Release BlackSTAR 1.1.0

.github/repository-settings.json

@@ -41,7 +41,13 @@
     },
     "required_status_checks": {
       "contexts": [
-        "build-and-test"
+        "build-and-test",
+        "compiler-gcc",
+        "compiler-clang",
+        "starlong-build-and-smoke",
+        "release-portability",
+        "codeql-c-cpp",
+        "codeql-python"
       ],
       "strict": true
     },

.github/workflows/blackstar-ci.yml

@@ -2,6 +2,8 @@ name: BlackSTAR CI
 
 on:
   push:
+    branches:
+      - main
   pull_request:
   workflow_dispatch:
 
@@ -26,7 +28,7 @@ jobs:
       - name: Install build dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y g++ jq make python3-yaml zlib1g-dev
+          sudo apt-get install -y g++ jq make python3-yaml samtools zlib1g-dev
 
       - name: Install architecture renderer
         run: npm ci --prefix extras/docs
@@ -41,13 +43,18 @@ jobs:
           bash -n extras/benchmarks/preparePublicAlignmentFixture.sh
           bash -n extras/benchmarks/runAlignmentA00.sh
           python3 -m py_compile \
+            extras/benchmarks/makeFastqSubset.py \
             extras/benchmarks/makePairedFastqSubset.py \
             extras/benchmarks/quietSystemGate.py \
             extras/benchmarks/summarizeAlignmentA00.py \
             extras/benchmarks/compareAlignmentRuns.py \
+            extras/benchmarks/compareGeneralizationRuns.py \
             extras/benchmarks/evaluateAlignmentNoninferiority.py \
-            extras/benchmarks/runAlignmentPairs.py
+            extras/benchmarks/runAlignmentPairs.py \
+            extras/benchmarks/runGeneralizationPairs.py
+          bash -n extras/benchmarks/runGeneralizationMode.sh
           extras/tests/scripts/testBenchmarkHarness.sh
+          extras/tests/scripts/testGeneralizationHarness.sh
 
       - name: Validate successor metadata
         run: |
@@ -57,13 +64,16 @@ jobs:
             extras/maintenance/check_detachment_readiness.py \
             extras/maintenance/finalize_successor_repo.py \
             extras/maintenance/validate_successor_metadata.py \
+            extras/scripts/inspectBlackSTARBinary.py \
             extras/scripts/generateBlackSTARSbom.py
           python3 extras/maintenance/validate_successor_metadata.py
 
-      - name: Build BlackSTAR
+      - name: Build BlackSTAR release variants
         env:
           JOBS: "2"
-        run: extras/scripts/buildBlackSTARRelease.sh
+        run: |
+          CPU_TARGET=baseline extras/scripts/buildBlackSTARRelease.sh
+          CPU_TARGET=avx2 extras/scripts/buildBlackSTARRelease.sh
 
       - name: Build independent release reproduction
         env:
@@ -72,34 +82,84 @@ jobs:
         run: |
           git worktree add --detach "${RUNNER_TEMP}/release-source-2" HEAD
           cd "${RUNNER_TEMP}/release-source-2"
-          extras/scripts/buildBlackSTARRelease.sh
+          CPU_TARGET=baseline extras/scripts/buildBlackSTARRelease.sh
+          CPU_TARGET=avx2 extras/scripts/buildBlackSTARRelease.sh
 
       - name: Verify cross-path release reproducibility
-        run: extras/scripts/compareBlackSTARReleases.sh dist "${RUNNER_TEMP}/release-build-2"
+        run: |
+          CPU_TARGET=baseline extras/scripts/compareBlackSTARReleases.sh dist "${RUNNER_TEMP}/release-build-2"
+          CPU_TARGET=avx2 extras/scripts/compareBlackSTARReleases.sh dist "${RUNNER_TEMP}/release-build-2"
 
