v0.0.2

gxfkit v0.0.2 Release Notes

Status: public GitHub Release and verified Bioconda package. Crates.io
publication is still pending maintainer credentials. Full public readiness is tracked by
scripts/release-evidence.sh --check-public and the strict public install audit.

Highlights

• Keeps gff2gtf as the focused alpha subcommand, with AGAT 1.7.0 as the
  correctness oracle.
• Reaches 100.00% normalized parity on the gated core corpus:
  human_chr1, human_chr21, and yeast.
• Adds the no-overwrite output guard for -o / --output, matching AGAT's
  safer pipeline rerun behavior.
• Preserves gzip input auto-detection and --sanitize diagnostics for malformed
  records.
• Hardens release distribution with GitHub Release archive verification,
  Bioconda install smoke tests, Crates.io publish ordering checks, public install
  audit tooling, release readiness checks, a deterministic local
  release-check.sh contract guard, and release evidence reporting.

Install Now

GitHub Release:

tar -xzf gxfkit-v0.0.2-linux-x86_64-static.tar.gz
./gxfkit-v0.0.2-linux-x86_64-static/gxfkit version

Bioconda:

conda install -c conda-forge -c bioconda gxfkit=0.0.2

Pending Install Channels

Crates.io 0.0.2 is pending maintainer credentials and publication from the
existing v0.0.2 tag:

cargo install gxfkit --version 0.0.2

Maintainer Verification

Before tagging:

set +e
RELEASE_CHECK_VERSION_SCOPE=cargo bash scripts/release-check.sh > release-check.log 2>&1
rc=$?
printf 'release-check-exit-code=%s\n' "$rc" >> release-check.log
set -e
python3 scripts/check-release-check.py
python3 scripts/release-readiness.py --phase tag
scripts/release-evidence.sh --allow-dirty --release-check-log release-check.log > release-evidence.md
exit "$rc"

After the GitHub source archive exists, update Bioconda metadata:

python3 scripts/github-source-sha256.py 0.0.2 --format prepare-command

After public propagation:

python3 scripts/release-readiness.py --phase public --check-public
python3 scripts/release-readiness.py --phase public --check-public --run-public-audit
VERIFY_PUBLIC_INSTALL_CHANNELS="github-linux github-parity bioconda crates" \
VERIFY_PUBLIC_INSTALLS_ALLOW_MISSING_CRATES=0 \
VERIFY_PUBLIC_INSTALLS_NO_OVERWRITE=1 \
VERIFY_PUBLIC_INSTALLS_MIN_PARITY=100 \
BENCH_FILES="human_chr1 human_chr21 yeast" \
VERSION=0.0.2 RELEASE_TAG=v0.0.2 bash scripts/verify-public-installs.sh
scripts/release-evidence.sh --check-public > release-evidence.md

The final public audit must keep the default strict settings:

• VERIFY_PUBLIC_INSTALL_CHANNELS="github-linux github-parity bioconda crates"
• VERIFY_PUBLIC_INSTALLS_ALLOW_MISSING_CRATES=0
• VERIFY_PUBLIC_INSTALLS_NO_OVERWRITE=1
• VERIFY_PUBLIC_INSTALLS_MIN_PARITY=100
• BENCH_FILES="human_chr1 human_chr21 yeast"

Known Limits

• gxfkit is still alpha and currently exposes one primary subcommand:
  gff2gtf.
• Public v0.0.1 packages predate the no-overwrite guard; do not use them as
  evidence for the v0.0.2 behavior.
• Extended Drosophila remains a documented stress-case divergence in
  docs/PARITY.md; the strict release gate is the core corpus.
• Bioconda 0.0.2 passed clean install verification, smoke conversion, and
  no-overwrite verification.

gxfkit v0.0.1

gxfkit v0.0.1

Alpha release for gff2gtf, a fast Rust implementation of the AGAT agat_convert_sp_gff2gtf.pl path.

Highlights

• gxfkit gff2gtf CLI with plain and gzip input support.
• AGAT 1.7.0 parity harness and CI gate.
• Prebuilt binaries for Linux x86_64/aarch64 and macOS x86_64/aarch64.
• Draft Crates.io/Bioconda publishing scaffolding is in the repo, but those channels are not published yet.

Verify downloads

Download the archive and matching .sha256, then run:

shasum -a 256 -c gxfkit-v0.0.1-<platform>.tar.gz.sha256

See docs/PARITY.md for known divergences and the AGAT baseline.