Elminate some codacy regressions, try to get tests working on GH Action

Author: gb119

Stoner/Image/kerr.py

@@ -115,7 +115,7 @@ def image(self: Self) -> ImageArray:  # pylint: disable=invalid-overridden-metho
         return self._image.view(KerrArray)
 
     @ImageFile.image.setter
-    def image(self: Self, v) -> None:  # noqa F811 pylint: disable=function-redefined
+    def image(self: Self, v) -> None:  # noqa: F811  # pylint: disable=redefined-outer-name
         """Ensure stored image is always an ImageArray."""
         filename = self.filename
         v = KerrArray(v)

Stoner/core/__init__.py

@@ -18,7 +18,6 @@
     "string_to_type",
     "exceptions",
     "utils",
-    "Typing",
 ]
 
 from . import array, base, exceptions, utils

Stoner/core/data.py

@@ -686,7 +686,7 @@ def _load(self, filename, *args, **kargs):
                     invalid_raise=False,
                     comments="\0",
                     missing_values=[""],
-                    filling_values=[np.nan],
+                    filling_values=[nan],
                     max_rows=max_rows,
                 )
         if data.ndim < 2:

Stoner/folders/__init__.py

@@ -1,5 +1,6 @@
 """Core support for working with collections of files in the :py:class:`Stoner.DataFolder`."""
 
+# pylint: disable=redefined-builtin
 __all__ = ["core", "each", "groups", "hdf5", "metadata", "mixins", "utils", "zip", "DataFolder", "PlotFolder"]
 
 from . import core, each, groups, hdf5, metadata, mixins, utils, zip

Stoner/folders/hdf5.py

@@ -15,8 +15,8 @@
 import h5py
 
 from ..compat import get_filedialog, path_types
-from ..core.data import Data  # noqa pylint: disable=unused-import
 from .mixins import DataFolder
+from ..tools import make_Class
 
 
 class HDF5Folder(DataFolder):
@@ -109,7 +109,7 @@ def _dialog(self, message="Select Folder", new_directory=True, mode="r+"):
     def _visit_func(self, name, obj):  # pylint: disable=unused-argument
         """Walker of the HDF5 tree."""
         if isinstance(obj, h5py.Group) and "type" in obj.attrs:
-            cls = globals()[obj.attrs["type"]]
+            cls = make_Class(obj.attrs["type"], None)
             if issubclass(self.loader, cls):
                 self.__setter__(obj.name, obj.name)
             elif obj.attrs["type"] == "HDF5Folder" and getattr(self, "recursive", True):

Stoner/folders/zip.py

@@ -39,6 +39,8 @@ class ZipFolder(DiskBasedFolderMixin, BaseFolder):
     def __init__(self, *args, **kargs):
         """Initialise the file attribute."""
         self.File = None
+        self.exclude = []
+        self.flat = False
         super().__init__(*args, **kargs)
 
     @property
@@ -58,7 +60,7 @@ def key(self, value):  # pylint: disable=invalid-overridden-method
         """Set the immediate filename that will be used when the file is saved."""
         self.path = pathjoin(self.directory, value)
 
-    def _dialog(self, mode="r"):
+    def _zip_file_dialog(self, mode="r"):
         """Create a file dialog box for working with.
 
         Args:
@@ -94,7 +96,7 @@ def getlist(self, recursive=None, directory=None, flatten=None, **_):
             flatten = self.flat
 
         if self.File is None and directory is None:
-            self.File = zf.ZipFile(self._dialog(), "r")
+            self.File = zf.ZipFile(self._zip_file_dialog(), "r")
             close_me = True
         elif isinstance(directory, zf.ZipFile):
             if directory.fp:
@@ -252,7 +254,7 @@ def save(self, root=None):
             A list of group paths in the Zip file
         """
         if root is None:
-            root = self._dialog(mode="w")
+            root = self._zip_file_dialog(mode="w")
         elif isinstance(root, bool) and not root and isinstance(self.File, zf.ZipFile):
             root = self.File.filename
             self.File.close()
@@ -261,14 +263,16 @@ def save(self, root=None):
             tmp = self.walk_groups(self._save)
         return tmp
 
-    def _save(self, f, trail):
+    def _save(self, f, trail, root=None):
         """Create a virtual path of groups in the Zip file and save data.
 
