From 8c98b46b40e5779eb789b3b510d0352dc45a34f0 Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 09:12:09 +0100
Subject: [PATCH 01/10] ci: ci test release

---
 .github/workflows/pr.yaml         |   2 +-
 .github/workflows/release.yaml    |  39 +++++++++
 .github/workflows/release_pr.yaml |  34 ++++++++
 .github/workflows/tag.yaml        | 139 ++++++++++++++++++++++++++++++
 pyproject.toml                    |  67 +++++++++++++-
 5 files changed, 279 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/release.yaml
 create mode 100644 .github/workflows/release_pr.yaml
 create mode 100644 .github/workflows/tag.yaml

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 10b99d8..2f09a10 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -20,4 +20,4 @@ jobs:
       - name: Install the latest version of rye
         run: make dev
       - name: Run checks
-      - uses: pre-commit/action@v3.0.1
+        uses: pre-commit/action@v3.0.1
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000..346efef
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,39 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+env:
+  PYTHON_VERSION_DEFAULT: "3.10.8"
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    environment: PyPI
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+      contents: write
+    steps:
+      - uses: actions/create-github-app-token@v1
+        id: trigger-token
+        with:
+          app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID}}
+          private-key: ${{ secrets.TRIGGER_WORKFLOW_GH_APP_KEY }}
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.10.8
+      - name: Install the latest version of rye
+        run: make dev
+      - name: Build package
+        run: make build
+      - name: Publish distribution 📦 to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          packages-dir: dist/
diff --git a/.github/workflows/release_pr.yaml b/.github/workflows/release_pr.yaml
new file mode 100644
index 0000000..441d43a
--- /dev/null
+++ b/.github/workflows/release_pr.yaml
@@ -0,0 +1,34 @@
+name: PR to trigger release
+
+"on":
+  schedule:
+    - cron: "15 16 * * 4"
+
+jobs:
+  pull-request:
+    runs-on: ubuntu-latest
+    environment: PyPI
+    steps:
+      - uses: actions/create-github-app-token@v1
+        id: trigger-token
+        with:
+          app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID}}
+          private-key: ${{ secrets.TRIGGER_WORKFLOW_GH_APP_KEY }}
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          repository: opentargets/gentropy
+          token: ${{ secrets.GITHUB_TOKEN }}
+          persist-credentials: false
+      - uses: actions/checkout@v3
+      - name: pull-request
+        uses: diillson/auto-pull-request@v1.0.1
+        with:
+          source_branch: "dev"
+          destination_branch: "main"
+          pr_title: "chore: trigger release process"
+          pr_body: ":warning: *This PR requires a MERGE COMMIT (Don't squash or rebase!)*"
+          pr_label: "auto-pr"
+          pr_draft: false
+          pr_allow_empty: true
+          github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/tag.yaml b/.github/workflows/tag.yaml
new file mode 100644
index 0000000..1722468
--- /dev/null
+++ b/.github/workflows/tag.yaml
@@ -0,0 +1,139 @@
+name: Release
+
+"on":
+  push:
+    branches: ["main"]
+
+concurrency:
+  group: deploy
+  cancel-in-progress: false # prevent hickups with semantic-release
+
+env:
+  PYTHON_VERSION_DEFAULT: "3.10.8"
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    concurrency: release
+    environment: PyPI
+    permissions:
+      contents: write
+
+    steps:
+      # NOTE: commits using GITHUB_TOKEN does not trigger workflows
+      - uses: actions/create-github-app-token@v1
+        id: trigger-token
+        with:
+          app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID}}
+          private-key: ${{ secrets.TRIGGER_WORKFLOW_GH_APP_KEY }}
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          repository: opentargets/gentropy
+          token: ${{ secrets.GITHUB_TOKEN }}
+          persist-credentials: false
+
+      - name: Python Semantic Release
