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Releases
v1.5.4
The circuit dashboard is now bundled with the installed package. Run:
pymagical dashboard --input_dir results/The command reads MAGICAL result tables from the required input directory, skips matrix and timing sidecars, saves dashboard.html, and opens it in a browser. No repository clone, separate update step, or Python visualization extra is needed.
- Support
--input-diras an alias,--outputfor a custom HTML path, and--no-openfor remote sessions. - Make the legacy
update_ui.pyhelper accept the same required input-directory flag. - Package the dashboard template without bundled demo results or frontend development files.
The browser still needs internet access for chart/table libraries and fonts.
Validation: five focused tests passed; version 1.5.4 wheel and source distribution built; the installed wheel generated a dashboard from real outputs outside the checkout.
v1.5.3
The CLI now uses the downloadable demo's filenames by default. Inputs in one folder run with --main-dir Demo_input_files --cell-dir Demo_input_files, using the header-free RefSeq file from the updated data release.
- Resolve
--main-dirand--cell-dirindependently from the working directory. For cell folders inside a main folder, pass the full relative path, such as--cell-dir data/astrocytes. - Report missing or invalid inputs with resolved absolute paths and their override flags; reject directories supplied as input files.
- Update README and tutorial examples, including a short demo smoke run.
Validation: 23 tests passed; wheel and source distribution built and checked as version 1.5.3.
v1.5.2
Original MAGICAL demo inputs now parse correctly: six-column scATAC peak files use their first four columns, and RefSeq files with headers produce a clear validation error. RefSeq headers must still be removed before running inference. Updated ATAC cache names prevent reuse of incorrectly parsed older caches.
Adds inference without a TAD prior through --no-tad, with --distance-control setting the maximum peak-center-to-TSS distance (default: 500 kb).
Validation: all 18 tests passed; source distribution and wheel built successfully as version 1.5.2.
Demo Dataset v1.0
Input files for pymagical demo and tutorial workflows.
Demo_input_files/hg38_Refseq.txt is header-free and ready to use with pymagical's default filenames. No tail command or separate RefSeq copy is needed.
The archive and SHA-256 checksum were updated on 2026-10-06 to remove the RefSeq header. All other file contents are unchanged.
v1.5.1
Documentation fidelity pass
- Corrected TSS selection logic, the programmatic
run_magicalsignature, and circuit output notation to match the code. - Reconciled all benchmark figures to the measured astrocytes 2000-iteration runs (~28x MATLAB-to-Numba sampling speedup); removed unverifiable averages.
- Stripped em/en dashes and tightened prose across the docs.
Robustness fixes
data_loader: raise on out-of-range 1-indexed COO indices instead of silently growing the sparse matrix.initialization: skip NaN OLS params/pvalues so degenerate regressions no longer seed NaN into the priors; useddof=1for L-prior variance to match MATLAB.