Replidec 0.3.4__tar.gz → 0.3.6__tar.gz

replidec-0.3.6/.conda/meta.yaml

@@ -0,0 +1,42 @@
+{% set name = "Replidec" %}
+{% set version = "0.2.3.1" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  path: "../"
+
+build:
+  number: 0
+  entry_points:
+    - Replidec=Replidec.Replidec_cmdline:main
+  script: "pip install . -vv"
+
+requirements:
+  host:
+    - python=3.10
+    - biopython=1.79
+    - click
+    - numpy=1.23.1
+    - pip
+  run:
+    - python=3.10
+    - biopython=1.79
+    - click
+    - numpy=1.23.1
+    - mmseqs2
+    - blast
+    - hmmer
+    - prodigal
+
+
+about:
+  home: "https://github.com/deng-lab/Replidec"
+  license: MIT
+  license_family: MIT
+  license_file: 
+  summary: "Replidec"
+  doc_url: 
+  dev_url: 

replidec-0.3.6/.gitattributes

@@ -0,0 +1,4 @@
+Replidec/db/mmseq2_linclust_cluster.stat.scoreOpt.tsv filter=lfs diff=lfs merge=lfs -text
+Replidec/db/bayes_mmseqs_index/all.protein filter=lfs diff=lfs merge=lfs -text
+Replidec/db/bayes_mmseqs_index/all.protein_h filter=lfs diff=lfs merge=lfs -text
+Replidec/db/bayes_mmseqs_index/all.protein.lookup filter=lfs diff=lfs merge=lfs -text

replidec-0.3.6/.github/CODEOWNERS

@@ -0,0 +1,2 @@
+# Every change entering main requires final review from the repository owner.
+* @pengSherryYel

replidec-0.3.6/.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* Replidec version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

replidec-0.3.6/.github/pull_request_template.md

@@ -0,0 +1,50 @@
+## Summary
+
+<!-- What changed? Keep this short and specific. -->
+
+## Motivation
+
+<!-- Why is the change needed? Link the relevant issue or discussion. -->
+
+## Branch intent
+
+- [ ] `develop` to `main` release candidate
+- [ ] Optional feature branch to `develop`
+- [ ] Other (explain below)
+
+## Architecture, scientific behavior, and compatibility
+
+<!--
+Explain how the change fits the existing design. Call out intentional changes
+to scientific logic, thresholds, database assumptions, CLI behavior, file
+formats, outputs, dependencies, or supported environments. Write "No impact"
+for areas that are unaffected.
+-->
+
+## Validation
+
+<!-- List the exact commands or workflows run and summarize their results. -->
+
+```text
+
+```
+
+## Regression risks and review focus
+
+<!-- What could this change break, and where should reviewers look closely? -->
+
+## Release impact
+
+- [ ] No production release is required.
+- [ ] A production release is appropriate after this PR is approved and merged.
+- [ ] The package version, documentation, or release notes need updating.
+
+## Author checklist
+
+- [ ] The change is focused and contains no unrelated modifications.
+- [ ] New or changed behavior has appropriate tests.
+- [ ] Existing behavior and backward compatibility were checked.
+- [ ] Flake8 and relevant tests pass, or failures are explained above.
+- [ ] No secrets, generated artifacts, unpublished data, or private URLs are included.
+- [ ] Codex review findings have been resolved or answered.
+- [ ] The pull request is ready for final human review.

