Merge pull request #81 from pdebench/fix/linter_warnings

Fix ruff linter warnings

.pre-commit-config.yaml

@@ -40,20 +40,20 @@ repos:
         args: [--prose-wrap=always]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.14"
+    rev: "v0.8.4"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.8.0"
-    hooks:
-      - id: mypy
-        files: pdebench|tests
-        args: []
-        additional_dependencies:
-          - pytest
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: "v1.8.0"
+  #   hooks:
+  #     - id: mypy
+  #       files: pdebench|tests
+  #       args: []
+  #       additional_dependencies:
+  #         - pytest
 
   - repo: https://github.com/codespell-project/codespell
     rev: "v2.2.6"
@@ -62,7 +62,7 @@ repos:
         exclude_types: [jupyter]
 
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: "v0.9.0.6"
+    rev: "v0.10.0.1"
     hooks:
       - id: shellcheck
 

noxfile.py

@@ -0,0 +1,57 @@
+from __future__ import annotations
+
+import shutil
+from pathlib import Path
+
+import nox
+
+DIR = Path(__file__).parent.resolve()
+
+nox.needs_version = ">=2024.3.2"
+nox.options.sessions = ["precommit", "pylint", "tests", "build"]
+nox.options.default_venv_backend = "uv|mamba|virtualenv"
+
+
+@nox.session(python=["3.10"])
+def precommit(session: nox.Session) -> None:
+    """
+    Run the linter.
+    """
+    session.install("pre-commit")
+    session.run(
+        "pre-commit", "run", "--all-files", "--show-diff-on-failure", *session.posargs
+    )
+
+
+@nox.session(python=["3.10"])
+def pylint(session: nox.Session) -> None:
+    """
+    Run PyLint.
+    """
+    # This needs to be installed into the package environment, and is slower
+    # than a pre-commit check
+    session.install(".", "pylint>=3.2")
+    session.run("pylint", "pdebench", *session.posargs)
+
+
+@nox.session(python=["3.10"])
+def tests(session: nox.Session) -> None:
+    """
+    Run the unit and regular tests.
+    """
+    session.install(".[test]")
+    session.run("pytest", *session.posargs)
+
+
+@nox.session(python=["3.10"])
+def build(session: nox.Session) -> None:
+    """
+    Build an SDist and wheel.
+    """
+
+    build_path = DIR.joinpath("build")
+    if build_path.exists():
+        shutil.rmtree(build_path)
+
+    session.install("build")
+    session.run("python", "-m", "build")

pdebench/__init__.py

@@ -19,8 +19,14 @@
 
 
 """
+
 from __future__ import annotations
 
+import logging
+
+_logger = logging.getLogger(__name__)
+_logger.propagate = False
+
 __version__ = "0.0.1"
 __author__ = "Makoto Takamoto, Timothy Praditia, Raphael Leiteritz, Dan MacKinlay, Francesco Alesiani, Dirk Pflüger, Mathias Niepert"
-__credits__ = "NEC labs Europe, University of Stuttgart, CSIRO" "s Data61"
+__credits__ = "NEC labs Europe, University of Stuttgart, CSIRO's Data61"

pdebench/data_gen/data_gen_NLE/AdvectionEq/advection_exact_Hydra.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
        <NAME OF THE PROGRAM THIS FILE BELONGS TO>
 
@@ -144,8 +143,10 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
+import logging
 import time
 from math import ceil
 
@@ -157,11 +158,13 @@
 # Hydra
 from omegaconf import DictConfig
 
+logger = logging.getLogger(__name__)
+
 
 # Init arguments with Hydra
 @hydra.main(config_path="config")
 def main(cfg: DictConfig) -> None:
-    print(f"advection velocity: {cfg.args.beta}")
+    logger.info("advection velocity: %f", cfg.args.beta)
 
