From c3d518fc1e3a1dae1316c2a375a7fe40ebf90175 Mon Sep 17 00:00:00 2001
From: Tobias Raabe <raabe@posteo.de>
Date: Tue, 12 Mar 2024 23:03:43 +0100
Subject: [PATCH 1/4] Update infra.

---
 .../.pre-commit-config.yaml                   |  4 --
 .../.readthedocs.yaml                         | 17 ++++--
 {{cookiecutter.project_slug}}/README.md       |  4 +-
 .../docs/docs_environment.yml                 | 22 -------
 {{cookiecutter.project_slug}}/environment.yml |  4 +-
 {{cookiecutter.project_slug}}/pyproject.toml  | 60 +++++++++++++++++++
 {{cookiecutter.project_slug}}/setup.cfg       | 41 -------------
 {{cookiecutter.project_slug}}/tox.ini         | 16 +++--
 8 files changed, 86 insertions(+), 82 deletions(-)
 delete mode 100644 {{cookiecutter.project_slug}}/docs/docs_environment.yml
 delete mode 100644 {{cookiecutter.project_slug}}/setup.cfg

diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
index 4d2146e..6560564 100644
--- a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -24,10 +24,6 @@ repos:
     -   id: python-no-log-warn
     -   id: python-use-type-annotations
     -   id: text-unicode-replacement-char
--   repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.2.0
-    hooks:
-    -   id: setup-cfg-fmt
 -   repo: https://github.com/aio-libs/sort-all
     rev: v1.2.0
     hooks:
diff --git a/{{cookiecutter.project_slug}}/.readthedocs.yaml b/{{cookiecutter.project_slug}}/.readthedocs.yaml
index b508b44..1478786 100644
--- a/{{cookiecutter.project_slug}}/.readthedocs.yaml
+++ b/{{cookiecutter.project_slug}}/.readthedocs.yaml
@@ -1,10 +1,17 @@
 version: 2
 
 build:
-  image: latest
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
 
-python:
-  version: 3.10
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: true
 
-conda:
-  environment: docs/docs_environment.yml
+python:
+  install:
+  - method: pip
+    path: .
+    extra_requirements:
+     - docs
diff --git a/{{cookiecutter.project_slug}}/README.md b/{{cookiecutter.project_slug}}/README.md
index 9bcbae0..bf38756 100644
--- a/{{cookiecutter.project_slug}}/README.md
+++ b/{{cookiecutter.project_slug}}/README.md
@@ -15,14 +15,14 @@ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}) {% endif %}
 cookiecutter.github_username }}/{{ cookiecutter.project_slug
 }}/main.svg)](https://results.pre-commit.ci/latest/github/{{
 cookiecutter.github_username }}/{{ cookiecutter.project_slug }}/main)
-[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 ## Usage
 
 To get started, create the environment with
 
 ```console
-$ conda/mamba env create
+$ mamba env create
 ```
 
 To build the project, type
diff --git a/{{cookiecutter.project_slug}}/docs/docs_environment.yml b/{{cookiecutter.project_slug}}/docs/docs_environment.yml
deleted file mode 100644
index 690a754..0000000
--- a/{{cookiecutter.project_slug}}/docs/docs_environment.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-channels:
-  - conda-forge
-  - nodefaults
-
-dependencies:
-  - python >= 3.10
-  - pip
-  - setuptools_scm
-  - toml
-
-  # Documentation
-  - furo
-  - ipython
-  - nbsphinx
-  - myst-parser
-  - sphinx
-  - sphinx-design
-  - sphinx-copybutton
-
-  - pip:
-    - ../
-    - sphinxext-opengraph
diff --git a/{{cookiecutter.project_slug}}/environment.yml b/{{cookiecutter.project_slug}}/environment.yml
index ff1f71c..e135210 100644
--- a/{{cookiecutter.project_slug}}/environment.yml
+++ b/{{cookiecutter.project_slug}}/environment.yml
@@ -14,7 +14,7 @@ dependencies:
   - conda-lock
 