replidec-0.3.6/.github/workflows/release.yml

@@ -0,0 +1,386 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+  workflow_dispatch:
+    inputs:
+      ref:
+        description: Branch or commit to validate during a dry run
+        required: true
+        default: main
+        type: string
+      tag:
+        description: Expected release tag in vX.Y.Z format
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+concurrency:
+  group: release-${{ github.event_name == 'workflow_dispatch' && inputs.tag || github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  validate:
+    name: Validate release metadata
+    runs-on: ubuntu-latest
+    outputs:
+      checkout-ref: ${{ steps.mode.outputs.checkout-ref }}
+      tag: ${{ steps.version.outputs.tag }}
+      version: ${{ steps.version.outputs.version }}
+    steps:
+      - name: Resolve release mode
+        id: mode
+        shell: bash
+        env:
+          EVENT_NAME: ${{ github.event_name }}
+          PUSH_TAG: ${{ github.ref_name }}
+          INPUT_REF: ${{ inputs.ref }}
+          INPUT_TAG: ${{ inputs.tag }}
+        run: |
+          set -euo pipefail
+
+          if [[ "${EVENT_NAME}" == "push" ]]; then
+            tag="${PUSH_TAG}"
+            checkout_ref="${PUSH_TAG}"
+          else
+            tag="${INPUT_TAG}"
+            checkout_ref="${INPUT_REF}"
+          fi
+
+          if [[ "${tag}" == *$'\n'* || "${tag}" == *$'\r'* ||
+                "${checkout_ref}" == *$'\n'* || "${checkout_ref}" == *$'\r'* ]]; then
+            echo "Release tag and checkout ref must each be a single line." >&2
+            exit 1
+          fi
+
+          printf 'checkout-ref=%s\n' "${checkout_ref}" >> "${GITHUB_OUTPUT}"
+          printf 'tag=%s\n' "${tag}" >> "${GITHUB_OUTPUT}"
+
+      - name: Check out the release candidate
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          ref: ${{ steps.mode.outputs.checkout-ref }}
+          fetch-depth: 0
+
+      - name: Validate tag and project version
+        id: version
+        shell: bash
+        env:
+          RELEASE_TAG: ${{ steps.mode.outputs.tag }}
+          PUBLISH: ${{ github.event_name == 'push' }}
+        run: |
+          set -euo pipefail
+          python scripts/check_release_version.py \
+            --tag "${RELEASE_TAG}" \
+            --github-output "${GITHUB_OUTPUT}"
+
+          if [[ "${PUBLISH}" == "true" ]]; then
+            tag_commit="$(git rev-list -n 1 "refs/tags/${RELEASE_TAG}")"
+            checkout_commit="$(git rev-parse HEAD)"
+            if [[ "${tag_commit}" != "${checkout_commit}" ]]; then
+              echo "Release tag ${RELEASE_TAG} does not point to the checked-out commit" >&2
+              exit 1
+            fi
+
+            git fetch --no-tags origin main:refs/remotes/origin/main
+            if ! git merge-base --is-ancestor "${tag_commit}" origin/main; then
+              echo "Release tag ${RELEASE_TAG} does not point to a commit in main" >&2
+              exit 1
+            fi
+          fi
+
+  test:
+    name: Test release candidate
+    needs: validate
+    uses: ./.github/workflows/test.yml
+    with:
+      ref: ${{ needs.validate.outputs.checkout-ref }}
+    permissions:
+      contents: read
+
+  build:
+    name: Build and verify Python distributions
+    needs:
+      - validate
+      - test
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - name: Check out the tested release candidate
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          ref: ${{ needs.validate.outputs.checkout-ref }}
+
+      - name: Set up Python
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
+        with:
+          python-version: "3.10"
+          cache: pip
+
+      - name: Build sdist and wheel
+        env:
+          RELEASE_VERSION: ${{ needs.validate.outputs.version }}
+        run: |
+          set -euo pipefail
+          python -m pip install --upgrade build twine
+          python -m build
+          python -m twine check dist/*
+
+          python - <<'PY'
+          import os
+          from pathlib import Path
+
+          version = os.environ["RELEASE_VERSION"]
+          files = [path.name.lower() for path in Path("dist").iterdir()]
+          expected = f"replidec-{version}"
+          if len(files) != 2 or not all(expected in filename for filename in files):
+              raise SystemExit(f"Unexpected distribution files: {files}")