+        id: semrelease
+        # v9.6.0 is required due to the python v3.12 in the newer version of semantic release action which
+        # breaks the poetry build command.
+        uses: python-semantic-release/python-semantic-release@v9.6.0
+        with:
+          github_token: ${{ steps.trigger-token.outputs.token }}
+
+      - name: Publish package to GitHub Release
+        uses: python-semantic-release/upload-to-gh-release@main
+        if: ${{ steps.semrelease.outputs.released }} == 'true'
+        with:
+          # NOTE: allow to start the workflow when push action on tag gets executed
+          # requires using GH_APP to authenitcate, otherwise push authorised with
+          # the GITHUB_TOKEN does not trigger the tag artifact workflow.
+          # see https://github.com/actions/create-github-app-token
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ steps.semrelease.outputs.tag }}
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    needs: release
+    name: >-
+      Publish 📦 in PyPI
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/gentropy
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-to-testpypi:
+    name: Publish 📦 in TestPyPI
+    needs: release
+    if: github.ref != 'refs/heads/main'
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/gentropy
+
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  documentation:
+    needs: release
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/main'
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION_DEFAULT }}
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: |
+            venv-${{ runner.os }}-\
+            ${{ env.PYTHON_VERSION_DEFAULT }}-\
+            ${{ hashFiles('**/poetry.lock') }}
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+      - name: Install library
+        run: poetry install --without tests --no-interaction
+      - name: Publish docs
+        run: poetry run mkdocs gh-deploy --force
diff --git a/pyproject.toml b/pyproject.toml
index 0e7f05b..abe20a7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "gentroutils"
-version = "0.1.0"
+version = "0.0.0"
 description = "Add your description here"
 authors = [
     { name = "Szymon Szyszkowski", email = "ss60@mib117351s.internal.sanger.ac.uk" },
@@ -126,3 +126,68 @@ warn_unused_ignores = true
 [[tool.mypy.overrides]]
 module = ["google.cloud", "pyfiglet", "click", "google.cloud.storage"]
 ignore_missing_imports = true
+
+
+[tool.semantic_release]
+version_toml = ["pyproject.tolm:project.version"]
+assets = []
+commit_message = "{version}\n\nAutomatically generated by python-semantic-release"
+commit_parser = "angular"
+logging_use_named_masks = false
+major_on_zero = true
+allow_zero_version = true
+tag_format = "v{version}"
+
+[tool.semantic_release.branches.main]
+match = "(main|master)"
+prerelease_token = "rc"
+prerelease = false
+
+[semantic_release.changelog]
+template_dir = "templates"
+changelog_file = "CHANGELOG.md"
+exclude_commit_patterns = []
+
+[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 = true
+
+[tool.semantic_release.commit_author]
+env = "GIT_COMMIT_AUTHOR"
+default = "semantic-release <semantic-release>"
+
+[tool.semantic_release.commit_parser_options]
+allowed_tags = [
+    "build",
+    "chore",
+    "ci",
+    "docs",
+    "feat",
+    "fix",
+    "perf",
+    "style",
+    "refactor",
+    "test",
+]
+minor_tags = ["feat"]
+patch_tags = ["fix", "perf", "docs", "style", "test", "ci"]
+default_bump_level = 0
+
+[tool.semantic_release.remote]
+name = "origin"
+type = "github"
+ignore_token_for_push = false
+
+[tool.semantic_release.publish]
+dist_glob_patterns = ["dist/*"]
+upload_to_vcs_release = true

From 7e1340f1fb4aa57092f149db0e9400d18a4a0cca Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 09:19:35 +0100
Subject: [PATCH 02/10] fix: add cargo to rc file

---
 setup.sh | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/setup.sh b/setup.sh
index e77988b..c02e690 100755
--- a/setup.sh
+++ b/setup.sh
@@ -5,24 +5,25 @@
 # It is intended to be run on a new system to quickly set up Rye.
 # It is recommended to review the script before running it.
 
