fixing flake8:

__init__:
    noqa: F401 on gTopRefinableObjRegistry
    import. Removing it will cause potential api
    breakage on downstream users. Also Exist at
    pyobjcryst.globals

crystal.py:
    Add except type (AttributeError)
    at UpdateDisplay(self) to avoid E722.

fourier.py:
    noqa E741 on ambigous variable
    name 'l'. (hkl)

globaloptim.py:
    clarify refinableobj imports

lsq.py:
    Expose LSQ from c++ extension

powderpattern.py:
    Add except type (AttributeError)
    at UpdateDisplay(self) to avoid E722.

    Add except type (AttributeError, RuntimeError, ValueError)
    at plot() (Force immediate display) with
    warning messages "Plot refresh failed..."

    Add except type (AttributeError, RuntimeError)
    at _do_plot_hkl (Force immediate display). Nested

utils.py:
    change lambda function to def

Author: Tieqiong

src/pyobjcryst/__init__.py

@@ -72,7 +72,9 @@
 import pyobjcryst.spacegroup
 import pyobjcryst.unitcell
 import pyobjcryst.zscatterer
-from pyobjcryst._pyobjcryst import gTopRefinableObjRegistry
+
+# could be api breaking if removed
+from pyobjcryst._pyobjcryst import gTopRefinableObjRegistry  # noqa: F401
 
 # Let's put this on the package level
 from pyobjcryst.general import ObjCrystException

src/pyobjcryst/crystal.py

@@ -36,8 +36,6 @@
 ]
 
 import warnings
-from multiprocessing import current_process
-from types import MethodType
 from urllib.request import urlopen
 
 import numpy as np
@@ -48,8 +46,6 @@
 )
 from pyobjcryst._pyobjcryst import Crystal as Crystal_orig
 
-from .refinableobj import wrap_boost_refinableobjregistry
-
 try:
     import py3Dmol
 except ImportError:
@@ -78,7 +74,7 @@ def UpdateDisplay(self):
         try:
             if self._display_update_disabled:
                 return
-        except:
+        except AttributeError:
             pass
         # test for _3d_widget is a bit ugly, but to correctly implement this we'd need an
         # __init__ function which overrides the 3 different Crystal constructors which
@@ -300,7 +296,7 @@ def _display_list(
                     name = scatt.GetComponentName(j)
                     name = name.replace("'", "_")
                     symbol = s.mpScattPow.GetSymbol()
-                    occ = s.Occupancy
+                    # occ = s.Occupancy
                     x, y, z = s.X, s.Y, s.Z
                     if enantiomer:
                         x = -x
@@ -413,8 +409,8 @@ def _display_list(
                                                     }
                                                 )
                     else:
-                        # TODO add 'visible' value in dictionary to determine which atoms are shown,
-                        # then update the bond and bondOrder lists
+                        # TODO add 'visible' value in dictionary to determine which atoms
+                        # are shown, then update the bond and bondOrder lists
                         for k in range(nsym):
                             for dx in (-1, 0, 1):
                                 for dy in (-1, 0, 1):
@@ -443,14 +439,14 @@ def _display_list(
                                             j = a["j"]
                                             vb = []
                                             vo = []
-                                            for l in range(len(a["bonds"])):
-                                                int_ptr = a["bonds"][l]
+                                            for i in range(len(a["bonds"])):
+                                                int_ptr = a["bonds"][i]
                                                 if atoms[int_ptr]["visible"]:
                                                     vb.append(
                                                         atoms[int_ptr]["idx"]
                                                     )
                                                     vo.append(
-                                                        a["bondOrder"][l]
+                                                        a["bondOrder"][i]
                                                     )
                                             x, y, z = vxyz[k, j] + np.array(
                                                 (dx, dy, dz)
@@ -479,7 +475,7 @@ def _display_list(
                         # 3dmol.js does not like ' in names,
                         # despite https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf
                         name = name.replace("'", "_")
-                        occ = s.Occupancy
+                        # occ = s.Occupancy
                         x, y, z = s.X, s.Y, s.Z
                         if enantiomer:
                             x = -x
@@ -514,7 +510,7 @@ def _display_list(
                         # 3dmol.js does not like ' in names,
                         # despite https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf
                         name = name.replace("'", "_")
-                        occ = s.Occupancy
+                        # occ = s.Occupancy
 
                         for k in range(nsym):
                             for dx in (-1, 0, 1):

src/pyobjcryst/fourier.py

@@ -67,7 +67,7 @@ def calc_fourier_map(
         # print(" Fourier map obs scale factor:", scale_fobs)
     vol = c.GetVolume()
     spg = c.GetSpaceGroup()
-    h, k, l = data.GetH()[:nb], data.GetK()[:nb], data.GetL()[:nb]
+    h, k, l = data.GetH()[:nb], data.GetK()[:nb], data.GetL()[:nb]  # noqa E741
     # Map size to achieve resolution
     nx = int(np.ceil(c.a / resolution))
     ny = int(np.ceil(c.b / resolution))

src/pyobjcryst/globaloptim.py

@@ -29,14 +29,21 @@
 from pyobjcryst._pyobjcryst import MonteCarlo as MonteCarlo_orig
 from pyobjcryst._pyobjcryst import OptimizationObjRegistry
 
