ChangeLog

Coalispr-1.0.0 (May, 2026)

‘Parquet’ release.

Pyarrow is an added requirement for running Coalispr now Pandas >= 3 relies on pyarrow to improve dataframe handling through the open source parquet format, which is used here to reduce I/O & disk storage:

  • Refactored binary storage from Shelve/Pickle to .parquet (BNY, PARQ).

  • Removed resources/numeric.py needed for python.shelve with Pandas >= 2.

  • Store only merged bedgraph data; this removes redundancy and in-between data I/O.

  • Removed editing of sample-names (because of fast data loading and counting).

  • Removed backup to text as chosen binary format (.parquet) is exchangeable.

  • Made saving counts to text files (.tsv) optional; defaults to .parquet.

  • Added a parquet-viewer to check outputs (in GUI and coalispr info -pV 1).

Changed multiprocessing to use spawn to start child processes:

  • Should facilitate usage on Windows or MacOS.

  • Previous default (fork) restricted multiprocessing to Linux/BSD.

  • Refactored datastore, countbams, info.

Manage memory usage to enable child-processes:

  • Large catalogs like chromosome indexes are no longer loaded into memory but read from file by each sub-process.

  • When needed, these catalogs are temporarily stored on disk.

Changed naming structure of created count and data files:

  • API breakage: old count files are no longer processed by the program.

Tested and developed with Python 3.12; updated zenodo archive (v6).

https://zenodo.org/badge/DOI/10.5281/zenodo.20328849.svg

Coalispr-0.9.7 (Mar, 2026)

Second public release.

Inclusion of a GUI (built with Tcl/Tk; start with coalispr_gui) to compose and run the same commands as via the CLI.

Refactoring of counting, now based around collections.Counter (replacing pandas.DataFrame). This gives a massive speed increase.

Multiprocessing used for counting and loading of bedgraph data (on linux).

Hand-cursor indicates interactive elements on interface of coalispr showgraphs.

Bin-analysis more refined and possibly more informative.

coalispr groupcompare refactored.

Counts for reads linked to extrageneous DNA (CHRXTRA) are now kept apart so that these do not inflate genomic counts.

A category for additional chromosomal DNA (ADD_GDNA) - that first was taken as extra DNA - is now included to enable inclusion into genomic counts.

Tested and developed with Python 3.12; updated zenodo archive (v4).

https://zenodo.org/badge/DOI/10.5281/zenodo.19390346.svg

Declared as “Production/Stable”.

Coalispr-0.7.8 (Oct, 2024)

First public, bioRχiv, release.

H99 and Mouse data @ https://doi.org/10.5281/zenodo.12822543

https://zenodo.org/badge/DOI/10.5281/zenodo.12822544.svg

Tested and developed with Python 3.9