fp-tools v0.2.9

fp-tools v0.2.9 fixes indexed fragment input in the Windows single-cell workflow.

Previously, the per-cell stage could fail when a .tbi file was present but the optional pysam library was unavailable. fp-tools now uses its existing sequential fragment reader in that case. The input index is preserved. The regression is covered by four source tests and an index-sidecar case in frozen Windows smoke tests.

This release includes the v0.2.8 documentation improvements and complete real peripheral blood mononuclear cell (PBMC) tutorial. The same versioned tutorial ZIP and checksums are attached below. The source-data preparation recipe now specifies its tested Python dependencies and gives complete input-preparation instructions.

Install with python -m pip install --upgrade fp-tools-bio==0.2.9, or use the Windows executable or Apple Silicon DMG. Verify desktop files against SHA256SUMS.txt; tutorial, runtime, and container archives have separate checksum files.

Local validation: 638 tests passed, one skipped; 30 focused signature/motif tests and 59 release/runtime/documentation preflight tests passed. The real tutorial's complete per-cell stage also passed with pysam explicitly unavailable, reusing the validated group-level outputs. The source distribution passed twine validation.

The scientific methods and defaults are unchanged. Research-branch methods and manuscript files are not included. The 300-cell tutorial demonstrates execution; it does not establish binding or qualify full-scale single-cell performance.

Public-release verification is complete:

• All three public-download jobs passed. Both the Windows EXE and Apple Silicon application completed fresh/cached managed motif discovery and the complete real tutorial, including three successful groups and per-cell outputs. Tutorial execution took 1422.4 seconds on Windows and 1271.6 seconds on macOS in these CI environments; these are execution checks, not a performance benchmark.
• Final main-branch CI passed all ten jobs, including the full Windows Python 3.11–3.13 suites. Documentation checks and deployment passed. The browser audit covered 33 pages at three viewport sizes.
• Desktop, managed-runtime, container and all 15 wheel builds plus the source distribution passed. The first Mac desktop GUI audit timed out waiting for a validation panel; an unchanged retry passed all assertions.
• All 14 GitHub archives and all 16 PyPI files matched their published SHA-256 digests. A fresh PyPI installation passed 53 tests and 51 subtests, console-script checks and pip check.
• PyPI metadata contains the corrected summary and absolute logo URL. A CAPTCHA prevented direct visual inspection of the final PyPI page; that rendering is not certified by this audit.

Start with the installation guide and complete single-cell tutorial.