Bump version to 4.4.16

Update version from 4.4.15 to 4.4.16 in version.go and version.txt files.

obitests/obitools/obisuperkmer/test.sh

@@ -4,8 +4,8 @@
 # Here give the name of the test serie
 #
 
-TEST_NAME=obisuperkmer
+TEST_NAME=obik-super
-CMD=obisuperkmer
+CMD=obik
 
 ######
 #
@@ -16,7 +16,7 @@ TEST_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
 OBITOOLS_DIR="${TEST_DIR/obitest*/}build"
 export PATH="${OBITOOLS_DIR}:${PATH}"
 
-MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
+MCMD="OBIk-super"
 
 TMPDIR="$(mktemp -d)"
 ntest=0
@@ -65,31 +65,10 @@ log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
 ####
 #### Below are the tests
 ####
-#### Before each test :
-####  - increment the variable ntest
-####
-#### Run the command as the condition of an if / then /else
-####  - The command must return 0 on success
-####  - The command must return an exit code different from 0 on failure
-####  - The datafiles are stored in the same directory than the test script
-####  - The test script directory is stored in the TEST_DIR variable
-####  - If result files have to be produced they must be stored
-####    in the temporary directory (TMPDIR variable)
-####
-#### then clause is executed on success of the command
-####  - Write a success message using the log function
-####  - increment the variable success
-####
-#### else clause is executed on failure of the command
-####  - Write a failure message using the log function
-####  - increment the variable failed
-####
 ######################################################################
 
-
-
 ((ntest++))
-if $CMD -h > "${TMPDIR}/help.txt" 2>&1
+if $CMD super -h > "${TMPDIR}/help.txt" 2>&1
 then
     log "$MCMD: printing help OK"
     ((success++))
@@ -100,7 +79,7 @@ fi
 
 # Test 1: Basic super k-mer extraction with default parameters
 ((ntest++))
-if obisuperkmer "${TEST_DIR}/test_sequences.fasta" \
+if $CMD super "${TEST_DIR}/test_sequences.fasta" \
     > "${TMPDIR}/output_default.fasta" 2>&1
 then
     log "$MCMD: basic extraction with default parameters OK"
@@ -148,7 +127,7 @@ fi
 
 # Test 5: Extract super k-mers with custom k and m parameters
 ((ntest++))
-if obisuperkmer -k 15 -m 7 "${TEST_DIR}/test_sequences.fasta" \
+if $CMD super -k 15 -m 7 "${TEST_DIR}/test_sequences.fasta" \
     > "${TMPDIR}/output_k15_m7.fasta" 2>&1
 then
     log "$MCMD: extraction with custom k=15, m=7 OK"
@@ -172,7 +151,7 @@ fi
 
 # Test 7: Test with different output format (FASTA output explicitly)
 ((ntest++))
-if obisuperkmer --fasta-output -k 21 -m 11 \
+if $CMD super --fasta-output -k 21 -m 11 \
     "${TEST_DIR}/test_sequences.fasta" \
     > "${TMPDIR}/output_fasta.fasta" 2>&1
 then
@@ -209,7 +188,7 @@ fi
 
 # Test 10: Test with output file option
 ((ntest++))
-if obisuperkmer -o "${TMPDIR}/output_file.fasta" \
+if $CMD super -o "${TMPDIR}/output_file.fasta" \
     "${TEST_DIR}/test_sequences.fasta" 2>&1
 then
     log "$MCMD: output to file with -o option OK"

pkg/obiformats/genbank_read.go

@@ -162,9 +162,10 @@ func GenbankChunkParser(withFeatureTable, UtoT bool) func(string, io.Reader) (ob
 					// log.Debugf("Chunk %d : Genbank: line %d, state = %d : %s", chunks.order, nl, state, line)
 
 					sl++
-					parts := strings.SplitN(line[10:], " ", 6)
+					cleanline := strings.TrimSpace(line)
+					parts := strings.SplitN(cleanline, " ", 7)
 					lparts := len(parts)
-					for i := 0; i < lparts; i++ {
+					for i := 1; i < lparts; i++ {
 						if UtoT {
 							parts[i] = strings.ReplaceAll(parts[i], "u", "t")
 						}

pkg/obioptions/version.go

@@ -3,7 +3,7 @@ package obioptions
 // Version is automatically updated by the Makefile from version.txt
 // The patch number (third digit) is incremented on each push to the repository
 
-var _Version = "Release 4.4.12"
+var _Version = "Release 4.4.16"
 