       - name: Verify release identity and OpenMP linkage
         run: |
+          version="$(sed -n 's/^#define BLACKSTAR_VERSION "\(.*\)"$/\1/p' source/VERSION)"
+          baseline="dist/blackstar-${version}-linux-x86_64-baseline"
+          avx2="dist/blackstar-${version}-linux-x86_64-avx2"
           test "$(source/STAR --version)" = "2.7.11b-blackstar.3"
-          extras/tests/scripts/testBlackstarVersion.sh
+          EXPECTED_CPU_TARGET=avx2 extras/tests/scripts/testBlackstarVersion.sh
           ldd source/STAR | grep -Eq 'libgomp|libomp'
-          test -f dist/blackstar-1.0.0-linux-x86_64.spdx.json
-          test -f dist/blackstar-1.0.0-linux-x86_64/LICENSE
-          test -f dist/blackstar-1.0.0-linux-x86_64/ATTRIBUTION.md
-          jq -e '
+          test -f "${baseline}.spdx.json"
+          test -x "${baseline}.STAR"
+          test -f "${baseline}.STAR.sha256"
+          test -f "${baseline}.build-info.tsv"
+          test -f "${baseline}.compatibility.tsv"
+          test -f "${baseline}.ldd.txt"
+          test -f "${baseline}/LICENSE"
+          test -f "${baseline}/ATTRIBUTION.md"
+          test -f "${avx2}.spdx.json"
+          test -x "${avx2}.STAR"
+          test -f "${avx2}.STAR.sha256"
+          test -f "${avx2}.build-info.tsv"
+          test -f "${avx2}.compatibility.tsv"
+          test -f "${avx2}.ldd.txt"
+          (
+            cd dist
+            sha256sum -c "$(basename "${baseline}").STAR.sha256"
+            sha256sum -c "$(basename "${avx2}").STAR.sha256"
+          )
+          grep -Fxq $'cpu_target\tbaseline' \
+            "${baseline}/compatibility.tsv"
+          grep -Fxq $'ymm_instructions\tabsent' \
+            "${baseline}/compatibility.tsv"
+          grep -Fxq $'cpu_target\tavx2' \
+            "${avx2}/compatibility.tsv"
+          grep -Fxq $'ymm_instructions\tpresent' \
+            "${avx2}/compatibility.tsv"
+          jq -e --arg version "${version}" '
             .spdxVersion == "SPDX-2.3" and
-            (.packages[] | select(.name == "BlackSTAR").versionInfo) == "1.0.0"
-          ' dist/blackstar-1.0.0-linux-x86_64.spdx.json
+            (.packages[] | select(.name == "BlackSTAR").versionInfo) == $version
+          ' "${baseline}.spdx.json"
+          test "$(
+            jq -r .documentNamespace \
+              "${baseline}.spdx.json"
+          )" != "$(
+            jq -r .documentNamespace \
+              "${avx2}.spdx.json"
+          )"
+
+      - name: Verify release variant result equivalence
+        run: extras/tests/scripts/testReleaseVariants.sh
 
       - name: Build upstream 2.7.11b compatibility oracle
         run: |
           git worktree add "${RUNNER_TEMP}/star-upstream-2.7.11b" 2.7.11b
           make -C "${RUNNER_TEMP}/star-upstream-2.7.11b/source" -j2 STAR
           echo "UPSTREAM_STAR_BIN=${RUNNER_TEMP}/star-upstream-2.7.11b/source/STAR" >> "${GITHUB_ENV}"
 
+      - name: Run specialized-mode compatibility tests
+        env:
+          KEEP_TEST_OUTPUT: "1"
+          OUT_DIR: ${{ runner.temp }}/specialized-modes
+          THREADS: "4"
+        run: extras/tests/scripts/testSpecializedModes.sh
+
       - name: Run focused sanitizer tests
         run: |
           extras/tests/scripts/testAlignmentThreadAffinity.sh
+          extras/tests/scripts/testNumaMemoryPolicy.sh
           extras/tests/scripts/testReadChunkConfig.sh
+          extras/tests/scripts/testTranscriptomePrimary.sh
+          extras/tests/scripts/testSystemMemory.sh
           extras/tests/scripts/testPackedArray.sh
           extras/tests/scripts/testSuffixComparator.sh
           extras/tests/scripts/testTranscriptInitialization.sh
@@ -141,6 +201,7 @@ jobs:
             ${{ runner.temp }}/release-build-2
             ${{ runner.temp }}/genome-insert-hardening
             ${{ runner.temp }}/saindex-strategies
+            ${{ runner.temp }}/specialized-modes
 
