From 3fe4f656c798a059ad3b0e6131fbf73bcba025b2 Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Fri, 4 Apr 2025 15:10:18 +0100
Subject: [PATCH 01/14] Converted to use uv and hatch over venv and tox

---
 .devcontainer/devcontainer.json               |  4 +-
 .../actions/install_requirements/action.yml   | 23 +++---
 .github/workflows/_hatch.yml                  | 27 +++++++
 .github/workflows/_release.yml                |  2 +-
 .github/workflows/_test.yml                   |  2 +-
 .github/workflows/ci.yml                      | 36 ++++++----
 .pre-commit-config.yaml                       | 16 ++++-
 Dockerfile                                    | 17 +++--
 pyproject.toml                                | 70 +++++++++++++------
 9 files changed, 144 insertions(+), 53 deletions(-)
 create mode 100644 .github/workflows/_hatch.yml

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index fce9dd59..7c480772 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -41,6 +41,6 @@
     ],
     // Mount the parent as /workspaces so we can pip install peers as editable
     "workspaceMount": "source=${localWorkspaceFolder}/..,target=/workspaces,type=bind",
-    // After the container is created, install the python project in editable form
-    "postCreateCommand": "pip install $([ -f dev-requirements.txt ] && echo '-c dev-requirements.txt') -e '.[dev]' && pre-commit install"
+    // After the container is created, install the uv env
+    "postCreateCommand": "uv pip install $([ -f dev-requirements.txt ] && echo '-c dev-requirements.txt') -e '.[dev]' && pre-commit install"
 }
diff --git a/.github/actions/install_requirements/action.yml b/.github/actions/install_requirements/action.yml
index d33e0805..998e2acb 100644
--- a/.github/actions/install_requirements/action.yml
+++ b/.github/actions/install_requirements/action.yml
@@ -4,9 +4,6 @@ inputs:
   python-version:
     description: Python version to install, default is from Dockerfile
     default: "dev"
-  pip-install:
-    description: Parameters to pass to pip install
-    default: "$([ -f dev-requirements.txt ] && echo '-c dev-requirements.txt') -e .[dev]"
 
 runs:
   using: composite
@@ -20,15 +17,25 @@ runs:
         echo "PYTHON_VERSION=$PYTHON_VERSION" >> "$GITHUB_ENV"
       shell: bash
 
-    - name: Setup python
-      uses: actions/setup-python@v5
+    - name: Install uv and set the python version
+      uses: astral-sh/setup-uv@v5
       with:
         python-version: ${{ env.PYTHON_VERSION }}
+        enable-cache: true
+        cache-dependency-glob: "uv.lock"
 
-    - name: Install packages
-      run: pip install ${{ inputs.pip-install }}
+    - name: Install dependencies
+      run: uv sync
       shell: bash
 
     - name: Report what was installed
-      run: pip freeze
+      run: uv pip list
+      shell: bash
+
+    - name: Add venv path to Github environment
+      run: echo "VENV_PATH=.venv" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Add venv path to Github Path
+      run: echo "${{ env.VENV_PATH }}/bin:$PATH" >> $GITHUB_PATH
       shell: bash
diff --git a/.github/workflows/_hatch.yml b/.github/workflows/_hatch.yml
new file mode 100644
index 00000000..e46c5758
--- /dev/null
+++ b/.github/workflows/_hatch.yml
@@ -0,0 +1,27 @@
+on:
+  workflow_call:
+    inputs:
+      hatch:
+        type: string
+        description: What to run under hatch
+        required: true
+
+
+jobs:
+  run:
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install python packages
+        uses: ./.github/actions/install_requirements
+
+      - name: Run hatch
+        run: |
+          IFS=',' read -ra SCRIPTS <<< "${{ inputs.hatch }}"
+          for script in "${SCRIPTS[@]}"; do
+            echo "Running $script"
+            hatch run $script
+          done
diff --git a/.github/workflows/_release.yml b/.github/workflows/_release.yml
index c7716829..517bcf8e 100644
--- a/.github/workflows/_release.yml
+++ b/.github/workflows/_release.yml
@@ -23,7 +23,7 @@ jobs:
       - name: Create GitHub Release
         # We pin to the SHA, not the tag, for security reasons.
         # https://docs.github.com/en/actions/learn-github-actions/security-hardening-for-github-actions#using-third-party-actions
-        uses: softprops/action-gh-release@7b4da11513bf3f43f9999e90eabced41ab8bb048 # v2.2.0
+        uses: softprops/action-gh-release@c95fe1489396fe8a9eb87c0abf8aa5b2ef267fda # v2.2.1
         with:
           prerelease: ${{ contains(github.ref_name, 'a') || contains(github.ref_name, 'b') || contains(github.ref_name, 'rc') }}
           files: "*"
diff --git a/.github/workflows/_test.yml b/.github/workflows/_test.yml
index 552b29d0..a3c535cd 100644
--- a/.github/workflows/_test.yml
+++ b/.github/workflows/_test.yml
@@ -51,7 +51,7 @@ jobs:
           pip-install: ".[dev]"
 
       - name: Run tests
-        run: tox -e tests
+        run: hatch run tests
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f198a244..a31c5c7c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,37 +11,45 @@ jobs:
   lint:
     needs: check
     if: needs.check.outputs.branch-pr == ''
-    uses: ./.github/workflows/_tox.yml
+    uses: ./.github/workflows/_hatch.yml
     with:
-      tox: pre-commit
+      hatch: precommit,type-check
 
   test:
     needs: check
     if: needs.check.outputs.branch-pr == ''
+    strategy:
+      matrix:
+        runs-on: ["ubuntu-latest"] # can add windows-latest, macos-latest
+        python-version: ["3.11"]
+        include:
+          # Include one that runs in the dev environment
+          - runs-on: "ubuntu-latest"
+            python-version: "dev"
+      fail-fast: false
     uses: ./.github/workflows/_test.yml
     with:
-      python-version: dev
-      runs-on: ubuntu-latest
+      runs-on: ${{ matrix.runs-on }}
+      python-version: ${{ matrix.python-version }}
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-  docs:
+  container:
     needs: check
     if: needs.check.outputs.branch-pr == ''
-    uses: ./.github/workflows/_docs.yml
+    uses: ./.github/workflows/_container.yml
     permissions:
-      contents: write
+      contents: read
+      packages: write
 
