Missing dependencies during installation of dingo

[adot-7]

I followed the README installation instructions. Running the tests fails with ModuleNotFoundError: No module named 'volestipy'.

Also, poetry install fails because build.py imports setuptools, which produces the error ModuleNotFoundError: No module named 'setuptools'. I believe this happens because setuptools is not included in the [build-system].requires list in pyproject.toml.

To Reproduce

1. Fork and clone the repository and cd into the clone directory
2. set the python version to 3.8.x( I did this by pyenv local 3.8.20 and confirmed the version by python --version)
3. git submodule update --init
4. Follow the README for downloading Boost & Ipsolve libraries.
5. Install system dependencies( since I am on Fedora, I did this by sudo dnf install suitesparse suitesparse-devel )
6. install poetry by curl -sSL https://install.python-poetry.org | python3 - --version 1.3.2
7. poetry install
   Observe the setuptools error. After I added 'setuptools' to the [build-system].requires list in pyproject.toml, the installation completed without errors.
8. install gurobi (not mandatory to reproduce the error)
9. Execute python tests/fba.py
   Observe the error:

Traceback (most recent call last):
  File "tests/fba.py", line 12, in <module>
    from dingo import MetabolicNetwork
  File "/home/adot/projects/geomscaleTesting/dingo/dingo/__init__.py", line 28, in <module>
    from dingo.PolytopeSampler import PolytopeSampler
  File "/home/adot/projects/geomscaleTesting/dingo/dingo/PolytopeSampler.py", line 22, in <module>
    from volestipy import HPolytope
ModuleNotFoundError: No module named 'volestipy'

Expected behavior

• poetry install should execute without error. Adding 'setuptools' to [build-system].requires list pyproject.toml is necessary for this.

• Running the tests should execute without error.

Environment
OS: Fedora Linux 42
Python: 3.8.20

Additional context
I can prepare a PR adding setuptools to the build-system requires list. I am still trying to figure out the volestipy dependency part though. I would appreciate any guidance on this.

[vissarion]

Thanks for the report. Could you please post the commands you type exactly and the error you are getting? Is it a Fedora issue? Since in ubuntu the workflow works correctly. See for examples the github actions.

[adot-7]

Yes, below are the commands I ran and their respective errors:

1. After cloning the fork and cding into the directory, I first set the local python environment to 3.8.20 and initialized the sub modules. Then I downloaded boost and lpsolve libraries. And then I installed the sparse QR library (for Fedora, I found it is called suitesparse). And then I installed poetry. No errors upto this point:

pyenv local 3.8.20
python --version # output: Python 3.8.20 
git submodule update --init

wget -O boost_1_76_0.tar.bz2 https://archives.boost.io/release/1.76.0/source/boost_1_76_0.tar.bz2
tar xjf boost_1_76_0.tar.bz2
rm boost_1_76_0.tar.bz2

wget https://sourceforge.net/projects/lpsolve/files/lpsolve/5.5.2.11/lp_solve_5.5.2.11_source.tar.gz
tar xzvf lp_solve_5.5.2.11_source.tar.gz
rm lp_solve_5.5.2.11_source.tar.gz

sudo dnf install -y suitesparse suitesparse-devel

curl -sSL https://install.python-poetry.org | python3 - --version 1.3.2
poetry shell
poetry install # got the first error here

Error:

Installing dependencies from lock file

No dependencies to install or update # as I had run the command earlier, it already installed the dependencies 

Installing the current project: dingo (0.1.0)Preparing build environment with build-system requirements poetry-core>=1.0.0, cython, numpy==1.20.1
Traceback (most recent call last):
  File "/home/adot/projects/geomscaleTesting/dingo/build.py", line 15, in <module>
    from setuptools import Extension
ModuleNotFoundError: No module named 'setuptools'

Command ['/tmp/tmp5nhzqs68/.venv/bin/python', '/home/adot/projects/geomscaleTesting/dingo/build.py'] errored with the following return code 1

Then, I added'setuptools' to '[build-system].requires list in pyproject.toml and re ran the command poetry install:

Installing dependencies from lock file

No dependencies to install or update

Installing the current project: dingo (0.1.0)Preparing build environment with build-system requirements poetry-core>=1.0.0, cython, numpy==1.20.1, setuptools
Installing the current project: dingo (0.1.0)

2. After that, I installed gurobi with a local free license. But the unit tests failed regardless of using gurobi or not.
3. I ran the command python tests/fba.py and got the following error (same for all other tests):

Traceback (most recent call last):
  File "tests/fba.py", line 12, in <module>
    from dingo import MetabolicNetwork
  File "/home/adot/projects/geomscaleTesting/dingo/dingo/__init__.py", line 28, in <module>
    from dingo.PolytopeSampler import PolytopeSampler
  File "/home/adot/projects/geomscaleTesting/dingo/dingo/PolytopeSampler.py", line 22, in <module>
    from volestipy import HPolytope
ModuleNotFoundError: No module named 'volestipy'

The dingo-ubuntu workflow runs fine, as you pointed out. So it does look like a Fedora-specific issue. My guess is that it comes down to package name or layout differences between Fedora and Ubuntu. I’ll look more closely at the sparse QR ( or suitesparse) part first since that’s the only step that really differs from the Ubuntu workflow.

