feat: Update 1.9.2

.github/ISSUE_TEMPLATE/config.yml

@@ -1 +1 @@
-blank_issues_enabled: false
+blank_issues_enabled: true

.github/pr-types.yml

@@ -0,0 +1,14 @@
+# .github/semantic.yml
+types:
+  - feat
+  - fix
+  - chore
+  - docs
+  - style
+  - refactor
+  - test
+  - perf
+  - build
+  - ci
+  - revert
+  - auto-sync

.github/releases.yml

@@ -0,0 +1,33 @@
+# .github/release.yml
+changelog:
+  # PRs carrying any of these labels will be omitted entirely
+  exclude:
+    labels:
+      - ignore-for-release
+    authors:
+      - dependabot[bot]
+
+  # Now define one or more categories for PRs you _do_ want to include
+  categories:
+    - title: Features
+      labels:
+        - feat
+
+    - title: Bug Fixes
+      labels:
+        - fix
+      # within this category you could also skip certain labels/authors
+      exclude:
+        labels:
+          - docs
+
+    - title: Maintenance
+      labels:
+        - chore
+        - ci
+        - refactor
+      exclude:
+        - build
+        - test
+        - perf
+        - style

.github/scripts/check_upstream_release.py

@@ -0,0 +1,77 @@
+import requests
+import toml
+import sys
+import os
+from packaging.version import Version, InvalidVersion
+
+UPSTREAM_REPO = "snakemake/snakemake-executor-plugin-slurm"
+PYPROJECT = "pyproject.toml"
+
+EXIT_OK = 0         # no changes
+EXIT_ERROR = 1      # script failure
+EXIT_NEW_RELEASE = 42  # desired trigger
+
+def error(msg):
+    print(f"ERROR: {msg}", file=sys.stderr)
+    sys.exit(EXIT_ERROR)
+
+def get_latest_upstream_version():
+    url = f"https://api.github.com/repos/{UPSTREAM_REPO}/releases/latest"
+    headers = {"Accept": "application/vnd.github+json"}
+
+    token = os.environ.get("GITHUB_TOKEN")
+    if token:
+        headers["Authorization"] = f"Bearer {token}"
+
+    r = requests.get(url, headers=headers)
+    if r.status_code != 200:
+        error(f"Failed to fetch upstream release info: {r.status_code}, response: {r.text}")
+
+    try:
+        version_str = r.json()["tag_name"].lstrip("v")
+        return Version(version_str)
+    except Exception:
+        error("Failed to parse upstream version from tag")
+
+def get_local_main_version():
+    try:
+        data = toml.load(PYPROJECT)
+        version_str = data["tool"]["poetry"]["version"]
+        base = Version(version_str).base_version  # base_version is a str
+        return Version(base)  # convert base_version string back to Version object
+    except Exception as e:
+        error(f"Could not parse pyproject.toml version: {e}")
+
+def main():
+    upstream = get_latest_upstream_version()
+    local = get_local_main_version()
+
+    print(f"Local main version = {local}")
+    print(f"Upstream version   = {upstream}")
+
+    if upstream > local:
+        print("New upstream release detected!")
+        sys.exit(EXIT_NEW_RELEASE)
+    else:
+        print("No new release")
+        sys.exit(EXIT_OK)
+
+if __name__ == "__main__":
+    ######
+    ## TESTS
+    # # Simulated version for testing
+    # simulated_upstream_version = "1.2.99"
+
+    # # Print output GitHub Actions will parse
+    # print(f"Local main version = 1.2.1")
+    # print(f"Upstream version   = {simulated_upstream_version}")
+    # print("New upstream release detected!")
+
+    # # Emit output for GitHub Actions
+    # #print(f"upstream-version={simulated_upstream_version}")
+
+    # # Exit code triggers the sync workflow
+    # sys.exit(42)
+    ######
+
+    main()

