Modernize Sphinx docs and fix docstring RST bugs - #87
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- Auto-generate module .rst stubs with sphinxcontrib.apidoc instead of hand-maintaining them, fixing dead references (ncempy.io.read, ncempy.algo.align/moments/rebin) and adding coverage for modules that had drifted out of the docs (dectris, eels, multicorr, viz.widgets). - Add sphinx.ext.intersphinx mappings (Python, NumPy, SciPy, h5py, Matplotlib) so docstring type references link out. - Add .readthedocs.yaml and docs/requirements.txt for an explicit, modern RTD build config. - Add a Dectris Arina usage example to docs/index.rst. - Fix RST syntax bugs in docstrings (eels.pre_post_fit, gaussND.gauss3D_FIT, multicorr_funcs.imageShifter, smv.smvWriter, line_profile.line_profile) and set napoleon_use_ivar to stop __slots__-based classes like fileDM from being documented twice. Verified with `sphinx-build -W`: warnings dropped from 30 to 7, all remaining ones pre-existing (missing edstomo extra, deprecated theme call, empty tools toctree entry). Co-Authored-By: Claude <noreply@anthropic.com>
Add a short description of python_titan as a set of open source automation packages for Thermo Fisher transmission electron microscopes, in both README.rst and docs/index.rst. Co-Authored-By: Claude <noreply@anthropic.com>
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Jul 13, 2026
Follow-up to the docs modernization merged in #87, which only included the first commit of the update-docs branch. This carries over the rest: - Link python_titan properly in the Components toctree instead of as plain bold text (it needs a real docs/python_titan.rst target). - Add docs/tools.rst and docs/python_titan.rst: docs/tools.rst had been deleted in a much older commit but the toctree entry pointing to it was never removed, so it silently failed to render on RTD. - Reword the ncempy.read()/fileDM examples in docs/index.rst to use `import ncempy` directly instead of `import ncempy.io as nio`. Co-authored-by: Claude <noreply@anthropic.com>
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Verified with
sphinx-build -W: warnings dropped from 30 to 7, all remaining ones pre-existing (missing edstomo extra, deprecated theme call, empty tools toctree entry).