From 3e2c4fc168741c2f2fa79c6630f23026c4e75103 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Oct 2026 16:20:14 +0000 Subject: [PATCH 1/2] chore(deps): bump CCBR/actions Bumps the github-actions group with 1 update in the / directory: [CCBR/actions](https://github.com/ccbr/actions). Updates `CCBR/actions` from 0.7 to 0.8 - [Release notes](https://github.com/ccbr/actions/releases) - [Changelog](https://github.com/CCBR/actions/blob/main/CHANGELOG.md) - [Commits](https://github.com/ccbr/actions/compare/v0.7...v0.8) --- updated-dependencies: - dependency-name: CCBR/actions dependency-version: '0.8' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions ... Signed-off-by: dependabot[bot] --- .github/workflows/draft-release.yml | 2 +- .github/workflows/post-release.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/draft-release.yml b/.github/workflows/draft-release.yml index eabd154..8d634b7 100644 --- a/.github/workflows/draft-release.yml +++ b/.github/workflows/draft-release.yml @@ -24,7 +24,7 @@ jobs: - uses: actions/checkout@v7 with: fetch-depth: 0 # required to include tags - - uses: CCBR/actions/draft-release@v0.7 + - uses: CCBR/actions/draft-release@v0.8 with: github-token: ${{ github.token }} version-tag: ${{ github.event.inputs.version-tag }} diff --git a/.github/workflows/post-release.yml b/.github/workflows/post-release.yml index 924aafa..ca1c382 100644 --- a/.github/workflows/post-release.yml +++ b/.github/workflows/post-release.yml @@ -17,6 +17,6 @@ jobs: - uses: actions/checkout@v7 with: fetch-depth: 0 - - uses: CCBR/actions/post-release@v0.7 + - uses: CCBR/actions/post-release@v0.8 with: github-token: ${{ github.token }} From 1f72bca30b4835bd8195f33c2c3987e62338268c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 1 Oct 2026 16:20:49 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .github/copilot-instructions.md | 7 +++++++ CHANGELOG.md | 1 - 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md index 6ac34dc..27b56ee 100644 --- a/.github/copilot-instructions.md +++ b/.github/copilot-instructions.md @@ -1,18 +1,24 @@ # Custom Instructions + (Migrated from old file) + # SUPERPOWERS PROTOCOL + You are an autonomous coding agent operating on a strict "Loop of Autonomy." ## CORE DIRECTIVE: The Loop + For every request, you must execute the following cycle: + 1. **PERCEIVE**: Read `plan.md`. Do not act without checking the plan. 2. **ACT**: Execute the next unchecked step in the plan. 3. **UPDATE**: Check off the step in `plan.md` when verified. 4. **LOOP**: If the task is large, do not stop. Continue to the next step. ## YOUR SKILLS (Slash Commands) + VS Code reserved commands are replaced with these Superpowers equivalents: - **Use `/write-plan`** (instead of /plan) to interview me and build `plan.md`. @@ -20,6 +26,7 @@ VS Code reserved commands are replaced with these Superpowers equivalents: - **Use `/tdd`** to write code. NEVER write code without a failing test. ## RULES + - If `plan.md` does not exist, your ONLY valid action is to ask to run `/write-plan`. - Do not guess. If stuck, write a theory in `scratchpad.md`. diff --git a/CHANGELOG.md b/CHANGELOG.md index 6163638..7894ca0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,6 @@ - Detect SLURM-killed Snakemake child jobs in classic cluster mode by adding a `--cluster-status` hook and `scancel` integration, so timed out, OOM-killed, cancelled, or otherwise failed child jobs now retry/fail cleanly instead of leaving the master workflow hanging indefinitely. (#148, @kopardev) - Clarify motif enrichment outputs and interpretation in the documentation: fix the reported location of HOMER/AME result folders, explain how ASPEN reuses HOMER-generated `target.fa`/`background.fa` in AME, document the AME parallelization strategy, and add simpler guidance for interpreting `knownResults.txt` and `ame_results.txt`. (#146, @kopardev) - ## ASPEN 1.4.0 - Add structured pipeline state tracking: a `pipeline.status.json` sidecar and `pipeline.{running,completed,failed,canceled}` marker files are now written to `WORKDIR` during `run`, with a live progress monitor that periodically updates `pipeline.running` with a step-completion percentage; a best-effort `jobby` TSV summary (`snakemake.log.jobby`) is now also generated when Slurm submission fails before Snakemake starts. Consolidated shared logging/banner/version-tag helper functions into a new staged library (`workflow/scripts/ccbr_pipeline_logging.sh`, slated for future migration to `ccbr_tools`); redesigned the `--version`/banner output. (#119, @kopardev)