[telatin]

Portable, faster release binaries

Fixes portability problems in the published binaries, removes the runtime PCRE dependency, and makes the build friendlier to packagers such as Bioconda.

Problems fixed

• macOS binaries required macOS 15+ (minos 15.0 in v1.29.0). The build now sets MACOSX_DEPLOYMENT_TARGET to 11.0 for arm64 and 10.13 for x86_64.
• Linux binaries required glibc ≥ 2.34 because they were built on ubuntu-24.04, so they would not run on RHEL/Rocky 8, Ubuntu 20.04, Debian 11 or many HPC systems. They are now built in manylinux_2_28 containers (glibc 2.28) with a pinned, checksum-verified Nim 2.2.10.
• Runtime libpcre lookup, pulled in by tableview's import re. The new minimum, tableview >= 0.6.0, uses the pure-Nim regex package, and the binary no longer references PCRE.

Release workflow (release-binaries.yml)

• Builds all tools (make all) and runs test/mini.sh on every platform before uploading.
• Release assets:
  • seqfu-<platform>: the main binary alone, same name as before, so existing download links keep working
  • seqfu-<version>-<platform>.tar.gz: all fu-* tools, plus LICENSE and README
  • SHA256SUMS
• Can also be started by hand (workflow_dispatch); a manual run builds and tests but doesn't upload anything. This replaces the duplicate build-binaries.yml, which is removed.
• Drops zlib1g-dev/libpcre3-dev from the release build (gzfast bundles zlib) and removes the no-op --threads:on append to nim.cfg. make.yaml no longer installs libpcre3-dev.

Makefile

• Faster, smaller binaries:
  • -d:lto is on by default. On Apple Silicon: seqfu stats ~20% faster, seqfu rc ~4% faster, gzipped input ~5% faster.
  • Stripping is on by default: seqfu shrinks from 2.49 to 2.22 MB. Linux uses -d:strip; macOS uses -Wl,-x, since Apple's ld ignores -s.
  • Switches: LTO=0 and NIMSTRIP=0 turn these off. NIMFLAGS=... passes extra Nim options.
• Uses the environment's compilers: CC/CXX are no longer hard-coded and CFLAGS/CXXFLAGS use ?=, so conda's toolchain is used without patching the Makefile with sed.
• Dependency handling:
  • src/deps.txt now depends on seqfu.nimble, so dependency bumps are actually installed.
  • Every Nim target depends on it, which makes make -j safe.
  • The rule fails when nimble reports a resolution error; nimble itself exits 0 in that case, which let builds silently fall back to an older tableview.

Other

• nim.cfg: documents why -d:danger stays. Re-enabling checks costs ~20% on seqfu rc.
• seqfu.nimble: license corrected from MIT to GPL-3.0-only, matching LICENSE and Bioconda.
• fu-split, fu-pecheck: shebang changed to python3.

Testing

• Clean make -j8 all on macOS arm64; bash test/mini.sh: all 657 tests pass.
• Checked MACOSX_DEPLOYMENT_TARGET=11.0 → minos 11.0.
• Checked the packaging script locally.
• Not yet run on GitHub: the manylinux container jobs. Before merging, trigger with
  gh workflow run release-binaries.yml --ref build/portable-release-binaries
  and confirm strings seqfu-linux-x86_64 | grep GLIBC_ | sort -V | tail -1 prints ≤ GLIBC_2.28.

Follow-up

• Update the Bioconda recipe after the next release: drop the pcre and sed patching, require nim >=2.2.0, add python as a run dependency, pin the osx-arm64 Nim download.
• Consider adding a nimble.lock so builds use fixed dependency versions.