From 63f1d56aa771338065808d2f016f3ffcb89e33ba Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 11 Jun 2026 12:01:00 -0400 Subject: [PATCH 1/2] docs: include nxf version hook in site --- docs/.gitignore | 2 ++ docs/_quarto.yml | 1 + docs/render_site.sh | 3 +-- src/ccbr_tools/hooks/sync_nextflow_version.py | 2 ++ 4 files changed, 6 insertions(+), 2 deletions(-) diff --git a/docs/.gitignore b/docs/.gitignore index b38a1f81..37cf5ad5 100644 --- a/docs/.gitignore +++ b/docs/.gitignore @@ -6,3 +6,5 @@ /_freeze/ /site_libs/ /_inv/ + +**/*.quarto_ipynb diff --git a/docs/_quarto.yml b/docs/_quarto.yml index b9f381c2..a0bc3509 100644 --- a/docs/_quarto.yml +++ b/docs/_quarto.yml @@ -83,6 +83,7 @@ quartodoc: contents: - hooks - hooks.detect_absolute_paths + - hooks.sync_nextflow_version - title: Legacy tools contents: - GSEA.deg2gs diff --git a/docs/render_site.sh b/docs/render_site.sh index dbbfa96f..0209fc02 100755 --- a/docs/render_site.sh +++ b/docs/render_site.sh @@ -1,4 +1,3 @@ ccbr_tools quarto-add fnl -python -m quartodoc build --verbose -python -m quartodoc interlinks +python -m quartodoc build --verbose && python -m quartodoc interlinks quarto render diff --git a/src/ccbr_tools/hooks/sync_nextflow_version.py b/src/ccbr_tools/hooks/sync_nextflow_version.py index 7cd2a934..0aef55d5 100644 --- a/src/ccbr_tools/hooks/sync_nextflow_version.py +++ b/src/ccbr_tools/hooks/sync_nextflow_version.py @@ -1,6 +1,8 @@ """ Synchronize `manifest.version` in `nextflow.config` with the repo `VERSION` file. +Whenever the `VERSION` file is updated, the `manifest.version` entry in `nextflow.config` will be updated to match it. + ## Usage with pre-commit Add this to your `.pre-commit-config.yaml` file: From a1edc0a0b36e14bd63c6e89ca7529bc4fd02c89d Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 11 Jun 2026 12:02:33 -0400 Subject: [PATCH 2/2] chore: update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index be739b05..ae1bf38e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,7 @@ ## Tools development version +- minor documentation improvements. (#197, #198, @kelly-sovacool) + ## Tools 0.7.0 - New pre-commit hook: `ccbr-hooks sync-nextflow-version`. Syncs `manifest.version` in `nextflow.config` from the repo `VERSION` file. (#193, @kelly-sovacool, @copilot)