diff --git a/.bumpversion.toml b/.bumpversion.toml
new file mode 100644
index 00000000..8a178596
--- /dev/null
+++ b/.bumpversion.toml
@@ -0,0 +1,27 @@
+[tool.bumpversion]
+current_version = "1.0.1"
+commit = true
+tag = false
+tag_name = "v{new_version}"
+tag_message = "Release version {new_version}"
+message = "bump: version {current_version} → {new_version}"
+
+[[tool.bumpversion.files]]
+filename = "src/cpg_flow/__init__.py"
+search = "__version__ = '{current_version}'"
+replace = "__version__ = '{new_version}'"
+
+[[tool.bumpversion.files]]
+filename = "Dockerfile"
+search = "# VERSION {current_version}"
+replace = "# VERSION {new_version}"
+
+[[tool.bumpversion.files]]
+filename = ".github/workflows/docker.yaml"
+search = "VERSION: {current_version}"
+replace = "VERSION: {new_version}"
+
+[[tool.bumpversion.files]]
+filename = ".github/workflows/test.yaml"
+search = "VERSION: {current_version}"
+replace = "VERSION: {new_version}"
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..d9e20df0
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,82 @@
+version: 2
+
+# Multi-ecosystem groups for Python dependencies
+multi-ecosystem-groups:
+  python-minor-patch:
+    applies-to: version-updates
+    update-types:
+      - "minor"
+      - "patch"
+  python-major:
+    applies-to: version-updates
+    update-types:
+      - "major"
+
+updates:
+  # pip ecosystem for pyproject.toml dependencies
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    multi-ecosystem-group: python-minor-patch
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+    ignore:
+      # Don't update hail - pinned at CPG's installed version
+      - dependency-name: "hail"
+      # Don't update Python version
+      - dependency-name: "python"
+    open-pull-requests-limit: 10
+
+  # uv ecosystem for uv.lock file
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    multi-ecosystem-group: python-minor-patch
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+    ignore:
+      # Don't update hail - pinned at CPG's installed version
+      - dependency-name: "hail"
+      # Don't update Python version
+      - dependency-name: "python"
+    open-pull-requests-limit: 10
+
+  # Separate update for major versions (pip)
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    multi-ecosystem-group: python-major
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+    ignore:
+      # Don't update hail - pinned at CPG's installed version
+      - dependency-name: "hail"
+      # Don't update Python version
+      - dependency-name: "python"
+      # Ignore minor and patch updates (handled by the other group)
+      - update-types: ["version-update:semver-minor", "version-update:semver-patch"]
+    open-pull-requests-limit: 10
+
+  # Separate update for major versions (uv)
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    multi-ecosystem-group: python-major
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+    ignore:
+      # Don't update hail - pinned at CPG's installed version
+      - dependency-name: "hail"
+      # Don't update Python version
+      - dependency-name: "python"
+      # Ignore minor and patch updates (handled by the other group)
+      - update-types: ["version-update:semver-minor", "version-update:semver-patch"]
+    open-pull-requests-limit: 10
diff --git a/.github/renovate-config.json b/.github/renovate-config.json
deleted file mode 100644
index 3317d2de..00000000
--- a/.github/renovate-config.json
+++ /dev/null
@@ -1,58 +0,0 @@
-{
-  "$schema": "https://docs.renovatebot.com/renovate-schema.json",
-  "onboarding": true,
-  "requireConfig": "ignored",
-  "platform": "github",
-  "repositories": [
-    "populationgenomics/cpg-flow"
-  ],
-  "prConcurrentLimit": 10,
-  "prHourlyLimit": 5,
-  "semanticCommits": "enabled",
-  "enabledManagers": [
-    "pep621"
-  ],
-  "constraints": {
-    "python": "==3.10"
-  },
-  "pep621": {
-    "lockFileMaintenance": {
-      "enabled": true
-    }
-  },
-  "packageRules": [
-    {
-      "matchManagers": [
-        "pep621"
-      ],
-      "matchPackageNames": [
-        "python",
-        "hail"
-      ],
-      "enabled": false
-    },
-    {
-      "groupName": "all non-major dependencies",
-      "groupSlug": "all-minor-patch",
-      "matchUpdateTypes": [
-        "minor",
-        "patch"
-      ],
-      "matchPackagePatterns": [
-        "*"
-      ],
-      "minimumReleaseAge": "48 hours"
-    },
-    {
-      "groupName": "all major dependencies",
-      "groupSlug": "all-major",
-      "matchUpdateTypes": [
-        "major"
-      ],
-      "matchPackagePatterns": [
-        "*"
-      ],
-      "minimumReleaseAge": "48 hours"
-    }
-  ]
-}
diff --git a/.github/workflows/package.yaml b/.github/workflows/package.yaml
index 36708743..a725c101 100644
--- a/.github/workflows/package.yaml
+++ b/.github/workflows/package.yaml
@@ -1,9 +1,8 @@
-name: Package
+name: Package and Release
 on:
   push:
     branches:
       - main
-      - alpha
 