-  example:
-    needs: test
-    if: github.ref_name == 'main'
-    uses: ./.github/workflows/_example.yml
-    secrets:
-      EXAMPLE_DEPLOY_KEY: ${{ secrets.EXAMPLE_DEPLOY_KEY }}
+  dist:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    uses: ./.github/workflows/_dist.yml
 
   release:
     if: github.ref_type == 'tag'
-    needs: docs
+    needs: [dist]
     uses: ./.github/workflows/_release.yml
     permissions:
       contents: write
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b5d4d7fa..6236246e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,21 +1,31 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-yaml
       - id: check-merge-conflict
       - id: end-of-file-fixer
 
-  - repo: local
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    # uv version.
+    rev: 0.6.3
     hooks:
+      - id: uv-lock
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.9.6
+    hooks:
+      # Run the linter.
       - id: ruff
         name: lint with ruff
         language: system
-        entry: ruff check --force-exclude --fix
+        entry: ruff check --force-exclude
         types: [python]
         require_serial: true
 
+      # Run the formatter.
       - id: ruff-format
         name: format with ruff
         language: system
diff --git a/Dockerfile b/Dockerfile
index 35d2abf7..bd5fdb40 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,9 +5,18 @@ FROM python:${PYTHON_VERSION} AS developer
 
 # Add any system dependencies for the developer/build environment here
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    graphviz \
+    graphviz vim \
     && rm -rf /var/lib/apt/lists/*
+# Install uv using the official installer script
+RUN curl -LsSf https://astral.sh/uv/install.sh | \
+    env UV_INSTALL_DIR="/usr/local/bin" sh
 
-# Set up a virtual environment and put it in PATH
-RUN python -m venv /venv
-ENV PATH=/venv/bin:$PATH
+# Configure environment
+ENV UV_CHECK_UPDATE=false
+# Configure UV to use system Python
+# ENV UV_SYSTEM_PYTHON=1
+
+# Creates virtual environment
+RUN uv venv --seed venv
+ENV VIRTUAL_ENV=/venv
+ENV PATH=$VIRTUAL_ENV/bin:$PATH
diff --git a/pyproject.toml b/pyproject.toml
index 44d1ca29..c16f6aac 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,9 +19,12 @@ dev = [
     "sphinx-copybutton",
     "sphinx-design",
     "tox",
-    "tox-direct",
 ]
 
+# # Without this, setuptools apparently try to scan the whole image's filesystem while working in /
+# [tool.setuptools.packages.find]
+# where = []
+
 [tool.setuptools_scm]
 
 [tool.pytest.ini_options]
@@ -32,27 +35,54 @@ addopts = """
 # Doctest python code in docs, python code in src docstrings, test functions in tests
 testpaths = "tests"
 
-# tox must currently be configured via an embedded ini string
-# See: https://github.com/tox-dev/tox/issues/999
+
 [tool.tox]
-legacy_tox_ini = """
-[tox]
-skipsdist=True
+skipsdist = true
+
+[tool.tox.env.pre-commit]
+description = "Run pre-commit"
+direct = true
+allowlist_externals = ["pre-commit"]
+commands = [
+    [
+        "pre-commit",
+        "run",
+        #"--all-files",
+        "--show-diff-on-failure",
+        "{posargs}",
+    ],
+]
 
-[testenv:{pre-commit,tests,docs}]
-# Don't create a virtualenv for the command, requires tox-direct plugin
-direct = True
-passenv = *
-allowlist_externals =
-    pre-commit
-    pytest
-    sphinx-build
-    sphinx-autobuild
-commands =
-    pre-commit: pre-commit run --all-files --show-diff-on-failure {posargs}
-    tests: pytest {posargs}
-    docs: sphinx-{posargs:build -EW --keep-going} -T docs build/html
-"""
+[tool.tox.env.tests]
+description = "Run tests"
+direct = true
+allowlist_externals = ["pytest"]
+commands = [
+    [
+        "pytest",
+        "--cov=phoebus_guibuilder",
+        "--cov-report",
+        "term",
+        "--cov-report",
+        "xml:cov.xml",
+        "{posargs}",
+    ],
+]
+
+[tool.tox.env.docs]
+description = "Run docs"
+direct = true
+allowlist_externals = ["sphinx-build", "sphinx-autobuild"]
+commands = [
+    [
+        "sphinx-{posargs:build}",
+        "-EW",
+        "--keep-going",
+        "-T",
+        "docs",
+        "build/html",
+    ],
+]
 
 [tool.ruff]
 src = ["src", "tests"]

From 6d03afeac9e4aeb002556296519f47e63aac2a54 Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Wed, 9 Apr 2025 15:54:10 +0000
Subject: [PATCH 02/14] Replace tox with tox-uv; Remove hatch.yml

---
 .github/workflows/_hatch.yml | 27 ---------------------------
 .github/workflows/ci.yml     |  4 ++--
 pyproject.toml               |  2 +-
 3 files changed, 3 insertions(+), 30 deletions(-)
 delete mode 100644 .github/workflows/_hatch.yml

diff --git a/.github/workflows/_hatch.yml b/.github/workflows/_hatch.yml
deleted file mode 100644
index e46c5758..00000000
--- a/.github/workflows/_hatch.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-on:
-  workflow_call:
-    inputs:
-      hatch:
-        type: string
-        description: What to run under hatch
-        required: true
-
-
-jobs:
-  run:
-    runs-on: "ubuntu-latest"
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - name: Install python packages
-        uses: ./.github/actions/install_requirements
-
-      - name: Run hatch
-        run: |
-          IFS=',' read -ra SCRIPTS <<< "${{ inputs.hatch }}"
-          for script in "${SCRIPTS[@]}"; do
-            echo "Running $script"
-            hatch run $script
-          done
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a31c5c7c..56036b42 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,9 +11,9 @@ jobs:
   lint:
     needs: check
     if: needs.check.outputs.branch-pr == ''
-    uses: ./.github/workflows/_hatch.yml
+    uses: ./.github/workflows/_tox.yml
     with:
-      hatch: precommit,type-check
+      tox: precommit,type-check
 
   test:
     needs: check
diff --git a/pyproject.toml b/pyproject.toml
index c16f6aac..dba5bb18 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,7 +18,7 @@ dev = [
     "sphinx-autobuild",
     "sphinx-copybutton",
     "sphinx-design",
-    "tox",
+    "tox-uv",
 ]
 
 # # Without this, setuptools apparently try to scan the whole image's filesystem while working in /

From 455efa56811162de6983bacf61ac6e336e65db7e Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Thu, 10 Apr 2025 08:14:11 +0000
Subject: [PATCH 03/14] Fix CI when building env

---
 .../actions/install_requirements/action.yml   |    2 +-
 .github/workflows/ci.yml                      |    2 +-
 uv.lock                                       | 1344 +++++++++++++++++
 3 files changed, 1346 insertions(+), 2 deletions(-)
 create mode 100644 uv.lock

diff --git a/.github/actions/install_requirements/action.yml b/.github/actions/install_requirements/action.yml
index 998e2acb..b14850d5 100644
--- a/.github/actions/install_requirements/action.yml
+++ b/.github/actions/install_requirements/action.yml
@@ -25,7 +25,7 @@ runs:
         cache-dependency-glob: "uv.lock"
 
     - name: Install dependencies
-      run: uv sync
+      run: uv sync --extra dev
       shell: bash
 
     - name: Report what was installed
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 56036b42..dd8e4250 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,7 +13,7 @@ jobs:
     if: needs.check.outputs.branch-pr == ''
     uses: ./.github/workflows/_tox.yml
     with:
-      tox: precommit,type-check
+      tox: pre-commit
 
   test:
     needs: check
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 00000000..26a7091a
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,1344 @@
+version = 1
+revision = 1
+requires-python = ">=3.10"
+resolution-markers = [
+    "python_full_version >= '3.11'",
+    "python_full_version < '3.11'",
+]
+
+[[package]]
+name = "accessible-pygments"
+version = "0.0.5"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pygments" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/bc/c1/bbac6a50d02774f91572938964c582fff4270eee73ab822a4aeea4d8b11b/accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872", size = 1377899 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/8d/3f/95338030883d8c8b91223b4e21744b04d11b161a3ef117295d8241f50ab4/accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7", size = 1395903 },
+]
+
+[[package]]
+name = "alabaster"
+version = "1.0.0"
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+]
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+[[package]]
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+version = "0.7.0"
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+[[package]]
+name = "anyio"
+version = "4.9.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "exceptiongroup", marker = "python_full_version < '3.11'" },
+    { name = "idna" },
+    { name = "sniffio" },
+    { name = "typing-extensions", marker = "python_full_version < '3.13'" },
+]
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+name = "babel"
+version = "2.17.0"
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+]

From 32c50ea63e3a5da8b49ae6b93a60dae33d46c5b6 Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Thu, 10 Apr 2025 08:31:44 +0000
Subject: [PATCH 04/14] Remove hatch run from _test.yml; Bump pre-commit hook
 versions

---
 .github/workflows/_test.yml | 2 +-
 .pre-commit-config.yaml     | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/_test.yml b/.github/workflows/_test.yml
index a3c535cd..552b29d0 100644
--- a/.github/workflows/_test.yml
+++ b/.github/workflows/_test.yml
@@ -51,7 +51,7 @@ jobs:
           pip-install: ".[dev]"
 
       - name: Run tests
-        run: hatch run tests
+        run: tox -e tests
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6236246e..3c6856c8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,13 +9,13 @@ repos:
 
   - repo: https://github.com/astral-sh/uv-pre-commit
     # uv version.
-    rev: 0.6.3
+    rev: 0.6.14
     hooks:
       - id: uv-lock
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.9.6
+    rev: v0.11.4
     hooks:
       # Run the linter.
       - id: ruff

From 0375c2d5468df921afb969bdb7233242267d761a Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Thu, 10 Apr 2025 08:42:27 +0000
Subject: [PATCH 05/14] Fix pytest runner

---
 pyproject.toml | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index dba5bb18..8858a31b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,17 +57,7 @@ commands = [
 description = "Run tests"
 direct = true
 allowlist_externals = ["pytest"]
-commands = [
-    [
-        "pytest",
-        "--cov=phoebus_guibuilder",
-        "--cov-report",
-        "term",
-        "--cov-report",
-        "xml:cov.xml",
-        "{posargs}",
-    ],
-]
+commands = [["pytest", "{posargs}"]]
 
 [tool.tox.env.docs]
 description = "Run docs"

From faea062a272a154abb0dd647f511084e5a1e0df6 Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Thu, 10 Apr 2025 08:46:26 +0000
Subject: [PATCH 06/14] Update template files for uv

---
 template/Dockerfile.jinja     | 24 ++++++++---
 template/pyproject.toml.jinja | 78 ++++++++++++++++++++++++-----------
 2 files changed, 72 insertions(+), 30 deletions(-)

diff --git a/template/Dockerfile.jinja b/template/Dockerfile.jinja
index c5ca109b..f969b8cb 100644
--- a/template/Dockerfile.jinja
+++ b/template/Dockerfile.jinja
@@ -5,24 +5,36 @@ FROM python:${PYTHON_VERSION} AS developer
 
 # Add any system dependencies for the developer/build environment here
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    graphviz \
+    graphviz vim \
     && rm -rf /var/lib/apt/lists/*
+# Install uv using the official installer script
+RUN curl -LsSf https://astral.sh/uv/install.sh | \
+    env UV_INSTALL_DIR="/usr/local/bin" sh
 
-# Set up a virtual environment and put it in PATH
-RUN python -m venv /venv
-ENV PATH=/venv/bin:$PATH{% if docker %}
+# Configure environment
+ENV UV_CHECK_UPDATE=false
+# Configure UV to use system Python
+# ENV UV_SYSTEM_PYTHON=1
+
+# Creates virtual environment
+RUN uv venv --seed venv
+ENV VIRTUAL_ENV=/venv
+ENV PATH=$VIRTUAL_ENV/bin:$PATH{% if docker %}
 
 # The build stage installs the context into the venv
 FROM developer AS build
 COPY . /context
 WORKDIR /context
-RUN touch dev-requirements.txt && pip install -c dev-requirements.txt .
+
+# install dependencies and project into the local packages directory
+RUN touch dev-requirements.txt && uv pip install -c dev-requirements.txt .
 