 // Version returns the version of the obitools package.
 //

pkg/obitools/obiconvert/sequence_reader.go

@@ -68,6 +68,8 @@ func ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 						strings.HasSuffix(path, "seq.gz") ||
 						strings.HasSuffix(path, "gb") ||
 						strings.HasSuffix(path, "gb.gz") ||
+						strings.HasSuffix(path, "gbff") ||
+						strings.HasSuffix(path, "gbff.gz") ||
 						strings.HasSuffix(path, "dat") ||
 						strings.HasSuffix(path, "dat.gz") ||
 						strings.HasSuffix(path, "ecopcr") ||
@@ -204,7 +206,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 					iterator = iterator.PairTo(ip)
 				}
 			} else {
-				iterator = obiiter.NilIBioSequence
+				return obiiter.NilIBioSequence, fmt.Errorf("no sequence files found in the provided paths")
 			}
 		}
 

release_notes.sh

@@ -0,0 +1,199 @@
+#!/bin/bash
+
+# Generate GitHub-compatible release notes for an OBITools4 version.
+#
+# Usage:
+#   ./release_notes.sh                 # latest version
+#   ./release_notes.sh -v 4.4.15       # specific version
+#   ./release_notes.sh -l              # list available versions
+#   ./release_notes.sh -r              # raw commit list (no LLM)
+#   ./release_notes.sh -c -v 4.4.16   # show LLM context for a version
+
+GITHUB_REPO="metabarcoding/obitools4"
+GITHUB_API="https://api.github.com/repos/${GITHUB_REPO}"
+VERSION=""
+LIST_VERSIONS=false
+RAW_MODE=false
+CONTEXT_MODE=false
+LLM_MODEL="ollama:qwen3-coder-next:latest"
+
+# ── Helpers ──────────────────────────────────────────────────────────────
+
+die() { echo "Error: $*" >&2; exit 1; }
+
+display_help() {
+  cat <<EOF
+Usage: $(basename "$0") [OPTIONS]
+
+Generate GitHub-compatible Markdown release notes for an OBITools4 version.
+
+Options:
+  -v, --version VERSION   Target version (e.g., 4.4.15). Default: latest.
+  -l, --list              List all available versions and exit.
+  -r, --raw               Output raw commit list without LLM summarization.
+  -c, --context           Show the exact context (commits + prompt) sent to the LLM.
+  -m, --model MODEL       LLM model for orla (default: $LLM_MODEL).
+  -h, --help              Display this help message.
+
+Examples:
+  $(basename "$0")                  # release notes for the latest version
+  $(basename "$0") -v 4.4.15       # release notes for a specific version
+  $(basename "$0") -l              # list versions
+  $(basename "$0") -r -v 4.4.15    # raw commit log for a version
+  $(basename "$0") -c -v 4.4.16    # show LLM context for a version
+EOF
+}
+
+# Fetch all Release tags from GitHub API (sorted newest first)
+fetch_versions() {
+  curl -sf "${GITHUB_API}/releases" \
+    | grep '"tag_name":' \
+    | sed -E 's/.*"tag_name": "Release_([0-9.]+)".*/\1/' \
+    | sort -V -r
+}
+
+# ── Parse arguments ──────────────────────────────────────────────────────
+
+while [ "$#" -gt 0 ]; do
+  case "$1" in
+    -v|--version)  VERSION="$2"; shift 2 ;;
+    -l|--list)     LIST_VERSIONS=true; shift ;;
+    -r|--raw)      RAW_MODE=true; shift ;;
+    -c|--context)  CONTEXT_MODE=true; shift ;;
+    -m|--model)    LLM_MODEL="$2"; shift 2 ;;
+    -h|--help)     display_help; exit 0 ;;
+    *)             die "Unsupported option: $1" ;;
+  esac
+done
+
+# ── List mode ────────────────────────────────────────────────────────────
+
+if [ "$LIST_VERSIONS" = true ]; then
+  echo "Available OBITools4 versions:" >&2
+  echo "==============================" >&2
+  fetch_versions
+  exit 0
+fi
+
+# ── Resolve versions ─────────────────────────────────────────────────────
+
+all_versions=$(fetch_versions)
+[ -z "$all_versions" ] && die "Could not fetch versions from GitHub"
+
+if [ -z "$VERSION" ]; then
+  VERSION=$(echo "$all_versions" | head -1)
+  echo "Using latest version: $VERSION" >&2
+fi
+
+tag_name="Release_${VERSION}"
+
+# Verify the requested version exists
