From 078c1be69ff5b3d055297ed10057e353dd52a90c Mon Sep 17 00:00:00 2001
From: Sebastian Straub <sebastian.straub@alexanderthamm.com>
Date: Fri, 8 Dec 2023 15:49:12 +0100
Subject: [PATCH 1/8] update and extend pyproject.toml

---
 {{cookiecutter.project_slug}}/pyproject.toml | 37 +++++++++++++++-----
 1 file changed, 29 insertions(+), 8 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index b03fe76..c8d3120 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -3,7 +3,7 @@ name = "{{ cookiecutter.project_slug }}"
 version = "0.1.0"
 description = "{{ cookiecutter.project_short_description }}"
 authors = ["{{ cookiecutter.full_name }} <{{ cookiecutter.email }}>"]
-license = "Proprietary"
+license = "proprietary"
 packages = [{ include = "{{ cookiecutter.module_name }}", from = "src" }, ]
 include = ["src/{{ cookiecutter.module_name }}/res/*"]
 {% if cookiecutter.create_cli == "yes" %}
@@ -11,17 +11,38 @@ include = ["src/{{ cookiecutter.module_name }}/res/*"]
 {{ cookiecutter.project_slug }} = "{{ cookiecutter.module_name }}.main:app" {% endif %}
 
 [tool.poetry.dependencies]
-python = "^3.10"{% if cookiecutter.config_file == 'hocon' %}
+python = "^3.11"{% if cookiecutter.config_file == 'hocon' %}
 pyhocon = "^0.3.59"{% elif cookiecutter.config_file == 'yaml' %}
 PyYAML = "^6.0"{% endif %}{% if cookiecutter.create_cli == 'yes' %}
-typer = {extras = ["all"], version = "^0.7.0"}{% endif %}
+typer = {extras = ["all"], version = "^0.9.0"}{% endif %}
 
-[tool.poetry.dev-dependencies]{% if cookiecutter.code_formatter == 'black' %}
-black = "^22.10"{% endif %}
-pre-commit = "^2.20"
-pytest = "^7.2"
-pytest-cov = "^4.0"{% if cookiecutter.use_notebooks == 'yes' %}
+[tool.poetry.group.test.dependencies]
+pytest = "^7.0"
+pytest-cov = "^4.0"
+
+[tool.poetry.group.linter.dependencies]{% if cookiecutter.code_formatter == 'black' %}
+black = "^23.11"{% else %}
+ruff = "^0.1.7"{% endif %}
+isort = "^5.12.0"
+
+[tool.poetry.group.dev.dependencies]
+pre-commit = "^3.0"{% if cookiecutter.use_notebooks == 'yes' %}
 jupyterlab = "^3.5"{% endif %}
+{% if cookiecutter.code_formatter != 'black' %}
+[tool.ruff]
+line-length = 100
+src = ["src", "tests"]
+ignore = ["F401"]
+{% endif %}
+[tool.isort]{% if cookiecutter.code_formatter == 'black' %}
+profile = "black"{% else %}
+py_version = 310
+line_length = 100
+multi_line_output = 3{% endif %}
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+testpaths = ["tests"]
 
 [build-system]
 requires = ["poetry-core"]

From 867a1d392a79f34e8b698fbc53b250bac85d31e9 Mon Sep 17 00:00:00 2001
From: Sebastian Straub <sebastian.straub@alexanderthamm.com>
Date: Fri, 8 Dec 2023 15:54:44 +0100
Subject: [PATCH 2/8] update and extend pre-commit hooks

---
 .../.pre-commit-config.yaml                   | 20 +++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
index 32091a9..a808417 100644
--- a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: 'v4.4.0'
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -13,13 +13,21 @@ repos:
       - id: mixed-line-ending
       - id: trailing-whitespace{% if cookiecutter.code_formatter == 'black' %}
   - repo: https://github.com/psf/black
-    rev: stable
+    rev: 'stable'
     hooks:
       - id: black
         language_version: python3.8
         exclude: ^notebooks{% else %}
-  - repo: https://github.com/PyCQA/flake8
-    rev: '5.0.4'
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: 'v0.1.7'
     hooks:
-      - id: flake8
-        args: ['--max-line-length=100', '--ignore=F401,W503', '--exclude=tests/*']{% endif %}
+      - id: ruff{% endif %}
+  - repo: https://github.com/pycqa/isort
+    rev: '5.12.0'
+    hooks:
+      - id: isort
+  - repo: https://github.com/asottile/pyupgrade
+    rev: 'v3.15.0'
+    hooks:
+      - id: pyupgrade
+        args: [ --py38-plus ]