 # The runtime stage copies the built venv into a slim runtime container
 FROM python:${PYTHON_VERSION}-slim AS runtime
 # Add apt-get system dependecies for runtime here if needed
 COPY --from=build /venv/ /venv/
-ENV PATH=/venv/bin:$PATH
+ENV VIRTUAL_ENV=/venv
+ENV PATH=$VIRTUAL_ENV/bin:$PATH
 
 # change this entrypoint if it is not the same as the repo
 ENTRYPOINT ["{{ repo_name }}"]
diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
index 93302aae..258b84e5 100644
--- a/template/pyproject.toml.jinja
+++ b/template/pyproject.toml.jinja
@@ -26,14 +26,14 @@ dev = [
     {% endif %}"pipdeptree",
     "pre-commit",
     {% if sphinx %}"pydata-sphinx-theme>=0.12",
-    {% endif %}{% if type_checker=="pyright" %}"pyright",
-    {% endif %}"pytest",
+    {% endif %} {% if type_checker=="pyright" %}"pyright",
+    {% endif %}"pytest>8.3.4",
     "pytest-cov",
     "ruff",
     {% if sphinx %}"sphinx-autobuild",
     "sphinx-copybutton",
     "sphinx-design",
-    {% endif %}"tox-direct",
+    {% endif %}"tox-uv",
     "types-mock",
 ]
 
@@ -77,30 +77,60 @@ data_file = "/tmp/{{ package_name }}.coverage"
 # Tests are run from installed location, map back to the src directory
 source = ["src", "**/site-packages/"]
 
-# tox must currently be configured via an embedded ini string
-# See: https://github.com/tox-dev/tox/issues/999
 [tool.tox]
-legacy_tox_ini = """
-[tox]
-skipsdist=True
+skipsdist = true
 
-[testenv:{pre-commit,type-checking,tests{% if sphinx %},docs{% endif %}}]
-# Don't create a virtualenv for the command, requires tox-direct plugin
-direct = True
-passenv = *
-allowlist_externals =
-    pytest
-    pre-commit
-    {{ type_checker }}
-{% if sphinx %}    sphinx-build
-    sphinx-autobuild
-{% endif %}commands =
-    pre-commit: pre-commit run --all-files --show-diff-on-failure {posargs}
-    type-checking: {{ type_checker }} src tests {posargs}
-    tests: pytest --cov={{ package_name }} --cov-report term --cov-report xml:cov.xml {posargs}
-{% if sphinx %}    docs: sphinx-{posargs:build -EW --keep-going} -T docs build/html
-{% endif %}"""
+[tool.tox.env.pre-commit]
+description = "Run pre-commit"
+direct = true
+allowlist_externals = ["pre-commit"]
+commands = [
+    [
+        "pre-commit",
+        "run",
+        #"--all-files",
+        "--show-diff-on-failure",
+        "{posargs}",
+    ],
+]
+
+[tool.tox.env.type-checking]
+description = "Run type-checking"
+direct = true
+allowlist_externals = ["{{ type_checker }}"]
+commands = [["{{ type_checker }}", "src", "{posargs}"]]
+
+[tool.tox.env.tests]
+description = "Run tests"
+direct = true
+allowlist_externals = ["pytest"]
+commands = [
+    [
+        "pytest",
+        "--cov={{ package_name}}",
+        "--cov-report",
+        "term",
+        "--cov-report",
+        "xml:cov.xml",
+        "{posargs}",
+    ],
+]
 
+{% if sphinx %}[tool.tox.env.docs]
+description = "Run docs"
+direct = true
+allowlist_externals = ["sphinx-build", "sphinx-autobuild"]
+commands = [
+    [
+        "sphinx-{posargs:build}",
+        "-EW",
+        "--keep-going",
+        "-T",
+        "docs",
+        "build/html",
+    ],
+]
+{% endif %}
 [tool.ruff]
 src = ["src", "tests"]
 line-length = 88

From 658a7948a5376617ac718e006520ef1f1bb3719b Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Thu, 10 Apr 2025 09:38:07 +0000
Subject: [PATCH 07/14] Tidy pyproject.toml

---
 pyproject.toml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8858a31b..716935c2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,9 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "python-copier-template"
 dynamic = ["version"]
 requires-python = ">=3.10"
-
-[project.optional-dependencies]
-dev = [
+optional-dependencies = { dev = [
     "copier",
     "myst-parser",
     "pre-commit",
@@ -19,7 +17,7 @@ dev = [
     "sphinx-copybutton",
     "sphinx-design",
     "tox-uv",
-]
+] }
 
 # # Without this, setuptools apparently try to scan the whole image's filesystem while working in /
 # [tool.setuptools.packages.find]

From 39b07b88c3610551fd5f43bc074a188a74246222 Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Mon, 14 Apr 2025 07:58:15 +0000
Subject: [PATCH 08/14] Revert unintended ci.yml changes

---
 .github/workflows/ci.yml | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dd8e4250..6ac1c4da 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,22 +34,23 @@ jobs:
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-  container:
+  docs:
     needs: check
     if: needs.check.outputs.branch-pr == ''
-    uses: ./.github/workflows/_container.yml
+    uses: ./.github/workflows/_docs.yml
     permissions:
-      contents: read
-      packages: write
+      contents: write
 
-  dist:
-    needs: check
-    if: needs.check.outputs.branch-pr == ''
-    uses: ./.github/workflows/_dist.yml
+  example:
+    needs: test
+    if: github.ref_name == 'main'
+    uses: ./.github/workflows/_example.yml
+    secrets:
+      EXAMPLE_DEPLOY_KEY: ${{ secrets.EXAMPLE_DEPLOY_KEY }}
 
   release:
     if: github.ref_type == 'tag'
-    needs: [dist]
+    needs: docs
     uses: ./.github/workflows/_release.yml
     permissions:
       contents: write

From ab7094bb3e4eb2bf99fbb60a299f36e5db22c58e Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Wed, 23 Apr 2025 09:31:00 +0000
Subject: [PATCH 09/14] Fix actions build, and updates to pyproject.toml

