Add pyflake to lint suite

bird/__init__.py

@@ -4,6 +4,10 @@
 
 from bird.version import __version__
 
+# Marks __version__ as an intentional re-export (read by setuptools as
+# bird.__version__); does not restrict attribute access to the module.
+__all__ = ["__version__"]
+
 BIRD_DIR = os.path.dirname(os.path.realpath(__file__))
 BIRD_CASE_DIR = os.path.join(BIRD_DIR, "../tutorial_cases")
 BIRD_CONST_DIR = os.path.join(BIRD_DIR, "constants")

bird/meshing/block_cyl_mesh.py

@@ -87,8 +87,6 @@ def assemble_mesh(input_file, geom_dict):
         raise ValueError(f"unknown input file ({input_file}) extension")
     R = geom_dict["R"]
     L = geom_dict["L"]
-    N1 = len(R)
-    N2 = len(L) - 1
     CW = []
     mCW = []
     C1 = []
@@ -313,16 +311,12 @@ def writeBlockMeshDict(out_folder, geom_dict, mesh_dict):
     BoundaryNames = geom_dict["names"]
     BoundaryType = geom_dict["types"]
     BoundaryRmin = geom_dict["rmin"]
-    BoundaryRmax = geom_dict["rmax"]
     BoundaryLmin = geom_dict["lmin"]
-    BoundaryLmax = geom_dict["lmax"]
 
     NR = mesh_dict["NR"]
     NS = mesh_dict["NS"]
     NVert = mesh_dict["NVert"]
     gradR = mesh_dict["gradR"]
-    gradR_l = mesh_dict["gradR_l"]
-    gradR_r = mesh_dict["gradR_r"]
     gradVert = mesh_dict["gradVert"]
     CW = mesh_dict["CW"]
     mCW = mesh_dict["mCW"]
@@ -420,8 +414,6 @@ def writeBlockMeshDict(out_folder, geom_dict, mesh_dict):
             # gradingR = 1
             # if il==N2-1:
             #    gradingVert = outletGrading
-            gradingR_l = gradR_l[ir]
-            gradingR_r = gradR_r[ir]
             gradingVert = gradVert[il]
             gradingR = gradR[ir]
             # Am I a wall
@@ -528,7 +520,6 @@ def writeBlockMeshDict(out_folder, geom_dict, mesh_dict):
             boundType = BoundaryType[i][ibound]
             if boundType == "lateral":
                 rminInd = BoundaryRmin[i][ibound]
-                rmaxInd = BoundaryRmax[i][ibound]
                 lInd = BoundaryLmin[i][ibound]
                 i1 = rminInd * (4 * (N2 + 1)) + 4 * lInd  # bottom
                 i2 = i1 - 4  # top
@@ -540,7 +531,6 @@ def writeBlockMeshDict(out_folder, geom_dict, mesh_dict):
 
             elif boundType == "top":
                 lminInd = BoundaryLmin[i][ibound]
-                lmaxInd = BoundaryLmax[i][ibound]
                 rInd = BoundaryRmin[i][ibound]
                 if rInd > 0:
                     i1 = 4 * (N2 + 1) * (rInd - 1) + 4 * lminInd  # right
@@ -556,7 +546,6 @@ def writeBlockMeshDict(out_folder, geom_dict, mesh_dict):
 
             elif boundType == "bottom":
                 lminInd = BoundaryLmin[i][ibound]
-                lmaxInd = BoundaryLmax[i][ibound]
                 rInd = BoundaryRmin[i][ibound]
                 i1 = 4 * (N2 + 1) * (rInd - 1) + 4 * lminInd  # right
                 i2 = i1 + 4 * (N2 + 1)  # left

bird/meshing/block_rect_mesh.py

@@ -44,7 +44,6 @@ def write_vertices(outfile, lengths, nboxes):
 def write_blocks(outfile, blockids, lengths, nboxes, points_per_len):
     nx = nboxes[0]
     ny = nboxes[1]
-    nz = nboxes[2]
 