[adot-7]

Update:

I compared the behavior on Ubuntu and Fedora by cloning the repository in an Ubuntu vm. On Ubuntu, poetry install created the compiledvolestipy.cpython-38-x86_64-linux-gnu.so shared object along with build and dingo.egg-info directories.
Whereas in Fedora, none of these files are created after poetry install even though the command executes without error (after adding setuptools to [build-system].requires in pyproject.toml.)

The final directory before running tests look like this in Fedora:

CODE_OF_CONDUCT.md
LICENSE
README.md
boost_1_76_0
build.py
dingo
doc
eigen
ext_data
lp_solve_5.5
poetry.lock
pyproject.toml
setup.py
tests
tutorials
volesti

Whereas in Ubuntu:

CODE_OF_CONDUCT.md
LICENSE
README.md
boost_1_76_0
build
build.py
dingo
dingo.egg-info
doc
eigen
ext_data
lp_solve_5.5
poetry.lock
pyproject.toml
setup.py
tests
tutorials
volesti
volestipy.cpython-38-x86_64-linux-gnu.so

This explains the ModuleNotFoundError: volestipy error, since the cython wrapper volestipy.pyx is not being built or compiled on fedora.

I believe the build step is skipped or failing without error on Fedora because of some missing header files or library path differences between both operating systems (possibly suitesparse related).

If anyone has insight into which part of the build process might be failing on Fedora (or any suitesparse requirement that differs from Ubuntu), that would be helpful.

[vissarion]

Thanks for your efforts @adot-7. Could you please run poetry install -vvv in Fedora and report the output here?

[adot-7]

Yes, following are outputs I got:

1. when no changes are made to the pyproject.toml file:

Using virtualenv: /home/adot/.cache/pypoetry/virtualenvs/dingo-qMK2hxJq-py3.8
Installing dependencies from lock file