         Args:
             f(DataFile):
                 A DataFile instance to save
             trail (list):
                 The trail of groups
+            root (string or None):
+                a replacement root directory
 
         Returns:
             The new filename of the saved DataFile.

Stoner/formats/maximus.py

@@ -75,10 +75,7 @@ def __init__(self, *args, **kargs):
     def _load(self, *args, **kargs):
         """Load an ImageStack from either an hdf file or textfiles."""
         filename, args, kargs = get_filename(args, kargs)
-        if filename is None or not filename:
-            self.get_filename("r")
-        else:
-            self.filename = filename
+        self.filename = filename
         pth = Path(self.filename)
         if h5py.is_hdf5(self.filename):
             return self.__class__.read_hdf5(self.filename)
@@ -219,14 +216,11 @@ def to_hdf5(self, filename=None):
         return self
 
     @classmethod
-    def read_hdf5(cls, filename, *args, **kargs):
+    def read_hdf5(cls, *args, **kargs):
         """Create a new instance from an hdf file."""
         self = cls(regrid=False)
-        if filename is None or not filename:
-            self.get_filename("r")
-            filename = self.filename
-        else:
-            self.filename = filename
+        filename, args, kargs = get_filename(args, kargs)
+        self.filename = filename
         with HDFFileManager(self.filename, "r") as f:
             self.scan_no = f.attrs["scan_no"]
             if "groups" in f.attrs:

Stoner/plot/formats.py

@@ -406,7 +406,10 @@ def update(self, other=(), /, **_):
                     if k in dir(self) and not callable(getattr(self, k)):
                         setattr(self, k, val)
                     elif not k.startswith("_"):
-                        setattr(self, f"template_{k}", val)
+                        try:
+                            setattr(self, f"template_{k}", val)
+                        except AttributeError:
+                            pass
             case _:
                 raise SyntaxError(
                     "Only one posotional argument which should be a Mapping subclass can be supplied toi update."

Stoner/tools/typing.py

@@ -8,7 +8,7 @@
 
 if TYPE_CHECKING:
     from ..core.data import Data
-    from ..core.setas import setas
+    from ..core.setas import Setas
     from ..image.core import ImageArray, ImageFile
 else:
     Setas = type("Setas", (), {})

scripts/BNL_FileSplitter.py

@@ -25,25 +25,25 @@
         break
     except IOError:
         print("Oops I couldn't find that file.")
-with open(filename, "r", encoding="utf-8") as mainFP, open(
+with open(filename, "r", encoding="utf-8") as main_fp, open(
     "title.txt", "w", encoding="utf-8"
-) as writeFP:
+) as write_fp:
 
     if "BNLSplitFiles" not in os.listdir(directory):
         os.mkdir("BNLSplitFiles")
     os.chdir("BNLSplitFiles")
 
     # writeName=re.split(r'[.]',filename)
     counter = 1  # this will label the files
-    for line in mainFP:
+    for line in main_fp:
         if line[0:2] == "#S":
             if int(line.split()[1]) != counter:
                 raise ValueError  # check for inconsistencies with filenames and scan numbers
-            writeFP.close()
-            writeFP = open(str(counter) + ".bnl", "w", encoding="utf-8")
+            write_fp.close()
+            write_fp = open(str(counter) + ".bnl", "w", encoding="utf-8")
             counter += 1
         if line[0:2] != "#C":
-            writeFP.write(line)
+            write_fp.write(line)
             # ignore #C statements which are usually abort and rarely useful, they come
             # after data and before the next #S"""