fix(linter): Fix the linter configuration (#131)

Fix the linter configuration for the project and the template.

Co-authored-by: Anavelyz <42752529+Anavelyz@users.noreply.github.com>

.pre-commit-config.yaml

@@ -1,50 +1,49 @@
 ---
+default_stages:
+  - commit
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0
     hooks:
       - id: end-of-file-fixer
+
   - repo: local
     hooks:
-    - entry: black
-      exclude: |
-       (?x)(
-           ^{{cookiecutter.project_slug}}/
-       )
-      files: ""
-      id: black
-      language: system
+    - id: black
+      entry: black
       name: black
+      language: system
       pass_filenames: true
-      stages:
-        - commit
       types:
         - python
-        - file
-        - python
-    - entry: mypy
-      exclude: ^$
-      files: "{{ cookiecutter.package_slug }}/"
-      id: mypy
-      language: python
+
+    - id: mypy
       name: mypy
+      entry: mypy
+      files: "src/scicookie/"
+      language: system
       pass_filenames: true
-      stages:
-        - commit
+      # pre-commit + mypy doesn't honor the exclusion defined in the config
+      exclude: |
+        (?x)(
+            src/scicookie/{{cookiecutter.project_slug}}/
+          | src/scicookie/hooks
+        )
       types:
         - python
+
     - id: ruff
       name: ruff
-      entry: ruff
-      language: python
+      entry: ruff --no-cache
+      language: system
       pass_filenames: true
+      files: "src/scicookie/"
+      # pre-commit + ruff doesn't honor the exclusion defined in the config
       exclude: |
-       (?x)^(
-        tests/.*|
-        src/scicookie/.*|
-        docs/.*|
-        )$
-      stages:
-        - commit
+        (?x)(
+            src/scicookie/{{cookiecutter.project_slug}}
+          | src/scicookie/hooks
+        )
       types:
         - python

pyproject.toml

@@ -17,25 +17,23 @@ include = [
 python = "^3.8.1"
 cookieninja = "1.0.0"
 sh = "^2.0.4"
-pyyaml = "<6.0"
+pyyaml = ">=5"
 colorama = "^0.4.6"
 inquirer = "^3.1.3"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7"
-black = "^22"
-isort = "^5"
-pre-commit = "^2"
-flake8 = "^4"
-ruff = "^0.0.272"
-mypy = "^0.931"
-pytest-cov = "^3.0.0"
-pytest-cookies = "^0.6.1"
-Sphinx = "^4.4.0"
-Flake8-pyproject = "^0.9.0"
-jupyterlab = "^3.5.1"
-jupyter-book = "^0.12.3"
-myst-parser = "^0.15"
+pytest = ">=7"
+black = ">=22"
+isort = ">=5"
+pre-commit = ">=3"
+ruff = ">=0.0.272"
+mypy = ">=1"
+pytest-cov = ">=3"
+pytest-cookies = ">=0.6.1"
+Sphinx = ">=4.4"
+jupyterlab = ">=3.5.1"
+jupyter-book = ">=0.12.3"
+myst-parser = ">=0.15"
 makim = "1.8.1"
 
 [build-system]
@@ -47,42 +45,48 @@ line-length = 79
 # note: for support "py39", we need to update black using poetry
 #       currently, it has conflicts with typing-extensions.
 target-version = ["py38"]
-force-exclude = '''
-/(
-  |  docs/*
-  |  hooks/*
-  |  {{cookiecutter.project_slug}}/*
+force-exclude = '''(?x)(
+    docs/*
+  | src/scicookie/{{cookiecutter.project_slug}}/*
+  | src/scicookie/hooks/*
   |.*\\.egg-info
-)/
-'''
+)'''  # TOML's single-quoted strings do not require escaping backslashes
 
-[tool.flake8]
-max-line-length = 79
-# Ignoring these erros will prevent conflicts with Flake8 and Jinja2 syntax.
-exclude = [
-  '.git/*',
-  '__pycache__/*',
-  'docs/*',
-  'src/scicookie/hooks/*',
-  'src/scicookie/{{cookiecutter.project_slug}}/*'
+[tool.mypy]
+no_strict_optional = false
+exclude = '''(?x)(
+      src/scicookie/{{cookiecutter.project_slug}}/
+    | src/scicookie/hooks/*
+)'''  # TOML's single-quoted strings do not require escaping backslashes
+
+[[tool.mypy.overrides]]
+module = [
+  "colorama",
+  "inquirer",
+  "sh",
+  "yaml",
 ]
+ignore_missing_imports = true
 
 [tool.ruff]
+line-length = 79
+force-exclude = true
+src = ["src/scicookie"]
 exclude = [
-  '.git/*',
-  '__pycache__/*',
-  'docs/*',
-  'src/scicookie/hooks/*',
-  'src/scicookie/{{cookiecutter.project_slug}}/*'
+   'src/scicookie/\{\{cookiecutter.project_slug\}\}',
+   'src/scicookie/hooks',
+]
+select = [
+  "E",   # pycodestyle
+  "F",   # pyflakes
+  "D",   # pydocstyle
+  "YTT", # flake8-2020
+  "PL",  # PL
+  "RUF", # Ruff-specific rules
 ]
 
-[tool.isort]
-ensure_newline_before_comments = true
-line_length = 79
-multi_line_output = 3
-include_trailing_comma = true
-skip_glob = ["docs/*", "*.egg-info"]
-
+[tool.ruff.pydocstyle]
+convention = "numpy"
 