     idarray = np.zeros(8, dtype=int)
     mesharray = np.zeros(3, dtype=int)
@@ -93,7 +92,6 @@ def make_fluid_blocks_from_corner(corners):
     assert isinstance(corners, list)
     fluid_blocks = []
     for multi_block in corners:
-        n_end_block = len(multi_block)
         for iend, end_block in enumerate(multi_block):
             # Add blocks that connect end points
             if iend == 0:
@@ -222,7 +220,6 @@ def from_block_rect_to_seg(input_geom_dict, rescale=True):
         )
         vec_conn = segments[iseg]["end"] - segments[iseg]["start"]
         segments[iseg]["conn"] = vec_conn
-        norm_vec_conn = np.linalg.norm(vec_conn)
         segments[iseg]["normal_dir"] = int(np.nonzero(vec_conn)[0][0])
         if segments[iseg]["normal_dir"] == 0:
             segments[iseg]["max_rad"] = (blocksize_y + blocksize_z) / 4

bird/meshing/stirred_tank_mesh.py

@@ -122,8 +122,6 @@ def get_globalindex_of(splti, ci, zi, react):
     centeroffset = react.centeroffset
     polyoffset = react.polyoffset
     nsplits = react.nsplits
-    hub_circ = react.hub_circ
-    tank_circ = react.tank_circ
 
     # also works for ci=-1
     global_id = (
@@ -173,8 +171,6 @@ def write_edges(outfile, react):
     for zi in range(nsections):
         outfile.write("\n//section " + str(zi) + "\n")
 
-        offset = 1 + nsplits  # one for center and nsplits for polygon
-
         outfile.write("\n//circles\n")
         for ci in range(ncirc):
             outfile.write("\n//circle " + str(ci) + "\n")

bird/postprocess/conditional_mean.py

@@ -20,7 +20,6 @@ def compute_cond_mean(
 ):
     time_float_sorted, time_str_sorted = get_case_times(case_folder)
     cell_centers, _ = read_cell_centers(case_folder)
-    nCells = len(cell_centers)
     assert len(diff_val_list) == len(diff_name_list)
     window_ave = min(window_ave, len(time_str_sorted))
 
@@ -38,11 +37,9 @@ def compute_cond_mean(
             field_file.append(
                 os.path.join(case_folder, time_folder, field_name)
             )
-
         for filename, name in zip(field_file, field_name_list):
-            val_dict = {}
             field_tmp, _ = read_field(
-                case_folder, time_folder, field_name=field_name
+                case_folder, time_folder, field_name=name
             )
             vert_axis, field_cond_tmp = conditional_average(
                 cell_centers[:, vert_ind], field_tmp, nbins=n_bins

bird/postprocess/early_pred.py

@@ -24,7 +24,7 @@
 
 
 def plotAllEarly(data_dict, color_files=None, chop=False, extrap=False):
-    fig = plt.figure()
+    plt.figure()
     for idat, datf in enumerate(data_dict):
         if color_files is not None:
             color = color_files[idat]
@@ -56,14 +56,13 @@ def plotAllEarly(data_dict, color_files=None, chop=False, extrap=False):
 
 
 def plotAllEarly_uq(data_dict, color_files=None):
-    fig = plt.figure()
+    plt.figure()
     for idat, datf in enumerate(data_dict):
         color = color_files[idat]
         text = data_dict[datf]["textrap"]
         t = data_dict[datf]["t"]
         y = data_dict[datf]["y"] * 100
         med_real = data_dict[datf]["med_real"] * 100
-        mean_real = data_dict[datf]["mean_real"] * 100
         std16_real = data_dict[datf]["std16_real"] * 100
         std84_real = data_dict[datf]["std84_real"] * 100
 

bird/postprocess/kla_utils.py

@@ -302,7 +302,6 @@ def post_cal(
     """
     np_hmc_samples = hmc_samples_2_np_samples(hmc_samples)
     labels_np = ["cstar", "kla", "sigma"]
-    nsamples = np_hmc_samples.shape[0]
     labels = list(hmc_samples.keys())
     nparams = len(labels)
 
@@ -322,7 +321,7 @@ def post_cal(
     p10_real = pred_dict["p10_pred"]
     p90_real = pred_dict["p90_pred"]
 
