Add type hints and MyPy checking to CI (#69)

* Add type hints and MyPy checking to CI

- Added MyPy as a dependency
- Added MyPy GitHub Actions workflow
- Added type hints to all Python files
- Added `type: ignore` comments for libraries without type stubs

* Update environment.yml

* Update mypy.yml

* Update _version.py

* Update share.py

* Update pyproject.toml

* Update test_cmd.py

* Update test_cmd.py

* Update test_core.py

* Update test_user_interface.py

* Update test_share.py

* Update test_share.py

* Create .pre-commit-config.yaml

* black formatting

* Delete .github/workflows/mypy.yml

* Merge CI

* Delete .pre-commit-config.yaml

* fixes

---------

Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

Author: jan-janssen

.github/workflows/black.yml

@@ -0,0 +1,126 @@
+name: Pipeline
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: psf/black@stable
+      with:
+        options: "--check --diff"
+        src: ./${{ github.event.repository.name }}
+
+  black_fix:  # in most cases pre-commit is faster
+    needs: [black]
+    if: failure()
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
+        ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
+        fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
+    - name: format black
+      uses: psf/black@stable
+      with:
+        options: ""
+        src: "./${{ github.event.repository.name }}"
+    - name: commit
+      run: |
+        git config --local user.email "pyiron@mpie.de"
+        git config --local user.name "pyiron-runner"
+        git commit -m "Format black" -a
+    - name: push
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
+        branch: ${{ github.event.pull_request.head.ref }}
+
+  mypy:
+    needs: [black]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+          architecture: x64
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Install mypy
+        run: pip install mypy
+      - name: Test
+        run: mypy --ignore-missing-imports ${{ github.event.repository.name }}
+
+  pip_check:
+    needs: [black]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Conda config
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: "3.13"
+        miniforge-version: latest
+        condarc-file: .condarc
+        environment-file: .ci_support/environment.yml
+    - name: Setup
+      shell: bash -l {0}
+      run: |
+        pip install tomlkit
+        pip install . --no-deps --no-build-isolation
+        pip check
+
+  unittest:
+    needs: [black]
+    runs-on: ${{ matrix.operating-system }}
+    strategy:
+      matrix:
+        operating-system: [ubuntu-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+    steps:
+    - uses: actions/checkout@v4
+    - name: Conda config
+      shell: bash -l {0}
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+        miniforge-version: latest
+        condarc-file: .condarc
+        environment-file: .ci_support/environment.yml
+    - name: Test
+      shell: bash -l {0}
+      run: |
+        pip install --no-deps .
+        coverage run -a -m unittest discover tests
+
+  coverage:
+    needs: [black]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Conda config
+      shell: bash -l {0}
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: '3.13'
+        miniforge-version: latest
+        condarc-file: .condarc
+        environment-file: .ci_support/environment.yml
+    - name: Test
+      shell: bash -l {0}
+      run: |
+        pip install --no-deps .
+        coverage run -a -m unittest discover tests
+        coverage combine
+        coverage xml
+    - name: Coveralls
+      uses: coverallsapp/github-action@v2

.github/workflows/coverage.yml

@@ -2,15 +2,16 @@
 Generate two factor authentication codes on the command line
 """
 
+from typing import Optional
 from . import _version
 from pyauthenticator.share import generate_qrcode
 from pyauthenticator.share import get_two_factor_code as get_two_factor_code_internal
 from pyauthenticator.share import load_config
 
-__version__ = _version.__version__
+__version__: str = _version.__version__
 
 
-def write_qrcode_to_file(service, file_name=None):
+def write_qrcode_to_file(service: str, file_name: Optional[str] = None) -> None:
     """
     Write qrcode to file to scan it with a mobile application
 
@@ -21,7 +22,7 @@ def write_qrcode_to_file(service, file_name=None):
     generate_qrcode(key=service, config_dict=load_config(), file_name=file_name)
 
 
-def get_two_factor_code(service):
+def get_two_factor_code(service: str) -> str:
     """
     Generate two factor authentication code
 

.github/workflows/pipeline.yml

@@ -4,6 +4,7 @@
 
 import argparse
 import sys
+from typing import Optional, Sequence
 
 from pyauthenticator.share import (
     add_service,
@@ -14,7 +15,7 @@
 )
 
 
-def command_line_parser(cmd_args=None):
+def command_line_parser(cmd_args: Optional[Sequence[str]] = None) -> None:
     """
     Main function primarly used for the command line interface
     """

.github/workflows/pypicheck.yml

@@ -5,17 +5,18 @@
 import json
 import os
 from inspect import signature
+from typing import Any, Dict, List, Optional
 
 import pyotp
 import qrcode
 from PIL import Image
 from pyzbar.pyzbar import decode
 
 # default configuration file
-config_file = "~/.pyauthenticator"
+config_file: str = "~/.pyauthenticator"
 
 
-def expand_path(path):
+def expand_path(path: str) -> str:
     """
     Expand path by expanding the user variable and converting the path to an absolute path
 
@@ -28,7 +29,7 @@ def expand_path(path):
     return os.path.abspath(os.path.expanduser(path))
 
 
-def load_config(config_file_to_load=config_file):
+def load_config(config_file_to_load: str = config_file) -> Dict[str, Any]:
     """
     Load configuration file
 
@@ -46,7 +47,9 @@ def load_config(config_file_to_load=config_file):
         return {}
 
 
-def write_config(config_dict, config_file_to_write=config_file):
+def write_config(
+    config_dict: Dict[str, Any], config_file_to_write: str = config_file
+) -> None:
     """
     Write configuration file
 
@@ -58,7 +61,7 @@ def write_config(config_dict, config_file_to_write=config_file):
         json.dump(config_dict, f)
 
 
-def get_otpauth_dict(otpauth_str):
+def get_otpauth_dict(otpauth_str: str) -> Dict[str, str]:
     """
     Parse otpauth url
 
@@ -76,7 +79,7 @@ def get_otpauth_dict(otpauth_str):
     }
 
 
-def check_if_key_in_config(key, config_dict):
+def check_if_key_in_config(key: str, config_dict: Dict[str, Any]) -> None:
     """
     Check if a given key is included in a dictionary, raise an ValueError if it is not.
 
@@ -88,7 +91,7 @@ def check_if_key_in_config(key, config_dict):
         raise ValueError()
 
 
-def get_two_factor_code(key, config_dict):
+def get_two_factor_code(key: str, config_dict: Dict[str, Any]) -> str:
     """
     Generate the two factor authentication code
 
@@ -123,8 +126,11 @@ def get_two_factor_code(key, config_dict):
 
 
 def add_service(
-    key, qrcode_png_file_name, config_dict, config_file_to_write=config_file
-):
+    key: str,
+    qrcode_png_file_name: str,
+    config_dict: Dict[str, Any],
+    config_file_to_write: str = config_file,
+) -> None:
     """
     Add new service to configuration file
 
@@ -139,7 +145,9 @@ def add_service(
     write_config(config_dict=config_dict, config_file_to_write=config_file_to_write)
 
 
-def generate_qrcode(key, config_dict, file_name=None):
+def generate_qrcode(
+    key: str, config_dict: Dict[str, Any], file_name: Optional[str] = None
+) -> None:
     """
     Write qrcode to file to scan it with a mobile application
 
@@ -154,7 +162,7 @@ def generate_qrcode(key, config_dict, file_name=None):
     qrcode.make(config_dict[key]).save(file_name, "PNG")
 
 
-def list_services(config_dict):
+def list_services(config_dict: Dict[str, Any]) -> List[str]:
     """
     List available services