From 98057c68ba52f1af19c525c054409f73f5af7091 Mon Sep 17 00:00:00 2001 From: Marius Lange Date: Wed, 14 Oct 2026 11:44:00 +0200 Subject: [PATCH 1/2] Drop the CLAUDE.md that only imported AGENTS.md Claude Code reads AGENTS.md itself when there is no CLAUDE.md, so one instruction file is enough (quadbio/claude-plugins#13). Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01Cu5AYoH46bk3rW3qivyPZ5 --- {{cookiecutter.project_name}}/CLAUDE.md | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 {{cookiecutter.project_name}}/CLAUDE.md diff --git a/{{cookiecutter.project_name}}/CLAUDE.md b/{{cookiecutter.project_name}}/CLAUDE.md deleted file mode 100644 index b06ba47..0000000 --- a/{{cookiecutter.project_name}}/CLAUDE.md +++ /dev/null @@ -1,3 +0,0 @@ -# {{ cookiecutter.project_name }} agent entry point - -@AGENTS.md From f4a5f8f9c9ccd475fa17ebbb16b65e5f2e9f802d Mon Sep 17 00:00:00 2001 From: Marius Lange Date: Wed, 14 Oct 2026 11:44:03 +0200 Subject: [PATCH 2/2] Take analysis-workflow from main, as its README says It no longer tags releases: the project's lock pins the commit, and `pixi update` moves it. Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01Cu5AYoH46bk3rW3qivyPZ5 --- {{cookiecutter.project_name}}/pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/{{cookiecutter.project_name}}/pixi.toml b/{{cookiecutter.project_name}}/pixi.toml index 04bd53e..0ff055c 100644 --- a/{{cookiecutter.project_name}}/pixi.toml +++ b/{{cookiecutter.project_name}}/pixi.toml @@ -59,7 +59,7 @@ session-info2 = "*" # Local editable package for path helpers {{ cookiecutter.package_name | replace('_', '-') }} = { path = ".", editable = true } # Task paths and additive write-back for agent-run tasks (README: "Working with coding agents") -analysis-workflow = { git = "https://github.com/quadbio/analysis-workflow", tag = "v0.1.1" } +analysis-workflow = { git = "https://github.com/quadbio/analysis-workflow" } igraph = ">=1.0.0, <2" celltypist = ">=1.7.1, <2"