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- 16 commits
- 18 files changed
- 1 contributor
Commits on Apr 11, 2025
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Check Assemblies for unrepresented asym IDs
Make sure that each Assembly used by a Model only includes asym IDs that are represented by Atoms or Spheres in at least one Model. Closes #165.
Commits on Apr 17, 2025
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Use pytest to run RPM tests in Fedora 42+
setuptools 72 no longer provides "setup.py test" so use pytest instead.
Commits on Apr 25, 2025
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Check for non-standard atoms in standard residues
Raise an error at dump time if the model contains any non-standard atom names (as per CCD) for any standard amino or nucleic acid. Closes #166.
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Make C extension optional at 'pip install' time
Mark the C extension as optional (since everything works OK without it) so that setuptools will still build and install python-ihm even if the compilation fails. Remove the --without-ext command line option, which doesn't work with modern pip/setuptools anyway.
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Test C extension in basic install test
Now that the C extension is optional, we should test to make sure it actually built in builds (such as RPM, .deb) where we want to use it.
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Revert "Test C extension in basic install test"
We also import this in tests where we don't have the C extension, so will have to test for that some other way. This reverts commit 7f85723.
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Make C extension non-optional for RPM, .deb builds
Patch setup.py during build of .rpm or .deb packages to make the C extension non-optional once again. This should fail the package build if building the extension fails.
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Modern setuptools wants us to use the 'license' argument now rather than a classifier.
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Move non-canonical atom name check to make_mmcif
Don't check for non-canonical atom names just yet in the dumper, but add an option to check them at make_mmcif time, defaulting to off.
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Commits on Apr 26, 2025
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Put back --without-ext command line setup.py option
We probably don't need the --without-ext option any more, and it doesn't work with modern pip/setuptools, but it shouldn't hurt to keep it for now in case it's needed on older operating systems.
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Use assembly's Python object ID, not _id attribute
python-modelcif doesn't assign _id to its Assembly objects, so we must use a different unique identifier.
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