feat!: rebuild py-ft as a pure-python toolkit over pysam + pyMA#119
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cademirch wants to merge 2 commits into
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feat!: rebuild py-ft as a pure-python toolkit over pysam + pyMA#119cademirch wants to merge 2 commits into
cademirch wants to merge 2 commits into
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Drops the Rust/pyo3 bindings (Fiberbam, Fiberdata, Fiberwriter, center) and the maturin build. py-ft is now plain Python: Fiberdata wraps a pysam record's molecular_annotation and exposes the fiber-seq accessors (m6a, cpg, nuc, msp, fire) over iter_type. fetch() iterates mapped and unmapped reads (so unaligned fiber-seq BAMs work), and Fiberdata.is_mapped lets callers filter. Plotting moves to an optional [viz] extra. region_to_* and the fiberplot CLI, which drove the old Rust Fiberbam, are stubbed with NotImplementedError until they're ported to fetch(); plot.py is unchanged. Adds a root release workflow for py-ft (py-ft-v* tags) using PyPI trusted publishing; the pyMA release workflow lives with the pyMA changes.
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The docs still built the old Rust/maturin package (rust toolchain + compiling the crate), which is why the Read the Docs build failed. py-ft is pure Python now, so: - .readthedocs.yaml drops rust/cmake; installing the package just pulls pysam + molecular-annotation from PyPI so autodoc can import pyft. - conf.py builds without nbsphinx; api.rst documents pyft.fiberdata via autodoc (Napoleon for the Google-style docstrings). - add __version__ to the package (conf.py reads it). - replace the old Fiberbam notebooks with a quickstart vignette on fetch() and the Fiberdata accessors; refresh index.rst.
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mrvollger
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Jul 22, 2026
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Drops the Rust/pyo3 bindings (Fiberbam, Fiberdata, Fiberwriter, center) and the maturin build. py-ft is now plain Python: Fiberdata wraps a pysam record's molecular_annotation and exposes the fiber-seq accessors (m6a, cpg, nuc, msp, fire) over iter_type. Plotting moves to an optional [viz] extra.
region_to_* and the fiberplot CLI are gone now. These are not currently implemented but can be if we decide this is the right direction for py-ft.
This depends on #118