seqpro 0.11.0__tar.gz → 0.12.0__tar.gz

seqpro-0.12.0/.github/workflows/bump.yaml

@@ -0,0 +1,94 @@
+name: Bump version
+
+on:
+  workflow_call:
+    inputs:
+      increment:
+        description: "Force a specific bump (auto|PATCH|MINOR|MAJOR)"
+        type: string
+        required: false
+        default: "auto"
+      dry_run:
+        description: "Compute the bump but do not commit/push"
+        type: boolean
+        required: false
+        default: false
+    outputs:
+      tag:
+        description: "The version string after the bump (or projected version in dry-run)"
+        value: ${{ jobs.bump.outputs.tag }}
+  workflow_dispatch:
+    inputs:
+      increment:
+        description: "Force a specific bump"
+        type: choice
+        required: false
+        default: "auto"
+        options: ["auto", "PATCH", "MINOR", "MAJOR"]
+      dry_run:
+        description: "Compute the bump but do not commit/push"
+        type: boolean
+        required: false
+        default: false
+
+jobs:
+  bump:
+    runs-on: ubuntu-latest
+    outputs:
+      tag: ${{ steps.emit.outputs.tag }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: "${{ secrets.GH_TOKEN }}"
+
+      - name: Install commitizen
+        run: pip install commitizen --quiet
+
+      - name: Detect partial bump
+        id: detect
+        run: |
+          PROJECT_VERSION=$(cz version --project)
+          LATEST_TAG=$(git tag --sort=-version:refname | grep -E '^[0-9]+\.[0-9]+\.[0-9]+$' | head -1)
+          if [ -n "$LATEST_TAG" ] && [ "$LATEST_TAG" != "$PROJECT_VERSION" ]; then
+            echo "partial=true" >> $GITHUB_OUTPUT
+            echo "tag=$LATEST_TAG" >> $GITHUB_OUTPUT
+          else
+            echo "partial=false" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Bump version (real)
+        if: steps.detect.outputs.partial != 'true' && inputs.dry_run == false
+        uses: commitizen-tools/commitizen-action@master
+        with:
+          github_token: ${{ secrets.GH_TOKEN }}
+          increment: ${{ inputs.increment != 'auto' && inputs.increment || '' }}
+
+      - name: Bump version (dry-run)
+        if: steps.detect.outputs.partial != 'true' && inputs.dry_run == true
+        run: |
+          ARGS="--dry-run --yes"
+          if [ "${{ inputs.increment }}" != "auto" ]; then
+            ARGS="$ARGS --increment ${{ inputs.increment }}"
+          fi
+          cz bump $ARGS
+
+      - name: Fix partial bump (tag exists on remote, update files only)
+        if: steps.detect.outputs.partial == 'true' && inputs.dry_run == false
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          NEW_VERSION="${{ steps.detect.outputs.tag }}"
+          cz bump --files-only --yes
+          BUMPED_VERSION=$(cz version --project)
+          git add pyproject.toml CHANGELOG.md
+          git commit -m "bump: version $NEW_VERSION"
+          git push origin main
+          git push origin "$BUMPED_VERSION"
+
+      - name: Emit resulting tag
+        id: emit
+        run: |
+          TAG=$(cz version --project)
+          echo "tag=$TAG" >> $GITHUB_OUTPUT
+          echo "Resolved tag: $TAG"

seqpro-0.12.0/.github/workflows/merge.yaml

@@ -0,0 +1,50 @@
+name: Merge main -> stable
+
+on:
+  workflow_call:
+    inputs:
+      dry_run:
+        description: 'Compute the rebase but do not push'
+        type: boolean
+        required: false
+        default: false
+  workflow_dispatch:
+    inputs:
+      dry_run:
+        description: 'Compute the rebase but do not push'
+        type: boolean
+        required: false
+        default: false
+
+jobs:
+  merge:
+    environment: pypi
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+        with:
+          ref: stable
+          fetch-depth: 0
+          token: "${{ secrets.GH_TOKEN }}"
+      - name: Config git
+        run: |
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
+      - name: Rebase stable onto main
+        run: git rebase origin/main
+      - name: Push to stable
+        if: inputs.dry_run == false
+        run: git push origin stable
+      - name: Dry-run summary (skipped push)
+        if: inputs.dry_run == true
+        run: |
+          {
+            echo "## Dry-run: would push the following to stable"
+            echo
+            echo '```'
+            git log --oneline origin/stable..HEAD
+            echo '```'
+          } >> "$GITHUB_STEP_SUMMARY"

