Modernize with new tooling and fix or update some code (#205)

.editorconfig

@@ -0,0 +1,21 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+insert_final_newline = true
+trim_trailing_whitespace = true
+charset = utf-8
+end_of_line = lf
+
+[*.py]
+max_line_length = 120
+
+[*.md]
+trim_trailing_whitespace = false
+
+[*.yml]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

.github/workflows/tests.yml

@@ -13,10 +13,10 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [
-            '3.8',
             '3.9',
             '3.10',
             '3.11',
+            '3.12',
         ]
     runs-on: ubuntu-latest
     steps:
@@ -30,19 +30,19 @@ jobs:
       - run: make unittests
       - run: coverage report
 
-  flake:
+  lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
-      - run: pip install flake8 flake8-isort pep8-naming
-      - run: make flaketest
+      - run: pip install ruff
+      - run: make linttest
 
   docs:
     if: github.ref == 'refs/heads/master'
-    needs: [tests, flake]
+    needs: [tests, lint]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

Makefile

@@ -1,16 +1,23 @@
-.PHONY: test unittests flaketest doctest update_data
-
+.PHONY: test
 test: unittests flaketest doctest
 
+.PHONY: unittests
 unittests:
 	coverage run -m unittest
 
-flaketest:
-	flake8 sapphire
+.PHONY: linttest
+linttest:
+	ruff check .
+
+.PHONY: lintfix
+lintfix:
+	ruff check --fix-only .
 
+.PHONY: doctest
 doctest:
 	sphinx-build -anW doc doc/_build/html
 
+.PHONY: update_data
 update_data:
 ifeq ($(strip $(shell git status --porcelain | wc -l)), 0)
 	@echo "Updating local data. Creating test data to match local data and committing."

doc/conf.py

@@ -9,13 +9,11 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import os
-import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('.'))
 
 # Often reused
 AUTHORS = 'David Fokkema, Arne de Laat, and Tom Kooij'
@@ -83,27 +81,26 @@
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'SAPPHiREdoc'
 
+
 def setup(app):
     app.add_css_file('hisparc_style.css')
 
+
 # -- Options for LaTeX output --------------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # The paper size ('letterpaper' or 'a4paper').
+    #'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'SAPPHiRE.tex', 'SAPPHiRE Documentation',
-   AUTHORS, 'manual'),
+    ('index', 'SAPPHiRE.tex', 'SAPPHiRE Documentation', AUTHORS, 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -116,8 +113,7 @@ def setup(app):
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'sapphire', 'SAPPHiRE Documentation',
-     [AUTHORS], 1)
+    ('index', 'sapphire', 'SAPPHiRE Documentation', [AUTHORS], 1),
 ]
 
 
@@ -127,10 +123,15 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'SAPPHiRE', 'SAPPHiRE Documentation',
-   AUTHORS, 'SAPPHiRE',
-   'One line description of project.',
-   'Miscellaneous'),
+    (
+        'index',
+        'SAPPHiRE',
+        'SAPPHiRE Documentation',
+        AUTHORS,
+        'SAPPHiRE',
+        'One line description of project.',
+        'Miscellaneous',
+    ),
 ]
 
 

doc/scripts/is_useful.py

@@ -1,5 +1,6 @@
 def square(x):
-    return x ** 2
+    return x**2
+
 
 print(1, 2, 3)
 print(square(1), square(2), square(3))

doc/scripts/is_useful_and_importable.py

@@ -1,5 +1,5 @@
 def square(x):
-    return x ** 2
+    return x**2
 
 
 if __name__ == '__main__':

doc/scripts/plot_zenith_distribution.py

@@ -13,8 +13,8 @@ def plot_zenith_distribution(data):
     zenith = zenith.compress(-isnan(zenith))
 
     plt.hist(degrees(zenith), bins=linspace(0, 90, 51), histtype='step')
-    plt.xlabel("zenith [deg]")
-    plt.ylabel("count")
+    plt.xlabel('zenith [deg]')
+    plt.ylabel('count')
 
 
 if __name__ == '__main__':

