Rename some identifiers to snake_case, refactor in ZipFolder

Author: gb119

Stoner/compat.py

@@ -124,12 +124,12 @@ def get_filedialog(what="file", **opts):
     Returns:
         A file name or directory or list of files.
     """
-    from .tools.widgets import fileDialog
+    from .tools.widgets import file_dialog
 
     funcs = {"file": "OpenFile", "directory": "SelectDirectory", "files": "OpenFiles", "save": "SaveFile"}
     if what not in funcs:
         raise RuntimeError(f"Unable to recognise required file dialog type:{what}")
-    return fileDialog.open_dialog(mode=funcs[what], **opts)
+    return file_dialog.open_dialog(mode=funcs[what], **opts)
 
 
 if np_version.major >= 2:

Stoner/folders/hdf5.py

@@ -160,7 +160,7 @@ def getlist(self, recursive=None, directory=None, flatten=False, **kwargs):  # p
         # At this point directory contains an open h5py.File object, or possibly a group
         directory.visititems(self._visit_func)
         if flatten:
-            self.flatten()
+            self.flatten()  # pylint: disable=no-member
         if closeme:
             self.File.close()
             self.File = None

Stoner/folders/zip.py

@@ -9,15 +9,56 @@
 import fnmatch
 import zipfile as zf
 from os import path
+from pathlib import Path
 
-from ..compat import _pattern_type, get_filedialog, path_types
+from ..compat import _pattern_type, get_filedialog
 from ..core.data import Data
 from ..formats.utils.zip import test_is_zip
 from .core import BaseFolder
 from .mixins import DiskBasedFolderMixin
 from .utils import pathjoin
 
 
+def _prune_list(p, files):
+    """Prune the files list of entries that match pattern p."""
+    if isinstance(p, str):
+        for f in list(fnmatch.filter(files, p)):
+            del files[files.index(f)]
+    if isinstance(p, _pattern_type):
+        matched = []
+        # For reg expts we iterate over all files, but we can't delete matched
+        # files as we go as we're iterating over them - so we store the
+        # indices and delete them later.
+        for f in files:
+            if p.search(f):
+                matched.append(files.index(f))
+        matched.sort(reverse=True)
+        for i in matched:  # reverse sort the matching indices to safely delete
+            del files[i]
+
+
+def _build_list(fldr, p, files):
+    """Add matching files from the list to folder if matching pattern p."""
+    if isinstance(p, str):
+        for f in fnmatch.filter(files, p):
+            del files[files.index(f)]
+            f.replace(path.sep, "/")
+            fldr.append(f)
+    elif isinstance(p, _pattern_type):
+        matched = []
+        # For reg expts we iterate over all files, but we can't delete matched
+        # files as we go as we're iterating over them - so we store the
+        # indices and delete them later.
+        for ix, f in enumerate(files):
+            if p.search(f):
+                f.replace(path.sep, "/")
+                fldr.append(f)
+            else:
+                matched.append(ix)
+        for i in reversed(matched):  # reverse sort the matching indices to safely delete
+            del files[i]
+
+
 class ZipFolder(DiskBasedFolderMixin, BaseFolder):
     """A sub class of DataFile that sores itself in a zip file.
 
@@ -95,72 +136,39 @@ def getlist(self, recursive=None, directory=None, flatten=None, **_):
         if flatten is None:
             flatten = self.flat
 