{seqpro-0.11.0 → seqpro-0.12.0}/.github/workflows/publish.yaml

@@ -1,22 +1,48 @@
-# This file is autogenerated by maturin v1.13.1
-# To update, run
+# This file was autogenerated by maturin v1.13.1 and has been hand-modified
+# to support workflow_call from release-pipeline.yaml.
+#
+# To regenerate, run:
 #
 #    maturin generate-ci -o .github/workflows/publish.yaml github
 #
+# Regenerating will overwrite the trigger block and the per-job `if:`
+# conditions below. Re-apply the workflow_call inputs (`dry_run`), delete
+# the `on.workflow_run` block, remove all `if: ${{ github.event_name ... }}`
+# guards, and wrap the `uv publish` step with the dry_run gate before
+# committing.
 name: Publish
 
 on:
-  workflow_run:
-    workflows: [Create release]
-    types: [completed]
+  workflow_call:
+    inputs:
+      dry_run:
+        description: 'Build wheels but skip uv publish'
+        type: boolean
+        required: false
+        default: false
+      tag:
+        description: 'Tag to check out and build wheels from (defaults to caller ref)'
+        type: string
+        required: false
+        default: ''
   workflow_dispatch:
+    inputs:
+      dry_run:
+        description: 'Build wheels but skip uv publish'
+        type: boolean
+        required: false
+        default: false
+      tag:
+        description: 'Tag to check out and build wheels from (defaults to current ref)'
+        type: string
+        required: false
+        default: ''
 
 permissions:
   contents: read
 
 jobs:
   linux:
-    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
@@ -35,6 +61,8 @@ jobs:
             target: ppc64le
     steps:
       - uses: actions/checkout@v6
+        with:
+          ref: ${{ inputs.tag }}
       - uses: actions/setup-python@v6
         with:
           python-version: '3.10'
@@ -59,7 +87,6 @@ jobs:
           path: dist
 
   musllinux:
-    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
@@ -74,6 +101,8 @@ jobs:
             target: armv7
     steps:
       - uses: actions/checkout@v6
+        with:
+          ref: ${{ inputs.tag }}
       - uses: actions/setup-python@v6
         with:
           python-version: '3.10'
@@ -98,7 +127,6 @@ jobs:
           path: dist
 
   windows:
-    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
@@ -114,6 +142,8 @@ jobs:
             python_arch: arm64
     steps:
       - uses: actions/checkout@v6
+        with:
+          ref: ${{ inputs.tag }}
       - uses: actions/setup-python@v6
         with:
           python-version: '3.13'
@@ -141,7 +171,6 @@ jobs:
           path: dist
 
   macos:
-    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
@@ -152,6 +181,8 @@ jobs:
             target: aarch64
     steps:
       - uses: actions/checkout@v6
+        with:
+          ref: ${{ inputs.tag }}
       - uses: actions/setup-python@v6
         with:
           python-version: '3.10'
@@ -177,10 +208,11 @@ jobs:
           path: dist
 
   sdist:
-    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
+        with:
+          ref: ${{ inputs.tag }}
       - name: Build sdist
         uses: PyO3/maturin-action@v1
         with:
@@ -196,7 +228,6 @@ jobs:
     environment: pypi
     name: Release
     runs-on: ubuntu-latest
-    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
     needs: [linux, musllinux, windows, macos, sdist]
     permissions:
       # Use to sign the release artifacts
@@ -214,4 +245,14 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v7
       - name: Publish to PyPI
+        if: inputs.dry_run == false
         run: uv publish 'wheels-*/*'
+
+      - name: Dry-run summary (skipped uv publish)
+        if: inputs.dry_run == true
+        run: |
+          {
+            echo "## Dry-run: would have published the following wheels"
+            echo
+            ls -1 wheels-*/* | sed 's/^/- /'
+          } >> "$GITHUB_STEP_SUMMARY"

seqpro-0.12.0/.github/workflows/release-pipeline.yaml

@@ -0,0 +1,101 @@
+name: Release pipeline
+
+on:
+  workflow_dispatch:
+    inputs:
+      increment:
+        description: "Force a specific bump (auto = let commitizen decide)"
+        type: choice
+        required: false
+        default: "auto"
+        options: ["auto", "PATCH", "MINOR", "MAJOR"]
+      skip_bump:
+        description: "Skip bump; release/publish/merge an existing tag instead"
+        type: boolean
+        required: false
+        default: false
+      tag:
+        description: "Existing tag to release (required when skip_bump=true)"
+        type: string
+        required: false
+        default: ""
+      dry_run:
+        description: "Run end-to-end without external side effects"
+        type: boolean
+        required: false
+        default: false
+
+permissions:
+  contents: write
+  id-token: write
+  attestations: write
+
+jobs:
+  resolve:
+    runs-on: ubuntu-latest
+    outputs:
+      tag: ${{ steps.out.outputs.tag }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Validate inputs
+        id: out
+        run: |
+          if [ "${{ inputs.skip_bump }}" = "true" ]; then
+            TAG="${{ inputs.tag }}"
+            if [ -z "$TAG" ]; then
+              echo "::error::skip_bump=true requires a tag input"
+              exit 1
+            fi
+            if ! echo "$TAG" | grep -Eq '^[0-9]+\.[0-9]+\.[0-9]+$'; then
+              echo "::error::tag '$TAG' does not match X.Y.Z"
+              exit 1
+            fi
+            git fetch --tags --quiet
+            if ! git rev-parse --verify --quiet "refs/tags/$TAG" >/dev/null; then
+              echo "::error::tag '$TAG' does not exist on the remote"
+              exit 1
+            fi
+            echo "tag=$TAG" >> "$GITHUB_OUTPUT"
+          else
+            echo "tag=" >> "$GITHUB_OUTPUT"
+          fi
+
+  bump:
+    needs: resolve
+    if: inputs.skip_bump == false
+    uses: ./.github/workflows/bump.yaml
+    secrets: inherit
+    with:
+      increment: ${{ inputs.increment }}
+      dry_run: ${{ inputs.dry_run }}
+
+  release:
+    needs: [resolve, bump]
+    if: |
+      always() &&
+      needs.resolve.result == 'success' &&
+      (needs.bump.result == 'success' || needs.bump.result == 'skipped')
+    uses: ./.github/workflows/release.yaml
+    secrets: inherit
+    with:
+      tag: ${{ needs.bump.outputs.tag || needs.resolve.outputs.tag }}
+      dry_run: ${{ inputs.dry_run }}
+
+  publish:
+    needs: [resolve, bump, release]
+    if: always() && needs.release.result == 'success'
+    uses: ./.github/workflows/publish.yaml
+    secrets: inherit
+    with:
+      dry_run: ${{ inputs.dry_run }}
+      tag: ${{ needs.bump.outputs.tag || needs.resolve.outputs.tag }}
+
+  merge:
+    needs: publish
+    if: always() && needs.publish.result == 'success'
+    uses: ./.github/workflows/merge.yaml
+    secrets: inherit
+    with:
+      dry_run: ${{ inputs.dry_run }}

