4.4.21: Parallel builds, robust installation, and rope-based parsing enhancements

This release introduces significant improvements to build reliability and performance, alongside key parsing enhancements for sequence data.

### Build & Installation Improvements
- Added support for parallel compilation via `-j/--jobs` option in both the Makefile and install script, enabling faster builds on multi-core systems. The default remains single-threaded for safety.
- Enhanced Makefile with `.DEFAULT_GOAL := all` for consistent behavior and a documented `help` target.
- Replaced fragile file operations with robust error handling, clear diagnostics, and automatic preservation of the build directory on copy failures to aid recovery.

### Rope-Based Parsing Enhancements (from 4.4.20)
- Introduced direct rope-based parsers for FASTA, EMBL, and FASTQ formats, improving memory efficiency for large files.
- Added U→T conversion support during sequence extraction and more reliable line ending detection.
- Unified rope scanning logic under a new `ropeScanner` for better maintainability.
- Added `TakeQualities()` method to BioSequence for more efficient handling of quality data.

### Bug Fixes (from 4.4.20)
- Fixed `CompressStream` to correctly respect the `compressed` variable.
- Replaced ambiguous string splitting utilities with precise left/right split variants (`LeftSplitInTwo`, `RightSplitInTwo`).

### Release Tooling (from 4.4.20)
- Streamlined release process with modular targets (`jjpush-notes`, `jjpush-push`, `jjpush-tag`) and AI-assisted note generation via `aichat`.
- Improved versioning support via the `VERSION` environment variable in `bump-version`.
- Switched PR submission from raw `jj git push` to `stakk` for consistency and reliability.

Note: This release incorporates key enhancements from 4.4.20 that impact end users, while focusing on build robustness and performance gains.

Makefile

@@ -2,6 +2,8 @@
 #export GOBIN=$(GOPATH)/bin
 #export PATH=$(GOBIN):$(shell echo $${PATH})
 
+.DEFAULT_GOAL := all
+
 GREEN  := \033[0;32m
 YELLOW := \033[0;33m
 BLUE   := \033[0;34m

README.md

@@ -32,8 +32,12 @@ The installation script offers several options:
 > 
 >  -p, --obitools-prefix   Prefix added to the obitools command names if you
 >                          want to have several versions of obitools at the
->                          same time on your system (as example `-p g` will produce 
+>                          same time on your system (as example `-p g` will produce
 >                          `gobigrep` command instead of `obigrep`).
+>
+>  -j, --jobs              Number of parallel jobs used for compilation
+>                          (default: 1). Increase this value to speed up
+>                          compilation on multi-core systems (e.g., `-j 4`).
 
 ### Examples
 

install_obitools.sh

@@ -7,6 +7,7 @@ INSTALL_DIR="/usr/local"
 OBITOOLS_PREFIX=""
 VERSION=""
 LIST_VERSIONS=false
+JOBS=1
 
 # Help message
 function display_help {
@@ -21,6 +22,7 @@ function display_help {
   echo "                          gobigrep command instead of obigrep)."
   echo "  -v, --version           Install a specific version (e.g., 4.4.8)."
   echo "                          If not specified, installs the latest version."
+  echo "  -j, --jobs              Number of parallel jobs for compilation (default: 1)."
   echo "  -l, --list              List all available versions and exit."
   echo "  -h, --help              Display this help message."
   echo ""
@@ -65,6 +67,10 @@ while [ "$#" -gt 0 ]; do
       VERSION="$2"
       shift 2
       ;;
+    -j|--jobs)
+      JOBS="$2"
+      shift 2
+      ;;
     -l|--list)
       LIST_VERSIONS=true
       shift
@@ -122,9 +128,15 @@ mkdir -p "${WORK_DIR}/cache" \
       exit 1)
 
 # Create installation directory
-mkdir -p "${INSTALL_DIR}/bin" 2> /dev/null \
-  || (echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
-      sudo mkdir -p "${INSTALL_DIR}/bin")
+if ! mkdir -p "${INSTALL_DIR}/bin" 2>/dev/null; then
+  if [ ! -w "$(dirname "${INSTALL_DIR}")" ] && [ ! -w "${INSTALL_DIR}" ]; then
+    echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
+    sudo mkdir -p "${INSTALL_DIR}/bin"
+  else
+    echo "Error: Could not create ${INSTALL_DIR}/bin (check path or disk space)" 1>&2
+    exit 1
+  fi
+fi
 
 if [[ ! -d "${INSTALL_DIR}/bin" ]]; then
   echo "Could not create ${INSTALL_DIR}/bin directory for installing obitools" 1>&2
@@ -208,16 +220,29 @@ mkdir -p vendor
 
 # Build with or without prefix
 if [[ -z "$OBITOOLS_PREFIX" ]] ; then
-  make GOFLAGS="-buildvcs=false"
+  make -j"${JOBS}" obitools GOFLAGS="-buildvcs=false"
 else
-  make GOFLAGS="-buildvcs=false" OBITOOLS_PREFIX="${OBITOOLS_PREFIX}"
+  make -j"${JOBS}" obitools GOFLAGS="-buildvcs=false" OBITOOLS_PREFIX="${OBITOOLS_PREFIX}"
 fi
 
 # Install binaries
 echo "Installing binaries to ${INSTALL_DIR}/bin..." 1>&2
-(cp build/* "${INSTALL_DIR}/bin" 2> /dev/null) \
-   || (echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
-       sudo cp build/* "${INSTALL_DIR}/bin")
+if ! cp build/* "${INSTALL_DIR}/bin" 2>/dev/null; then
+  if [ ! -w "${INSTALL_DIR}/bin" ]; then
+    echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
+    sudo cp build/* "${INSTALL_DIR}/bin"
+  else
+    echo "Error: Could not copy binaries to ${INSTALL_DIR}/bin" 1>&2
+    echo "  Source files: $(ls build/ 2>/dev/null || echo 'none found')" 1>&2
+    echo "" 1>&2
+    echo "The build directory has been preserved for manual recovery:" 1>&2
+    echo "  $(pwd)/build/" 1>&2
+    echo "You can install manually with:" 1>&2
+    echo "  cp $(pwd)/build/* ${INSTALL_DIR}/bin/" 1>&2
+    popd > /dev/null || true
+    exit 1
+  fi
+fi
 
 popd > /dev/null || exit
 

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 4.4.19"
+var _Version = "Release 4.4.21"
 
 // Version returns the version of the obitools package.
 //

version.txt

@@ -1 +1 @@
-4.4.19
+4.4.21