+if ! echo "$all_versions" | grep -qx "$VERSION"; then
+  die "Version $VERSION not found. Use -l to list available versions."
+fi
+
+# Find the previous version (the one right after in the sorted-descending list)
+previous_version=$(echo "$all_versions" | grep -A1 -x "$VERSION" | tail -1)
+
+if [ "$previous_version" = "$VERSION" ] || [ -z "$previous_version" ]; then
+  previous_tag=""
+  echo "No previous version found -- will include all commits for $tag_name" >&2
+else
+  previous_tag="Release_${previous_version}"
+  echo "Generating notes: $previous_tag -> $tag_name" >&2
+fi
+
+# ── Fetch commit messages between tags via GitHub compare API ────────────
+
+if [ -n "$previous_tag" ]; then
+  commits_json=$(curl -sf "${GITHUB_API}/compare/${previous_tag}...${tag_name}")
+  if [ -z "$commits_json" ]; then
+    die "Could not fetch commit comparison from GitHub"
+  fi
+  commit_list=$(echo "$commits_json" \
+    | jq -r '.commits[] | (.sha[:8] + " " + (.commit.message | split("\n")[0]))' 2>/dev/null)
+else
+  # First release: get commits up to this tag
+  commits_json=$(curl -sf "${GITHUB_API}/commits?sha=${tag_name}&per_page=50")
+  if [ -z "$commits_json" ]; then
+    die "Could not fetch commits from GitHub"
+  fi
+  commit_list=$(echo "$commits_json" \
+    | jq -r '.[] | (.sha[:8] + " " + (.commit.message | split("\n")[0]))' 2>/dev/null)
+fi
+
+if [ -z "$commit_list" ]; then
+  die "No commits found between $previous_tag and $tag_name"
+fi
+
+# ── LLM prompt (shared by context mode and summarization) ────────────────
+
+LLM_PROMPT="Summarize the following commits into a GitHub release note for version ${VERSION}. \
+Ignore commits related to version bumps, .gitignore changes, or any internal housekeeping \
+that is irrelevant to end users. Describe each user-facing change precisely without exposing \
+code. Eliminate redundancy. Output strictly valid JSON with no surrounding text, using this \
+exact schema: {\"title\": \"<short release title>\", \"body\": \"<detailed markdown release notes>\"}"
+
+# ── Raw mode: just output the commit list ────────────────────────────────
+
+if [ "$RAW_MODE" = true ]; then
+  echo "# Release ${VERSION}"
+  echo ""
+  echo "## Commits"
+  echo ""
+  echo "$commit_list" | while IFS= read -r line; do
+    echo "- ${line}"
+  done
+  exit 0
+fi
+
+# ── Context mode: show what would be sent to the LLM ────────────────────
+
+if [ "$CONTEXT_MODE" = true ]; then
+  echo "=== LLM Model ==="
+  echo "$LLM_MODEL"
+  echo ""
+  echo "=== Prompt ==="
+  echo "$LLM_PROMPT"
+  echo ""
+  echo "=== Stdin (commit list) ==="
+  echo "$commit_list"
+  exit 0
+fi
+
+# ── LLM summarization ───────────────────────────────────────────────────
+
+if ! command -v orla >/dev/null 2>&1; then
+  die "orla is required for LLM summarization. Use -r for raw output."
+fi
+
+if ! command -v jq >/dev/null 2>&1; then
+  die "jq is required for JSON parsing. Use -r for raw output."
+fi
+
+echo "Summarizing with LLM ($LLM_MODEL)..." >&2
+
+raw_output=$(echo "$commit_list" | \
+  ORLA_MAX_TOOL_CALLS=50 orla agent -m "$LLM_MODEL" \
+  "$LLM_PROMPT" \
+  2>/dev/null) || true
+
+if [ -z "$raw_output" ]; then
+  echo "Warning: LLM returned empty output, falling back to raw mode" >&2
+  exec "$0" -r -v "$VERSION"
+fi
+
+# Sanitize: extract JSON object, strip control characters
+sanitized=$(echo "$raw_output" | sed -n '/^{/,/^}/p' | tr -d '\000-\011\013-\014\016-\037')
+
+release_title=$(echo "$sanitized" | jq -r '.title // empty' 2>/dev/null)
+release_body=$(echo "$sanitized" | jq -r '.body // empty' 2>/dev/null)
+
+if [ -n "$release_title" ] && [ -n "$release_body" ]; then
+  echo "# ${release_title}"
+  echo ""
+  echo "$release_body"
+else
+  echo "Warning: JSON parsing failed, falling back to raw mode" >&2
+  exec "$0" -r -v "$VERSION"
+fi

version.txt

@@ -1 +1 @@
-4.4.12
+4.4.17