Finding the necessary packages for the current system

Package operations: 0 installs, 0 updates, 0 removals, 54 skipped

  - Installing anyio (4.4.0): Pending...
  - Installing anyio (4.4.0): Skipped for the following reason: Already installed
  - Installing argparse (1.4.0): Pending...
  - Installing argparse (1.4.0): Skipped for the following reason: Already installed
  - Installing certifi (2024.7.4): Pending...
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  - Installing python-dateutil (2.9.0.post0): Pending...
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Installing the current project: dingo (0.1.0)
  - Building package dingo in editable mode
[virtualenv:virtualenv.discovery.builtin] find interpreter for spec PythonSpec(path=/home/adot/.pyenv/versions/3.8.20/bin/python3.8)
[virtualenv:virtualenv.info] filesystem is case-sensitive
[virtualenv:virtualenv.discovery.builtin] proposed PythonInfo(spec=CPython3.8.20.final.0-64, exe=/home/adot/.pyenv/versions/3.8.20/bin/python3.8, platform=linux, version='3.8.20 (default, Nov 24 2025, 16:18:50) \n[GCC 15.2.1 20251111 (Red Hat 15.2.1-4)]', encoding_fs_io=utf-8-utf-8)
[virtualenv:virtualenv.discovery.builtin] accepted PythonInfo(spec=CPython3.8.20.final.0-64, exe=/home/adot/.pyenv/versions/3.8.20/bin/python3.8, platform=linux, version='3.8.20 (default, Nov 24 2025, 16:18:50) \n[GCC 15.2.1 20251111 (Red Hat 15.2.1-4)]', encoding_fs_io=utf-8-utf-8)
[virtualenv:virtualenv.info] symlink on filesystem does work
[virtualenv:virtualenv.run.session] create virtual environment via CPython3Posix(dest=/tmp/tmpeqxtf3z7/.venv, clear=False, no_vcs_ignore=False, global=False)
[virtualenv:virtualenv.util.path._sync] create folder /tmp/tmpeqxtf3z7/.venv/bin
[virtualenv:virtualenv.util.path._sync] create folder /tmp/tmpeqxtf3z7/.venv/lib/python3.8/site-packages
[virtualenv:virtualenv.create.pyenv_cfg] write /tmp/tmpeqxtf3z7/.venv/pyvenv.cfg
[virtualenv:virtualenv.create.pyenv_cfg] 	home = /home/adot/.pyenv/versions/3.8.20/bin
[virtualenv:virtualenv.create.pyenv_cfg] 	implementation = CPython
[virtualenv:virtualenv.create.pyenv_cfg] 	version_info = 3.8.20.final.0
[virtualenv:virtualenv.create.pyenv_cfg] 	virtualenv = 20.35.4
[virtualenv:virtualenv.create.pyenv_cfg] 	include-system-site-packages = false
[virtualenv:virtualenv.create.pyenv_cfg] 	base-prefix = /home/adot/.pyenv/versions/3.8.20
[virtualenv:virtualenv.create.pyenv_cfg] 	base-exec-prefix = /home/adot/.pyenv/versions/3.8.20
[virtualenv:virtualenv.create.pyenv_cfg] 	base-executable = /home/adot/.pyenv/versions/3.8.20/bin/python3.8
[virtualenv:virtualenv.util.path._sync] symlink /home/adot/.pyenv/versions/3.8.20/bin/python3.8 to /tmp/tmpeqxtf3z7/.venv/bin/python
[virtualenv:virtualenv.create.via_global_ref.api] create virtualenv import hook file /tmp/tmpeqxtf3z7/.venv/lib/python3.8/site-packages/_virtualenv.pth
[virtualenv:virtualenv.create.via_global_ref.api] create /tmp/tmpeqxtf3z7/.venv/lib/python3.8/site-packages/_virtualenv.py
[virtualenv:virtualenv.run.session] ============================== target debug ==============================
[virtualenv:virtualenv.create.creator] debug via /tmp/tmpeqxtf3z7/.venv/bin/python /home/adot/.pyenv/versions/3.8.20/lib/python3.8/site-packages/virtualenv/create/debug.py
[virtualenv:virtualenv.run.session] {
[virtualenv:virtualenv.run.session]   "sys": {
[virtualenv:virtualenv.run.session]     "executable": "/tmp/tmpeqxtf3z7/.venv/bin/python",
[virtualenv:virtualenv.run.session]     "_base_executable": "/tmp/tmpeqxtf3z7/.venv/bin/python",
[virtualenv:virtualenv.run.session]     "prefix": "/tmp/tmpeqxtf3z7/.venv",
[virtualenv:virtualenv.run.session]     "base_prefix": "/home/adot/.pyenv/versions/3.8.20",
[virtualenv:virtualenv.run.session]     "real_prefix": null,
[virtualenv:virtualenv.run.session]     "exec_prefix": "/tmp/tmpeqxtf3z7/.venv",
[virtualenv:virtualenv.run.session]     "base_exec_prefix": "/home/adot/.pyenv/versions/3.8.20",
[virtualenv:virtualenv.run.session]     "path": [
[virtualenv:virtualenv.run.session]       "/home/adot/.pyenv/versions/3.8.20/lib/python38.zip",
[virtualenv:virtualenv.run.session]       "/home/adot/.pyenv/versions/3.8.20/lib/python3.8",
[virtualenv:virtualenv.run.session]       "/home/adot/.pyenv/versions/3.8.20/lib/python3.8/lib-dynload",
[virtualenv:virtualenv.run.session]       "/tmp/tmpeqxtf3z7/.venv/lib/python3.8/site-packages"
[virtualenv:virtualenv.run.session]     ],
[virtualenv:virtualenv.run.session]     "meta_path": [
[virtualenv:virtualenv.run.session]       "<class '_virtualenv._Finder'>",
[virtualenv:virtualenv.run.session]       "<class '_frozen_importlib.BuiltinImporter'>",
[virtualenv:virtualenv.run.session]       "<class '_frozen_importlib.FrozenImporter'>",
[virtualenv:virtualenv.run.session]       "<class '_frozen_importlib_external.PathFinder'>"
[virtualenv:virtualenv.run.session]     ],
[virtualenv:virtualenv.run.session]     "fs_encoding": "utf-8",
[virtualenv:virtualenv.run.session]     "io_encoding": "utf-8"
[virtualenv:virtualenv.run.session]   },
[virtualenv:virtualenv.run.session]   "version": "3.8.20 (default, Nov 24 2025, 16:18:50) \n[GCC 15.2.1 20251111 (Red Hat 15.2.1-4)]",
[virtualenv:virtualenv.run.session]   "makefile_filename": "/home/adot/.pyenv/versions/3.8.20/lib/python3.8/config-3.8-x86_64-linux-gnu/Makefile",
[virtualenv:virtualenv.run.session]   "os": "<module 'os' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/os.py'>",
[virtualenv:virtualenv.run.session]   "site": "<module 'site' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/site.py'>",
[virtualenv:virtualenv.run.session]   "datetime": "<module 'datetime' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/datetime.py'>",
[virtualenv:virtualenv.run.session]   "math": "<module 'math' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/lib-dynload/math.cpython-38-x86_64-linux-gnu.so'>",
[virtualenv:virtualenv.run.session]   "json": "<module 'json' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/json/__init__.py'>"
[virtualenv:virtualenv.run.session] }
[virtualenv:virtualenv.run.session] add activators for Bash, CShell, Fish, Nushell, PowerShell, Python
[virtualenv:virtualenv.create.pyenv_cfg] write /tmp/tmpeqxtf3z7/.venv/pyvenv.cfg
[virtualenv:virtualenv.create.pyenv_cfg] 	home = /home/adot/.pyenv/versions/3.8.20/bin
[virtualenv:virtualenv.create.pyenv_cfg] 	implementation = CPython
[virtualenv:virtualenv.create.pyenv_cfg] 	version_info = 3.8.20.final.0
[virtualenv:virtualenv.create.pyenv_cfg] 	virtualenv = 20.35.4
[virtualenv:virtualenv.create.pyenv_cfg] 	include-system-site-packages = false
[virtualenv:virtualenv.create.pyenv_cfg] 	base-prefix = /home/adot/.pyenv/versions/3.8.20
[virtualenv:virtualenv.create.pyenv_cfg] 	base-exec-prefix = /home/adot/.pyenv/versions/3.8.20
[virtualenv:virtualenv.create.pyenv_cfg] 	base-executable = /home/adot/.pyenv/versions/3.8.20/bin/python3.8
Preparing build environment with build-system requirements poetry-core>=1.0.0, cython, numpy==1.20.1
Collecting poetry-core>=1.0.0
  Using cached poetry_core-1.9.1-py3-none-any.whl.metadata (3.5 kB)
Collecting cython
  Using cached cython-3.2.2-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (4.7 kB)
Collecting numpy==1.20.1
  Using cached numpy-1.20.1-cp38-cp38-manylinux2010_x86_64.whl.metadata (2.0 kB)
Using cached numpy-1.20.1-cp38-cp38-manylinux2010_x86_64.whl (15.4 MB)
Using cached poetry_core-1.9.1-py3-none-any.whl (309 kB)
Using cached cython-3.2.2-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (3.5 MB)
Installing collected packages: poetry-core, numpy, cython
Successfully installed cython-3.2.2 numpy-1.20.1 poetry-core-1.9.1
  - Executing build script: build.py
Traceback (most recent call last):
  File "/home/adot/projects/geomscaleTesting/dingo/build.py", line 15, in <module>
    from setuptools import Extension
ModuleNotFoundError: No module named 'setuptools'

