Replace pylint + autopep8 with ruff for Python linting and formatting

- Replace autopep8 with ruff format, pylint with ruff check
- Add ruff.toml config at repo root (E, F, W, I, PL rule sets)
- Enable ruff check --fix in format.sh and lint.sh for safe auto-fixes
- Remove all ~229 inline pylint: disable comments
- Fix code violations: E731 (lambda), E741 (ambiguous var), E721 (type
  comparison), PLW1641 (hash), PLR1722 (sys.exit), F541 (f-string),
  E501 (line length), E702 (semicolons), PLW2901 (loop var overwrite)
- Add ~12 noqa comments for intentional global statements (PLW0603/PLW0602)
- Remove 8 zero-violation rules from ignore list to keep config minimal
- Fix lint.sh symlink path resolution breaking ruff config discovery
- Replace pylint and autopep8 deps with ruff in pyproject.toml

Resolves #1281

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: sbryngelson

benchmarks/5eq_rk3_weno3_hllc/case.py

@@ -6,9 +6,9 @@
 # - weno_order : 3
 # - riemann_solver : 2
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarking Case 1", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

benchmarks/hypo_hll/case.py

@@ -4,9 +4,9 @@
 # - hypoelasticity : T
 # - riemann_solver : 1
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarkin Case 3", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

benchmarks/ibm/case.py

@@ -3,9 +3,9 @@
 # Additional Benchmarked Features
 # - ibm : T
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarking Case 4", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

benchmarks/igr/case.py

@@ -5,9 +5,9 @@
 # - viscous : T
 # - igr_order : 5
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarking Case 5", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

benchmarks/viscous_weno5_sgb_acoustic/case.py

@@ -8,9 +8,9 @@
 # - bubble_model : 3
 # - acoustic_source : T
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarking Case 2", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

examples/0D_bubblecollapse_adap/case.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
-import math
 import json
+import math
 
 # FLUID PROPERTIES
 # Water

examples/1D_bubblescreen/case.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
-import math
 import json
+import math
 
 # FLUID PROPERTIES
 R_uni = 8314.0  # [J/kmol/K]
@@ -53,7 +53,6 @@
 u0 = math.sqrt(p0 / rho0)  # [m/s]
 t0 = x0 / u0  # [s]
 
-#
 cfl = 0.1
 Nx = 100
 Ldomain = 20.0e-03

examples/1D_convergence/case.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
-import math
-import json
 import argparse
+import json
+import math
 
 # Parsing command line arguments
 parser = argparse.ArgumentParser(description="Generate JSON case configuration for two-fluid convergence simulation.")
@@ -67,10 +67,10 @@
             "patch_icpp(1)%length_x": 1.0,
             "patch_icpp(1)%vel(1)": 1.0,
             "patch_icpp(1)%pres": 1.0,
-            "patch_icpp(1)%alpha_rho(1)": f"0.5 - 0.5*sin(2*pi*x)",
-            "patch_icpp(1)%alpha(1)": f"0.5 - 0.5*sin(2*pi*x)",
-            "patch_icpp(1)%alpha_rho(2)": f"0.5 + 0.5*sin(2*pi*x)",
-            "patch_icpp(1)%alpha(2)": f"0.5 + 0.5*sin(2*pi*x)",
+            "patch_icpp(1)%alpha_rho(1)": "0.5 - 0.5*sin(2*pi*x)",
+            "patch_icpp(1)%alpha(1)": "0.5 - 0.5*sin(2*pi*x)",
+            "patch_icpp(1)%alpha_rho(2)": "0.5 + 0.5*sin(2*pi*x)",
+            "patch_icpp(1)%alpha(2)": "0.5 + 0.5*sin(2*pi*x)",
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (1.4 - 1.0e00),
             "fluid_pp(1)%pi_inf": 0.0,

examples/1D_exp_bubscreen/case.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
-import math
 import json
+import math
 
 # FLUID PROPERTIES
 R_uni = 8314.0  # [J/kmol/K]

examples/1D_exp_tube_phasechange/case.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
-import math
-import json
 import argparse
+import json
+import math
 
 parser = argparse.ArgumentParser(prog="phasechange", description="phase change considering both 5 and 6 equation models.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 parser.add_argument("--mfc", type=json.loads, default="{}", metavar="DICT", help="MFC's toolchain's internal state.")