From b3aa85f5ecd608a1e69dc11bfb9301b0cbefb77f Mon Sep 17 00:00:00 2001
From: Jon Palmer <nextgenusfs@gmail.com>
Date: Tue, 9 Jun 2026 17:26:09 -0700
Subject: [PATCH 1/2] fix(hooks): make pre-commit CITATION sync portable

The pre-commit hook auto-updates CITATION.cff whenever pyproject.toml
changes, but two bugs caused it to silently corrupt the file on
macOS/BSD:

1. The version-extraction regex used \s (GNU-only) in grep -E / sed -E.
   On BSD this matches a literal 's', so the capture fails and VERSION
   falls back to the entire matched line ('version = "X.Y.Z"').
2. The CITATION.cff substitution `s/version: .*/.../` was unanchored,
   so it also rewrote the `cff-version:` line.

Together these turned `cff-version: 1.2.0` and `version: X.Y.Z` into
`cff-version: version = "X.Y.Z"` and `version: version = "X.Y.Z"`,
which is invalid CFF (this is what PR #73 had to repair).

Fix both by using POSIX [[:space:]] and anchoring the substitutions
with ^.
---
 .githooks/pre-commit | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/.githooks/pre-commit b/.githooks/pre-commit
index d6371c9..d48ef0e 100755
--- a/.githooks/pre-commit
+++ b/.githooks/pre-commit
@@ -3,21 +3,25 @@
 
 # Check if pyproject.toml is being modified
 if git diff --cached --name-only | grep -q "pyproject.toml"; then
-    # Extract the version from pyproject.toml
-    VERSION=$(grep -E 'version\s*=\s*"[^"]+"' pyproject.toml | head -1 | sed -E 's/.*version\s*=\s*"([^"]+)".*/\1/')
-    
+    # Extract the version from pyproject.toml.
+    # Use [[:space:]] instead of \s so the regex works on both GNU and BSD
+    # (macOS) grep/sed — BSD treats \s as a literal 's', which silently
+    # falls back to capturing the whole line and corrupts CITATION.cff.
+    VERSION=$(grep -E '^[[:space:]]*version[[:space:]]*=[[:space:]]*"[^"]+"' pyproject.toml | head -1 | sed -E 's/.*version[[:space:]]*=[[:space:]]*"([^"]+)".*/\1/')
+
     if [ -n "$VERSION" ]; then
         # Get current date in YYYY-MM-DD format
         TODAY=$(date +"%Y-%m-%d")
-        
-        # Update version and date in CITATION.cff
-        sed -i.bak -E "s/version: .*/version: $VERSION/" CITATION.cff
-        sed -i.bak -E "s/date-released: .*/date-released: '$TODAY'/" CITATION.cff
+
+        # Update version and date in CITATION.cff. Anchor with ^ so the
+        # `version:` rule does not also clobber the `cff-version:` line.
+        sed -i.bak -E "s/^version: .*/version: $VERSION/" CITATION.cff
+        sed -i.bak -E "s/^date-released: .*/date-released: '$TODAY'/" CITATION.cff
         rm CITATION.cff.bak
-        
+
         # Add the updated CITATION.cff to the commit
         git add CITATION.cff
-        
+
         echo "Updated CITATION.cff to version $VERSION and date $TODAY"
     fi
 fi

From a49c0092bd101e9f931d04abec308d9f11254fcb Mon Sep 17 00:00:00 2001
From: Jon Palmer <nextgenusfs@gmail.com>
Date: Tue, 9 Jun 2026 17:26:09 -0700
Subject: [PATCH 2/2] build: bump version to 2026.6.9

Release cut after #73. Switches to CalVer (YYYY.M.D) matching the
prior v2025.11.1 tag rather than the intermediate YY.M.DD form used
in 26.5.22.

- pyproject.toml: 26.5.22 -> 2026.6.9
- CITATION.cff: version + date-released for today's tag
---
 CITATION.cff   | 4 ++--
 pyproject.toml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index babe0cb..6a48c29 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -17,5 +17,5 @@ keywords:
   - functional annotation
   - consensus gene models
 license: BSD-2-Clause
-version: 26.5.22
-date-released: '2026-05-24'
+version: 2026.6.9
+date-released: '2026-06-09'
diff --git a/pyproject.toml b/pyproject.toml
index 1a16fa4..84aada9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "funannotate2"
-version = "26.5.22"
+version = "2026.6.9"
 description = "Funannotate2: eukarytoic genome annotation pipeline"
 readme = {file = "README.md", content-type = "text/markdown"}
 authors = [