  Stack trace:

  1  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/poetry/utils/env/base_env.py:335 in _run
      333│             if call:
      334│                 assert stderr != subprocess.PIPE
    → 335│                 subprocess.check_call(cmd, stderr=stderr, env=env, **kwargs)
      336│                 output = ""
      337│             else:

  CalledProcessError

  Command '['/tmp/tmpeqxtf3z7/.venv/bin/python', '/home/adot/projects/geomscaleTesting/dingo/build.py']' returned non-zero exit status 1.

  at ~/.pyenv/versions/3.8.20/lib/python3.8/subprocess.py:364 in check_call
       360│     if retcode:
       361│         cmd = kwargs.get("args")
       362│         if cmd is None:
       363│             cmd = popenargs[0]
    →  364│         raise CalledProcessError(retcode, cmd)
       365│     return 0
       366│ 
       367│ 
       368│ def check_output(*popenargs, timeout=None, **kwargs):

The following error occurred when trying to handle this error:


  Stack trace:

  12  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/cleo/application.py:327 in run
       325│ 
       326│             try:
     → 327│                 exit_code = self._run(io)
       328│             except BrokenPipeError:
       329│                 # If we are piped to another process, it may close early and send a

  11  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/poetry/console/application.py:190 in _run
       188│         self._load_plugins(io)
       189│ 
     → 190│         exit_code: int = super()._run(io)
       191│         return exit_code
       192│ 

  10  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/cleo/application.py:431 in _run
       429│             io.input.interactive(interactive)
       430│ 
     → 431│         exit_code = self._run_command(command, io)
       432│         self._running_command = None
       433│ 

   9  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/cleo/application.py:473 in _run_command
       471│ 
       472│         if error is not None:
     → 473│             raise error
       474│ 
       475│         return terminate_event.exit_code

   8  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/cleo/application.py:457 in _run_command
       455│ 
       456│             if command_event.command_should_run():
     → 457│                 exit_code = command.run(io)
       458│             else:
       459│                 exit_code = ConsoleCommandEvent.RETURN_CODE_DISABLED

   7  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/cleo/commands/base_command.py:117 in run
       115│         io.input.validate()
       116│ 
     → 117│         return self.execute(io) or 0
       118│ 
       119│     def merge_application_definition(self, merge_args: bool = True) -> None:

   6  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/cleo/commands/command.py:61 in execute
        59│ 
        60│         try:
     →  61│             return self.handle()
        62│         except KeyboardInterrupt:
        63│             return 1

   5  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/poetry/console/commands/install.py:183 in handle
       181│         try:
       182│             builder = EditableBuilder(self.poetry, self.env, self.io)
     → 183│             builder.build()
       184│         except (ModuleOrPackageNotFound, FileNotFoundError) as e:
       185│             # This is likely due to the fact that the project is an application

   4  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/poetry/masonry/builders/editable.py:66 in build
        64│                 return self._path
        65│ 
     →  66│             self._run_build_script(self._package.build_script)
        67│ 
        68│         for removed in self._env.site_packages.remove_distribution_files(

   3  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/poetry/masonry/builders/editable.py:86 in _run_build_script
        84│         with build_environment(poetry=self._poetry, env=self._env, io=self._io) as env:
        85│             self._debug(f"  - Executing build script: {build_script}")
     →  86│             env.run("python", str(self._path.joinpath(build_script)), call=True)
        87│ 
        88│     def _setup_build(self) -> None:

   2  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/poetry/utils/env/base_env.py:305 in run
       303│     def run(self, bin: str, *args: str, **kwargs: Any) -> str:
       304│         cmd = self.get_command_from_bin(bin) + list(args)
     → 305│         return self._run(cmd, **kwargs)
       306│ 
       307│     def run_pip(self, *args: str, **kwargs: Any) -> str:

   1  ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/poetry/utils/env/virtual_env.py:88 in _run
        86│     def _run(self, cmd: list[str], **kwargs: Any) -> str:
        87│         kwargs["env"] = self.get_temp_environ(environ=kwargs.get("env"))
     →  88│         return super()._run(cmd, **kwargs)
        89│ 
        90│     def get_temp_environ(