.github/scripts/merge_test.sh

@@ -0,0 +1,85 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+# CONFIGURATION
+UPSTREAM_REMOTE="upstream"
+UPSTREAM_BRANCH="main"
+FORK_BRANCH="main"
+TEMP_DIR=".merge-tmp"
+
+EXCLUDES=(
+    "TODO.md"
+    "tests/Snakefile"
+    "tests/tests.py"
+    "tests/__pycache__"
+    "tests/profiles"
+)
+# Check if the script is run from the correct directory
+echo "Preparing for local 3-way sync test (upstream → cannon)..."
+
+# Ensure remotes are up to date
+git fetch $UPSTREAM_REMOTE
+git fetch origin
+
+# Find the common ancestor (merge base)
+BASE_COMMIT=$(git merge-base origin/$FORK_BRANCH $UPSTREAM_REMOTE/$UPSTREAM_BRANCH)
+echo "Using merge base: $BASE_COMMIT"
+
+# Prepare temp workspace
+mkdir -p $TEMP_DIR/base $TEMP_DIR/theirs $TEMP_DIR/mine $TEMP_DIR/preview
+
+MERGED=false
+
+# Gather tracked files from upstream
+FILES=$(git ls-tree -r --name-only $UPSTREAM_REMOTE/$UPSTREAM_BRANCH)
+
+for SRC in $FILES; do
+    # (skip exclusions and map paths as before)
+
+    # Map slurm ➞ cannon
+    if [[ "$SRC" == snakemake_executor_plugin_slurm/* ]]; then
+        DEST="${SRC/snakemake_executor_plugin_slurm/snakemake_executor_plugin_cannon}"
+    else
+        DEST="$SRC"
+    fi
+
+    [[ ! -f "$DEST" ]] && continue
+
+    echo "Merging $SRC -> $DEST"
+
+    TMP_BASE="$TEMP_DIR/base/$(basename "$DEST")"
+    TMP_THEIRS="$TEMP_DIR/theirs/$(basename "$DEST")"
+    TMP_MINE="$TEMP_DIR/mine/$(basename "$DEST")"
+
+    git show "$BASE_COMMIT:$SRC" > "$TMP_BASE" 2>/dev/null || continue
+    git show "$UPSTREAM_REMOTE/$UPSTREAM_BRANCH:$SRC" > "$TMP_THEIRS" || continue
+    cp "$DEST" "$TMP_MINE"
+
+    if git merge-file --marker-size=30 "$TMP_MINE" "$TMP_BASE" "$TMP_THEIRS"; then
+        echo "Clean merge completed: $DEST"
+    else
+        echo "Conflict detected: $DEST (manual resolution may be required)"
+    fi
+
+    echo "Diff between $DEST and merged result:"
+    diff -u "$DEST" "$TMP_MINE" || true
+    echo
+
+    read -p "Apply merged result to $DEST? [y/N]: " CONFIRM
+    if [[ "$CONFIRM" == "y" || "$CONFIRM" == "Y" ]]; then
+        cp "$TMP_MINE" "$DEST"
+        echo "Applied merged version to $DEST"
+        MERGED=true
+    else
+        echo "Skipped applying merged version to $DEST"
+    fi
+
+    rm -f "$TMP_BASE" "$TMP_THEIRS" "$TMP_MINE"
+done
+
+echo ""
+echo "Merge simulation complete."
+echo "Merged files are available under: $TEMP_DIR/preview/"
+echo "No files in your working directory were modified."
+echo "To apply changes, manually copy from preview/ into your repo and commit."

.github/workflows/announce-release.yml → .github/workflows/announce-release.yml.disabled

@@ -18,12 +18,21 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Verify logo file exists
+        run: |
+          ls -la ${{ github.workspace }}/pr_logo/
+          if [ ! -f "${{ github.workspace }}/pr_logo/long_logo_hpc.png" ]; then
+            echo "ERROR: Logo file not found!"
+            exit 1
+          fi
+          echo "Logo file found at: ${{ github.workspace }}/pr_logo/long_logo_hpc.png"
+
       - name: Post to Mastodon
         uses: snakemake/mastodon-release-post-action@main # == latest
         with:
           access-token: ${{ secrets.MASTODONBOT }}
           pr-title: ${{ github.event.head_commit.message }}
-          image: "${{ github.workspace }}/pr_logo/long_logo_hpc.png"
+          image: "long_logo_hpc.png"
           image-description: "Snakemake HPC logo for Mastodon"
           message: |
             Beep, Beep - I am your friendly #Snakemake release announcement bot.

.github/workflows/bump-and-tag.yml.disabled

@@ -0,0 +1,79 @@
+name: Version Bump
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  bump-and-tag:
+    name: Bump version & optionally tag
+    if: |
+      github.event_name == 'workflow_dispatch' ||
+      (
+        github.event_name == 'push' &&
+        startsWith(github.ref, 'refs/heads/main') &&
+        contains(github.event.head_commit.message, '[bump-')
+      )
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python & Poetry
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+      - run: pip install poetry
+
+      - name: Detect bump mode
+        id: mode
+        run: |
+          MSG="${{ github.event.head_commit.message }}"
+          if [[ "$MSG" == *"[bump-release]"* ]]; then
+            MODE=release
+          else
+            MODE=local
+          fi
+          echo "mode=$MODE" >> "$GITHUB_OUTPUT"
+          echo "MODE=$MODE" >> "$GITHUB_ENV"
+          echo "::notice::Detected bump mode: $MODE"
+
+      - name: Compute next post-release version
+        id: bump
+        run: |
+          FULL=$(poetry version -s)
+          UPSTREAM="${FULL%%.post*}"
+          if [[ "$FULL" =~ \.post([0-9]+)$ ]]; then
+            NEXT=$((BASH_REMATCH[1] + 1))
+          else
+            NEXT=1
+          fi
+          NEW="${UPSTREAM}.post${NEXT}"
+          poetry version "$NEW"
+          echo "new_version=$NEW" >> "$GITHUB_OUTPUT"
+          echo "::notice::Will bump to: $NEW"
+
+      - name: Commit bumped version
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git commit -am "Version ${{ steps.bump.outputs.new_version }}"
+
+      - name: Tag release (only in release mode)
+        if: env.MODE == 'release'
+        run: |
+          echo "Tagging v${{ steps.bump.outputs.new_version }}"
+          git tag "v${{ steps.bump.outputs.new_version }}"
+
+      - name: Push commit and tag
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          git push origin HEAD
+          if [ "$MODE" = "release" ]; then
+            git push origin "v${{ steps.bump.outputs.new_version }}"
+          fi