Drop distutils for Python 3.12 compatibility (closes #58) by wshlavacek · Pull Request #75 · RuleWorld/PyBioNetGen

wshlavacek · 2026-05-10T21:16:07Z

Summary

distutils was removed from the stdlib in Python 3.12 (and emits a DeprecationWarning before then). This PR replaces the two remaining usages with stdlib / setuptools equivalents:

bionetgen/core/utils/utils.py: distutils.spawn.find_executable → shutil.which. Same arg, same return semantics (absolute path or None).
bionetgen/simulator/csimulator.py: distutils.ccompiler → lazy setuptools._distutils.ccompiler via a small _new_ccompiler() helper. The import is deferred to CSimulator.__init__, so plain import bionetgen does not require setuptools at runtime — only instantiating CSimulator (the cpy simulator path) does, and that path already requires a local CVODE install. Missing setuptools raises a clear BNGCompileError with install guidance.

Closes#58.

Note on #59 / #61

Both #59 and #61 are about from pkg_resources import packaging failing under newer setuptools / Python. That import was already replaced in c392f2b ("CI fixes") and is in main today (line 21 of bionetgen/main.py). The tickets are still open but the underlying bug is gone — they could be closed at the same time as this PR.

Test plan

CI passes on the supported Python versions
import bionetgen works on Python 3.12 with no distutils available
bionetgen run -i ... (CLI path that uses find_BNG_path → shutil.which) works
CSimulator(...) raises a clear BNGCompileError on a system without setuptools, and works normally with setuptools installed

distutils was removed from the stdlib in Python 3.12 and emits a DeprecationWarning before then. shutil.which is the modern stdlib equivalent, takes the same argument, and returns the same result (absolute path or None).

distutils was removed from the stdlib in Python 3.12. setuptools vendors the same API as setuptools._distutils. The ccompiler import is wrapped in a lazy _new_ccompiler() helper called from CSimulator.__init__, so plain 'import bionetgen' does not require setuptools at runtime — only the cpy simulator path does, which already requires CVODE installed locally. Missing setuptools yields a clear BNGCompileError with install guidance.

wshlavacek · 2026-05-10T21:16:07Z

Summary

distutils was removed from the stdlib in Python 3.12 (and emits a DeprecationWarning before then). This PR replaces the two remaining usages with stdlib / setuptools equivalents:

bionetgen/core/utils/utils.py: distutils.spawn.find_executable → shutil.which. Same arg, same return semantics (absolute path or None).
bionetgen/simulator/csimulator.py: distutils.ccompiler → lazy setuptools._distutils.ccompiler via a small _new_ccompiler() helper. The import is deferred to CSimulator.__init__, so plain import bionetgen does not require setuptools at runtime — only instantiating CSimulator (the cpy simulator path) does, and that path already requires a local CVODE install. Missing setuptools raises a clear BNGCompileError with install guidance.

Closes#58.

Note on #59 / #61

Both #59 and #61 are about from pkg_resources import packaging failing under newer setuptools / Python. That import was already replaced in c392f2b ("CI fixes") and is in main today (line 21 of bionetgen/main.py). The tickets are still open but the underlying bug is gone — they could be closed at the same time as this PR.

Test plan

CI passes on the supported Python versions
import bionetgen works on Python 3.12 with no distutils available
bionetgen run -i ... (CLI path that uses find_BNG_path → shutil.which) works
CSimulator(...) raises a clear BNGCompileError on a system without setuptools, and works normally with setuptools installed

distutils was removed from the stdlib in Python 3.12 and emits a DeprecationWarning before then. shutil.which is the modern stdlib equivalent, takes the same argument, and returns the same result (absolute path or None).

distutils was removed from the stdlib in Python 3.12. setuptools vendors the same API as setuptools._distutils. The ccompiler import is wrapped in a lazy _new_ccompiler() helper called from CSimulator.__init__, so plain 'import bionetgen' does not require setuptools at runtime — only the cpy simulator path does, which already requires CVODE installed locally. Missing setuptools yields a clear BNGCompileError with install guidance.