seqpro-0.12.0/.github/workflows/release.yaml

@@ -0,0 +1,71 @@
+name: Create release
+
+on:
+  push:
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Tag to release (e.g. 0.10.0)'
+        required: true
+  workflow_call:
+    inputs:
+      tag:
+        description: 'Tag to release'
+        type: string
+        required: true
+      dry_run:
+        description: 'Build the release body but do not create a GH release'
+        type: boolean
+        required: false
+        default: false
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Resolve tag
+        id: tag
+        run: |
+          case "${{ github.event_name }}" in
+            push)          echo "tag=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT ;;
+            workflow_dispatch) echo "tag=${{ inputs.tag }}" >> $GITHUB_OUTPUT ;;
+            workflow_call) echo "tag=${{ inputs.tag }}" >> $GITHUB_OUTPUT ;;
+          esac
+
+      - name: Extract changelog section
+        run: |
+          TAG="${{ steps.tag.outputs.tag }}"
+          awk -v tag="$TAG" '
+            $0 ~ "^## " tag " " { flag=1; next }
+            flag && /^## / { exit }
+            flag { print }
+          ' CHANGELOG.md > body.md
+
+      - name: Dry-run summary
+        if: github.event_name == 'workflow_call' && inputs.dry_run == true
+        run: |
+          {
+            echo "## Dry-run: release ${{ steps.tag.outputs.tag }}"
+            echo
+            echo "Would create a GitHub Release with the following body:"
+            echo
+            echo '```markdown'
+            cat body.md
+            echo '```'
+          } >> "$GITHUB_STEP_SUMMARY"
+
+      - name: Create GitHub release
+        if: ${{ !(github.event_name == 'workflow_call' && inputs.dry_run == true) }}
+        uses: softprops/action-gh-release@v3
+        with:
+          tag_name: ${{ steps.tag.outputs.tag }}
+          body_path: body.md
+          token: ${{ secrets.GH_TOKEN }}

{seqpro-0.11.0 → seqpro-0.12.0}/CHANGELOG.md

@@ -1,3 +1,59 @@
+## 0.12.0 (2026-05-29)
+
+### Feat
+
+- **translate**: validate OHE inputs are one-hot
+- **translate**: add validate flag for nucleotide input checking
+
+### Fix
+
+- **ci**: merge runs when publish succeeded after a transitive skip
+- **ci**: allow publish to run when bump was skipped
+- **ci**: publish.yaml checks out the bumped tag, not the dispatch SHA
+
+### Refactor
+
+- **translate**: gate LUT build with predicate, drop exception control-flow
+- **translate**: single source of truth for codon LUT index
+
+### Perf
+
+- **translate**: route Ragged path through codon LUT
+- **translate**: O(1) LUT codon→AA lookup — 179× speedup on bench
+
+## 0.11.1 (2026-05-21)
+
+### Feat
+
+- **ci**: add release-pipeline.yaml orchestrator
+- add on_path flag to Vertex and path stack to ShuffleBuffers
+- specialize k=2 path to skip LUT and codes lookup
+- add ShuffleBuffers with sparse-reset LUT
+- add KmerIndex trait with DirectLut and HashLut impls
+- add kmer_encode module with rolling integer encoder
+- ragged support for ohe, decode_ohe, tokenize, decode_tokens
+
+### Fix
+
+- **ci**: grant orchestrator permissions required by called workflows
+- **ci**: make merge.yaml workflow_call-able, drop workflow_run
+- **ci**: make publish.yaml workflow_call-able, drop workflow_run
+- **ci**: make release.yaml workflow_call-able with dry_run
+- **ci**: make bump.yaml workflow_call-able with increment and dry_run
+- derive per-row seeds so batches get independent shuffles
+- support arbitrary leading/trailing dims across public functions
+- types
+
+### Refactor
+
+- pool LUT and reuse buffers via ShuffleBuffers
+- rewrite k_shuffle1 with KmerIndex strategy + u32 Vertex
+
+### Perf
+
+- replace two-pass Wilson with single-pass loop-erased random walk
+- add criterion benchmark for k_shuffle
+
 ## 0.11.0 (2026-05-07)
 
 ### Feat

{seqpro-0.11.0 → seqpro-0.12.0}/CLAUDE.md

@@ -72,3 +72,7 @@ Only `kshuffle.rs` is compiled. It's exposed as `seqpro._k_shuffle` (called by `
 - Axis arguments (`length_axis`, `ohe_axis`) are always integers referring to the NumPy axis index; negative indexing is supported.
 - The `transforms/` module wraps functional ops into callable objects with `__call__` for use in data pipelines.
 - Conventional commits are enforced — use `feat:`, `fix:`, `ci:`, `bump:`, `refactor:`, `docs:`, etc. prefixes.
+
+## Skills
+
+This repo ships an installable skill at `skills/seqpro/SKILL.md` (skills.sh layout) describing how to use seqpro. **Any PR that adds a new public feature, changes a public signature, or makes a breaking change MUST update `skills/seqpro/SKILL.md` in the same PR.** Doc-only edits and internal refactors do not require updates unless they change conventions documented in the skill. Reviewers should reject feature/breaking PRs that don't touch the skill.