---
 .../actions/install_requirements/action.yml   |   7 +-
 .github/workflows/_test.yml                   |   2 +-
 .pre-commit-config.yaml                       |   2 +-
 pyproject.toml                                |  20 +-
 uv.lock                                       | 433 +++++++++++++++---
 5 files changed, 400 insertions(+), 64 deletions(-)

diff --git a/.github/actions/install_requirements/action.yml b/.github/actions/install_requirements/action.yml
index b14850d5..21faff5c 100644
--- a/.github/actions/install_requirements/action.yml
+++ b/.github/actions/install_requirements/action.yml
@@ -4,6 +4,9 @@ inputs:
   python-version:
     description: Python version to install, default is from Dockerfile
     default: "dev"
+  pip-install:
+    description: Parameters to pass to uv pip install
+    default: "$([ -f dev-requirements.txt ] && echo '-c dev-requirements.txt') -e .[dev]"
 
 runs:
   using: composite
@@ -24,8 +27,8 @@ runs:
         enable-cache: true
         cache-dependency-glob: "uv.lock"
 
-    - name: Install dependencies
-      run: uv sync --extra dev
+    - name: Install packages
+      run: uv pip install ${{ inputs.pip-install }}
       shell: bash
 
     - name: Report what was installed
diff --git a/.github/workflows/_test.yml b/.github/workflows/_test.yml
index 552b29d0..977f161f 100644
--- a/.github/workflows/_test.yml
+++ b/.github/workflows/_test.yml
@@ -34,7 +34,7 @@ jobs:
 
       - if: inputs.python-version == 'dev'
         name: Write the requirements as an artifact
-        run: pip freeze --exclude-editable > /tmp/dev-requirements.txt
+        run: uv pip freeze --exclude-editable > /tmp/dev-requirements.txt
 
       - if: inputs.python-version == 'dev'
         name: Upload dev-requirements.txt
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3c6856c8..39abe952 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
       - id: ruff
         name: lint with ruff
         language: system
-        entry: ruff check --force-exclude
+        entry: ruff check --force-exclude --fix
         types: [python]
         require_serial: true
 
diff --git a/pyproject.toml b/pyproject.toml
index 716935c2..3f1a5420 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,6 +17,7 @@ optional-dependencies = { dev = [
     "sphinx-copybutton",
     "sphinx-design",
     "tox-uv",
+    "twine>=6.1.0",
 ] }
 
 # # Without this, setuptools apparently try to scan the whole image's filesystem while working in /
@@ -36,10 +37,17 @@ testpaths = "tests"
 
 [tool.tox]
 skipsdist = true
+requires = ["tox-uv>=1.25.0"]
+# envs to runs automatically with tox -p
+env_list = ["pre-commit", "tests", "docs"]
+
+[tool.tox.env]
+passenv = { "*" = "" }
+# Include setuptools, pip, ... in the tox envs
+uv_seed = { enabled = true }
 
 [tool.tox.env.pre-commit]
 description = "Run pre-commit"
-direct = true
 allowlist_externals = ["pre-commit"]
 commands = [
     [
@@ -53,22 +61,22 @@ commands = [
 
 [tool.tox.env.tests]
 description = "Run tests"
-direct = true
 allowlist_externals = ["pytest"]
 commands = [["pytest", "{posargs}"]]
 
 [tool.tox.env.docs]
 description = "Run docs"
-direct = true
 allowlist_externals = ["sphinx-build", "sphinx-autobuild"]
 commands = [
     [
-        "sphinx-{posargs:build}",
-        "-EW",
-        "--keep-going",
+        "sphinx-build",
         "-T",
         "docs",
         "build/html",
+        { replace = "posargs", default = [
+            "-EW",
+            "--keep-going",
+        ], extend = true },
     ],
 ]
 
diff --git a/uv.lock b/uv.lock
index 26a7091a..76f83bd4 100644
--- a/uv.lock
+++ b/uv.lock
@@ -60,6 +60,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/b7/b8/3fe70c75fe32afc4bb507f75563d39bc5642255d1d94f1f23604725780bf/babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2", size = 10182537 },
 ]
 
+[[package]]
+name = "backports-tarfile"
+version = "1.2.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/86/72/cd9b395f25e290e633655a100af28cb253e4393396264a98bd5f5951d50f/backports_tarfile-1.2.0.tar.gz", hash = "sha256:d75e02c268746e1b8144c278978b6e98e85de6ad16f8e4b0844a154557eca991", size = 86406 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/b9/fa/123043af240e49752f1c4bd24da5053b6bd00cad78c2be53c0d1e8b975bc/backports.tarfile-1.2.0-py3-none-any.whl", hash = "sha256:77e284d754527b01fb1e6fa8a1afe577858ebe4e9dad8919e34c862cb399bc34", size = 30181 },
+]
+
 [[package]]
 name = "beautifulsoup4"
 version = "4.13.3"
@@ -91,6 +100,47 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/38/fc/bce832fd4fd99766c04d1ee0eead6b0ec6486fb100ae5e74c1d91292b982/certifi-2025.1.31-py3-none-any.whl", hash = "sha256:ca78db4565a652026a4db2bcdf68f2fb589ea80d0be70e03929ed730746b84fe", size = 166393 },
 ]
 
+[[package]]
+name = "cffi"
+version = "1.17.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pycparser" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/fc/97/c783634659c2920c3fc70419e3af40972dbaf758daa229a7d6ea6135c90d/cffi-1.17.1.tar.gz", hash = "sha256:1c39c6016c32bc48dd54561950ebd6836e1670f2ae46128f67cf49e789c52824", size = 516621 }
+wheels = [
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+    { url = "https://files.pythonhosted.org/packages/d3/48/1b9283ebbf0ec065148d8de05d647a986c5f22586b18120020452fff8f5d/cffi-1.17.1-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:ad9413ccdeda48c5afdae7e4fa2192157e991ff761e7ab8fdd8926f40b160cc3", size = 455571 },
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 version = "3.4.0"
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 ]
 