pyproject.toml

@@ -0,0 +1,189 @@
+[build-system]
+requires = ['flit_core>=3.9']
+build-backend = 'flit_core.buildapi'
+
+[project]
+name = 'hisparc-sapphire'
+version = '2.0.0'
+description = 'A framework for the HiSPARC experiment'
+readme = 'README.rst'
+requires-python = '>=3.9'
+license = {file = 'LICENSE'}
+authors = [
+    {name = 'Arne de Laat', email = 'arne@delaat.net'},
+    {name = 'David Fokkema'},
+    {name = 'Tom Kooij'},
+]
+maintainers = [
+    {name = 'Arne de Laat', email = 'arne@delaat.net'},
+]
+keywords = [
+    'cosmic rays',
+    'detectors',
+    'astrophysics',
+    'HiSPARC',
+    'Nikhef',
+    'University of Utah',
+]
+classifiers = [
+    'Intended Audience :: Education',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+    'Operating System :: OS Independent',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python',
+    'Topic :: Education',
+    'Topic :: Scientific/Engineering',
+]
+dependencies = [
+    'numpy>=1.25.2',
+    'scipy>=1.13.0',
+    'tables>=3.9.2',
+    'progressbar2>=4.4.2',
+]
+
+[project.optional-dependencies]
+dev = [
+    'Sphinx',
+    'coverage==7.4.4',
+    'ruff==0.4.1',
+]
+astropy = [
+    'astropy>=5.0.0',
+]
+publish = [
+    'flit==3.9.0',
+]
+
+[project.urls]
+Homepage = 'https://data.hisparc.nl'
+Documentation = 'https://docs.hisparc.nl/sapphire/'
+Repository = 'https://github.com/hisparc/sapphire/'
+Issues = 'https://github.com/HiSPARC/sapphire/issues'
+
+[project.scripts]
+create_and_store_test_data = 'sapphire.tests.create_and_store_test_data:main'
+update_local_data = 'sapphire.data.update_local_data:main'
+extend_local_data = 'sapphire.data.extend_local_data:main'
+
+[tool.flit.module]
+name = 'sapphire'
+
+[tool.ruff]
+line-length = 120
+target-version = 'py39'
+extend-exclude = [
+    'doc/',
+    'scripts/',
+]
+
+[tool.ruff.format]
+quote-style = 'single'  # Prefer single quotes, except for triple quotes strings
+
+[tool.ruff.lint]
+select = ['ALL']  # https://docs.astral.sh/ruff/rules/
+ignore = [
+    'ANN',  # No type annotations yet
+    'ARG002',  # Allow unused arguments to keep signature equal for similar functions
+    'B028',  # Allow warnings.warn without stacklevel
+    'B904',  # Allow skipping causes for exceptions
+    'BLE001',  # Allow catching Exception
+    'CPY001',  # Do not require copyright notices
+    'D',  # Ignore docstring checks
+    'DTZ',  # Ignore timezones for datetime
+    'E731',  # Allow assigning lambda to variable
+    'EM',  # Allow messages directly in exceptions
+    'ERA001',  # Allow commented code
+    'F405',  # Allow star imports
+    'FBT001',  # Allow positional for boolean arguments
+    'FBT002',  # Allow default value for boolean arguments
+    'PD',  # Not using pandas
+    'PERF203',  # Allow try-except in loop
+    'PLR0913',  # Allow functions with many arguments
+    'PLR6301',  # Allow not using self in methods
+    'PT',  # Not using pytest
+    'PTH',  # Allow using os.path
+    'RET504',  # Allow variable assignment before return
+    'RET505',  # Allow elif after return
+    'RET506',  # Allow elif after raise
+    'RET507',  # Allow elif after continue
+    'RET508',  # Allow elif after break
+    'S311',  # Allow using random for non-cryptographic purposes
+    'SIM108',  # Allow if-else block instead of ternary
+    'SIM117',  # Allow separate with statements to preserve context
+    'SLF001',  # Allow accessing private members
+    'T201',  # Allow using print
+    'TD002',  # Allow TODO without author
+    'TD003',  # Allow TODO without issue link
+    'TID252',  # Allow relative imports
+    'TRY003',  # Specific messages for common exception classes
+
+    # TODO these still need to be checked (i.e. ignored or fixed)
+    'ARG001',
+    'ARG003',
+    'ARG005',
+    'B018',
+    'C901',
+    'FBT003',
+    'FIX002',
+    'G002',
+    'G004',
+    'NPY002',
+    'PLR0911',
+    'PLR0912',
+    'PLR0915',
+    'PLR2004',
+    'PLW2901',
+    'RET503',
+    'RUF005',
+    'RUF012',
+    'S103',
+    'S108',
+    'S310',
+    'S602',
+    'S603',
+    'S604',
+    'S607',
+    'SIM102',
+    'SIM105',
+    'SIM115',
+    'TRY301',
+    'TRY400',
+    'UP031',
+]
+
+[tool.ruff.lint.per-file-ignores]
+'sapphire/corsika/units.py' = ['N816']  # Allow mixed case variables
+'sapphire/esd.py' = ['A002']  # Some keyword arguments shadow a builtin
+'sapphire/kascade.py' = ['N806']  # Allow non lower case variables to match KASCADE
+'sapphire/storage.py' = ['N815']  # Allow mixed case variables
+'sapphire/tests/simulations/test_gammas.py' = ['N806']  # Allow upper case variables
+'sapphire/tests/transformations/test_celestial.py' = ['N806']  # Allow upper case variables
+
+[tool.ruff.lint.flake8-quotes]
+inline-quotes = 'single'
+
+[tool.ruff.lint.isort]
+lines-between-types = 1
+section-order = [
+    'future',
+    'standard-library',
+    'third-party',
+    'extras',
+    'first-party',
+    'local-folder',
+]
+
+[tool.ruff.lint.isort.sections]
+extras = ['artist', 'pylab']
+
+[tool.coverage.run]
+branch = true
+source = [
+    'sapphire',
+]
+
+[tool.coverage.report]
+show_missing = true
+skip_empty = true
+skip_covered = true

sapphire/README.md

@@ -0,0 +1 @@
+# Simulation and Analysis Program Package for HiSPARC Research (SAPPHiRE)