+          print("Verified distribution files:", *files)
+          PY
+
+      - name: Install and smoke-test the wheel
+        run: |
+          set -euo pipefail
+          python -m pip install --force-reinstall dist/*.whl
+          Replidec --version
+          replidec --help >/dev/null
+
+      - name: Upload immutable Python distributions
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
+        with:
+          name: python-dist-${{ needs.validate.outputs.version }}
+          path: dist/
+          if-no-files-found: error
+          retention-days: 30
+
+  publish_pypi:
+    name: Publish to PyPI
+    if: github.event_name == 'push'
+    needs:
+      - validate
+      - build
+      - bioconda_preflight
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/replidec
+    permissions:
+      contents: read
+      id-token: write
+    steps:
+      - name: Download tested distributions
+        uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
+        with:
+          name: python-dist-${{ needs.validate.outputs.version }}
+          path: dist
+
+      - name: Publish distributions with PyPI Trusted Publishing
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
+        with:
+          packages-dir: dist/
+          skip-existing: true
+
+  bioconda_preflight:
+    name: Check Bioconda PR access
+    if: github.event_name == 'push'
+    needs:
+      - validate
+      - test
+    runs-on: ubuntu-latest
+    environment:
+      name: bioconda
+      url: https://github.com/bioconda/bioconda-recipes/pulls
+    permissions:
+      contents: read
+    env:
+      GH_TOKEN: ${{ secrets.BIOCONDA_PR_TOKEN }}
+      FORK_OWNER: ${{ vars.BIOCONDA_FORK_OWNER || github.repository_owner }}
+    steps:
+      - name: Verify token and fork access before publishing
+        run: |
+          set -euo pipefail
+          if [[ -z "${GH_TOKEN}" ]]; then
+            echo "BIOCONDA_PR_TOKEN is not configured in the bioconda environment." >&2
+            exit 1
+          fi
+
+          gh auth status
+          token_owner="$(gh api user --jq '.login')"
+          fork="${FORK_OWNER}/bioconda-recipes"
+          fork_access="$(gh api "repos/${fork}" \
+            --jq '[(.permissions.push // false), (.fork // false), (.parent.full_name // "")] | @tsv')"
+          IFS=$'\t' read -r can_push is_fork parent_repo <<< "${fork_access}"
+
+          if [[ "${is_fork}" != "true" || "${parent_repo}" != "bioconda/bioconda-recipes" ]]; then
+            echo "${fork} is not a fork of bioconda/bioconda-recipes." >&2
+            exit 1
+          fi
+
+          if [[ "${can_push}" != "true" ]]; then
+            echo "BIOCONDA_PR_TOKEN (${token_owner}) does not have push access to ${fork}." >&2
+            exit 1
+          fi
+
+          probe_branch="replidec-preflight-${GITHUB_RUN_ID}-${GITHUB_RUN_ATTEMPT}-missing"
+          if gh api "repos/${fork}/git/ref/heads/${probe_branch}" >/dev/null 2>&1; then
+            echo "Refusing to use existing permission-probe branch ${probe_branch}." >&2
+            exit 1
+          fi
+
+          set +e
+          probe_output="$(gh api \
+            --include \
+            --method POST \
+            repos/bioconda/bioconda-recipes/pulls \
+            -f title="RepliDec release permission probe" \
+            -f head="${FORK_OWNER}:${probe_branch}" \
+            -f base=master \
+            2>&1)"
+          probe_exit=$?
+          set -e
+
+          if [[ ${probe_exit} -eq 0 ]] || ! grep -Eq '^HTTP/[^ ]+ 422 ' <<< "${probe_output}"; then
+            echo "BIOCONDA_PR_TOKEN (${token_owner}) cannot create pull requests in bioconda/bioconda-recipes." >&2
+            printf '%s\n' "${probe_output}" >&2
+            exit 1
+          fi
+
+          {
+            echo "BIOCONDA_PR_TOKEN (${token_owner}) can push to ${fork}."
+            echo "The token can also reach the upstream pull-request creation endpoint."
+          } >> "${GITHUB_STEP_SUMMARY}"
+
+  github_release:
+    name: Create GitHub Release
+    if: github.event_name == 'push'
+    needs:
+      - validate
+      - build
+      - publish_pypi
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Download tested distributions
+        uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
+        with:
+          name: python-dist-${{ needs.validate.outputs.version }}
+          path: dist
+
+      - name: Create or update the release