From 7e1cf570c9d2ea8017d2bc342a872c08a180fbeb Mon Sep 17 00:00:00 2001
From: Sebastian Straub <sebastian.straub@alexanderthamm.com>
Date: Fri, 8 Dec 2023 16:02:11 +0100
Subject: [PATCH 3/8] update and extend .gitlab-ci.yml

---
 {{cookiecutter.project_slug}}/.gitlab-ci.yml | 22 +++++++++++++-------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/.gitlab-ci.yml b/{{cookiecutter.project_slug}}/.gitlab-ci.yml
index 316e614..65790a0 100644
--- a/{{cookiecutter.project_slug}}/.gitlab-ci.yml
+++ b/{{cookiecutter.project_slug}}/.gitlab-ci.yml
@@ -16,7 +16,7 @@ variables:
   {%- if cookiecutter.package_manager == 'conda' %}
   CONDA_PKGS_DIRS: $CI_PROJECT_DIR/.cache/conda
   {%- elif cookiecutter.package_manager == 'poetry' %}
-  POETRY_VERSION: 1.0.5
+  POETRY_VERSION: 1.7.1
   POETRY_CACHE_DIR: $CI_PROJECT_DIR/.cache/poetry
   {%- endif %}
 
@@ -30,7 +30,7 @@ stages:
 
 {% if cookiecutter.package_manager == 'poetry' -%}
 build-wheel:
-  image: python:3-slim
+  image: python:3.11
   stage: build
   artifacts:
     name: 'app-wheel'
@@ -41,7 +41,7 @@ build-wheel:
     - pip install poetry==$POETRY_VERSION
     - poetry build -f wheel {% else -%}
 build-wheel:
-  image: python:3-slim
+  image: python:3.11
   stage: build
   artifacts:
     name: 'app-wheel'
@@ -54,20 +54,26 @@ build-wheel:
 {% if cookiecutter.package_manager == 'poetry' -%}
 test-unit:
   stage: test
-  image: python:3-slim
+  image: python:3.11
   cache:
     key:
       files:
-        - pyproject.toml
+        - poetry.lock
     paths:
       - $PIP_CACHE_DIR
       - $POETRY_CACHE_DIR
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+  coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
   before_script:
     - pip install poetry==$POETRY_VERSION
-    - poetry install --no-root
+    - poetry install --only=main,test
     - source `poetry env info --path`/bin/activate
   script:
-    - pytest tests {% elif cookiecutter.package_manager == 'conda' -%}
+    - pytest tests --cov src --cov-report=term --cov-report xml:coverage.xml{% elif cookiecutter.package_manager == 'conda' -%}
 test-unit:
   stage: test
   image: continuumio/miniconda3
@@ -89,7 +95,7 @@ test-unit:
     - pytest tests {% elif cookiecutter.package_manager == 'pip' -%}
 test-unit:
   stage: test
-  image: python:3-slim
+  image: python:3.11
   cache:
     key:
       files:

From 4ad6065406c2fe994ad0c10106c31cba100d420f Mon Sep 17 00:00:00 2001
From: Sebastian Straub <sebastian.straub@alexanderthamm.com>
Date: Fri, 8 Dec 2023 16:07:53 +0100
Subject: [PATCH 4/8] update poetry info in readme

---
 {{cookiecutter.project_slug}}/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/README.md b/{{cookiecutter.project_slug}}/README.md
index 44f892f..617689e 100644
--- a/{{cookiecutter.project_slug}}/README.md
+++ b/{{cookiecutter.project_slug}}/README.md
@@ -96,9 +96,9 @@ Note that we mainly use notebooks for experiments, visualizations and reports. E
 
 To build a distribution package (wheel), please use
 
-    python setup.py bdist_wheel
+    {% if cookiecutter.package_manager == 'poetry' %}poetry build{% else %}python setup.py bdist_wheel{% endif %}
 
-this will clean up the build folder and then run the `bdist_wheel` command.
+You will find your distribution package in the `dist` folder.
 