   # Package dependencies
-  - pytask >=0.2
+  - pytask >=0.4
 
   # Misc
   - black
@@ -34,5 +34,5 @@ dependencies:
   - sphinx-panels
 
   - pip:
-    - -e .
     - sphinxext-opengraph
+    - -e .
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index 83670b4..c6c349f 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -4,6 +4,66 @@ requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
 [tool.setuptools_scm]
 write_to = "src/{{ cookiecutter.project_slug }}/_version.py"
 
+[project]
+name = "{{ cookiecutter.project_slug }}"
+description = "{{ cookiecutter.project_description }}"
+requires-python = ">=3.8"
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: {{ cookiecutter.open_source_license }} License",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+]
+dynamic = ["version"]
+dependencies = ["pytask"]
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.license]
+text = "{{ cookiecutter.open_source_license }}"
+
+[[project.authors]]
+name = "{{ cookiecutter.author }}"
+email = "{{ cookiecutter.email }}"
+
+[project.optional-dependencies]
+docs = [
+  "furo",
+  "ipython",
+  "myst-parser",
+  "nbsphinx",
+  "sphinx",
+  "sphinx-copybutton",
+  "sphinx-design>=0.3",
+  "sphinx-toolbox",
+  "sphinxext-opengraph",
+]
+test = []
+
+[project.urls]
+Changelog = "https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}"
+Documentation = "https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}"
+Github = "https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}"
+Tracker = "https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}/issues"
+
+[tool.setuptools]
+include-package-data = true
+zip-safe = false
+platforms = ["unix", "linux", "osx", "win32"]
+license-files = ["LICENSE"]
+
+[tool.setuptools.package-dir]
+"" = "src"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+namespaces = false
+
 {% if cookiecutter.add_mypy == "yes" %}[tool.mypy]
 files = ["src", "tests"]
 check_untyped_defs = true
diff --git a/{{cookiecutter.project_slug}}/setup.cfg b/{{cookiecutter.project_slug}}/setup.cfg
deleted file mode 100644
index 39f8479..0000000
--- a/{{cookiecutter.project_slug}}/setup.cfg
+++ /dev/null
@@ -1,41 +0,0 @@
-[metadata]
-name = {{ cookiecutter.project_slug }}
-description = {{ cookiecutter.project_description }}
-long_description = file: README.md
-long_description_content_type = text/markdown
-url = https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}
-author = {{ cookiecutter.author }}
-author_email = {{ cookiecutter.email }}
-license = {{ cookiecutter.open_source_license }}
-{% if cookiecutter.open_source_license != 'Not open source' %}license_file = LICENSE
-{% endif %}platforms = unix, linux, osx, cygwin, win32
-classifiers =
-    Intended Audience :: Science/Research
-    License :: OSI Approved :: {{ cookiecutter.open_source_license }} License
-    Operating System :: MacOS :: MacOS X
-    Operating System :: Microsoft :: Windows
-    Operating System :: POSIX
-    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3 :: Only
-project_urls =
-    Changelog = https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}
-    Documentation = https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}
-    Github = https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}
-    Tracker = https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.project_slug }}/issues
-
-[options]
-packages = find:
-install_requires =
-    pytask
-python_requires = >=3.8
-include_package_data = True
-package_dir =
-    =src
-zip_safe = False
-
-[options.packages.find]
-where = src
-
-[check-manifest]
-ignore =
-    src/{{ cookiecutter.project_slug }}/_version.py
diff --git a/{{cookiecutter.project_slug}}/tox.ini b/{{cookiecutter.project_slug}}/tox.ini
index 1f2169e..76e568a 100644
--- a/{{cookiecutter.project_slug}}/tox.ini
+++ b/{{cookiecutter.project_slug}}/tox.ini
@@ -1,10 +1,11 @@
 [tox]
-envlist = pytest, sphinx
+requires = tox>=4
+envlist = docs, test
 
 [testenv]
-usedevelop = true
+package = editable
 
-[testenv:pytest]
+[testenv:test]
 conda_channels =
     conda-forge
     nodefaults
@@ -14,8 +15,11 @@ conda_deps =
     pytest-cov
     pytest-xdist
 
-    # Package dependencies
-    pytask
-
 commands =
     pytest {posargs}
+
+[testenv:docs]
+extras = docs, test
+commands =
+    - sphinx-build -n -T -b html -d {envtmpdir}/doctrees docs/source docs/build/html
+    - sphinx-build -n -T -b doctest -d {envtmpdir}/doctrees docs/source docs/build/html

From 1ca0e1709fa3e0ecb5752991fb21e8977422a4cc Mon Sep 17 00:00:00 2001
From: Tobias Raabe <raabe@posteo.de>
Date: Tue, 12 Mar 2024 23:08:40 +0100
Subject: [PATCH 2/4] Update.

---
 .github/workflows/main.yml                    |  7 +---
 codecov.yml                                   |  1 -
 .../.github/dependabot.yml                    |  5 +++
 .../.github/workflows/main.yml                | 32 +++----------------
 {{cookiecutter.project_slug}}/codecov.yml     | 26 +++++++++++++++
 {{cookiecutter.project_slug}}/dependabot.yml  | 12 +++++++
 {{cookiecutter.project_slug}}/pyproject.toml  | 13 +-------
 7 files changed, 50 insertions(+), 46 deletions(-)
 create mode 100644 {{cookiecutter.project_slug}}/codecov.yml
 create mode 100644 {{cookiecutter.project_slug}}/dependabot.yml

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index f9fb346..4eaae9f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -5,9 +5,6 @@ concurrency:
   group: ${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-env:
-  CONDA_EXE: mamba
-
 on:
   push:
     branches:
@@ -43,6 +40,4 @@ jobs:
         run: tox -e test -- --cov=./ --cov-report=xml
 
       - name: Upload coverage reports of tests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.10'
-        shell: bash -l {0}
-        run: bash <(curl -s https://codecov.io/bash)
+        uses: codecov/codecov-action@v4
diff --git a/codecov.yml b/codecov.yml
index 4892c14..7fc9643 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -24,4 +24,3 @@ coverage:
 
 ignore:
   - ".tox/**/*"
-  - "setup.py"
diff --git a/{{cookiecutter.project_slug}}/.github/dependabot.yml b/{{cookiecutter.project_slug}}/.github/dependabot.yml
index 718572b..fbb58d4 100644
--- a/{{cookiecutter.project_slug}}/.github/dependabot.yml
+++ b/{{cookiecutter.project_slug}}/.github/dependabot.yml
@@ -5,3 +5,8 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+
+    groups:
+      github-actions:
+        patterns:
+          - "*"
diff --git a/{{cookiecutter.project_slug}}/.github/workflows/main.yml b/{{cookiecutter.project_slug}}/.github/workflows/main.yml
index 45adfcc..f61c9b2 100644
--- a/{{cookiecutter.project_slug}}/.github/workflows/main.yml
+++ b/{{cookiecutter.project_slug}}/.github/workflows/main.yml
@@ -30,7 +30,7 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: mamba-org/provision-with-micromamba@main
         with:
           environment-file: false
@@ -42,31 +42,9 @@ jobs:
             tox-conda
           cache-downloads: true
 
-      # Unit, integration, and end-to-end tests.
-
-      - name: Run unit tests and doctests.
-        shell: bash -l {0}
-        run: tox -e pytest -- src tests -m "unit or (not integration and not end_to_end)" --cov=./ --cov-report=xml -n auto
-
-      - name: Upload coverage report for unit tests and doctests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.10'
-        shell: bash -l {0}
-        run: bash <(curl -s https://codecov.io/bash) -F unit -c
-
-      - name: Run integration tests.
+      - name: Run tests and doctests.
         shell: bash -l {0}
-        run: tox -e pytest -- src tests -m integration --cov=./ --cov-report=xml -n auto
+        run: tox -e pytest
 