   workflow_dispatch:
     inputs:
@@ -16,9 +15,9 @@ on:
 permissions: {}
 
 jobs:
-  package:
-    name: Package
-    if: startsWith(github.event.head_commit.message, 'bump:') != true
+  release:
+    name: Release
+    if: startsWith(github.event.head_commit.message, 'bump:')
     environment: production
     permissions:
       id-token: write
@@ -29,45 +28,29 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - name: Setup | Force correct release branch on workflow sha
-        env:
-          REPO: ${{ github.repository }}
-          REF_NAME: ${{ github.ref_name }}
-          SHA: ${{ github.sha }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          set -euo pipefail
-          git clone https://github.com/${REPO} .
-          git checkout -B "${REF_NAME}" "${SHA}"
-          git config user.name "cpg-software-ci-bot"
-          git config user.email "software-team+githubcibot@populationgenomics.org.au"
-          git remote set-url origin "https://x-access-token:${GITHUB_TOKEN}@github.com/${REPO}"
-
-      - name: Action | Semantic Version Release
-        id: release
-        uses: python-semantic-release/python-semantic-release@0dc72ac9058a62054a45f6344c83a423d7f906a8 #v9.21.1
+      - name: Checkout
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 #v4.2.2
         with:
-          root_options: '-v'
-          git_committer_email: 'software-team+githubcibot@populationgenomics.org.au'
-          git_committer_name: 'cpg-software-ci-bot'
-          github_token: ${{ secrets.BOT_ACCESS_TOKEN }}
+          fetch-depth: 0
 
-      - name: Build on no release
-        if: steps.release.outputs.released != 'true'
+      - name: Extract version from commit message
+        id: version
+        env:
+          COMMIT_MESSAGE: ${{ github.event.head_commit.message }}
         run: |
-          echo "No release was made, manual build"
-          make ci-build
+          # Extract version from commit message like "bump: version 1.0.1 → 1.0.2"
+          VERSION=$(echo "$COMMIT_MESSAGE" | grep -oP '→ \K[0-9]+\.[0-9]+\.[0-9]+')
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "Detected version: $VERSION"
 
-      - name: Publish | Upload package to PyPI
-        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc #v1.12.4
-        if: steps.release.outputs.released == 'true' || github.event.inputs.force_pypi_release == 'true'
-
-      - name: Publish | Upload to GitHub Release Assets
-        uses: python-semantic-release/publish-action@1aa9f41fac5d531e6764e1991b536783337f3a56 #v9.21.1
-        if: steps.release.outputs.released == 'true'
-        with:
-          github_token: ${{ secrets.BOT_ACCESS_TOKEN }}
-          tag: ${{ steps.release.outputs.tag }}
+      - name: Create and push tag
+        env:
+          VERSION: ${{ steps.version.outputs.version }}
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git tag -a "v${VERSION}" -m "Release version ${VERSION}"
+          git push origin "v${VERSION}"
 
       - name: Install uv
         uses: astral-sh/setup-uv@6b9c6063abd6010835644d4c2e1bef4cf5cd0fca #v6.0.1
@@ -78,12 +61,18 @@ jobs:
         run: |
           uv sync
 