 ### Contributions
 

From 0f6013276ae2d79d439e8d822a197b7118ac1bf9 Mon Sep 17 00:00:00 2001
From: Sebastian Straub <sebastian.straub@alexanderthamm.com>
Date: Fri, 8 Dec 2023 16:08:07 +0100
Subject: [PATCH 5/8] cleanup imports in setup.py

---
 {{cookiecutter.project_slug}}/setup.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/setup.py b/{{cookiecutter.project_slug}}/setup.py
index 8ff3637..fc5e4e5 100644
--- a/{{cookiecutter.project_slug}}/setup.py
+++ b/{{cookiecutter.project_slug}}/setup.py
@@ -1,8 +1,4 @@
 import os
-import shutil
-import subprocess
-import sys
-from distutils.cmd import Command
 from runpy import run_path
 
 from setuptools import find_packages, setup

From 47c474ad3fb341a31b05349fec7a90f6e668876d Mon Sep 17 00:00:00 2001
From: Sebastian Straub <sebastian.straub@alexanderthamm.com>
Date: Fri, 8 Dec 2023 16:24:10 +0100
Subject: [PATCH 6/8] remove pytest.ini for poetry

---
 hooks/post_gen_project.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py
index 3cf7a48..c52ca3c 100644
--- a/hooks/post_gen_project.py
+++ b/hooks/post_gen_project.py
@@ -18,12 +18,14 @@
     'requirements.txt',
     'requirements-dev.txt',
     'setup.py',
+    'tests/pytest.ini',
 }
 
 files_conda = {
     'environment.yml',
     'environment-dev.yml',
     'setup.py',
+    'tests/pytest.ini',
 }
 
 files_poetry = {
@@ -165,6 +167,7 @@ def handle_editor_settings():
         print(f"Error: unsupported editor {editor_settings}")
         sys.exit(1)
 
+
 def handle_ci():
     ci_pipeline = '{{ cookiecutter.ci_pipeline }}'
     if ci_pipeline == "gitlab":

From b298d3ee0913ed7a1aa55ac2f7fba71c8f702348 Mon Sep 17 00:00:00 2001
From: Sebastian Straub <sebastian.straub@alexanderthamm.com>
Date: Fri, 8 Dec 2023 16:24:22 +0100
Subject: [PATCH 7/8] readme update

---
 {{cookiecutter.project_slug}}/README.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/README.md b/{{cookiecutter.project_slug}}/README.md
index 617689e..1239186 100644
--- a/{{cookiecutter.project_slug}}/README.md
+++ b/{{cookiecutter.project_slug}}/README.md
@@ -98,14 +98,13 @@ To build a distribution package (wheel), please use
 
     {% if cookiecutter.package_manager == 'poetry' %}poetry build{% else %}python setup.py bdist_wheel{% endif %}
 
-You will find your distribution package in the `dist` folder.
+You can find the build artifacts in the `dist` folder.
 
 ### Contributions
 
 Before contributing, please set up the pre-commit hooks to reduce errors and ensure consistency
 
     pip install -U pre-commit
-
     pre-commit install
 
 If you run into any issues, you can remove the hooks again with `pre-commit uninstall`.

From 095871db904e38c6f9e900c20edf38d72f5e5b40 Mon Sep 17 00:00:00 2001
From: Sebastian Straub <sebastian.straub@alexanderthamm.com>
Date: Fri, 8 Dec 2023 16:38:55 +0100
Subject: [PATCH 8/8] small changes so pre-commit hooks don't fail

---
 {{cookiecutter.project_slug}}/.gitlab-ci.yml    |  8 ++++----
 {{cookiecutter.project_slug}}/pyproject.toml    |  2 +-
 .../src/{{cookiecutter.module_name}}/main.py    |  1 -
 .../{{cookiecutter.module_name}}/main__cli.py   | 17 +++++++----------
 .../{{cookiecutter.module_name}}/util__yaml.py  |  2 +-
 .../tests/test_example.py                       |  1 -
 6 files changed, 13 insertions(+), 18 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/.gitlab-ci.yml b/{{cookiecutter.project_slug}}/.gitlab-ci.yml
index 65790a0..90700c2 100644
--- a/{{cookiecutter.project_slug}}/.gitlab-ci.yml
+++ b/{{cookiecutter.project_slug}}/.gitlab-ci.yml
@@ -39,7 +39,7 @@ build-wheel:
     expire_in: 6 mos
   script:
     - pip install poetry==$POETRY_VERSION
-    - poetry build -f wheel {% else -%}
+    - poetry build -f wheel{% else -%}
 build-wheel:
   image: python:3.11
   stage: build
@@ -49,7 +49,7 @@ build-wheel:
       - dist/{{ cookiecutter.module_name }}-*.whl
     expire_in: 6 mos
   script:
-    - python setup.py dist {%- endif %}
+    - python setup.py dist{%- endif %}
 
