Skip to content

chore: post-release cleanup for v1.3.0 #142

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
kopardev merged 2 commits into from
Sep 17, 2026
Merged

chore: post-release cleanup for v1.3.0 #142

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0183dde
chore: 🤖 prepare release v1.3.0
github-actions[bot] Sep 17, 2026
eb527bf
chore: bump changelog & version after release of v1.3.0
github-actions[bot] Sep 17, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
## ASPEN development version

## ASPEN 1.3.0

- Generate Tn5 nicking-site and read counts matrices, and the corresponding DiffATAC/DESeq2 results, from both `dedup.bam` (PCR/optical duplicates removed) and `filtered.bam` (duplicates retained, labeled `nondedup`), written to separate `dedup`/`nondedup` output subfolders under `visualization/` and `peaks/{peakcaller}/{fixed_width/counts,DiffATAC}/`; previously only the duplicate-retaining `filtered.bam` was used. `dedup` is recommended for standard differential accessibility testing. (#138, @kopardev)
- Fail fast with a clear, actionable error message when a replicate has 0 reads aligned to the spike-in genome, instead of crashing with an opaque `ZeroDivisionError` in `_compute_downsampling_scaling_factors.py`; the error is now also captured in a dedicated `results/spikein/compute_scaling_factors.log`. (#139, @kopardev)
- Overhaul documentation for accuracy and clarity across `docs/overview.md`, `docs/outputs.md`, `docs/introduction.md`, `docs/deployment.md`, and `docs/index.md`: fix stale claims left over from the dedup/nondedup change, clarify how consensus peaks and ROIs are generated, add ENCODE-referenced QC rule-of-thumb callouts (library complexity, TSS enrichment, FRiP), consolidate scattered spike-in "when should I use this" guidance into a single decision-tree callout, and remove the outdated, unreferenced `docs/extra.md` page whose content is now covered by `docs/outputs.md`. (#138, @kopardev)
Expand Down
4 changes: 2 additions & 2 deletions CITATION.cff
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,5 +29,5 @@ identifiers:
type: doi
value: 10.5281/zenodo.13755867
doi: 10.5281/zenodo.13755867
version: v1.1.2
date-released: "2025-07-17"
version: v1.3.0
date-released: "2026-09-17"
2 changes: 1 addition & 1 deletion VERSION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
1.2.0-dev
1.3.0-dev
Loading