   compiler-build:
     name: compiler-${{ matrix.name }}
@@ -169,6 +230,107 @@ jobs:
           CXX: ${{ matrix.cxx }}
         run: |
           make -C source -j2 STAR CXX="${CXX}"
+          version="$(sed -n 's/^#define BLACKSTAR_VERSION "\(.*\)"$/\1/p' source/VERSION)"
           test "$(source/STAR --version)" = "2.7.11b-blackstar.3"
-          source/STAR --version-json | jq -e '.blackstar_version == "1.0.0"'
+          source/STAR --version-json |
+            jq -e --arg version "${version}" '.blackstar_version == $version'
           ldd source/STAR | grep -Eq 'libgomp|libomp'
+
+  starlong-build-and-smoke:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 35
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+
+      - name: Install build dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y g++ make zlib1g-dev
+
+      - name: Build short-read and long-read binaries in one tree
+        run: |
+          make -C source -j2 STAR
+          make -C source -j2 STARlong
+          test -x source/STAR
+          test -x source/STARlong
+
+      - name: Build official STARlong compatibility oracle
+        run: |
+          git worktree add --detach "${RUNNER_TEMP}/star-upstream-long" 2.7.11b
+          make -C "${RUNNER_TEMP}/star-upstream-long/source" -j2 STARlong
+          echo "UPSTREAM_STARLONG_BIN=${RUNNER_TEMP}/star-upstream-long/source/STARlong" >> "${GITHUB_ENV}"
+
+      - name: Exercise STARlong-only code and high-thread chunk sizing
+        env:
+          THREADS: "96"
+          KEEP_TEST_OUTPUT: "1"
+          OUT_DIR: ${{ runner.temp }}/starlong-smoke
+          REQUIRE_UPSTREAM_STARLONG: "1"
+        run: extras/tests/scripts/testSTARlong.sh
+
+      - name: Upload STARlong smoke evidence
+        if: always()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: blackstar-starlong-${{ github.run_id }}
+          if-no-files-found: ignore
+          retention-days: 14
+          path: ${{ runner.temp }}/starlong-smoke
+
+  release-portability:
+    runs-on: ubuntu-24.04
+    container: ubuntu:20.04
+    timeout-minutes: 45
+    steps:
+      - name: Install older-userspace build dependencies
+        env:
+          DEBIAN_FRONTEND: noninteractive
+        run: |
+          apt-get update
+          apt-get install -y binutils g++ git gzip make python3 xxd zlib1g-dev
+
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+
+      - name: Build explicit CPU variants on glibc 2.31
+        env:
+          DIST_DIR: ${{ runner.temp }}/portable-dist
+          JOBS: "2"
+        run: |
+          git config --global --add safe.directory "${GITHUB_WORKSPACE}"
+          CPU_TARGET=baseline extras/scripts/buildBlackSTARRelease.sh
+          CPU_TARGET=avx2 extras/scripts/buildBlackSTARRelease.sh
+
+      - name: Verify ABI and ISA floors
+        env:
+          DIST_DIR: ${{ runner.temp }}/portable-dist
+        run: |
+          version="$(sed -n 's/^#define BLACKSTAR_VERSION "\(.*\)"$/\1/p' source/VERSION)"
+          for target in baseline avx2; do
+            compatibility="${DIST_DIR}/blackstar-${version}-linux-x86_64-${target}/compatibility.tsv"
+            minimum_glibc="$(awk -F '\t' '$1=="minimum_glibc" {print $2}' "${compatibility}")"
+            dpkg --compare-versions "${minimum_glibc}" le "2.31"
+          done
+          awk -F '\t' \
+            '$1=="ymm_instructions" && $2=="absent" {found=1} END {exit !found}' \
+            "${DIST_DIR}/blackstar-${version}-linux-x86_64-baseline/compatibility.tsv"
+          awk -F '\t' \
+            '$1=="ymm_instructions" && $2=="present" {found=1} END {exit !found}' \
+            "${DIST_DIR}/blackstar-${version}-linux-x86_64-avx2/compatibility.tsv"
+
+      - name: Verify release variant result equivalence
+        env:
+          DIST_DIR: ${{ runner.temp }}/portable-dist
+        run: extras/tests/scripts/testReleaseVariants.sh
+
+      - name: Upload portability evidence
+        if: always()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: blackstar-portable-release-${{ github.run_id }}
+          if-no-files-found: error
+          retention-days: 14
+          path: ${{ runner.temp }}/portable-dist