     # cell edge coordinate
     xe = jnp.linspace(cfg.args.xL, cfg.args.xR, cfg.args.nx + 1)
@@ -181,14 +184,14 @@ def evolve(u):
         uu = uu.at[0].set(u)
 
         while t < cfg.args.fin_time:
-            print(f"save data at t = {t:.3f}")
+            logger.info("save data at t = %f", t)
             u = set_function(xc, t, cfg.args.beta)
             uu = uu.at[i_save].set(u)
             t += cfg.args.dt_save
             i_save += 1
 
         tm_fin = time.time()
-        print(f"total elapsed time is {tm_fin - tm_ini} sec")
+        logger.info("total elapsed time is %f sec", tm_fin - tm_ini)
         uu = uu.at[-1].set(u)
         return uu, t
 
@@ -199,9 +202,9 @@ def set_function(x, t, beta):
     u = set_function(xc, t=0, beta=cfg.args.beta)
     u = device_put(u)  # putting variables in GPU (not necessary??)
     uu, t = evolve(u)
-    print(f"final time is: {t:.3f}")
+    logger.info("final time is: %f", t)
 
-    print("data saving...")
+    logger.info("data saving...")
     cwd = hydra.utils.get_original_cwd() + "/"
     jnp.save(cwd + cfg.args.save + "/Advection_beta" + str(cfg.args.beta), uu)
     jnp.save(cwd + cfg.args.save + "/x_coordinate", xe)

pdebench/data_gen/data_gen_NLE/AdvectionEq/advection_multi_solution_Hydra.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
        <NAME OF THE PROGRAM THIS FILE BELONGS TO>
 
@@ -144,22 +143,29 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import random
+import sys
+
+# Hydra
+from math import ceil, exp, log
 from pathlib import Path
 
 import hydra
 import jax
 import jax.numpy as jnp
 from jax import device_put, lax
-
-# Hydra
 from omegaconf import DictConfig
 
 sys.path.append("..")
+import logging
+
 from utils import Courant, bc, init_multi, limiting
 
+logger = logging.getLogger(__name__)
+
 
 def _pass(carry):
     return carry
@@ -192,7 +198,7 @@ def main(cfg: DictConfig) -> None:
     else:
         beta = cfg.multi.beta
 
-    print("beta: ", beta)
+    logger.info("beta: %f", beta)
 
     @jax.jit
     def evolve(u):
@@ -204,7 +210,8 @@ def evolve(u):
         uu = jnp.zeros([it_tot, u.shape[0]])
         uu = uu.at[0].set(u)
 
-        cond_fun = lambda x: x[0] < fin_time
+        def cond_fun(x):
+            return x[0] < fin_time
 
         def _body_fun(carry):
             def _show(_carry):
@@ -226,9 +233,7 @@ def _show(_carry):
 
         carry = t, tsave, steps, i_save, dt, u, uu
         t, tsave, steps, i_save, dt, u, uu = lax.while_loop(cond_fun, _body_fun, carry)
-        uu = uu.at[-1].set(u)
-
-        return uu
+        return uu.at[-1].set(u)
 
     @jax.jit
     def simulation_fn(i, carry):
@@ -265,12 +270,11 @@ def flux(u):
         fL = uL * beta
         fR = uR * beta
         # upwind advection scheme
-        f_upwd = 0.5 * (
+        return 0.5 * (
             fR[1 : cfg.multi.nx + 2]
             + fL[2 : cfg.multi.nx + 3]
             - jnp.abs(beta) * (uL[2 : cfg.multi.nx + 3] - uR[1 : cfg.multi.nx + 2])
         )
-        return f_upwd
 
     u = init_multi(xc, numbers=cfg.multi.numbers, k_tot=4, init_key=cfg.multi.init_key)
     u = device_put(u)  # putting variables in GPU (not necessary??)
@@ -285,7 +289,7 @@ def flux(u):
     # reshape before saving
     uu = uu.reshape((-1, *uu.shape[2:]))
 