 [[package]]
 name = "uvicorn"
-version = "0.34.0"
+version = "0.34.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "click" },
     { name = "h11" },
     { name = "typing-extensions", marker = "python_full_version < '3.11'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/4b/4d/938bd85e5bf2edeec766267a5015ad969730bb91e31b44021dfe8b22df6c/uvicorn-0.34.0.tar.gz", hash = "sha256:404051050cd7e905de2c9a7e61790943440b3416f49cb409f965d9dcd0fa73e9", size = 76568 }
+sdist = { url = "https://files.pythonhosted.org/packages/86/37/dd92f1f9cedb5eaf74d9999044306e06abe65344ff197864175dbbd91871/uvicorn-0.34.1.tar.gz", hash = "sha256:af981725fc4b7ffc5cb3b0e9eda6258a90c4b52cb2a83ce567ae0a7ae1757afc", size = 76755 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/61/14/33a3a1352cfa71812a3a21e8c9bfb83f60b0011f5e36f2b1399d51928209/uvicorn-0.34.0-py3-none-any.whl", hash = "sha256:023dc038422502fa28a09c7a30bf2b6991512da7dcdb8fd35fe57cfc154126f4", size = 62315 },
+    { url = "https://files.pythonhosted.org/packages/5f/38/a5801450940a858c102a7ad9e6150146a25406a119851c993148d56ab041/uvicorn-0.34.1-py3-none-any.whl", hash = "sha256:984c3a8c7ca18ebaad15995ee7401179212c59521e67bfc390c07fa2b8d2e065", size = 62404 },
 ]
 
 [[package]]
@@ -1342,3 +1658,12 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/68/a1/dcb68430b1d00b698ae7a7e0194433bce4f07ded185f0ee5fb21e2a2e91e/websockets-15.0.1-pp310-pypy310_pp73-win_amd64.whl", hash = "sha256:cad21560da69f4ce7658ca2cb83138fb4cf695a2ba3e475e0559e05991aa8122", size = 176884 },
     { url = "https://files.pythonhosted.org/packages/fa/a8/5b41e0da817d64113292ab1f8247140aac61cbf6cfd085d6a0fa77f4984f/websockets-15.0.1-py3-none-any.whl", hash = "sha256:f7a866fbc1e97b5c617ee4116daaa09b722101d4a3c170c787450ba409f9736f", size = 169743 },
 ]
+
+[[package]]
+name = "zipp"
+version = "3.21.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/3f/50/bad581df71744867e9468ebd0bcd6505de3b275e06f202c2cb016e3ff56f/zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4", size = 24545 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/b7/1a/7e4798e9339adc931158c9d69ecc34f5e6791489d469f5e50ec15e35f458/zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931", size = 9630 },
+]

From bb18724b39e0d61f6571c5889c7b2c328e801299 Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Wed, 23 Apr 2025 14:57:33 +0000
Subject: [PATCH 10/14] Improvements to template pyproject.toml

---
 template/pyproject.toml.jinja | 46 ++++++++++++++++++-----------------
 1 file changed, 24 insertions(+), 22 deletions(-)

diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
index 258b84e5..ffa0b55e 100644
--- a/template/pyproject.toml.jinja
+++ b/template/pyproject.toml.jinja
@@ -17,16 +17,15 @@ dynamic = ["version"]
 license.file = "LICENSE"
 readme = "README.md"
 requires-python = ">=3.10"
-
-[project.optional-dependencies]
-dev = [
+optional-dependencies = { dev = [
+    "build",
     "copier",
     {% if type_checker=="mypy" %}"mypy",
     {% endif %}{% if sphinx %}"myst-parser",
     {% endif %}"pipdeptree",
     "pre-commit",
     {% if sphinx %}"pydata-sphinx-theme>=0.12",
-    {% endif %} {% if type_checker=="pyright" %}"pyright",
+    {% endif %}{% if type_checker=="pyright" %}"pyright",
     {% endif %}"pytest>8.3.4",
     "pytest-cov",
     "ruff",
@@ -34,18 +33,13 @@ dev = [
     "sphinx-copybutton",
     "sphinx-design",
     {% endif %}"tox-uv",
+    "twine",
     "types-mock",
-]
-
-[project.scripts]
-{{ repo_name }} = "{{ package_name }}.__main__:main"
-
-[project.urls]
-GitHub = "{{ repo_url }}"
-
-[[project.authors]] # Further authors may be added by duplicating this section
-email = "{{ author_email }}"
-name = "{{ author_name }}"
+] }
+scripts = { {{ repo_name }} = "{{ package_name }}.__main__:main" }
+urls = { GitHub = "{{ repo_url }}" }
+# Further authors may be added by appending to this list
+authors = [ { email = "{{ author_email }}", name = "{{ author_name }}" } ]
 
 
 [tool.setuptools_scm]
@@ -79,10 +73,17 @@ source = ["src", "**/site-packages/"]
 
 [tool.tox]
 skipsdist = true
+requires = ["tox-uv>=1.25.0"]
+# envs to runs automatically with tox -p
+env_list = ["pre-commit", "type-checking", "docs"] # "tests"]
+
+[tool.tox.env]
+passenv = { "*" = "" }
+# Include setuptools, pip, ... in the tox envs
+uv_seed = { enabled = true }
 
 [tool.tox.env.pre-commit]
 description = "Run pre-commit"
-direct = true
 allowlist_externals = ["pre-commit"]
 commands = [
     [
@@ -96,13 +97,13 @@ commands = [
 
 [tool.tox.env.type-checking]
 description = "Run type-checking"
-direct = true
 allowlist_externals = ["{{ type_checker }}"]
+# needed otherwise throws reportUnknownMemberType errors
+deps = ["pytest"]
 commands = [["{{ type_checker }}", "src", "{posargs}"]]
 
 [tool.tox.env.tests]
 description = "Run tests"
-direct = true
 allowlist_externals = ["pytest"]
 commands = [
     [
@@ -118,16 +119,17 @@ commands = [
 
 {% if sphinx %}[tool.tox.env.docs]
 description = "Run docs"
-direct = true
 allowlist_externals = ["sphinx-build", "sphinx-autobuild"]
 commands = [
     [
-        "sphinx-{posargs:build}",
-        "-EW",
-        "--keep-going",
+        "sphinx-build",
         "-T",
         "docs",
         "build/html",
+        { replace = "posargs", default = [
+            "-EW",
+            "--keep-going",
+        ], extend = true },
     ],
 ]
 {% endif %}

From 99f8aa59775c99c005da7d121cf5bad9344386a9 Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Wed, 30 Apr 2025 10:36:59 +0000
Subject: [PATCH 11/14] Fixes to dev container and tests (but some test cases
 fail, e.g. running test_template_mypy