+export SHELL_RC=$(echo "$HOME/.${SHELL##*/}rc")
 
-export SHELL_ZSH=$(echo "$HOME/.${SHELL##*/}rc")
-
-if ! command -v rye &> /dev/null; then
+if ! command -v rye &>/dev/null; then
     echo "Rye is not installed. Installing..."
     curl -sSf https://rye.astral.sh/get | bash
-    echo "Updating $SHELL_ZSH"
-    echo "source $HOME/.rye/env" >> $SHELL_ZSH
+    echo "Updating $SHELL_RC"
+    echo "source $HOME/.rye/env" >>$SHELL_RC
+    echo "source $HOME/.cargo/bin" >>$SHELL_RC
 else
     echo "Rye is already installed."
 fi
 
-if ! command -v uv &> /dev/null; then
+if ! command -v uv &>/dev/null; then
     echo "uv is not installed. Installing..."
     curl -LsSf https://astral.sh/uv/install.sh | sh
 else
     echo "uv is already installed."
 fi
+source $SHELL_RC
 rye sync
 rye run pre-commit install --hook-type commit-msg --hook-type pre-commit
 

From cd0c7eda865af9df5bf1ab65dfa405b3a13e605c Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 09:28:47 +0100
Subject: [PATCH 03/10] fix: debug ci

---
 setup.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.sh b/setup.sh
index c02e690..b8c451b 100755
--- a/setup.sh
+++ b/setup.sh
@@ -24,6 +24,7 @@ else
     echo "uv is already installed."
 fi
 source $SHELL_RC
+cat $SHELL_RC
 rye sync
 rye run pre-commit install --hook-type commit-msg --hook-type pre-commit
 

From 332e0d58dee315c9aa5f57f20464d1097c41cb59 Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 10:12:03 +0100
Subject: [PATCH 04/10] fix: debug v2

---
 .github/workflows/tag.yaml | 86 --------------------------------------
 setup.sh                   |  4 +-
 2 files changed, 3 insertions(+), 87 deletions(-)

diff --git a/.github/workflows/tag.yaml b/.github/workflows/tag.yaml
index 1722468..0997101 100644
--- a/.github/workflows/tag.yaml
+++ b/.github/workflows/tag.yaml
@@ -51,89 +51,3 @@ jobs:
           # see https://github.com/actions/create-github-app-token
           github_token: ${{ secrets.GITHUB_TOKEN }}
           tag: ${{ steps.semrelease.outputs.tag }}
-
-      - name: Store the distribution packages
-        uses: actions/upload-artifact@v4
-        with:
-          name: python-package-distributions
-          path: dist/
-
-  publish-to-pypi:
-    needs: release
-    name: >-
-      Publish 📦 in PyPI
-    if: github.ref == 'refs/heads/main'
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/p/gentropy
-    permissions:
-      id-token: write # IMPORTANT: mandatory for trusted publishing
-    steps:
-      - name: Download all the dists
-        uses: actions/download-artifact@v4
-        with:
-          name: python-package-distributions
-          path: dist/
-      - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-
-  publish-to-testpypi:
-    name: Publish 📦 in TestPyPI
-    needs: release
-    if: github.ref != 'refs/heads/main'
-    runs-on: ubuntu-latest
-
-    environment:
-      name: testpypi
-      url: https://test.pypi.org/p/gentropy
-
-    permissions:
-      id-token: write # IMPORTANT: mandatory for trusted publishing
-
-    steps:
-      - name: Download all the dists
-        uses: actions/download-artifact@v4
-        with:
-          name: python-package-distributions
-          path: dist/
-      - name: Publish distribution 📦 to TestPyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          repository-url: https://test.pypi.org/legacy/
-
-  documentation:
-    needs: release
-    runs-on: ubuntu-latest
-    if: github.ref == 'refs/heads/main'
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          token: ${{ secrets.GITHUB_TOKEN }}
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ env.PYTHON_VERSION_DEFAULT }}
-      - name: Install and configure Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-          installer-parallel: true
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v4
-        with:
-          path: .venv
-          key: |
-            venv-${{ runner.os }}-\
-            ${{ env.PYTHON_VERSION_DEFAULT }}-\
-            ${{ hashFiles('**/poetry.lock') }}
-      - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root
-      - name: Install library
-        run: poetry install --without tests --no-interaction
-      - name: Publish docs
-        run: poetry run mkdocs gh-deploy --force
diff --git a/setup.sh b/setup.sh
index b8c451b..8c7883e 100755
--- a/setup.sh
+++ b/setup.sh
@@ -24,7 +24,9 @@ else
     echo "uv is already installed."
 fi
 source $SHELL_RC
-cat $SHELL_RC
+which rye
+echo $PATH
+cat $HOME/.rye/env
 rye sync
 rye run pre-commit install --hook-type commit-msg --hook-type pre-commit
 

