pyproject.toml: tool.chimerax.extra-files fails on second run

[Tristan Croll]

Server seems to be down, so reporting the old-fashioned way...


Rebuilding Clipper *without* doing a "make clean" in between fails:


{{{

chimerax --nogui --safemode --cmd "devel install . ; exit"

Executing: devel install .

Traceback (most recent call last):

File
"/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/devel.py",
line 180, in _run

unbound_method(bb, *args, **kw)

File
"/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder_toml.py",
line 553, in make_install

wheel = self.build_wheel()

^^^^^^^^^^^^^^^^^^

File
"/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder_toml.py",
line 839, in build_wheel

self._clear_distutils_dir_and_prep_srcdir(build_exts=True)

File
"/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder_toml.py",
line 791, in _clear_distutils_dir_and_prep_srcdir

self._copy_extrafiles()

File
"/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder_toml.py",
line 686, in _copy_extrafiles

shutil.copytree(entry, destination)

File "/usr/lib/ucsf-chimerax/lib/python3.11/shutil.py", line 561, in
copytree

return _copytree(entries=entries, src=src, dst=dst, symlinks=symlinks,

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/usr/lib/ucsf-chimerax/lib/python3.11/shutil.py", line 459, in
_copytree

os.makedirs(dst, exist_ok=dirs_exist_ok)

File "<frozen os>", line 225, in makedirs

FileExistsError: [Errno 17] File exists: 'src/include/clipper_ext'

}}}


Culprit is this section of pyproject.toml:
https://github.com/tristanic/chimerax-clipper/blob/59c09818a0c9f9a53a31b5776e0e77114dee129c/pyproject.toml#L53-L56


Looks like the call to `shutil.copytree` should include
`dirs_include_ok=True`?

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[Tom Goddard]

Zach have you looked at this? At the SLAC cryoEM workshop Alexis Rohou wasted a good bit of time trying to build Clipper failing because of this ticket from 3 months ago.

[Zach Pearson]

Should be fixed in tomorrow's daily build. Tristan's suggested fix worked.