 [tool.pytest.ini_options]
 testpaths = [

src/scicookie/__init__.py

@@ -0,0 +1 @@
+"""SciCookie is a wrap around cookiecutter/cookieninja with a better TUI."""

src/scicookie/__main__.py

@@ -1,3 +1,4 @@
+"""Interface for the `python -m scicookie`."""
 from scicookie.cli import app
 
 if __name__ == "__main__":

src/scicookie/cli.py

@@ -1,3 +1,4 @@
+"""Module with CLI functions."""
 import json
 import os
 import sys
@@ -30,6 +31,7 @@ def _get_cookiecutter_default_answer(
 
 
 def call_cookiecutter(profile: Profile, answers: dict):
+    """Call coociecutter/cookieninja with the parameters from the TUI."""
     answers_profile = {}
     cookie_args = []
     questions = profile.config
@@ -96,8 +98,7 @@ def call_cookiecutter(profile: Profile, answers: dict):
 
 
 def app():
-    """CLI main function."""
-
+    """Run SciCookie."""
     # note: this parameter should be provided by a CLI argument
     profile = Profile("osl")
 

src/scicookie/hooks/post_gen_project.py

@@ -92,11 +92,6 @@ def clean_up_project_layout():
             shutil.move('{{cookiecutter.package_slug}}', 'src')
 
 
-def clean_up_bandit():
-    if not USE_BANDIT:
-        remove_project_file(PROJECT_DIRECTORY / '.bandit')
-
-
 def clean_up_code_of_conduct():
     if COC_PATH:
         shutil.move(
@@ -192,7 +187,6 @@ def post_gen():
     # keep this one first, because it changes the package folder
     clean_up_project_layout()
 
-    clean_up_bandit()
     clean_up_cli()
     clean_up_code_of_conduct()
     clean_up_conda()

src/scicookie/logs.py

@@ -1,10 +1,13 @@
+"""Module for functions and classes for systen logs."""
 import os
 from enum import Enum
 
 from colorama import Fore
 
 
 class SciCookieErrorType(Enum):
+    """Enum class for the error codes."""
+
     SH_ERROR_RETURN_CODE = 1
     SH_KEYBOARD_INTERRUPT = 2
     SCICOOKIE_INVALID_PARAMETER = 3
@@ -13,15 +16,20 @@ class SciCookieErrorType(Enum):
 
 
 class SciCookieLogs:
+    """Main log for print and raise messages to the system."""
+
     @staticmethod
     def raise_error(message: str, message_type: SciCookieErrorType):
+        """Print an error message and exit with the given error code."""
         print(Fore.RED, f"[EE] {message}", Fore.RESET)
         os._exit(message_type.value)
 
     @staticmethod
     def info(message: str):
+        """Print an info message."""
         print(Fore.BLUE, message, Fore.RESET)
 
     @staticmethod
     def warning(message: str):
+        """Print a warning message."""
         print(Fore.YELLOW, message, Fore.RESET)

src/scicookie/profile.py

@@ -1,3 +1,4 @@
+"""Profile handles "profiles" defined in the .yaml files."""
 from pathlib import Path
 
 import yaml
@@ -9,9 +10,11 @@
 
 
 class Profile:
+    """Profile class that handles profiles defined in the .yaml files."""
+
     profile_name: str = ""
     config: dict = {}
-    profiles_available = []
+    profiles_available: list = []
 
     def __init__(self, profile_name: str):
         self._load_profiles_available()
@@ -30,6 +33,7 @@ def _load_profiles_available(self):
         self.profiles_available = ["osl"]
 
     def read_config(self):
+        """Read the config file."""
         config = {}
         with open(PROFILE_DIR_PATH / "base.yaml") as f:
             config = yaml.safe_load(f)

src/scicookie/ui.py

@@ -1,17 +1,20 @@
+"""Define functions for the interface with the user."""
+from typing import Optional, Type, Dict
 import inquirer
-
 from scicookie.logs import SciCookieErrorType, SciCookieLogs
 
 
-def _create_question(question_id: str, question: dict):
+def _create_question(
+    question_id: str, question: dict
+) -> Optional[inquirer.questions.Question]:
     # validation
     if not question.get("enabled", False):
-        return
+        return None
 
     # config required
-    default_answer = question.get("default")
-    question_message = question.get("message")
-    question_type = question.get("type")
+    default_answer = question.get("default", "")
+    question_message = question.get("message", "")
+    question_type = question.get("type", "")
     # todo: implement help text int he prompt
     # question_help = question.get("help")
     # todo: implement depends on workflow, it needs refactoring the code
@@ -43,7 +46,7 @@ def _create_question(question_id: str, question: dict):
     if question.get("choices"):
         content["choices"] = question.get("choices")
 
-    fn_questions = {
+    fn_questions: Dict[str, Type[inquirer.questions.Question]] = {
         "text": inquirer.Text,
         "single-choice": inquirer.List,
         "multiple-choices": inquirer.Checkbox,
@@ -57,6 +60,7 @@ def _create_question(question_id: str, question: dict):
 
 
 def make_questions(questions: dict):
+    """Generate all the enabled questions."""
     questions_ui = []
 
     for question_id, question in questions.items():

src/scicookie/{{cookiecutter.project_slug}}/.pre-commit-config.yaml

@@ -46,6 +46,7 @@ repos:
       entry: ruff
       language: system
       pass_filenames: true
+      files: "{{ package_path }}"
       types:
         - python
 {%- endif %}