Revert discussed changes and remove commented out parts

Author: callumforrester

Dockerfile

@@ -5,18 +5,17 @@ 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 vim \
+    graphviz \
     && 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
 
 # Configure environment
 ENV UV_CHECK_UPDATE=false
-# Configure UV to use system Python
-# ENV UV_SYSTEM_PYTHON=1
 
-# Creates virtual environment
+# Create virtual environment
 RUN uv venv --seed venv
 ENV VIRTUAL_ENV=/venv
 ENV PATH=$VIRTUAL_ENV/bin:$PATH

pyproject.toml

@@ -6,7 +6,9 @@ build-backend = "setuptools.build_meta"
 name = "python-copier-template"
 dynamic = ["version"]
 requires-python = ">=3.11"
-optional-dependencies = { dev = [
+
+[project.optional-dependencies]
+dev = [
     "copier",
     "myst-parser",
     "pre-commit",
@@ -18,11 +20,7 @@ optional-dependencies = { dev = [
     "sphinx-design",
     "tox-uv",
     "twine>=6.1.0",
-] }
-
-# # Without this, setuptools apparently try to scan the whole image's filesystem while working in /
-# [tool.setuptools.packages.find]
-# where = []
+]
 
 [tool.setuptools_scm]
 
@@ -55,14 +53,14 @@ commands = [
         "run",
         #"--all-files",
         "--show-diff-on-failure",
-        "{posargs}",
+        { replace = "posargs", default = [], extend = true },
     ],
 ]
 
 [tool.tox.env.tests]
 description = "Run tests"
 allowlist_externals = ["pytest"]
-commands = [["pytest", "{posargs}"]]
+commands = [["pytest", { replace = "posargs", default = [], extend = true }]]
 
 [tool.tox.env.docs]
 description = "Run docs"

template/Dockerfile.jinja

@@ -5,18 +5,17 @@ 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 vim \
+    graphviz \
     && 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
 
 # Configure environment
 ENV UV_CHECK_UPDATE=false
-# Configure UV to use system Python
-# ENV UV_SYSTEM_PYTHON=1
 
-# Creates virtual environment
+# Create virtual environment
 RUN uv venv --seed venv
 ENV VIRTUAL_ENV=/venv
 ENV PATH=$VIRTUAL_ENV/bin:$PATH{% if docker %}

template/pyproject.toml.jinja

@@ -63,8 +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