wshlavacek · 2026-05-10T21:16:07Z

Summary

distutils was removed from the stdlib in Python 3.12 (and emits a DeprecationWarning before then). This PR replaces the two remaining usages with stdlib / setuptools equivalents:

bionetgen/core/utils/utils.py: distutils.spawn.find_executable → shutil.which. Same arg, same return semantics (absolute path or None).
bionetgen/simulator/csimulator.py: distutils.ccompiler → lazy setuptools._distutils.ccompiler via a small _new_ccompiler() helper. The import is deferred to CSimulator.__init__, so plain import bionetgen does not require setuptools at runtime — only instantiating CSimulator (the cpy simulator path) does, and that path already requires a local CVODE install. Missing setuptools raises a clear BNGCompileError with install guidance.

Closes#58.

Note on #59 / #61

Both #59 and #61 are about from pkg_resources import packaging failing under newer setuptools / Python. That import was already replaced in c392f2b ("CI fixes") and is in main today (line 21 of bionetgen/main.py). The tickets are still open but the underlying bug is gone — they could be closed at the same time as this PR.

Test plan

CI passes on the supported Python versions
import bionetgen works on Python 3.12 with no distutils available
bionetgen run -i ... (CLI path that uses find_BNG_path → shutil.which) works
CSimulator(...) raises a clear BNGCompileError on a system without setuptools, and works normally with setuptools installed

distutils was removed from the stdlib in Python 3.12 and emits a DeprecationWarning before then. shutil.which is the modern stdlib equivalent, takes the same argument, and returns the same result (absolute path or None).

distutils was removed from the stdlib in Python 3.12. setuptools vendors the same API as setuptools._distutils. The ccompiler import is wrapped in a lazy _new_ccompiler() helper called from CSimulator.__init__, so plain 'import bionetgen' does not require setuptools at runtime — only the cpy simulator path does, which already requires CVODE installed locally. Missing setuptools yields a clear BNGCompileError with install guidance.

wshlavacek · 2026-05-10T21:16:07Z

Summary

distutils was removed from the stdlib in Python 3.12 (and emits a DeprecationWarning before then). This PR replaces the two remaining usages with stdlib / setuptools equivalents:

bionetgen/core/utils/utils.py: distutils.spawn.find_executable → shutil.which. Same arg, same return semantics (absolute path or None).
bionetgen/simulator/csimulator.py: distutils.ccompiler → lazy setuptools._distutils.ccompiler via a small _new_ccompiler() helper. The import is deferred to CSimulator.__init__, so plain import bionetgen does not require setuptools at runtime — only instantiating CSimulator (the cpy simulator path) does, and that path already requires a local CVODE install. Missing setuptools raises a clear BNGCompileError with install guidance.

Closes#58.

Note on #59 / #61

Both #59 and #61 are about from pkg_resources import packaging failing under newer setuptools / Python. That import was already replaced in c392f2b ("CI fixes") and is in main today (line 21 of bionetgen/main.py). The tickets are still open but the underlying bug is gone — they could be closed at the same time as this PR.

Test plan

CI passes on the supported Python versions
import bionetgen works on Python 3.12 with no distutils available
bionetgen run -i ... (CLI path that uses find_BNG_path → shutil.which) works
CSimulator(...) raises a clear BNGCompileError on a system without setuptools, and works normally with setuptools installed

distutils was removed from the stdlib in Python 3.12 and emits a DeprecationWarning before then. shutil.which is the modern stdlib equivalent, takes the same argument, and returns the same result (absolute path or None).

distutils was removed from the stdlib in Python 3.12. setuptools vendors the same API as setuptools._distutils. The ccompiler import is wrapped in a lazy _new_ccompiler() helper called from CSimulator.__init__, so plain 'import bionetgen' does not require setuptools at runtime — only the cpy simulator path does, which already requires CVODE installed locally. Missing setuptools yields a clear BNGCompileError with install guidance.

wshlavacek · 2026-05-10T21:16:07Z

Summary

distutils was removed from the stdlib in Python 3.12 (and emits a DeprecationWarning before then). This PR replaces the two remaining usages with stdlib / setuptools equivalents:

bionetgen/core/utils/utils.py: distutils.spawn.find_executable → shutil.which. Same arg, same return semantics (absolute path or None).
bionetgen/simulator/csimulator.py: distutils.ccompiler → lazy setuptools._distutils.ccompiler via a small _new_ccompiler() helper. The import is deferred to CSimulator.__init__, so plain import bionetgen does not require setuptools at runtime — only instantiating CSimulator (the cpy simulator path) does, and that path already requires a local CVODE install. Missing setuptools raises a clear BNGCompileError with install guidance.

