From c44d36ab20b04e70ba5574d493a346cadbfb2a6d Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 20 Apr 2026 14:10:42 +0000
Subject: [PATCH 1/2] Initial plan


From ff798616a3b6cb310bd58b507f8725cb82a488ec Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 20 Apr 2026 14:15:37 +0000
Subject: [PATCH 2/2] chore: add copilot coding agent instructions

Agent-Logs-Url: https://github.com/precimed/container_template/sessions/86b9e70f-a0b6-43c8-8e47-c3c039c367f3

Co-authored-by: espenhgn <2492641+espenhgn@users.noreply.github.com>
---
 .github/copilot-instructions.md | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 .github/copilot-instructions.md

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
new file mode 100644
index 0000000..3e7fcb8
--- /dev/null
+++ b/.github/copilot-instructions.md
@@ -0,0 +1,25 @@
+# Copilot instructions for `precimed/container_template`
+
+## Repository purpose
+- This repository is a reusable template for containerized projects (Docker/Singularity/Apptainer) and workflow scaffolding.
+- Keep changes minimal and scoped to the issue; avoid broad template rewrites unless explicitly requested.
+
+## Key project structure
+- `containers/`: container recipes and built image references.
+- `tests/`: pytest-based validation for runtime/container behavior.
+- `scripts/init.py`: initialization script that customizes this template for downstream projects.
+- `.github/workflows/`: CI checks (including Python linting and container workflows).
+
+## Validation commands
+- Install test/lint dependencies:
+  - `python -m pip install -r test-requirements.txt flake8`
+- Run tests:
+  - `python -m pytest -q`
+- Run lint:
+  - `flake8 .`
+
+## Contribution expectations for agent changes
+- Prefer surgical edits over refactors.
+- Do not modify unrelated files to fix pre-existing lint issues unless the task asks for it.
+- If modifying behavior, update or add focused tests under `tests/`.
+- Keep workflow and container changes backward-compatible with template usage.