Add pytest CI and pre-commit

.github/workflows/ci.yaml

@@ -0,0 +1,27 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Test with pytest
+        run: |
+          pytest

.pre-commit-config.yaml

@@ -0,0 +1,62 @@
+# https://pre-commit.com/
+ci:
+    # The repos are quite stable and doesn't effectively change the code that
+    # often. So no need for the bot to update the rev that often.
+    autoupdate_schedule: quarterly
+
+# Dont format test dcm-files at all as they contain typical errors that the
+# parser has to handle.
+exclude: "tests/Sample.dcm"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: debug-statements
+      - id: mixed-line-ending
+  - repo: https://github.com/MarcoGorelli/absolufy-imports
+    rev: v0.3.1
+    hooks:
+      - id: absolufy-imports
+        name: absolufy-imports
+        files: ^src/dcmReader/
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.0.235'
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+  # https://github.com/python/black#version-control-integration
+  - repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.8
+    hooks:
+      - id: blackdoc
+        additional_dependencies: ["black==22.12.0"]
+      - id: blackdoc-autoupdate-black
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.991
+    hooks:
+      - id: mypy
+        # This is slow and so we take it out of the fast-path; requires passing
+        # `--hook-stage manual` to pre-commit
+        stages: [manual]
+        additional_dependencies: [
+            # Type stubs
+            types-python-dateutil,
+            types-pkg_resources,
+            types-PyYAML,
+            types-pytz,
+            typing-extensions,
+          ]

README.md

@@ -55,4 +55,4 @@ This can also be used to sort a DCM file:
 
 ## UnitTests
 The UnitTests can be run in the tests directory by running
-    python Tests.py
+    python Tests.py

pyproject.toml

@@ -19,4 +19,34 @@ disable = [
     "too-many-statements",
     "duplicate-code",
     "invalid-name",
-]
+]
+
+[tool.ruff]
+target-version = "py39"
+builtins = ["ellipsis"]
+exclude = [
+    ".eggs",
+    "doc",
+]
+# E402: module level import not at top of file
+# E501: line too long - let black worry about that
+# E731: do not assign a lambda expression, use a def
+ignore = [
+    "E402",
+    "E501",
+    "E731",
+]
+select = [
+    # Pyflakes
+    "F",
+    # Pycodestyle
+    "E",
+    "W",
+    # isort
+    "I",
+    # Pyupgrade
+    "UP",
+]
+
+[tool.ruff.isort]
+known-first-party = ["dcmReader"]

requirements.txt

@@ -0,0 +1,5 @@
+# This file is redundant with setup.cfg;
+# it exists to let GitHub build the repository dependency graph
+# https://help.github.com/en/github/visualizing-repository-data-with-graphs/listing-the-packages-that-a-repository-depends-on
+
+numpy >= 1.21

setup.cfg

@@ -19,7 +19,30 @@ classifiers =
 package_dir =
     = src
 packages = find:
-python_requires = >=3.6
+python_requires = >=3.9
+install_requires =
+    numpy >= 1.21
 
 [options.packages.find]
-where = src
+where = src
+
+[flake8]
+ignore =
+    # E203: whitespace before ':' - doesn't work well with black
+    # E402: module level import not at top of file
+    # E501: line too long - let black worry about that
+    # E731: do not assign a lambda expression, use a def
+    # W503: line break before binary operator
+    E203, E402, E501, E731, W503
+exclude =
+    .eggs
+    doc
+builtins =
+    ellipsis
+
+[isort]
+profile = black
+skip_gitignore = true
+float_to_top = true
+default_section = THIRDPARTY
+known_first_party = dcmReader

setup.py

@@ -1,6 +1,6 @@
 import setuptools
 
-with open("README.md", "r", encoding="utf-8") as fh:
+with open("README.md", encoding="utf-8") as fh:
     long_description = fh.read()
 
 setuptools.setup(

src/dcmReader/dcm_characteristic_line.py

@@ -54,15 +54,15 @@ def __str__(self):
         if self.unit_values:
             value += f'  EINHEIT_W     "{self.unit_values}"\n'
         if self.x_mapping:
-            value += f'*SSTX   {self.x_mapping}\n'
+            value += f"*SSTX   {self.x_mapping}\n"
         if self.values:
             x_entries = ""
             value_entries = ""
             for x_entry, value_entry in self.values.items():
                 x_entries += f"{str(x_entry)} "
                 value_entries += f"{str(value_entry)} "
-            value += f'  ST/X          {x_entries.strip()}\n'
-            value += f'  WERT          {value_entries.strip()}\n'
+            value += f"  ST/X          {x_entries.strip()}\n"
+            value += f"  WERT          {value_entries.strip()}\n"
         for var_name, var_value in self.variants.items():
             value += f"  VAR           {var_name}={var_value}\n"
 

src/dcmReader/dcm_characteristic_map.py

@@ -64,9 +64,9 @@ def __str__(self):
         if self.unit_values:
             value += f'  EINHEIT_W     "{self.unit_values}"\n'
         if self.x_mapping:
-            value += f'*SSTX   {self.x_mapping}\n'
+            value += f"*SSTX   {self.x_mapping}\n"
         if self.y_mapping:
-            value += f'*SSTY   {self.y_mapping}\n'
+            value += f"*SSTY   {self.y_mapping}\n"
         stx_written = False
         for y_entry, map_values in self.values.items():
             x_entries = ""
@@ -75,10 +75,10 @@ def __str__(self):
                 x_entries += f"{str(x_entry)} "
                 value_entries += f"{str(value_entry)} "
             if not stx_written:
-                value += f'  ST/X          {x_entries.strip()}\n'
+                value += f"  ST/X          {x_entries.strip()}\n"
                 stx_written = True
-            value += f'  ST/Y          {str(y_entry).strip()}\n'
-            value += f'  WERT          {value_entries.strip()}\n'
+            value += f"  ST/Y          {str(y_entry).strip()}\n"
+            value += f"  WERT          {value_entries.strip()}\n"
         for var_name, var_value in self.variants.items():
             value += f"  VAR           {var_name}={var_value}\n"
 

src/dcmReader/dcm_distribution.py

@@ -49,7 +49,7 @@ def __str__(self):
             x_entries = ""
             for x_entry in self.values:
                 x_entries += f"{str(x_entry)} "
-            value += f'  ST/X          {x_entries.strip()}\n'
+            value += f"  ST/X          {x_entries.strip()}\n"
         for var_name, var_value in self.variants.items():
             value += f"  VAR           {var_name}={var_value}\n"
 

src/dcmReader/dcm_fixed_characteristic_line.py

@@ -3,6 +3,7 @@
 """
 
 from dataclasses import dataclass
+
 from dcmReader.dcm_characteristic_line import DcmCharacteristicLine
 
 

src/dcmReader/dcm_fixed_characteristic_map.py

@@ -3,6 +3,7 @@
 """
 
 from dataclasses import dataclass
+
 from dcmReader.dcm_characteristic_map import DcmCharacteristicMap
 
 

src/dcmReader/dcm_group_characteristic_line.py

@@ -2,6 +2,7 @@
 Definition of DCM group characteristic line
 """
 from dataclasses import dataclass
+
 from dcmReader.dcm_characteristic_line import DcmCharacteristicLine
 
 

src/dcmReader/dcm_group_characteristic_map.py

@@ -2,6 +2,7 @@
 Definition of DCM fixed characteristic map
 """
 from dataclasses import dataclass
+
 from dcmReader.dcm_characteristic_map import DcmCharacteristicMap