---
 __init__.py                   |  0
 template/Dockerfile.jinja     |  4 ++--
 template/pyproject.toml.jinja |  5 +++++
 tests/test_example.py         | 28 +++++++++++++++-------------
 4 files changed, 22 insertions(+), 15 deletions(-)
 create mode 100644 __init__.py

diff --git a/__init__.py b/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/template/Dockerfile.jinja b/template/Dockerfile.jinja
index f969b8cb..46e6f8ca 100644
--- a/template/Dockerfile.jinja
+++ b/template/Dockerfile.jinja
@@ -32,8 +32,8 @@ RUN touch dev-requirements.txt && uv pip install -c dev-requirements.txt .
 # The runtime stage copies the built venv into a slim runtime container
 FROM python:${PYTHON_VERSION}-slim AS runtime
 # Add apt-get system dependecies for runtime here if needed
-COPY --from=build /venv/ /venv/
-ENV VIRTUAL_ENV=/venv
+COPY --from=build /venv/ .venv/
+ENV VIRTUAL_ENV=./.venv
 ENV PATH=$VIRTUAL_ENV/bin:$PATH
 
 # change this entrypoint if it is not the same as the repo
diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
index ffa0b55e..ed87b89b 100644
--- a/template/pyproject.toml.jinja
+++ b/template/pyproject.toml.jinja
@@ -41,6 +41,8 @@ urls = { GitHub = "{{ repo_url }}" }
 # Further authors may be added by appending to this list
 authors = [ { email = "{{ author_email }}", name = "{{ author_name }}" } ]
 
+[tool.uv]
+default-groups = []
 
 [tool.setuptools_scm]
 version_file = "src/{{ package_name }}/_version.py"
@@ -53,6 +55,8 @@ typeCheckingMode = "standard"
 {% endif %}{% if type_checker=="mypy" %}
 [tool.mypy]
 ignore_missing_imports = true # Ignore missing stubs in imported modules
+explicit_package_bases = true
+#no_namespace_packages = true
 {% endif %}
 [tool.pytest.ini_options]
 # Run pytest with all our checkers, and don't spam us with massive tracebacks on error
@@ -108,6 +112,7 @@ allowlist_externals = ["pytest"]
 commands = [
     [
         "pytest",
+        "-vv",
         "--cov={{ package_name}}",
         "--cov-report",
         "term",
diff --git a/tests/test_example.py b/tests/test_example.py
index a8c0f9ac..a54be57c 100644
--- a/tests/test_example.py
+++ b/tests/test_example.py
@@ -37,10 +37,12 @@ def run_pipe(cmd: str, cwd=None):
 
 
 def make_venv(project_path: Path) -> callable:
-    venv_path = project_path / "venv"
-    run_pipe(f"python -m venv {venv_path}")
+    venv_path = project_path / ".venv"
+    run_pipe(f"uv venv {venv_path}")
     run = functools.partial(run_pipe, cwd=str(project_path))
-    run("./venv/bin/pip install -e .[dev]")
+    # install to this env (hence the -p)
+    run(f"uv pip install -e .[dev] -p {venv_path}/bin/python")
+    # run("ls -la .venv/bin >&2")
     return run
 
 
@@ -53,14 +55,14 @@ def test_template_defaults(tmp_path: Path):
     catalog_info = tmp_path / "catalog-info.yaml"
     assert catalog_info.exists()
     assert 'typeCheckingMode = "strict"' in pyproject_toml.read_text()
-    run("./venv/bin/tox -p")
+    run(".venv/bin/tox -p")
     if not run_pipe("git tag --points-at HEAD"):
         # Only run linkcheck if not on a tag, as the CI might not have pushed
         # the docs for this tag yet, so we will fail
-        run("./venv/bin/tox -e docs build -- -b linkcheck")
-    run("./venv/bin/pip install build twine")
-    run("./venv/bin/python -m build")
-    run("./venv/bin/twine check --strict dist/*")
+        run(".venv/bin/tox -p -e docs -- -b linkcheck")
+    run(".venv/bin/uv pip install build twine")
+    run(".venv/bin/python -m build")
+    run(".venv/bin/twine check --strict dist/*")
 
 
 def test_template_with_extra_code_and_api_docs(tmp_path: Path):
@@ -100,7 +102,7 @@ class Thing:
     # Add to make sure pre-commit doesn't moan
     run("git add .")
     # Build
-    run("./venv/bin/tox -p")
+    run(".venv/bin/tox -p")
     # Check it generates the right output
     api_dir = tmp_path / "build" / "html" / "_api"
     top_html = api_dir / "python_copier_template_example.html"
@@ -121,13 +123,13 @@ class Thing:
 def test_template_mypy(tmp_path: Path):
     copy_project(tmp_path, type_checker="mypy")
     run = make_venv(tmp_path)
-    run("./venv/bin/tox -p")
+    run(".venv/bin/tox -p")
 
 
 def test_template_no_docs(tmp_path: Path):
     copy_project(tmp_path, docs_type="README")
     run = make_venv(tmp_path)
-    run("./venv/bin/tox -p")
+    run(".venv/bin/tox -p")
 
 
 def test_template_in_different_org_has_no_catalog(tmp_path: Path):
@@ -141,7 +143,7 @@ def test_template_no_docker_has_no_docs_and_works(tmp_path: Path):
     container_doc = tmp_path / "docs" / "how-to" / "run-container.md"
     assert not container_doc.exists()
     run = make_venv(tmp_path)
-    run("./venv/bin/tox -p")
+    run(".venv/bin/tox -p")
 
 
 def test_bad_repo_name(tmp_path: Path):
@@ -232,7 +234,7 @@ def test_pyright_works_in_standard_typing_mode(tmp_path: Path):
 
     # Ensure pyright is still happy
     run = make_venv(tmp_path)
-    run(f"./venv/bin/pyright {tmp_path}")
+    run(f".venv/bin/pyright {tmp_path}")
 
 
 def test_ignores_mypy_strict_mode(tmp_path: Path):

From daa725badec21d9c9052e92675f89d7f9af23795 Mon Sep 17 00:00:00 2001
From: Callum Forrester <callum.forrester@diamond.ac.uk>
Date: Thu, 1 May 2025 11:18:32 +0000
Subject: [PATCH 12/14] Fix posargs being passed to tox commands as list

---
 template/pyproject.toml.jinja | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
index ed87b89b..305fe139 100644
--- a/template/pyproject.toml.jinja
+++ b/template/pyproject.toml.jinja
@@ -95,7 +95,7 @@ commands = [
         "run",
         #"--all-files",
         "--show-diff-on-failure",
-        "{posargs}",
+        { replace = "posargs", default = [], extend = true },
     ],
 ]
 