  EnvCommandError

  Command ['/tmp/tmpeqxtf3z7/.venv/bin/python', '/home/adot/projects/geomscaleTesting/dingo/build.py'] errored with the following return code 1

  at ~/.pyenv/versions/3.8.20/lib/python3.8/site-packages/poetry/utils/env/base_env.py:342 in _run
      338│                 output = subprocess.check_output(
      339│                     cmd, stderr=stderr, env=env, text=True, **kwargs
      340│                 )
      341│         except CalledProcessError as e:
    → 342│             raise EnvCommandError(e)
      343│ 
      344│         return output
      345│ 
      346│     def execute(self, bin: str, *args: str, **kwargs: Any) -> int:

2. when I added "setuptools" to [build-system].requires list in pyproject.toml:

Using virtualenv: /home/adot/.cache/pypoetry/virtualenvs/dingo-qMK2hxJq-py3.8
Installing dependencies from lock file

Finding the necessary packages for the current system

Package operations: 0 installs, 0 updates, 0 removals, 54 skipped

  - Installing anyio (4.4.0): Pending...
  - Installing anyio (4.4.0): Skipped for the following reason: Already installed
  - Installing certifi (2024.7.4): Pending...
  - Installing certifi (2024.7.4): Skipped for the following reason: Already installed
  - Installing argparse (1.4.0): Pending...
  - Installing argparse (1.4.0): Skipped for the following reason: Already installed
  - Installing cffi (1.17.0): Pending...
  - Installing cffi (1.17.0): Skipped for the following reason: Already installed
  - Installing cobra (0.26.3): Pending...
  - Installing cobra (0.26.3): Skipped for the following reason: Already installed
  - Installing contourpy (1.1.1): Pending...
  - Installing contourpy (1.1.1): Skipped for the following reason: Already installed
  - Installing cycler (0.12.1): Pending...
  - Installing cycler (0.12.1): Skipped for the following reason: Already installed
  - Installing cython (0.29.37): Pending...
  - Installing cython (0.29.37): Skipped for the following reason: Already installed
  - Installing depinfo (1.7.0): Pending...
  - Installing depinfo (1.7.0): Skipped for the following reason: Already installed
  - Installing diskcache (5.6.3): Pending...
  - Installing diskcache (5.6.3): Skipped for the following reason: Already installed
  - Installing exceptiongroup (1.2.2): Pending...
  - Installing exceptiongroup (1.2.2): Skipped for the following reason: Already installed
  - Installing fonttools (4.53.1): Pending...
  - Installing fonttools (4.53.1): Skipped for the following reason: Already installed
  - Installing future (1.0.0): Pending...
  - Installing future (1.0.0): Skipped for the following reason: Already installed
  - Installing appdirs (1.4.4): Pending...
  - Installing appdirs (1.4.4): Skipped for the following reason: Already installed
  - Installing h11 (0.14.0): Pending...
  - Installing h11 (0.14.0): Skipped for the following reason: Already installed
  - Installing highsbox (1.7.2.post1): Pending...
  - Installing highsbox (1.7.2.post1): Skipped for the following reason: Already installed
  - Installing httpcore (1.0.5): Pending...
  - Installing httpcore (1.0.5): Skipped for the following reason: Already installed
  - Installing httpx (0.27.0): Pending...
  - Installing httpx (0.27.0): Skipped for the following reason: Already installed
  - Installing idna (3.7): Pending...
  - Installing idna (3.7): Skipped for the following reason: Already installed
  - Installing importlib-resources (6.4.2): Pending...
  - Installing importlib-resources (6.4.2): Skipped for the following reason: Already installed
  - Installing kaleido (0.2.1): Pending...
  - Installing kaleido (0.2.1): Skipped for the following reason: Already installed
  - Installing kiwisolver (1.4.5): Pending...
  - Installing kiwisolver (1.4.5): Skipped for the following reason: Already installed
  - Installing markdown-it-py (3.0.0): Pending...
  - Installing markdown-it-py (3.0.0): Skipped for the following reason: Already installed
  - Installing mdurl (0.1.2): Pending...
  - Installing mdurl (0.1.2): Skipped for the following reason: Already installed
  - Installing mpmath (1.3.0): Pending...
  - Installing mpmath (1.3.0): Skipped for the following reason: Already installed
  - Installing networkx (3.1): Pending...
  - Installing networkx (3.1): Skipped for the following reason: Already installed
  - Installing numpy (1.23.5): Pending...
  - Installing numpy (1.23.5): Skipped for the following reason: Already installed
  - Installing optlang (1.8.2): Pending...
  - Installing optlang (1.8.2): Skipped for the following reason: Already installed
  - Installing packaging (24.1): Pending...
  - Installing packaging (24.1): Skipped for the following reason: Already installed
  - Installing pandas (1.5.3): Pending...
  - Installing pandas (1.5.3): Skipped for the following reason: Already installed
  - Installing pillow (10.4.0): Pending...
  - Installing pillow (10.4.0): Skipped for the following reason: Already installed
  - Installing plotly (5.23.0): Pending...
  - Installing plotly (5.23.0): Skipped for the following reason: Already installed
  - Installing pycparser (2.22): Pending...
  - Installing pycparser (2.22): Skipped for the following reason: Already installed
  - Installing matplotlib (3.7.5): Pending...
  - Installing matplotlib (3.7.5): Skipped for the following reason: Already installed
  - Installing pydantic (1.10.17): Pending...
  - Installing pydantic (1.10.17): Skipped for the following reason: Already installed
  - Installing pyoptinterface (0.2.7): Pending...
  - Installing pyoptinterface (0.2.7): Skipped for the following reason: Already installed
  - Installing python-dateutil (2.9.0.post0): Pending...
  - Installing python-dateutil (2.9.0.post0): Skipped for the following reason: Already installed
  - Installing python-libsbml (5.20.4): Pending...
  - Installing python-libsbml (5.20.4): Skipped for the following reason: Already installed
  - Installing pytz (2024.1): Pending...
  - Installing pytz (2024.1): Skipped for the following reason: Already installed
  - Installing rich (13.7.1): Pending...
  - Installing rich (13.7.1): Skipped for the following reason: Already installed
  - Installing ruamel-yaml (0.18.6): Pending...
  - Installing ruamel-yaml (0.18.6): Skipped for the following reason: Already installed
  - Installing pygments (2.18.0): Pending...
  - Installing pygments (2.18.0): Skipped for the following reason: Already installed
  - Installing ruamel-yaml-clib (0.2.8): Pending...
  - Installing ruamel-yaml-clib (0.2.8): Skipped for the following reason: Already installed
  - Installing scipy (1.9.3): Pending...
  - Installing scipy (1.9.3): Skipped for the following reason: Already installed
  - Installing simplejson (3.19.3): Pending...
  - Installing simplejson (3.19.3): Skipped for the following reason: Already installed
  - Installing pyparsing (3.1.2): Pending...
  - Installing pyparsing (3.1.2): Skipped for the following reason: Already installed
  - Installing six (1.16.0): Pending...
  - Installing six (1.16.0): Skipped for the following reason: Already installed
  - Installing sniffio (1.3.1): Pending...
  - Installing sniffio (1.3.1): Skipped for the following reason: Already installed
  - Installing sparseqr (1.2.1 42989e9): Pending...
  - Installing sparseqr (1.2.1 42989e9): Skipped for the following reason: Already installed
  - Installing swiglpk (5.0.10): Pending...
  - Installing swiglpk (5.0.10): Skipped for the following reason: Already installed
  - Installing sympy (1.13.2): Pending...
  - Installing sympy (1.13.2): Skipped for the following reason: Already installed
  - Installing typing-extensions (4.12.2): Pending...
  - Installing typing-extensions (4.12.2): Skipped for the following reason: Already installed
  - Installing zipp (3.20.0): Pending...
  - Installing zipp (3.20.0): Skipped for the following reason: Already installed
  - Installing tenacity (9.0.0): Pending...
  - Installing tenacity (9.0.0): Skipped for the following reason: Already installed