-      - run: uv pip install mike
-
-      - name: Clean stale build metadata
+      - name: Build package
         run: |
-          rm -rf src/*.egg-info || true
+          uv build --sdist --wheel
+
+      - name: Publish | Upload package to PyPI
+        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e #v1.13.0
+        if: github.event_name == 'push' || github.event.inputs.force_pypi_release == 'true'
 
       - name: Publish | Update docs version
+        env:
+          VERSION: ${{ steps.version.outputs.version }}
+          GIT_COMMITTER_NAME: github-actions[bot]
+          GIT_COMMITTER_EMAIL: github-actions[bot]@users.noreply.github.com
         run: |
-          uv run mike deploy -F docs/mkdocs.yml --push --update-aliases ${{ steps.release.outputs.tag }} latest
+          uv run mike deploy -F docs/mkdocs.yml --push --update-aliases "${VERSION}" latest
diff --git a/.github/workflows/renovate.yaml b/.github/workflows/renovate.yaml
deleted file mode 100644
index dc0f51c4..00000000
--- a/.github/workflows/renovate.yaml
+++ /dev/null
@@ -1,35 +0,0 @@
-name: Renovate
-on:
-  schedule:
-    - cron: '0 0 * * Sun'
-  workflow_dispatch:
-
-permissions: {}
-
-jobs:
-  renovate:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-      pull-requests: write
-    steps:
-      - uses: actions/create-github-app-token@df432ceedc7162793a195dd1713ff69aefc7379e #v2.0.6
-        id: app-token
-        with:
-          app-id: ${{ vars.RENOVATE_APP_ID }}
-          private-key: ${{ secrets.RENOVATE_PRIVATE_KEY }}
-
-      - name: Checkout
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 #v4.2.2
-        with:
-          persist-credentials: false
-
-      - name: Self-hosted Renovate
-        uses: renovatebot/github-action@e854b273e774bce1ef8cb05f128b8ce8aee2a887 #v42.0.1
-        with:
-          token: '${{ steps.app-token.outputs.token }}'
-          docker-user: root
-          configurationFile: .github/renovate-config.json
-        env:
-          LOG_LEVEL: 'debug'
-          RENOVATE_PLATFORM_COMMIT: 'true'
diff --git a/.github/workflows/web-docs.yaml b/.github/workflows/web-docs.yaml
deleted file mode 100644
index 16b2dddb..00000000
--- a/.github/workflows/web-docs.yaml
+++ /dev/null
@@ -1,44 +0,0 @@
-name: mkdocs
-on:
-  push:
-    branches:
-      - alpha
-      - main
-
-permissions: {}
-
-jobs:
-  deploy:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 #v4.2.2
-        with:
-          persist-credentials: true
-
-      - name: Configure Git Credentials
-        run: |
-          git config user.name github-actions[bot]
-          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@6b9c6063abd6010835644d4c2e1bef4cf5cd0fca #v6.0.1
-
-      - name: Install project dependencies
-        run: |
-          uv sync
-          source .venv/bin/activate
-
-      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
-      - uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 #v4.2.3
-        with:
-          key: mkdocs-material-${{ env.cache_id }}
-          path: .cache
-          restore-keys: |
-            mkdocs-material-
-
-      - run: uv pip install mkdocs-material
-      - run: uv pip install "mkdocstrings[python]"
-      - run: uv pip install griffe-typingdoc
-      - run: uv run mkdocs gh-deploy -f docs/mkdocs.yml --force
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d9066bc1..2217e20d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -52,11 +52,3 @@ repos:
   #   rev: v1.1.400
   #   hooks:
   #     - id: pyright
-
-  - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
-    rev: v9.22.0
-    hooks:
-      - id: commitlint
-        stages: [commit-msg]
-        args: [--config, .commitlintrc.json]
-        additional_dependencies: ['@commitlint/config-conventional']
diff --git a/Dockerfile b/Dockerfile
index 41a659d4..66e54202 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,5 @@
 FROM australia-southeast1-docker.pkg.dev/analysis-runner/images/driver:latest
+# VERSION 1.0.1
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
 # Set up working directory for the project
diff --git a/Makefile b/Makefile
index 0371427b..a10b6893 100644
--- a/Makefile
+++ b/Makefile
@@ -6,7 +6,7 @@ init: venv
 	uv run pre-commit install
 
 init-dev: init install-local
-	uv run pre-commit install --hook-type commit-msg
+
 