-    fig = plt.figure()
+    plt.figure()
     plt.plot(
         time_obs, mean_real, color="k", linewidth=3, label="mean predictions"
     )
@@ -367,6 +366,6 @@ def print_res_dict(res_dict: dict) -> None:
     if bs:
         logger.info(f"\tkla = {kla*3600:.4g} +/- {kla_err*3600:.4g} [h-1]")
         logger.info(f"\tcstar = {cs:.4g} +/- {cs_err:.4g} [mol/m3]")
-        logger.info(f"Without data bootstrap")
+        logger.info("Without data bootstrap")
     logger.info(f"\tkla = {kla_nb*3600:.4g} +/- {kla_err_nb*3600:.4g} [h-1]")
     logger.info(f"\tcstar = {cs_nb:.4g} +/- {cs_err_nb:.4g} [mol/m3]")

bird/postprocess/post_quantities/__init__.py

@@ -61,3 +61,12 @@
     "sherwood",
     "weber",
 ]
+
+# Private cell-selection helpers re-exported for the test suite (imported by tests/).
+__all__ += [
+    "_field_filter",
+    "_get_ind_gas",
+    "_get_ind_liq",
+    "_get_ind_slice",
+    "_weighted_average",
+]

bird/preprocess/dynamic_mixer/io_fvModels.py

@@ -42,14 +42,14 @@ def write_preamble(output_folder):
         f.write("\t\tconst volVectorField& UL =\n")
         f.write('\t\t\tmesh().lookupObject<volVectorField>("U.liquid");\n')
         f.write("\t\tdouble pi=3.141592654;\n")
-        f.write(f"\t\tdouble source_pt_x;\n")
-        f.write(f"\t\tdouble source_pt_y;\n")
-        f.write(f"\t\tdouble source_pt_z;\n")
-        f.write(f"\t\tdouble disk_rad;\n")
+        f.write("\t\tdouble source_pt_x;\n")
+        f.write("\t\tdouble source_pt_y;\n")
+        f.write("\t\tdouble source_pt_z;\n")
+        f.write("\t\tdouble disk_rad;\n")
         f.write("\t\tdouble disk_area;\n")
-        f.write(f"\t\tdouble power;\n")
-        f.write(f"\t\tdouble smear_factor;\n")
-        f.write(f"\t\tdouble startTime;\n")
+        f.write("\t\tdouble power;\n")
+        f.write("\t\tdouble smear_factor;\n")
+        f.write("\t\tdouble startTime;\n")
 
 
 def write_mixer(mixer, output_folder):

bird/preprocess/json_gen/generate_designs.py

@@ -152,29 +152,29 @@ def write_script_start(filename, n):
         for i in range(n):
             sim_folder = id2simfolder(i)
             f.write(f"cd {sim_folder}\n")
-            f.write(f"sbatch script\n")
-            f.write(f"cd ..\n")
+            f.write("sbatch script\n")
+            f.write("cd ..\n")
 
 
 def write_script_post(filename, n):
     with open(filename, "w+") as f:
         for i in range(n):
             sim_folder = id2simfolder(i)
             f.write(f"cd {sim_folder}\n")
-            f.write(f"sbatch script_post\n")
-            f.write(f"cd ..\n")
+            f.write("sbatch script_post\n")
+            f.write("cd ..\n")
 
 
 def write_prep(filename, n):
     with open(filename, "w+") as f:
         f.write("prep () {\n")
-        f.write(f"\tcd $1\n")
-        f.write(f"\treconstructPar -newTimes\n")
-        f.write(f"\tcd ..\n")
+        f.write("\tcd $1\n")
+        f.write("\treconstructPar -newTimes\n")
+        f.write("\tcd ..\n")
         f.write("}\n")
-        f.write(f"\n")
+        f.write("\n")
         f.write(
-            f"source /projects/gas2fuels/ofoam_cray_mpich/OpenFOAM-dev/etc/bashrc\n"
+            "source /projects/gas2fuels/ofoam_cray_mpich/OpenFOAM-dev/etc/bashrc\n"
         )
         for i in range(n):
             sim_folder = id2simfolder(i)

bird/preprocess/stl_patch/stl_shapes.py

@@ -65,7 +65,6 @@ def make_circle(radius, center, normal_dir, npts=3):
 
 
 def make_spider(centerRad, nArms, widthArms, lengthArms, center, normal_dir):
-    globalArea = 0
     if nArms < 2:
         error_msg = f"nArms ({nArms}) must be >= 2"
         logger.error(error_msg)