Installing the current project: dingo (0.1.0)
  - Building package dingo in editable mode
[virtualenv:virtualenv.discovery.builtin] find interpreter for spec PythonSpec(path=/home/adot/.pyenv/versions/3.8.20/bin/python3.8)
[virtualenv:virtualenv.info] filesystem is case-sensitive
[virtualenv:virtualenv.discovery.builtin] proposed PythonInfo(spec=CPython3.8.20.final.0-64, exe=/home/adot/.pyenv/versions/3.8.20/bin/python3.8, platform=linux, version='3.8.20 (default, Nov 24 2025, 16:18:50) \n[GCC 15.2.1 20251111 (Red Hat 15.2.1-4)]', encoding_fs_io=utf-8-utf-8)
[virtualenv:virtualenv.discovery.builtin] accepted PythonInfo(spec=CPython3.8.20.final.0-64, exe=/home/adot/.pyenv/versions/3.8.20/bin/python3.8, platform=linux, version='3.8.20 (default, Nov 24 2025, 16:18:50) \n[GCC 15.2.1 20251111 (Red Hat 15.2.1-4)]', encoding_fs_io=utf-8-utf-8)
[virtualenv:virtualenv.info] symlink on filesystem does work
[virtualenv:virtualenv.run.session] create virtual environment via CPython3Posix(dest=/tmp/tmp_9id0ats/.venv, clear=False, no_vcs_ignore=False, global=False)
[virtualenv:virtualenv.util.path._sync] create folder /tmp/tmp_9id0ats/.venv/bin
[virtualenv:virtualenv.util.path._sync] create folder /tmp/tmp_9id0ats/.venv/lib/python3.8/site-packages
[virtualenv:virtualenv.create.pyenv_cfg] write /tmp/tmp_9id0ats/.venv/pyvenv.cfg
[virtualenv:virtualenv.create.pyenv_cfg] 	home = /home/adot/.pyenv/versions/3.8.20/bin
[virtualenv:virtualenv.create.pyenv_cfg] 	implementation = CPython
[virtualenv:virtualenv.create.pyenv_cfg] 	version_info = 3.8.20.final.0
[virtualenv:virtualenv.create.pyenv_cfg] 	virtualenv = 20.35.4
[virtualenv:virtualenv.create.pyenv_cfg] 	include-system-site-packages = false
[virtualenv:virtualenv.create.pyenv_cfg] 	base-prefix = /home/adot/.pyenv/versions/3.8.20
[virtualenv:virtualenv.create.pyenv_cfg] 	base-exec-prefix = /home/adot/.pyenv/versions/3.8.20
[virtualenv:virtualenv.create.pyenv_cfg] 	base-executable = /home/adot/.pyenv/versions/3.8.20/bin/python3.8
[virtualenv:virtualenv.util.path._sync] symlink /home/adot/.pyenv/versions/3.8.20/bin/python3.8 to /tmp/tmp_9id0ats/.venv/bin/python
[virtualenv:virtualenv.create.via_global_ref.api] create virtualenv import hook file /tmp/tmp_9id0ats/.venv/lib/python3.8/site-packages/_virtualenv.pth
[virtualenv:virtualenv.create.via_global_ref.api] create /tmp/tmp_9id0ats/.venv/lib/python3.8/site-packages/_virtualenv.py
[virtualenv:virtualenv.run.session] ============================== target debug ==============================
[virtualenv:virtualenv.create.creator] debug via /tmp/tmp_9id0ats/.venv/bin/python /home/adot/.pyenv/versions/3.8.20/lib/python3.8/site-packages/virtualenv/create/debug.py
[virtualenv:virtualenv.run.session] {
[virtualenv:virtualenv.run.session]   "sys": {
[virtualenv:virtualenv.run.session]     "executable": "/tmp/tmp_9id0ats/.venv/bin/python",
[virtualenv:virtualenv.run.session]     "_base_executable": "/tmp/tmp_9id0ats/.venv/bin/python",
[virtualenv:virtualenv.run.session]     "prefix": "/tmp/tmp_9id0ats/.venv",
[virtualenv:virtualenv.run.session]     "base_prefix": "/home/adot/.pyenv/versions/3.8.20",
[virtualenv:virtualenv.run.session]     "real_prefix": null,
[virtualenv:virtualenv.run.session]     "exec_prefix": "/tmp/tmp_9id0ats/.venv",
[virtualenv:virtualenv.run.session]     "base_exec_prefix": "/home/adot/.pyenv/versions/3.8.20",
[virtualenv:virtualenv.run.session]     "path": [
[virtualenv:virtualenv.run.session]       "/home/adot/.pyenv/versions/3.8.20/lib/python38.zip",
[virtualenv:virtualenv.run.session]       "/home/adot/.pyenv/versions/3.8.20/lib/python3.8",
[virtualenv:virtualenv.run.session]       "/home/adot/.pyenv/versions/3.8.20/lib/python3.8/lib-dynload",
[virtualenv:virtualenv.run.session]       "/tmp/tmp_9id0ats/.venv/lib/python3.8/site-packages"
[virtualenv:virtualenv.run.session]     ],