 # Actions
 test:
@@ -27,10 +27,6 @@ docs:
 	uv pip install mkdocs-material "mkdocstrings[python]" griffe-typingdoc
 	uv run mkdocs serve -f docs/mkdocs.yml
 
-ci-build: clean
-	python -m pip install build "setuptools>=42" setuptools-scm wheel
-	SETUPTOOLS_SCM_PRETEND_VERSION="$$NEW_VERSION" python -m build --sdist --wheel
-
 build: clean
 	uv build --sdist --wheel
 
@@ -44,4 +40,14 @@ upload: clean build
 	uv run twine check dist/*
 	uv run twine upload -r testpypi dist/*
 
-.PHONY: venv init test docs clean ci-build build install-build install-local upload
+# Version Management
+bump-major:
+	uv run bump-my-version bump major
+
+bump-minor:
+	uv run bump-my-version bump minor
+
+bump-patch:
+	uv run bump-my-version bump patch
+
+.PHONY: venv init test docs clean build install-build install-local upload bump-major bump-minor bump-patch
diff --git a/pyproject.toml b/pyproject.toml
index abcc49a4..b61c4bcc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,19 +47,17 @@ classifiers = [
 ]
 keywords = ["hail", "flow", "api", "bioinformatics", "genomics"]
 
-[tool.uv]
-dev-dependencies = [
+[dependency-groups]
+dev = [
     "black>=24.10.0",
     "build>=1.2.2.post1",
-    "bump2version>=1.0.1",
-    "commitizen>=3.30.0",
+    "bump-my-version>=0.30.0",
     "coverage>=7.6.4",
     "hail>=0.2.133",
     "pip-audit>=2.7.3",
     "pylint>=3.3.1",
     "pytest-mock>=3.14.0",
     "pytest>=8.3.3",
-    "python-semantic-release>=9.4.1",
     "pyyaml>=6.0.2",
     "ruff>=0.5.2",
     "toml>=0.10.2",
@@ -71,6 +69,7 @@ dev-dependencies = [
     "pyright>=1.1.400",
 ]
 
+
 [project.urls]
 Repository = "https://github.com/populationgenomics/cpg-flow"
 
@@ -101,91 +100,7 @@ venvPath = "."
 venv = ".venv"
 typeCheckingMode = "basic"
 
-[tool.semantic_release]
-version_variables = [
-    "src/cpg_flow/__init__.py:__version__",
-    "Dockerfile:VERSION",
-    ".github/workflows/docker.yaml:VERSION",
-    ".github/workflows/test.yaml:VERSION",
-]
-assets = []
-build_command_env = []
-commit_message = "bump: {version}\n\nAutomatically generated by python-semantic-release"
-commit_parser = "angular"
-logging_use_named_masks = false
-major_on_zero = true
-allow_zero_version = true
-repo_dir = "."
-no_git_verify = false
-tag_format = "v{version}"
-build_command = "make ci-build"
-
-[tool.semantic_release.branches.main]
-match = "main"
-prerelease = false
-
-[tool.semantic_release.branches.prerelease]
-match = "alpha"
-prerelease_token = "alpha"
-prerelease = true
-
-[tool.semantic_release.changelog]
-exclude_commit_patterns = []
-mode = "init"
-insertion_flag = "<!-- version list -->"
-template_dir = "templates"
-
-[tool.semantic_release.changelog.default_templates]
-changelog_file = "CHANGELOG.md"
-output_format = "md"
-
-[tool.semantic_release.changelog.environment]
-block_start_string = "{%"
-block_end_string = "%}"
-variable_start_string = "{{"
-variable_end_string = "}}"
-comment_start_string = "{#"
-comment_end_string = "#}"
-trim_blocks = false
-lstrip_blocks = false
-newline_sequence = "\n"
-keep_trailing_newline = false
-extensions = []
-autoescape = false
-
-[tool.semantic_release.commit_author]
-env = "GIT_COMMIT_AUTHOR"
-default = "semantic-release <semantic-release>"
-
-[tool.semantic_release.commit_parser_options]
-allowed_tags = [
-    "build",
-    "ci",
-    "docs",
-    "feat",
-    "fix",
-    "perf",
-    "style",
-    "refactor",
-    "test",
-    "chore",
-]
-minor_tags = ["feat"]
-patch_tags = ["fix", "perf"]
-default_bump_level = 0
-
-[tool.semantic_release.remote]
-name = "origin"
-type = "github"
-token = { env = "GITHUB_TOKEN" }
-ignore_token_for_push = false
-insecure = false
-
-[tool.semantic_release.publish]
-dist_glob_patterns = ["dist/*"]
-upload_to_pypi = false
-upload_to_test_pypi = true
-upload_to_vcs_release = false
+
 