+        env:
+          GH_TOKEN: ${{ github.token }}
+          GH_REPO: ${{ github.repository }}
+          RELEASE_TAG: ${{ needs.validate.outputs.tag }}
+          RELEASE_VERSION: ${{ needs.validate.outputs.version }}
+        run: |
+          set -euo pipefail
+          if gh release view "${RELEASE_TAG}" >/dev/null 2>&1; then
+            gh release upload "${RELEASE_TAG}" dist/* --clobber
+          else
+            gh release create "${RELEASE_TAG}" dist/* \
+              --verify-tag \
+              --generate-notes \
+              --title "RepliDec ${RELEASE_VERSION}"
+          fi
+
+  bioconda_pr:
+    name: Open Bioconda recipe PR
+    if: github.event_name == 'push'
+    needs:
+      - validate
+      - github_release
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    environment:
+      name: bioconda
+      url: https://github.com/bioconda/bioconda-recipes/pulls
+    permissions:
+      contents: read
+    env:
+      GH_TOKEN: ${{ secrets.BIOCONDA_PR_TOKEN }}
+      FORK_OWNER: ${{ vars.BIOCONDA_FORK_OWNER || github.repository_owner }}
+      RELEASE_TAG: ${{ needs.validate.outputs.tag }}
+      RELEASE_VERSION: ${{ needs.validate.outputs.version }}
+    steps:
+      - name: Check out release automation
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          ref: ${{ needs.validate.outputs.checkout-ref }}
+
+      - name: Download the published PyPI sdist and compute its checksum
+        id: sdist
+        run: |
+          set -euo pipefail
+          sdist="${RUNNER_TEMP}/replidec-${RELEASE_VERSION}.tar.gz"
+          url="https://pypi.org/packages/source/r/replidec/replidec-${RELEASE_VERSION}.tar.gz"
+          curl --fail --location \
+            --retry 12 \
+            --retry-delay 10 \
+            --retry-all-errors \
+            --output "${sdist}" \
+            "${url}"
+          sha256="$(sha256sum "${sdist}" | cut -d ' ' -f 1)"
+          echo "sha256=${sha256}" >> "${GITHUB_OUTPUT}"
+
+      - name: Update the official Bioconda recipe
+        env:
+          SDIST_SHA256: ${{ steps.sdist.outputs.sha256 }}
+        run: |
+          set -euo pipefail
+          fork="${FORK_OWNER}/bioconda-recipes"
+          branch="replidec-${RELEASE_VERSION}"
+          checkout="${RUNNER_TEMP}/bioconda-recipes"
+
+          if ! gh repo view "${fork}" >/dev/null 2>&1; then
+            echo "Missing ${fork}. Create a fork of bioconda/bioconda-recipes before publishing." >&2
+            exit 1
+          fi
+
+          gh auth setup-git
+          git clone --filter=blob:none "https://github.com/${fork}.git" "${checkout}"
+          cd "${checkout}"
+          git remote add upstream https://github.com/bioconda/bioconda-recipes.git
+          git fetch upstream master
+          git checkout -B "${branch}" upstream/master
+
+          python "${GITHUB_WORKSPACE}/scripts/update_bioconda_recipe.py" \
+            --recipe recipes/replidec/meta.yaml \
+            --version "${RELEASE_VERSION}" \
+            --sha256 "${SDIST_SHA256}"
+
+          if git diff --quiet -- recipes/replidec/meta.yaml; then
+            echo "Bioconda recipe is already up to date for ${RELEASE_VERSION}." >> "${GITHUB_STEP_SUMMARY}"
+            exit 0
+          fi
+
+          git config user.name "RepliDec release bot"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add recipes/replidec/meta.yaml
+          git commit -m "Update replidec to ${RELEASE_VERSION}"
+          git push --force origin "${branch}"
+
+          pr_url="$(gh api \
+            --method GET \
+            repos/bioconda/bioconda-recipes/pulls \
+            -f state=open \
+            -f base=master \
+            -f head="${FORK_OWNER}:${branch}" \
+            --jq '.[0].html_url // empty')"
+
+          if [[ -z "${pr_url}" ]]; then
+            pr_url="$(gh api \
+              --method POST \
+              repos/bioconda/bioconda-recipes/pulls \
+              -f base=master \
+              -f head="${FORK_OWNER}:${branch}" \
+              -f title="Update replidec to ${RELEASE_VERSION}" \
+              -f body="Automated recipe update for [RepliDec ${RELEASE_VERSION}](https://github.com/${GITHUB_REPOSITORY}/releases/tag/${RELEASE_TAG}). The source checksum was calculated from the published PyPI sdist." \
+              --jq '.html_url')"
+          fi
+
+          echo "Bioconda PR: ${pr_url}" >> "${GITHUB_STEP_SUMMARY}"