-      - name: Upload coverage reports of integration tests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.10'
-        shell: bash -l {0}
-        run: bash <(curl -s https://codecov.io/bash) -F integration -c
-
-      - name: Run end-to-end tests.
-        shell: bash -l {0}
-        run: tox -e pytest -- src tests -m end_to_end --cov=./ --cov-report=xml -n auto
-
-      - name: Upload coverage reports of end-to-end tests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.10'
-        shell: bash -l {0}
-        run: bash <(curl -s https://codecov.io/bash) -F end_to_end -c
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v4
diff --git a/{{cookiecutter.project_slug}}/codecov.yml b/{{cookiecutter.project_slug}}/codecov.yml
new file mode 100644
index 0000000..7fc9643
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/codecov.yml
@@ -0,0 +1,26 @@
+codecov:
+  branch: main
+
+coverage:
+  precision: 2
+  round: down
+  range: 80...100
+  status:
+    project:
+      default:
+        threshold: 1%
+      unit:
+        threshold: 1%
+        flags:
+          - unit
+      integration:
+        threshold: 1%
+        flags:
+          - integration
+      end_to_end:
+        threshold: 1%
+        flags:
+          - end_to_end
+
+ignore:
+  - ".tox/**/*"
diff --git a/{{cookiecutter.project_slug}}/dependabot.yml b/{{cookiecutter.project_slug}}/dependabot.yml
new file mode 100644
index 0000000..fbb58d4
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/dependabot.yml
@@ -0,0 +1,12 @@
+version: 2
+
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+
+    groups:
+      github-actions:
+        patterns:
+          - "*"
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index c6c349f..f06690c 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -106,16 +106,5 @@ convention = "numpy"
 
 [tool.pytest.ini_options]
 addopts = ["--doctest-modules"]
-testpaths = ["tests"]
-filterwarnings = [
-    "ignore: the imp module is deprecated in favour of importlib",
-    "ignore: Using or importing the ABCs from 'collections' instead of from",
-    "ignore: The (parser|symbol) module is deprecated and will be removed in future",
-]
-markers = [
-    "wip: Tests that are work-in-progress.",
-    "unit: Flag for unit tests which target mainly a single function.",
-    "integration: Flag for integration tests which may comprise of multiple unit tests.",
-    "end_to_end: Flag for tests that cover the whole program.",
-]
+testpaths = ["src", "tests"]
 norecursedirs = [".idea", ".tox"]

From b1e25c223438993b7065b4906857be76480328c9 Mon Sep 17 00:00:00 2001
From: Tobias Raabe <raabe@posteo.de>
Date: Tue, 12 Mar 2024 23:09:28 +0100
Subject: [PATCH 3/4] Fix.

---
 docs/source/changes.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/changes.md b/docs/source/changes.md
index e6ec852..7cf458d 100644
--- a/docs/source/changes.md
+++ b/docs/source/changes.md
@@ -6,6 +6,7 @@ them in reverse chronological order.
 ## 1.7.0 - 2024-xx-xx
 
 - {pull}`39` updates the pre-commit hooks.
+- {pull}`41` updates the infrastructure.
 
 ## 1.6.0 - 2023-11-23
 

From cac138a714efe4247155137121abf90146d4a997 Mon Sep 17 00:00:00 2001
From: Tobias Raabe <raabe@posteo.de>
Date: Tue, 12 Mar 2024 23:23:44 +0100
Subject: [PATCH 4/4] update hooks.

---
 {{cookiecutter.project_slug}}/.pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
index 6560564..a8ba69d 100644
--- a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -29,12 +29,12 @@ repos:
     hooks:
     -   id: sort-all
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.3.2
     hooks:
       - id: ruff
       - id: ruff-format
 {% if cookiecutter.python_version in ["3.10", "3.11", "3.12"] %}-   repo: https://github.com/dosisod/refurb
-    rev: v1.24.0
+    rev: v2.0.0
     hooks:
     -   id: refurb
 {% endif %}
@@ -59,7 +59,7 @@ repos:
         args: [--wrap, "88"]
         files: (docs/.)
 {% if cookiecutter.add_mypy == "yes" %}-   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.7.0'
+    rev: 'v1.9.0'
     hooks:
     -   id: mypy
         args: [