[virtualenv:virtualenv.run.session]     "meta_path": [
[virtualenv:virtualenv.run.session]       "<class '_virtualenv._Finder'>",
[virtualenv:virtualenv.run.session]       "<class '_frozen_importlib.BuiltinImporter'>",
[virtualenv:virtualenv.run.session]       "<class '_frozen_importlib.FrozenImporter'>",
[virtualenv:virtualenv.run.session]       "<class '_frozen_importlib_external.PathFinder'>"
[virtualenv:virtualenv.run.session]     ],
[virtualenv:virtualenv.run.session]     "fs_encoding": "utf-8",
[virtualenv:virtualenv.run.session]     "io_encoding": "utf-8"
[virtualenv:virtualenv.run.session]   },
[virtualenv:virtualenv.run.session]   "version": "3.8.20 (default, Nov 24 2025, 16:18:50) \n[GCC 15.2.1 20251111 (Red Hat 15.2.1-4)]",
[virtualenv:virtualenv.run.session]   "makefile_filename": "/home/adot/.pyenv/versions/3.8.20/lib/python3.8/config-3.8-x86_64-linux-gnu/Makefile",
[virtualenv:virtualenv.run.session]   "os": "<module 'os' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/os.py'>",
[virtualenv:virtualenv.run.session]   "site": "<module 'site' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/site.py'>",
[virtualenv:virtualenv.run.session]   "datetime": "<module 'datetime' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/datetime.py'>",
[virtualenv:virtualenv.run.session]   "math": "<module 'math' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/lib-dynload/math.cpython-38-x86_64-linux-gnu.so'>",
[virtualenv:virtualenv.run.session]   "json": "<module 'json' from '/home/adot/.pyenv/versions/3.8.20/lib/python3.8/json/__init__.py'>"
[virtualenv:virtualenv.run.session] }
[virtualenv:virtualenv.run.session] add activators for Bash, CShell, Fish, Nushell, PowerShell, Python
[virtualenv:virtualenv.create.pyenv_cfg] write /tmp/tmp_9id0ats/.venv/pyvenv.cfg
[virtualenv:virtualenv.create.pyenv_cfg] 	home = /home/adot/.pyenv/versions/3.8.20/bin
[virtualenv:virtualenv.create.pyenv_cfg] 	implementation = CPython
[virtualenv:virtualenv.create.pyenv_cfg] 	version_info = 3.8.20.final.0
[virtualenv:virtualenv.create.pyenv_cfg] 	virtualenv = 20.35.4
[virtualenv:virtualenv.create.pyenv_cfg] 	include-system-site-packages = false
[virtualenv:virtualenv.create.pyenv_cfg] 	base-prefix = /home/adot/.pyenv/versions/3.8.20
[virtualenv:virtualenv.create.pyenv_cfg] 	base-exec-prefix = /home/adot/.pyenv/versions/3.8.20
[virtualenv:virtualenv.create.pyenv_cfg] 	base-executable = /home/adot/.pyenv/versions/3.8.20/bin/python3.8
Preparing build environment with build-system requirements poetry-core>=1.0.0, cython, numpy==1.20.1, setuptools
Collecting poetry-core>=1.0.0
  Using cached poetry_core-1.9.1-py3-none-any.whl.metadata (3.5 kB)
Collecting cython
  Using cached cython-3.2.2-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (4.7 kB)
Collecting numpy==1.20.1
  Using cached numpy-1.20.1-cp38-cp38-manylinux2010_x86_64.whl.metadata (2.0 kB)
Collecting setuptools
  Using cached setuptools-75.3.2-py3-none-any.whl.metadata (6.9 kB)
Using cached numpy-1.20.1-cp38-cp38-manylinux2010_x86_64.whl (15.4 MB)
Using cached poetry_core-1.9.1-py3-none-any.whl (309 kB)
Using cached cython-3.2.2-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (3.5 MB)
Using cached setuptools-75.3.2-py3-none-any.whl (1.3 MB)
Installing collected packages: setuptools, poetry-core, numpy, cython
Successfully installed cython-3.2.2 numpy-1.20.1 poetry-core-1.9.1 setuptools-75.3.2
  - Executing build script: build.py
  - Removed dingo-0.1.0.dist-info directory from /home/adot/.cache/pypoetry/virtualenvs/dingo-qMK2hxJq-py3.8/lib/python3.8/site-packages
  - Adding dingo.pth to /home/adot/.cache/pypoetry/virtualenvs/dingo-qMK2hxJq-py3.8/lib/python3.8/site-packages for /home/adot/projects/geomscaleTesting/dingo
  - Adding the dingo-0.1.0.dist-info directory to /home/adot/.cache/pypoetry/virtualenvs/dingo-qMK2hxJq-py3.8/lib/python3.8/site-packages