Closes#58.

Note on #59 / #61

Both #59 and #61 are about from pkg_resources import packaging failing under newer setuptools / Python. That import was already replaced in c392f2b ("CI fixes") and is in main today (line 21 of bionetgen/main.py). The tickets are still open but the underlying bug is gone — they could be closed at the same time as this PR.

Test plan

CI passes on the supported Python versions
import bionetgen works on Python 3.12 with no distutils available
bionetgen run -i ... (CLI path that uses find_BNG_path → shutil.which) works
CSimulator(...) raises a clear BNGCompileError on a system without setuptools, and works normally with setuptools installed

distutils was removed from the stdlib in Python 3.12 and emits a DeprecationWarning before then. shutil.which is the modern stdlib equivalent, takes the same argument, and returns the same result (absolute path or None).

distutils was removed from the stdlib in Python 3.12. setuptools vendors the same API as setuptools._distutils. The ccompiler import is wrapped in a lazy _new_ccompiler() helper called from CSimulator.__init__, so plain 'import bionetgen' does not require setuptools at runtime — only the cpy simulator path does, which already requires CVODE installed locally. Missing setuptools yields a clear BNGCompileError with install guidance.

wshlavacek · 2026-05-10T21:16:07Z

Summary

distutils was removed from the stdlib in Python 3.12 (and emits a DeprecationWarning before then). This PR replaces the two remaining usages with stdlib / setuptools equivalents:

bionetgen/core/utils/utils.py: distutils.spawn.find_executable → shutil.which. Same arg, same return semantics (absolute path or None).
bionetgen/simulator/csimulator.py: distutils.ccompiler → lazy setuptools._distutils.ccompiler via a small _new_ccompiler() helper. The import is deferred to CSimulator.__init__, so plain import bionetgen does not require setuptools at runtime — only instantiating CSimulator (the cpy simulator path) does, and that path already requires a local CVODE install. Missing setuptools raises a clear BNGCompileError with install guidance.

Closes#58.

Note on #59 / #61

Both #59 and #61 are about from pkg_resources import packaging failing under newer setuptools / Python. That import was already replaced in c392f2b ("CI fixes") and is in main today (line 21 of bionetgen/main.py). The tickets are still open but the underlying bug is gone — they could be closed at the same time as this PR.

Test plan

CI passes on the supported Python versions
import bionetgen works on Python 3.12 with no distutils available
bionetgen run -i ... (CLI path that uses find_BNG_path → shutil.which) works
CSimulator(...) raises a clear BNGCompileError on a system without setuptools, and works normally with setuptools installed

distutils was removed from the stdlib in Python 3.12 and emits a DeprecationWarning before then. shutil.which is the modern stdlib equivalent, takes the same argument, and returns the same result (absolute path or None).

distutils was removed from the stdlib in Python 3.12. setuptools vendors the same API as setuptools._distutils. The ccompiler import is wrapped in a lazy _new_ccompiler() helper called from CSimulator.__init__, so plain 'import bionetgen' does not require setuptools at runtime — only the cpy simulator path does, which already requires CVODE installed locally. Missing setuptools yields a clear BNGCompileError with install guidance.

wshlavacek · 2026-05-10T21:16:07Z

Summary

distutils was removed from the stdlib in Python 3.12 (and emits a DeprecationWarning before then). This PR replaces the two remaining usages with stdlib / setuptools equivalents:

bionetgen/core/utils/utils.py: distutils.spawn.find_executable → shutil.which. Same arg, same return semantics (absolute path or None).
bionetgen/simulator/csimulator.py: distutils.ccompiler → lazy setuptools._distutils.ccompiler via a small _new_ccompiler() helper. The import is deferred to CSimulator.__init__, so plain import bionetgen does not require setuptools at runtime — only instantiating CSimulator (the cpy simulator path) does, and that path already requires a local CVODE install. Missing setuptools raises a clear BNGCompileError with install guidance.