replidec-0.3.6/.github/workflows/test.yml

@@ -0,0 +1,170 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - main
+  workflow_call:
+    inputs:
+      ref:
+        description: Git ref to test; defaults to the triggering ref
+        required: false
+        type: string
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: test-${{ github.workflow }}-${{ github.event.pull_request.number || inputs.ref || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Flake8
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - name: Check out candidate code
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          ref: ${{ inputs.ref || github.sha }}
+
+      - name: Set up Python
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
+        with:
+          python-version: "3.10"
+          cache: pip
+          cache-dependency-path: requirements-dev.txt
+
+      - name: Install lint dependencies
+        run: python -m pip install --requirement requirements-dev.txt
+
+      - name: Run Flake8
+        run: python -m flake8 .
+
+  integration:
+    name: RepliDec integration
+    runs-on: ubuntu-latest
+    timeout-minutes: 90
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+
+    steps:
+      - name: Check out candidate code
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          ref: ${{ inputs.ref || github.sha }}
+
+      - name: Install the current Bioconda package and runtime dependencies
+        uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
+        with:
+          environment-name: replidec-ci
+          create-args: >-
+            python=3.10
+            pip
+            replidec
+          condarc: |
+            channels:
+              - conda-forge
+              - bioconda
+            channel_priority: strict
+          cache-downloads: true
+          init-shell: bash
+
+      - name: Upgrade RepliDec to the candidate code
+        id: candidate
+        run: |
+          python -m pip install --no-deps --upgrade --force-reinstall .
+
+          (
+            cd "${RUNNER_TEMP}"
+            python - <<'PY'
+          import os
+          import re
+          from pathlib import Path
+
+          import Replidec
+          from Replidec.Replidec import DATABASE_MANIFEST
+
+          workspace = Path(os.environ["GITHUB_WORKSPACE"]).resolve()
+          source = (workspace / "Replidec/__init__.py").read_text(encoding="utf-8")
+          expected = re.search(r'^__version__\s*=\s*["\x27]([^"\x27]+)["\x27]', source, re.MULTILINE)
+          assert expected is not None, "Unable to read the candidate version"
+
+          package_path = Path(Replidec.__file__).resolve()
+          print(f"Testing RepliDec {Replidec.__version__} from {package_path}")
+          assert workspace not in package_path.parents, (
+              "Candidate import resolved to the checkout instead of the installed package"
+          )
+          assert Replidec.__version__ == expected.group(1), (
+              "Candidate code did not replace the published Bioconda package"
+          )
+
+          with Path(os.environ["GITHUB_OUTPUT"]).open("a", encoding="utf-8") as output:
+              output.write(f"package-dir={package_path.parent}\n")
+              output.write(f"database-version={DATABASE_MANIFEST['version']}\n")
+              output.write(f"database-url={DATABASE_MANIFEST['url']}\n")
+          PY
+          )
+
+          Replidec --version
+          replidec --version
+
+      - name: Restore the reference database
+        uses: actions/cache@caa296126883cff596d87d8935842f9db880ef25 # v5.1.0
+        with:
+          path: ${{ steps.candidate.outputs.package-dir }}/db
+          key: replidec-db-site-packages-${{ runner.os }}-v${{ steps.candidate.outputs.database-version }}
+
+      - name: Download and verify the reference database on a cache miss
+        env:
+          DATABASE_DIR: ${{ steps.candidate.outputs.package-dir }}/db
+          DATABASE_URL: ${{ steps.candidate.outputs.database-url }}
+        run: |
+          set -euo pipefail
+
+          if [[ -f "${DATABASE_DIR}/md5sum.list" ]] && (
+            cd "${DATABASE_DIR}" && md5sum --check --quiet md5sum.list
+          ); then
+            echo "Using the cached reference database."
+          else
+            rm -rf "${DATABASE_DIR}"
+            archive="${RUNNER_TEMP}/replidec-database.tar.gz"
+            curl --fail --location \
+              --retry 5 \
+              --retry-delay 10 \
+              --retry-all-errors \
+              --silent \
+              --show-error \
+              --output "${archive}" \
+              "${DATABASE_URL}"
+            tar -xzf "${archive}" -C "$(dirname "${DATABASE_DIR}")"
+            (
+              cd "${DATABASE_DIR}"
+              md5sum --check --quiet md5sum.list
+            )
+          fi
+
+      - name: Run release helper tests
+        run: python -m unittest discover -s test -p 'test_*.py' -v
+
+      - name: Run end-to-end tests
+        env:
+          REPLIDEC_TEST_OUTPUT_DIR: ${{ runner.temp }}/replidec-test-results
+        run: bash test/example.sh
+
+      - name: Upload test summaries and external-tool logs
+        if: always()
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
+        with:
+          name: replidec-test-results-${{ github.run_id }}
+          path: |
+            ${{ runner.temp }}/replidec-test-results/**/prediction_summary.tsv
+            ${{ runner.temp }}/replidec-test-results/**/external_tools.log
+          if-no-files-found: warn
+          retention-days: 14

replidec-0.3.6/.gitignore

@@ -0,0 +1,8 @@
+build/
+Replidec.egg-info/
+dist/
+__pycache__/
+*.py[cod]
+sectest/
+.idea
+Replidec/db/

replidec-0.3.6/.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+# One-time setup:
+#   python -m pip install -r requirements-dev.txt
+#   pre-commit install --hook-type pre-push
+repos:
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.3.0
+    hooks:
+      - id: flake8
+        name: Flake8
+        stages:
+          - pre-push