@@ -104,7 +104,15 @@ description = "Run type-checking"
 allowlist_externals = ["{{ type_checker }}"]
 # needed otherwise throws reportUnknownMemberType errors
 deps = ["pytest"]
-commands = [["{{ type_checker }}", "src", "{posargs}"]]
+commands = [
+    [
+        "{{ type_checker }}",
+        "src",
+        "tests",
+        { replace = "posargs", default = [
+        ], extend = true },
+    ],
+]
 
 [tool.tox.env.tests]
 description = "Run tests"
@@ -113,12 +121,13 @@ commands = [
     [
         "pytest",
         "-vv",
-        "--cov={{ package_name}}",
+        "--cov=python_copier_template_example",
         "--cov-report",
         "term",
         "--cov-report",
         "xml:cov.xml",
-        "{posargs}",
+        { replace = "posargs", default = [
+        ], extend = true },
     ],
 ]
 

From d4bcfecb7a53bcfa72d6d5047b4639e7fb5987d3 Mon Sep 17 00:00:00 2001
From: Callum Forrester <callum.forrester@diamond.ac.uk>
Date: Tue, 6 May 2025 10:29:02 +0000
Subject: [PATCH 13/14] Revert more non-relevant changes

---
 template/pyproject.toml.jinja | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
index 305fe139..9b3c8f98 100644
--- a/template/pyproject.toml.jinja
+++ b/template/pyproject.toml.jinja
@@ -17,7 +17,9 @@ dynamic = ["version"]
 license.file = "LICENSE"
 readme = "README.md"
 requires-python = ">=3.10"
-optional-dependencies = { dev = [
+
+[project.optional-dependencies]
+dev = [
     "build",
     "copier",
     {% if type_checker=="mypy" %}"mypy",
@@ -35,11 +37,17 @@ optional-dependencies = { dev = [
     {% endif %}"tox-uv",
     "twine",
     "types-mock",
-] }
-scripts = { {{ repo_name }} = "{{ package_name }}.__main__:main" }
-urls = { GitHub = "{{ repo_url }}" }
-# Further authors may be added by appending to this list
-authors = [ { email = "{{ author_email }}", name = "{{ author_name }}" } ]
+]
+
+[project.scripts]
+{{ repo_name }} = "{{ package_name }}.__main__:main"
+
+[project.urls]
+GitHub = "{{ repo_url }}"
+
+[[project.authors]] # Further authors may be added by duplicating this section
+email = "{{ author_email }}"
+name = "{{ author_name }}"
 
 [tool.uv]
 default-groups = []
@@ -55,8 +63,6 @@ typeCheckingMode = "standard"
 {% endif %}{% if type_checker=="mypy" %}
 [tool.mypy]
 ignore_missing_imports = true # Ignore missing stubs in imported modules
-explicit_package_bases = true
-#no_namespace_packages = true
 {% endif %}
 [tool.pytest.ini_options]
 # Run pytest with all our checkers, and don't spam us with massive tracebacks on error

From 3ac8a8a85baba49be553421c91bb6a550f8734c8 Mon Sep 17 00:00:00 2001
From: Ollie Copping <oliver.copping@diamond.ac.uk>
Date: Fri, 9 May 2025 15:53:12 +0100
Subject: [PATCH 14/14] Tidy pyproject.toml

---
 template/pyproject.toml.jinja | 39 +++++++++++------------------------
 1 file changed, 12 insertions(+), 27 deletions(-)

diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
index 9b3c8f98..ed87b89b 100644
--- a/template/pyproject.toml.jinja
+++ b/template/pyproject.toml.jinja
@@ -17,9 +17,7 @@ dynamic = ["version"]
 license.file = "LICENSE"
 readme = "README.md"
 requires-python = ">=3.10"
-
-[project.optional-dependencies]
-dev = [
+optional-dependencies = { dev = [
     "build",
     "copier",
     {% if type_checker=="mypy" %}"mypy",
@@ -37,17 +35,11 @@ dev = [
     {% endif %}"tox-uv",
     "twine",
     "types-mock",
-]
-
-[project.scripts]
-{{ repo_name }} = "{{ package_name }}.__main__:main"
-
-[project.urls]
-GitHub = "{{ repo_url }}"
-
-[[project.authors]] # Further authors may be added by duplicating this section
-email = "{{ author_email }}"
-name = "{{ author_name }}"
+] }
+scripts = { {{ repo_name }} = "{{ package_name }}.__main__:main" }
+urls = { GitHub = "{{ repo_url }}" }
+# Further authors may be added by appending to this list
+authors = [ { email = "{{ author_email }}", name = "{{ author_name }}" } ]
 
 [tool.uv]
 default-groups = []
@@ -63,6 +55,8 @@ typeCheckingMode = "standard"
 {% endif %}{% if type_checker=="mypy" %}
 [tool.mypy]
 ignore_missing_imports = true # Ignore missing stubs in imported modules
+explicit_package_bases = true
+#no_namespace_packages = true
 {% endif %}
 [tool.pytest.ini_options]
 # Run pytest with all our checkers, and don't spam us with massive tracebacks on error
@@ -101,7 +95,7 @@ commands = [
         "run",
         #"--all-files",
         "--show-diff-on-failure",
-        { replace = "posargs", default = [], extend = true },
+        "{posargs}",
     ],
 ]
 
@@ -110,15 +104,7 @@ description = "Run type-checking"
 allowlist_externals = ["{{ type_checker }}"]
 # needed otherwise throws reportUnknownMemberType errors
 deps = ["pytest"]
-commands = [
-    [
-        "{{ type_checker }}",
-        "src",
-        "tests",
-        { replace = "posargs", default = [
-        ], extend = true },
-    ],
-]
+commands = [["{{ type_checker }}", "src", "{posargs}"]]
 
 [tool.tox.env.tests]
 description = "Run tests"
@@ -127,13 +113,12 @@ commands = [
     [
         "pytest",
         "-vv",
-        "--cov=python_copier_template_example",
+        "--cov={{ package_name}}",
         "--cov-report",
         "term",
         "--cov-report",
         "xml:cov.xml",
-        { replace = "posargs", default = [
-        ], extend = true },
+        "{posargs}",
     ],
 ]