bird/utilities/ofio/__init__.py

@@ -50,3 +50,14 @@
     "species_name_to_mw",
     "write_openfoam_dict",
 ]
+
+# Helpers
+__all__ += [
+    "_find_header_size",
+    "_get_mesh_time",
+    "_get_volume_time",
+    "_read_mesh",
+    "_readOF",
+    "_readOFScal",
+    "_readOFVec",
+]

bird/utilities/ofio/foam_field_io.py

@@ -142,7 +142,6 @@ def _read_meta_data(filename: str, mode: str | None = None) -> dict:
                             sline = line.split()
                             for ientry, entry in enumerate(sline):
                                 if ";" in entry:
-                                    ind_end = ientry
                                     break
                             line_cropped = " ".join(sline[2 : ientry + 1])
                             unif_value = _ofvec2arr(line_cropped.strip(";"))

bird/utilities/ofio/global_vars.py

@@ -94,7 +94,7 @@ def repl(match):
                     #    result = int(result)
                     cross_referenced_globalVars_dict[key] = result
 
-                except Exception as e:
+                except Exception:
                     logger.warning(
                         f"Could not evaluate globalVars expression for {key}: {expr}"
                     )
@@ -124,7 +124,7 @@ def repl_direct(match):
                     # if result.is_integer():
                     #    result = int(result)
                     cross_referenced_globalVars_dict[key] = result
-                except Exception as e:
+                except Exception:
                     logger.warning(
                         f"Could not evaluate globalVars expression for {key}: {expr}"
                     )

bird/utilities/ofio/thermo.py

@@ -163,7 +163,7 @@ def read_mu_liquid(
                 mu_liq = globalVars["muMixLiq"]
             if mu_liq is None:
                 logger.error(
-                    f"Liquid viscosity is not constant, yet could not find thermo:mu.liquid"
+                    "Liquid viscosity is not constant, yet could not find thermo:mu.liquid"
                 )
                 raise FileNotFoundError(err)
             else:

noxfile.py

@@ -48,7 +48,7 @@ def run_cleanup(session: nox.Session) -> None:
 @nox.session(name="linter", python=False)
 def run_lint(session: nox.Session) -> None:
     """
-    Run black and isort with the github config file
+    Run black and isort, then pyflakes on the bird library
 
     """
 
@@ -59,9 +59,6 @@ def run_lint(session: nox.Session) -> None:
         "black",
         "--line-length",
         "79",
-        # Target the OLDEST python supported in pyproject.toml, not the newest.
-        # This flag tells black which syntax it may emit, so targeting py314
-        # let it rewrite `except (A, B):` into py3.14-only `except A, B:`
         "--target-version",
         "py311",
         "--exclude",
@@ -97,6 +94,48 @@ def run_lint(session: nox.Session) -> None:
     session.run(*black_command)
     session.run(*isort_command)
 
+    run_pyflakes(session)
+
+
+@nox.session(name="pyflakes", python=False)
+def run_pyflakes(session: nox.Session) -> None:
+    """
+    Run pyflakes on the bird library only
+    """
+
+    session.run("pip", "install", "--upgrade", "--quiet", "pyflakes")
+
+    output = session.run(
+        "pyflakes",
+        "bird",
+        external=True,
+        silent=True,
+        success_codes=[0, 1],
+    )
+
+    ignored_messages = (
+        "unable to detect undefined names",
+        "may be undefined, or defined from star imports",
+    )
+    # Script-only subtrees under bird/
+    excluded_paths = (
+        "bird/preprocess/data_case_gen/",
+        "bird/preprocess/inhomogeneousBC/",
+        "bird/postprocess/SA_optimization/",
+        "bird/postprocess/computeQoI/",
+    )
+
+    problems = [
+        line
+        for line in (output or "").splitlines()
+        if line.strip()
+        and not any(msg in line for msg in ignored_messages)
+        and not any(path in line for path in excluded_paths)
+    ]
+
+    if problems:
+        session.error("pyflakes found issues:\n" + "\n".join(problems))
+
 
 @nox.session(name="spell", python=False)
 @nox.session(name="codespell", python=False)