Closes#58.

Note on #59 / #61

Both #59 and #61 are about from pkg_resources import packaging failing under newer setuptools / Python. That import was already replaced in c392f2b ("CI fixes") and is in main today (line 21 of bionetgen/main.py). The tickets are still open but the underlying bug is gone — they could be closed at the same time as this PR.

Test plan

CI passes on the supported Python versions
import bionetgen works on Python 3.12 with no distutils available
bionetgen run -i ... (CLI path that uses find_BNG_path → shutil.which) works
CSimulator(...) raises a clear BNGCompileError on a system without setuptools, and works normally with setuptools installed

distutils was removed from the stdlib in Python 3.12 and emits a DeprecationWarning before then. shutil.which is the modern stdlib equivalent, takes the same argument, and returns the same result (absolute path or None).

distutils was removed from the stdlib in Python 3.12. setuptools vendors the same API as setuptools._distutils. The ccompiler import is wrapped in a lazy _new_ccompiler() helper called from CSimulator.__init__, so plain 'import bionetgen' does not require setuptools at runtime — only the cpy simulator path does, which already requires CVODE installed locally. Missing setuptools yields a clear BNGCompileError with install guidance.

wshlavacek · 2026-05-10T21:16:07Z

Summary

distutils was removed from the stdlib in Python 3.12 (and emits a DeprecationWarning before then). This PR replaces the two remaining usages with stdlib / setuptools equivalents:

bionetgen/core/utils/utils.py: distutils.spawn.find_executable → shutil.which. Same arg, same return semantics (absolute path or None).
bionetgen/simulator/csimulator.py: distutils.ccompiler → lazy setuptools._distutils.ccompiler via a small _new_ccompiler() helper. The import is deferred to CSimulator.__init__, so plain import bionetgen does not require setuptools at runtime — only instantiating CSimulator (the cpy simulator path) does, and that path already requires a local CVODE install. Missing setuptools raises a clear BNGCompileError with install guidance.

Closes#58.

Note on #59 / #61

Both #59 and #61 are about from pkg_resources import packaging failing under newer setuptools / Python. That import was already replaced in c392f2b ("CI fixes") and is in main today (line 21 of bionetgen/main.py). The tickets are still open but the underlying bug is gone — they could be closed at the same time as this PR.

Test plan

CI passes on the supported Python versions
import bionetgen works on Python 3.12 with no distutils available
bionetgen run -i ... (CLI path that uses find_BNG_path → shutil.which) works
CSimulator(...) raises a clear BNGCompileError on a system without setuptools, and works normally with setuptools installed

distutils was removed from the stdlib in Python 3.12 and emits a DeprecationWarning before then. shutil.which is the modern stdlib equivalent, takes the same argument, and returns the same result (absolute path or None).

distutils was removed from the stdlib in Python 3.12. setuptools vendors the same API as setuptools._distutils. The ccompiler import is wrapped in a lazy _new_ccompiler() helper called from CSimulator.__init__, so plain 'import bionetgen' does not require setuptools at runtime — only the cpy simulator path does, which already requires CVODE installed locally. Missing setuptools yields a clear BNGCompileError with install guidance.

wshlavacek added 3 commits May 10, 2026 15:12

Replace distutils.spawn.find_executable with shutil.which
3e886a5
distutils was removed from the stdlib in Python 3.12 and emits a DeprecationWarning before then. shutil.which is the modern stdlib equivalent, takes the same argument, and returns the same result (absolute path or None).

Apply black formatting to _new_ccompiler helper
514f247

jrfaeder merged commit ea60e0a into RuleWorld:mainMay 11, 2026
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