From ce4fd37ed2483c353bc552e6d9e91b5f9883dc52 Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 10:29:07 +0100
Subject: [PATCH 05/10] feat: attempt to install rye with cargo

---
 setup.sh | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/setup.sh b/setup.sh
index 8c7883e..9460f0f 100755
--- a/setup.sh
+++ b/setup.sh
@@ -7,12 +7,21 @@
 
 export SHELL_RC=$(echo "$HOME/.${SHELL##*/}rc")
 
+if ! command -v cargo &>/dev/null; then
+    echo "Cargo is not installed. Installing..."
+    curl https://sh.rustup.rs -sSf | sh
+    echo "Updating $SHELL_RC"
+    echo "source $HOME/.cargo/bin" >>$SHELL_RC
+else
+    echo "Cargo is installed."
+fi
+source $SHELL_RC
+
 if ! command -v rye &>/dev/null; then
     echo "Rye is not installed. Installing..."
-    curl -sSf https://rye.astral.sh/get | bash
+    cargo install --git https://github.com/astral-sh/rye --tag 0.38.0 rye
     echo "Updating $SHELL_RC"
     echo "source $HOME/.rye/env" >>$SHELL_RC
-    echo "source $HOME/.cargo/bin" >>$SHELL_RC
 else
     echo "Rye is already installed."
 fi

From e7c9e5e2dec910aa9cef2b14b1d88d4e669c057a Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 10:39:32 +0100
Subject: [PATCH 06/10] ci: changed how uv and rye are installed

---
 .github/workflows/pr.yaml      | 10 ++++++++--
 .github/workflows/release.yaml | 10 ++++++++--
 setup.sh                       | 16 ++--------------
 3 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 2f09a10..178a69f 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -17,7 +17,13 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.10.8
-      - name: Install the latest version of rye
-        run: make dev
+      - name: Install uv
+        uses: yezz123/setup-uv@v4
+      - name: Install rye
+        uses: eifinger/setup-rye@v4
+        with:
+          version: "latest"
+      - name: Sync dependencies
+        run: rye sync
       - name: Run checks
         uses: pre-commit/action@v3.0.1
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index 346efef..bf783ff 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -28,8 +28,14 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.10.8
-      - name: Install the latest version of rye
-        run: make dev
+      - name: Install uv
+        uses: yezz123/setup-uv@v4
+      - name: Install rye
+        uses: eifinger/setup-rye@v4
+        with:
+          version: "latest"
+      - name: Sync dependencies
+        run: rye sync
       - name: Build package
         run: make build
       - name: Publish distribution 📦 to TestPyPI
diff --git a/setup.sh b/setup.sh
index 9460f0f..c02e690 100755
--- a/setup.sh
+++ b/setup.sh
@@ -7,21 +7,12 @@
 
 export SHELL_RC=$(echo "$HOME/.${SHELL##*/}rc")
 