I also ran the same command in the ubuntu machine but it just showed A setup.py file already exists. Using it. after installing dependencies.

[DhanashreePetare]

I would like to work on the issue. Can you please assign it to me.

[adot-7]

@DhanashreePetare are you working on Fedora as well? If yes, are you seeing the same installation errors?
Regarding assignment, I don’t see any assignee on other open issues either, so I assume it’s fine to start working on it without a formal assignment.

[DhanashreePetare]

@adot-7 ..I haven't started working on anything else currently. If you want, I can check and then tell. and I will start working on the issue.

[adot-7]

@DhanashreePetare Yeah that works. I had been busy with my finals but now I can also work on this. Do let me know if you can reproduce the issue on your system.

[adot-7]

@vissarion following up on your request to run poetry install -vvv and compare the behavior across systems:

I also ran the same command in the ubuntu machine but it just showed A setup.py file already exists. Using it. after installing dependencies.

I then added a print statement to build.py to check whether it is executed.
The print statement appears during poetry install on Fedora, but not on Ubuntu.

This shows that Poetry executes build.py on Fedora, while on Ubuntu it falls back to setup.py.

Since build.py does not replicate the compilation process of setup.py, no compiled binary is produced on Fedora, whereas Ubuntu does build via setup.py.

I executed poetry run python setup.py develop on Fedora to verify this. This produced the compiled binaries, and after this step, all unit tests run successfully on Fedora.

I added the following line at the top of build.py to verify whether it is executed:

print("build.py executed")

Output of poetry install on Fedora:

- Executing build script: build.py
build.py executed
  - Removed dingo-0.1.0.dist-info directory from /home/adot/.cache/pypoetry/virtualenvs/dingo-qMK2hxJq-py3.8/lib/python3.8/site-packages
  - Adding dingo.pth to /home/adot/.cache/pypoetry/virtualenvs/dingo-qMK2hxJq-py3.8/lib/python3.8/site-packages for /home/adot/projects/geomscaleTesting/dingo
  - Adding the dingo-0.1.0.dist-info directory to /home/adot/.cache/pypoetry/virtualenvs/dingo-qMK2hxJq-py3.8/lib/python3.8/site-packages

Whereas on Ubuntu:

Installing the current project: dingo (0.1.0)
  - Building package dingo in editable mode
  - Falling back on using a setup.py
A setup.py file already exists. Using it.

The difference matters because the build logic is defined in setup.py. While the build.py script used in the install path does contain build logic, it only cythonizes volestipy.pyx and does not replicate the same configuration as in setup.py, which explains why there is no compiled binary in Fedora, since Fedora only runs build.py.

Based on this, the issue does not appear to be Fedora-specific or related to external libraries. The root cause is the difference in Poetry’s install path (build.py vs setup.py) across environments.

As a temporary workaround, documenting that Fedora users should run:

poetry run python setup.py develop

since the full build currently happens only via setup.py.