BUILD_TYPE=Release', '-DMorphIO_CXX_WARNINGS=OFF', '-GNinja']' returned non-zero exit status 1.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for morphio
Failed to build morphio
ERROR: Could not build wheels for morphio, which is required to install pyproject.toml-based projects

Do you know of a workaround I might be able to employ?

[IanQS]

Okay, I figured it out.

1. clone the repo via git clone git@github.com:openbraininstitute/MorphI O.git --recursive

2. Install any pre-reqs e.g. sudo apt install libhdf5-dev hdf5-tools cmake

3. cd MorphIO && mkdir build && cd build && cmake .. && make install

4. copy the build/binds/python/*.so into wherever is good for your code

5. Add the .so to your path - I used uv.

---

Using UV

Modify pyproject.toml to include the following:

[tool.setuptools.packages.find]
where = ["."]
include = ["some_dir*"]

[tool.setuptools.package-data]
"some_dir.morphio" = ["*.so"]

where some_dir is the name of your main package code. You'll probably have to adapt this for your (the reader) specific case, but this should help get you started.