 [tool.setuptools.dynamic.version]
 attr = "cpg_flow.__version__"
diff --git a/uv.lock b/uv.lock
index 948995cc..bdbe65c7 100644
--- a/uv.lock
+++ b/uv.lock
@@ -95,15 +95,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/a1/ee/48ca1a7c89ffec8b6a0c5d02b89c305671d5ffd8d3c94acf8b8c408575bb/anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c", size = 100916, upload-time = "2025-03-17T00:02:52.713Z" },
 ]
 
-[[package]]
-name = "argcomplete"
-version = "3.6.2"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/16/0f/861e168fc813c56a78b35f3c30d91c6757d1fd185af1110f1aec784b35d0/argcomplete-3.6.2.tar.gz", hash = "sha256:d0519b1bc867f5f4f4713c41ad0aba73a4a5f007449716b16f385f2166dc6adf", size = 73403, upload-time = "2025-04-03T04:57:03.52Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/31/da/e42d7a9d8dd33fa775f467e4028a47936da2f01e4b0e561f9ba0d74cb0ca/argcomplete-3.6.2-py3-none-any.whl", hash = "sha256:65b3133a29ad53fb42c48cf5114752c7ab66c1c38544fdf6460f450c09b42591", size = 43708, upload-time = "2025-04-03T04:57:01.591Z" },
-]
-
 [[package]]
 name = "astroid"
 version = "3.3.10"
@@ -360,6 +351,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/7e/83/a753562020b69fa90cebc39e8af2c753b24dcdc74bee8355ee3f6cefdf34/botocore-1.38.27-py3-none-any.whl", hash = "sha256:a785d5e9a5eda88ad6ab9ed8b87d1f2ac409d0226bba6ff801c55359e94d91a8", size = 13580545, upload-time = "2025-05-30T19:32:26.712Z" },
 ]
 
+[[package]]
+name = "bracex"
+version = "2.6"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/63/9a/fec38644694abfaaeca2798b58e276a8e61de49e2e37494ace423395febc/bracex-2.6.tar.gz", hash = "sha256:98f1347cd77e22ee8d967a30ad4e310b233f7754dbf31ff3fceb76145ba47dc7", size = 26642, upload-time = "2025-06-22T19:12:31.254Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/9d/2a/9186535ce58db529927f6cf5990a849aa9e052eea3e2cfefe20b9e1802da/bracex-2.6-py3-none-any.whl", hash = "sha256:0b0049264e7340b3ec782b5cb99beb325f36c3782a32e36e876452fd49a09952", size = 11508, upload-time = "2025-06-22T19:12:29.781Z" },
+]
+
 [[package]]
 name = "build"
 version = "1.2.2.post1"
@@ -377,12 +377,23 @@ wheels = [
 ]
 
 [[package]]
-name = "bump2version"
-version = "1.0.1"
+name = "bump-my-version"
+version = "1.2.4"
 source = { registry = "https://pypi.org/simple" }
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