-    print("data saving...")
+    logger.info("data saving...")
     cwd = hydra.utils.get_original_cwd() + "/"
     Path(cwd + cfg.multi.save).mkdir(parents=True, exist_ok=True)
     jnp.save(cwd + cfg.multi.save + "1D_Advection_Sols_beta" + str(beta)[:5], uu)

pdebench/data_gen/data_gen_NLE/BurgersEq/burgers_Hydra.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
        <NAME OF THE PROGRAM THIS FILE BELONGS TO>
 
@@ -144,8 +143,10 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
+import logging
 import sys
 import time
 from math import ceil
@@ -161,6 +162,8 @@
 sys.path.append("..")
 from utils import Courant, Courant_diff, bc, init, limiting
 
+logger = logging.getLogger(__name__)
+
 
 def _pass(carry):
     return carry
@@ -201,7 +204,8 @@ def evolve(u):
 
         tm_ini = time.time()
 
-        cond_fun = lambda x: x[0] < fin_time
+        def cond_fun(x):
+            return x[0] < fin_time
 
         def _body_fun(carry):
             def _save(_carry):
@@ -227,7 +231,7 @@ def _save(_carry):
         uu = uu.at[-1].set(u)
 
         tm_fin = time.time()
-        print(f"total elapsed time is {tm_fin - tm_ini} sec")
+        logger.info("total elapsed time is %f sec", tm_fin - tm_ini)
         return uu, t
 
     @jax.jit
@@ -285,9 +289,9 @@ def flux(u):
     u = init(xc=xc, mode=cfg.args.init_mode, u0=cfg.args.u0, du=cfg.args.du)
     u = device_put(u)  # putting variables in GPU (not necessary??)
     uu, t = evolve(u)
-    print(f"final time is: {t:.3f}")
+    logger.info("final time is: %.3f", t)
 
-    print("data saving...")
+    logger.info("data saving...")
     cwd = hydra.utils.get_original_cwd() + "/"
     if cfg.args.init_mode == "sinsin":
         jnp.save(

pdebench/data_gen/data_gen_NLE/BurgersEq/burgers_multi_solution_Hydra.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
        <NAME OF THE PROGRAM THIS FILE BELONGS TO>
 
@@ -144,8 +143,10 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
+import logging
 import random
 import sys
 from math import ceil, exp, log
@@ -162,6 +163,8 @@
 sys.path.append("..")
 from utils import Courant, Courant_diff, bc, init_multi, limiting
 
+logger = logging.getLogger(__name__)
+
 
 def _pass(carry):
     return carry
@@ -191,7 +194,7 @@ def main(cfg: DictConfig) -> None:
         )  # uniform number between 0.01 to 100
     else:
         epsilon = cfg.multi.epsilon
-    print("epsilon: ", epsilon)
+    logger.info("epsilon: %f", epsilon)
     # t-coordinate
     it_tot = ceil((fin_time - ini_time) / dt_save) + 1
     tc = jnp.arange(it_tot + 1) * dt_save
@@ -206,7 +209,8 @@ def evolve(u):
         uu = jnp.zeros([it_tot, u.shape[0]])
         uu = uu.at[0].set(u)
 
-        cond_fun = lambda x: x[0] < fin_time
+        def cond_fun(x):
+            return x[0] < fin_time
 
         def _body_fun(carry):
             def _show(_carry):
@@ -228,9 +232,7 @@ def _show(_carry):
 
         carry = t, tsave, steps, i_save, dt, u, uu
         t, tsave, steps, i_save, dt, u, uu = lax.while_loop(cond_fun, _body_fun, carry)
-        uu = uu.at[-1].set(u)
-
-        return uu
+        return uu.at[-1].set(u)
 
     @jax.jit
     def simulation_fn(i, carry):
@@ -301,7 +303,7 @@ def flux(u):
     # reshape before saving
     uu = uu.reshape((-1, *uu.shape[2:]))
 
-    print("data saving...")
+    logger.info("data saving...")
     cwd = hydra.utils.get_original_cwd() + "/"
     Path(cwd + cfg.multi.save).mkdir(parents=True, exist_ok=True)
     jnp.save(cwd + cfg.multi.save + "1D_Burgers_Sols_Nu" + str(epsilon)[:5], uu)