-if ! command -v cargo &>/dev/null; then
-    echo "Cargo is not installed. Installing..."
-    curl https://sh.rustup.rs -sSf | sh
-    echo "Updating $SHELL_RC"
-    echo "source $HOME/.cargo/bin" >>$SHELL_RC
-else
-    echo "Cargo is installed."
-fi
-source $SHELL_RC
-
 if ! command -v rye &>/dev/null; then
     echo "Rye is not installed. Installing..."
-    cargo install --git https://github.com/astral-sh/rye --tag 0.38.0 rye
+    curl -sSf https://rye.astral.sh/get | bash
     echo "Updating $SHELL_RC"
     echo "source $HOME/.rye/env" >>$SHELL_RC
+    echo "source $HOME/.cargo/bin" >>$SHELL_RC
 else
     echo "Rye is already installed."
 fi
@@ -33,9 +24,6 @@ else
     echo "uv is already installed."
 fi
 source $SHELL_RC
-which rye
-echo $PATH
-cat $HOME/.rye/env
 rye sync
 rye run pre-commit install --hook-type commit-msg --hook-type pre-commit
 

From 7d74378a45c307b9ae64cd6dfd707948113b5e7d Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 10:45:04 +0100
Subject: [PATCH 07/10] fix: ensure pip is installed for pre-commit action

---
 .github/workflows/pr.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 178a69f..eeebb5a 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -25,5 +25,7 @@ jobs:
           version: "latest"
       - name: Sync dependencies
         run: rye sync
+      - name: ensure pip
+        run: python -m ensurepip # required as pre-commit requires pip to install
       - name: Run checks
         uses: pre-commit/action@v3.0.1

From 4345691c7e3a352b72d5003fbfe5781d7d111c90 Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 10:52:05 +0100
Subject: [PATCH 08/10] feat: local pre-commit execution without action

---
 .github/workflows/pr.yaml | 4 +---
 Makefile                  | 2 +-
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index eeebb5a..4cf20ae 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -25,7 +25,5 @@ jobs:
           version: "latest"
       - name: Sync dependencies
         run: rye sync
-      - name: ensure pip
-        run: python -m ensurepip # required as pre-commit requires pip to install
       - name: Run checks
-        uses: pre-commit/action@v3.0.1
+        run: pre-commit run --all-files
diff --git a/Makefile b/Makefile
index 4717f5a..a9f49d0 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
 SHELL := /bin/bash
 .PHONY: $(shell sed -n -e '/^$$/ { n ; /^[^ .\#][^ ]*:/ { s/:.*$$// ; p ; } ; }' $(MAKEFILE_LIST))
 VERSION := $$(grep '^version' pyproject.toml | sed 's%version = "\(.*\)"%\1%')
-APP_NAME := $$(grep '^name' pyproject.toml | sed 's%name = "\(.*\)"%\1%')
+APP_NAME := $$(grep '^name' pyproject.toml | head -1 | sed 's%name = "\(.*\)"%\1%')
 
 .DEFAULT_GOAL := help
 

From 10584a56790cf4693bd47ee3e50672bc4bb78068 Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 10:54:06 +0100
Subject: [PATCH 09/10] fix: typo in package name

---
 .github/workflows/release.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index bf783ff..f6b461c 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -41,5 +41,5 @@ jobs:
       - name: Publish distribution 📦 to TestPyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          repository-url: https://test.pypi.org/legacy/
+          repository-url: https://test.pypi.org/gentroutils/
           packages-dir: dist/

From 7fbd06cbeb42563f6c2a66f768e490f554a7c07b Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Date: Tue, 13 Aug 2024 10:55:10 +0100
Subject: [PATCH 10/10] fix: run pre-commit by rye

---
 .github/workflows/pr.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 4cf20ae..bf8ce5d 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -26,4 +26,4 @@ jobs:
       - name: Sync dependencies
         run: rye sync
       - name: Run checks
-        run: pre-commit run --all-files
+        run: rye run pre-commit run --all-files