-from .refinableobj import *
+from .refinableobj import (
+    refpartype_scattdata_background,
+    refpartype_scattdata_corr,
+    refpartype_scattdata_profile,
+    refpartype_scattdata_radiation,
+    refpartype_scattdata_scale,
+    refpartype_unitcell,
+)
 
 
 class MonteCarlo(MonteCarlo_orig):
 
     def Optimize(self, nb_step: int, final_cost=0, max_time=-1):
         self._fix_parameters_for_global_optim()
-        if type(self) == MonteCarlo_orig:
+        if type(self) is MonteCarlo_orig:
             self._Optimize(int(nb_step), True, final_cost, max_time)
         else:
             super().Optimize(int(nb_step), True, final_cost, max_time)
@@ -45,7 +52,7 @@ def MultiRunOptimize(
         self, nb_run: int, nb_step: int, final_cost=0, max_time=-1
     ):
         self._fix_parameters_for_global_optim()
-        if type(self) == MonteCarlo_orig:
+        if type(self) is MonteCarlo_orig:
             self._MultiRunOptimize(
                 int(nb_run), int(nb_step), True, final_cost, max_time
             )
@@ -56,7 +63,7 @@ def MultiRunOptimize(
 
     def RunSimulatedAnnealing(self, nb_step: int, final_cost=0, max_time=-1):
         self._fix_parameters_for_global_optim()
-        if type(self) == MonteCarlo_orig:
+        if type(self) is MonteCarlo_orig:
             self._RunSimulatedAnnealing(
                 int(nb_step), True, final_cost, max_time
             )
@@ -67,7 +74,7 @@ def RunSimulatedAnnealing(self, nb_step: int, final_cost=0, max_time=-1):
 
     def RunParallelTempering(self, nb_step: int, final_cost=0, max_time=-1):
         self._fix_parameters_for_global_optim()
-        if type(self) == MonteCarlo_orig:
+        if type(self) is MonteCarlo_orig:
             self._RunParallelTempering(
                 int(nb_step), True, final_cost, max_time
             )
@@ -116,7 +123,7 @@ def UpdateDisplay(self):
         try:
             if self._display_update_disabled:
                 return
-        except:
+        except AttributeError:
             pass
         try:
             if self._widget is not None:

src/pyobjcryst/lsq.py

@@ -17,4 +17,6 @@
         In development !
 """
 
+__all__ = ["LSQ"]
+
 from pyobjcryst._pyobjcryst import LSQ

src/pyobjcryst/powderpattern.py

@@ -17,7 +17,8 @@
         Additional functions for plotting, basic QPA and profile fitting.
 """
 
-from multiprocessing import current_process
+import inspect
+import warnings
 from urllib.request import urlopen
 
 import numpy as np
@@ -33,9 +34,6 @@
     "SpaceGroupExplorer",
 ]
 
-from types import MethodType
-
-from pyobjcryst.general import ObjCrystException
 from pyobjcryst._pyobjcryst import LSQ
 from pyobjcryst._pyobjcryst import (
     CreatePowderPatternFromCIF as CreatePowderPatternFromCIF_orig,
@@ -48,6 +46,7 @@
     ReflectionProfileType,
     SpaceGroupExplorer,
 )
+from pyobjcryst.general import ObjCrystException
 from pyobjcryst.refinableobj import refpartype_scattdata_background
 
 
@@ -82,7 +81,7 @@ def UpdateDisplay(self):
         try:
             if self._display_update_disabled:
                 return
-        except:
+        except AttributeError:
             pass
         if self._plot_fig is not None:
             if self._plot_fig is not None:
@@ -225,8 +224,17 @@ def plot(
                 self._plot_fig.canvas.draw()
                 if "ipympl" not in plt.get_backend():
                     plt.pause(0.001)
-            except:
-                pass
+            except (AttributeError, RuntimeError, ValueError) as e:
+                cls_name = type(self).__name__
+                func_name = inspect.currentframe().f_code.co_name
+                backend = plt.get_backend()
+                fig_id = getattr(self._plot_fig, "number", None)
+                warnings.warn(
+                    f"[{cls_name}.{func_name}] "
+                    f"Plot refresh failed ({type(e).__name__}): {e}. "
+                    f"Matplotlib backend={backend}, figure id={fig_id}",
+                    stacklevel=2,
+                )
             # plt.gca().callbacks.connect('xlim_changed', self._on_xlims_change)
             # plt.gca().callbacks.connect('ylim_changed', self._on_ylims_change)
             self._plot_fig.canvas.mpl_connect(
@@ -273,15 +281,15 @@ def _do_plot_hkl(self, nb_max=100, fontsize_hkl=None):
                 try:
                     # need the renderer to avoid text overlap
                     renderer = plt.gcf().canvas.get_renderer()
-                except:
+                except (AttributeError, RuntimeError):
                     # Force immediate display. Not supported on all backends (e.g. nbagg)
                     ax.draw()
                     self._plot_fig.canvas.draw()
                     if "ipympl" not in plt.get_backend():
                         plt.pause(0.001)
                     try:
                         renderer = self._plot_fig.canvas.get_renderer()
-                    except:
+                    except (AttributeError, RuntimeError):
                         renderer = None
             else:
                 renderer = None

src/pyobjcryst/utils.py

@@ -54,7 +54,8 @@ def putAtomsInMolecule(crystal, alist=None, name=None):
     # mapping fractional coords back into [0, 1)
     from math import floor
 
-    f = lambda v: v - floor(v)
+    def f(v):
+        return v - floor(v)
 
     scat = []
     for idx in alist: