Linting

.git-blame-ignore-revs

@@ -0,0 +1,14 @@
+81d65dae23119d7626c1280868064fd6d83adf98
+b8bf10e010ce4c2dad1bc0c85367f573a5d0b881
+6f2eee122c42eee8306b29491e85118d1c0ff81d
+d87f9dfec164991649fc6a33a9a25e387ae4fa5b
+245d5ffe2b07a6c6b59afe0f18520297d2ebf776
+a9cc5f3393cf87713155e8c6582a2724748185da
+21c334c5d2d7438382cd6b18cfc0080b93db905b
+5b123eb06e941570e20292d72a27b978a8ea0315
+4c6aac5ba123b770c44a86fe0008fd8e63755432
+f4017e4911d8ef9cd49315a5a86fb22f5f75ef95
+b7472c592e028533850d953905290f6e6a3014f4
+2c4e08432d06ceec2faebd82243a2a5bced96d0a
+e6458e20673d8385d85bcfe8e552a403734326a7
+0d71d450598d0a399794ab3621cab74fb064f95c

.github/workflows/lint.yml

@@ -0,0 +1,28 @@
+# This workflow will install Python dependencies and run the linter
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Lint
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  ruff:
+    name: Lint with Ruff
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v6
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --editable .[dev]
+
+    - name: Run linter check
+      run: |
+        python -m ruff check --output-format=github src/ tests/

.gitignore

@@ -173,7 +173,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
 
 # Abstra
 # Abstra is an AI-powered process automation framework.

pyproject.toml

@@ -1,6 +1,24 @@
 [project]
 name = "zdPlasmaPy"
-version = "0.1.0"
+requires-python = ">=3.12"
+license-files = ["LICEN[CS]E*"]
+dynamic = ["version"]
+dependencies = [
+    "h5py>=3.16.0",
+    "ipykernel>=7.3.0",
+    "jsonschema>=4.26.0",
+    "matplotlib>=3.11.0",
+    "numpy<2.0.0",
+    "pytest>=9.1.0",
+    "pyyaml>=6.0.3",
+    "scipy>=1.17.1",
+    "streamlit>=1.58.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "ruff>=0.15.17",
+]
 
 [project.scripts]
 zdplasmapy = "main:main"
@@ -12,6 +30,33 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools]
 py-modules = ["main"]
 
+[tool.setuptools_scm]
+
 [tool.setuptools.packages.find]
 where = ["."]
-include = ["src*"]
+include = ["src*"]
+
+[tool.ruff.lint]
+select = [
+  "F", # Pyflakes
+  "E", # pycodestyle error
+  "W", # pycodestyle warning
+  "I", # isort
+  "B", # flake8-bugbear
+  "A", # flake8-builtins
+  "C4", # flake8-comprehensions
+  "T10", # flake8-debugger
+  "SIM", # flake8-simplify
+  "TCH", # flake8-type-checking
+  "UP", # pyupgrade
+  "FURB", # refurb
+  "PERF", # perflint
+  "NPY", # NumPy specific
+]
+ignore = [
+  "B904", # `except` clause raise
+  "E401", # Multiple imports on one line
+  "E501", # Line too long
+  "E701", # Multiple statements on one line
+  "E741", # Ambiguous variable name
+]

src/build_model_dict.py

@@ -1,30 +1,31 @@
 # src/build_model_dict.py
 
-from .config_loader import load_config
 from .chemistry_parser import load_chemistry
+from .config_loader import load_config
+
 
 def build_model_definition(config_path):
     """
     Builds the model_definition dictionary that GlobalModel expects.
-    
+
     Args:
         config_path: Path to config.yml
-        
+
     Returns:
         dict: Complete model definition for GlobalModel
     """
     # Load config
     config = load_config(config_path)
-    
+
     # Load chemistry
     species, reactions, mass_dict = load_chemistry(config['chemistry']['absolute_path'])
-    
+
     # --- Item 3: Extract ion species masses for generalized wall loss ---
     ion_species = {}
     for sp in species:
         if '+' in sp.get('name', '') and sp.get('name') != 'e':
             ion_species[sp['name']] = sp.get('mass_amu', 1.0)
-    
+
     # Build the model definition dictionary
     model_def = {
         'name': config.get('name', 'Unnamed Model'),
@@ -61,19 +62,19 @@ def build_model_definition(config_path):
         'transport_model': config.get('transport_model', 'none'),
         'declarations_func': lambda p: {}  # Empty for now, transport models will populate
     }
-    
+
     # --- Item 2: Dynamic Gas Density from pressure + composition ---
     k_B = 1.380649e-23
     P = config['parameters']['pressure_Pa']
     Tg = config['parameters']['gas_temp_K']
     N_total = P / (k_B * Tg)
-    
+
     gas_composition = config['parameters'].get('gas_composition', {})
     for gas_species, fraction in gas_composition.items():
         # Only inject if NOT explicitly set in species_densities (override wins)
         if gas_species not in config['initial_conditions'].get('species_densities', {}):
             model_def['initial_values'][gas_species] = fraction * N_total
             print(f"INFO: Auto-computed {gas_species} density = {fraction} × {N_total:.3e} = {fraction * N_total:.3e} m⁻³")
-    
+
     return model_def
 

src/case_utils.py

@@ -4,36 +4,37 @@
 """
 import os
 
+
 def discover_cases(cases_dir='cases'):
     """
     Discover all valid case folders in the cases/ directory.
     A valid case has a config.yml file.
-    
+
     Returns:
         list: List of case names (subdirectory names)
     """
     if not os.path.isdir(cases_dir):
         return []
-    
+
     cases = []
     for entry in os.listdir(cases_dir):
         case_path = os.path.join(cases_dir, entry)
         if os.path.isdir(case_path):
             config_path = os.path.join(case_path, 'config.yml')
             if os.path.isfile(config_path):
                 cases.append(entry)
-    
+
     return sorted(cases)
 
 
 def get_case_config_path(case_name, cases_dir='cases'):
     """
     Get the full path to a case's config.yml file.
-    
+
     Args:
         case_name (str): Name of the case folder
         cases_dir (str): Base cases directory
-    
+
     Returns:
         str: Full path to config.yml
     """
@@ -43,43 +44,43 @@ def get_case_config_path(case_name, cases_dir='cases'):
 def group_parameters(params, species_list, geometry_dict, constants_dict):
     """
     Group flat parameter dictionary into structured groups for cleaner access.
-    
+
     Args:
         params (dict): Flat parameter dictionary
         species_list (list): List of species names
         geometry_dict (dict): Geometry parameters
         constants_dict (dict): Physical constants
-    
+
     Returns:
         dict: Grouped parameters with keys: constants, variables, geometry, species
     """
     # Extract known variable keys
     variable_keys = ['Te_eV', 'Th_eV', 'na', 'ne', 'Ti_eV', 'Tg_K', 'Th_K']
-    
+
     # Extract known species-specific keys (concentrations, mass, sigma, etc.)
     # Start with existing species dict if provided (to avoid double-grouping loss)
     species_keys = params.get('species', {}).copy()
-    for key in params.keys():
+    for key in params:
         if key.startswith('mass_') or key.startswith('sigma_') or key in species_list:
             species_keys[key] = params[key]
-    
+
     # Also add geometry parameters that might be in params but should be in geometry
     for key in ['R', 'L', 'radius_m', 'length_m', 'Reff', 'volume', 'area']:
         if key in params:
             geometry_dict[key] = params[key]
-    
+
     grouped = {
         'constants': constants_dict.copy(),
         'variables': {k: params[k] for k in variable_keys if k in params},
         'geometry': geometry_dict.copy(),
         'species': species_keys.copy()
     }
-    
+
     # Add any remaining params to variables (fallback)
     for key, value in params.items():
         if key not in variable_keys and key not in species_keys and key not in constants_dict and key not in ['R', 'L', 'radius_m', 'length_m', 'Reff', 'volume', 'area', 't']:
             grouped['variables'][key] = value
-            
+
     # Explicitly pull 't' to the top-level as many declarations expect it there
     if 't' in params:
         grouped['t'] = params['t']
@@ -88,5 +89,5 @@ def group_parameters(params, species_list, geometry_dict, constants_dict):
     grouped.update(grouped['constants'])
     grouped.update(grouped['geometry'])
     grouped.update(grouped['variables'])
-    
+
     return grouped

src/chemistry.py

@@ -8,9 +8,9 @@ def __init__(self, name, mass_amu=0.0):
 
 class Reaction:
     """A class to hold data about a single reaction, including its compiled functions."""
-    def __init__(self, formula, rate_coeff_func, energy_loss_func, type, reference):
+    def __init__(self, formula, rate_coeff_func, energy_loss_func, type_, reference):
         self.formula = formula
         self.rate_coeff_func = rate_coeff_func
         self.energy_loss_func = energy_loss_func
-        self.type = type
-        self.reference = reference
+        self.type = type_
+        self.reference = reference