 {% if cookiecutter.package_manager == 'poetry' -%}
 test-unit:
@@ -92,7 +92,7 @@ test-unit:
     - source activate .venv
     - pip install dist/{{ cookiecutter.module_name }}-*.whl
   script:
-    - pytest tests {% elif cookiecutter.package_manager == 'pip' -%}
+    - pytest tests{% elif cookiecutter.package_manager == 'pip' -%}
 test-unit:
   stage: test
   image: python:3.11
@@ -109,7 +109,7 @@ test-unit:
     - pip install -r requirements.txt -r requirements-dev.txt
     - pip install dist/{{ cookiecutter.module_name }}-*.whl
   script:
-    - pytest tests {%- endif %}
+    - pytest tests{%- endif %}
 
 # Nonprod deployments
 
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index c8d3120..feb3d7b 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -8,7 +8,7 @@ packages = [{ include = "{{ cookiecutter.module_name }}", from = "src" }, ]
 include = ["src/{{ cookiecutter.module_name }}/res/*"]
 {% if cookiecutter.create_cli == "yes" %}
 [tool.poetry.scripts]
-{{ cookiecutter.project_slug }} = "{{ cookiecutter.module_name }}.main:app" {% endif %}
+{{ cookiecutter.project_slug }} = "{{ cookiecutter.module_name }}.main:app"{% endif %}
 
 [tool.poetry.dependencies]
 python = "^3.11"{% if cookiecutter.config_file == 'hocon' %}
diff --git a/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/main.py b/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/main.py
index 4d27bd2..021ce3e 100644
--- a/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/main.py
+++ b/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/main.py
@@ -1,4 +1,3 @@
-
 def main():
     # TODO your journey starts here
     print("hello :)")
diff --git a/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/main__cli.py b/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/main__cli.py
index 755a70e..3df7895 100644
--- a/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/main__cli.py
+++ b/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/main__cli.py
@@ -2,14 +2,11 @@
 
 import typer
 
-from {{ cookiecutter.module_name }} import __title__ , __version__{% if cookiecutter.config_file != 'none' %}, util{% endif %}
+from {{ cookiecutter.module_name }} import __title__, __version__{% if cookiecutter.config_file != 'none' %}, util{% endif %}
 
 logger = logging.getLogger('{{ cookiecutter.module_name }}')
 
-app = typer.Typer(
-    name='{{ cookiecutter.module_name }}',
-    help="{{ cookiecutter.project_short_description }}"
-)
+app = typer.Typer(name='{{ cookiecutter.module_name }}')
 
 
 def version_callback(version: bool):
@@ -25,8 +22,6 @@ def version_callback(version: bool):
     metavar='PATH',
     help="path to the program configuration"
 )
-
-
 VersionOption = typer.Option(
     None,
     '-v',
@@ -40,11 +35,13 @@ def version_callback(version: bool):
 @app.command()
 def main(config_file: str = ConfigOption, version: bool = VersionOption):
     """
-    This is the entry point of your command line application. The values of the CLI params that
-    are passed to this application will show up als parameters to this function.
+    {{ cookiecutter.project_short_description }}
 
+    Note: This is the entry point of your command line application. The values of the CLI params
+    that are passed to this application will show up als parameters to this function.
     This docstring is where you describe what your command line application does.
-    Try running `python -m {{ cookiecutter.module_name }} --help` to see how this shows up in the command line.
+    Try running `python -m {{ cookiecutter.module_name }} --help` to see how this shows up in the
+    command line.
     """
     {% if cookiecutter.config_file != 'none' %}config = util.load_config(config_file)
     util.logging_setup(config){% endif %}
diff --git a/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/util__yaml.py b/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/util__yaml.py
index 78b62e8..5bf8e33 100644
--- a/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/util__yaml.py
+++ b/{{cookiecutter.project_slug}}/src/{{cookiecutter.module_name}}/util__yaml.py
@@ -28,7 +28,7 @@ def load_config(config_file: Union[str, Path]) -> Dict[str, Any]:
     :param config_file: path of the config file to load
     :return: the parsed config as dictionary
     """
-    with open(config_file, 'r') as fp:
+    with open(config_file) as fp:
         return yaml.safe_load(fp)
 
 
diff --git a/{{cookiecutter.project_slug}}/tests/test_example.py b/{{cookiecutter.project_slug}}/tests/test_example.py
index e6ae4d9..6ef09e2 100644
--- a/{{cookiecutter.project_slug}}/tests/test_example.py
+++ b/{{cookiecutter.project_slug}}/tests/test_example.py
@@ -1,3 +1,2 @@
-
 def test_the_universe():
     assert 6 * 7 == 42