-        if self.File is None and directory is None:
-            self.File = zf.ZipFile(self._zip_file_dialog(), "r")
-            close_me = True
-        elif isinstance(directory, zf.ZipFile):
-            if directory.fp:
+        match directory:
+            case None if self.File is None:
+                self.File = zf.ZipFile(self._zip_file_dialog(), "r")  # pylint: disable=R1732
+                close_me = True
+            case zf.ZipFile() if directory.fp:
                 self.File = directory
                 close_me = False
-            else:
-                self.File = zf.ZipFile(directory, "r")
+            case zf.ZipFile():
+                self.File = zf.ZipFile(directory, "r")  # pylint: disable=R1732
                 close_me = True
-        elif isinstance(directory, path_types) and path.isdir(directory):  # Fall back to DataFolder
-            return super().getlist(recursive=recursive, directory=directory, flatten=flatten)
-        elif isinstance(directory, path_types) and zf.is_zipfile(directory):
-            self.File = zf.ZipFile(directory, "r")
-            close_me = True
-        elif isinstance(self.File, zf.ZipFile):
-            if self.File.fp:
+            case str() | Path() if path.isdir(directory):
+                return super().getlist(recursive=recursive, directory=directory, flatten=flatten)
+            case str() | Path() if zf.is_zipfile(directory):
+                self.File = zf.ZipFile(directory, "r")  # pylint: disable=R1732
+                close_me = True
+            case _ if isinstance(self.File, zf.ZipFile) and self.File.fp:
                 close_me = False
-            else:
+            case _ if isinstance(self.File, zf.ZipFile):
                 self.File = zf.ZipFile(self.File.filename, "r")  # pylint: disable=R1732
                 close_me = True
-        else:
-            raise IOError(f"{directory} does not appear to be zip file!")
+            case _:
+                raise IOError(f"{directory} does not appear to be zip file!")
         # At this point directory contains an open h5py.File object, or possibly a group
         self.path = self.File.filename
         files = [x.filename for x in self.File.filelist]
         for p in self.exclude:  # Remove excluded files
-            if isinstance(p, str):
-                for f in list(fnmatch.filter(files, p)):
-                    del files[files.index(f)]
-            if isinstance(p, _pattern_type):
-                matched = []
-                # For reg expts we iterate over all files, but we can't delete matched
-                # files as we go as we're iterating over them - so we store the
-                # indices and delete them later.
-                for f in files:
-                    if p.search(f):
-                        matched.append(files.index(f))
-                matched.sort(reverse=True)
-                for i in matched:  # reverse sort the matching indices to safely delete
-                    del files[i]
-
+            _prune_list(p, files)
         for p in self.pattern:  # pattern is a list of strings and regeps
-            if isinstance(p, str):
-                for f in fnmatch.filter(files, p):
-                    del files[files.index(f)]
-                    f.replace(path.sep, "/")
-                    self.append(f)
-            elif isinstance(p, _pattern_type):
-                matched = []
-                # For reg expts we iterate over all files, but we can't delete matched
-                # files as we go as we're iterating over them - so we store the
-                # indices and delete them later.
-                for ix, f in enumerate(files):
-                    if p.search(f):
-                        f.replace(path.sep, "/")
-                        self.append(f)
-                    else:
-                        matched.append(ix)
-                for i in reversed(matched):  # reverse sort the matching indices to safely delete
-                    del files[i]
-
+            _build_list(self, p, files)
         self._zip_contents = files
 
         if flatten is None or not flatten:
-            self.unflatten()
+            self.unflatten()  # pylint: disable=no-member
         if close_me:
             self.File.close()
         return self
@@ -260,7 +268,7 @@ def save(self, root=None):
             self.File.close()
         mode = "a" if path.exists(root) else "w"
         with zf.ZipFile(root, mode) as self.File:
-            tmp = self.walk_groups(self._saver)
+            tmp = self.walk_groups(self._saver)  # pylint: disable=no-member
         return tmp
 
     def _saver(self, f, trail):

Stoner/tools/file.py

@@ -18,7 +18,7 @@
 from ..core.exceptions import StonerLoadError, StonerUnrecognisedFormat
 from ..tools.typing import Filename
 from .decorators import make_Data, make_Image
-from .widgets import fileDialog
+from .widgets import file_dialog as _file_dialog
 
 __all__ = [
     "get_hdf_loader",
@@ -152,7 +152,7 @@ def file_dialog(mode: str, filename: Filename, filetype: str) -> Union[pathlib.P
         mode = "SaveFile"
     else:
         mode = "SelectDirectory"
-    filename = fileDialog.open_dialog(start=dirname, mode=mode, patterns=patterns)
+    filename = _file_dialog.open_dialog(start=dirname, mode=mode, patterns=patterns)
     return filename if filename else None
 
 

Stoner/tools/widgets.py

@@ -3,7 +3,7 @@
 
 Code based on the PyQt5 Tutorial code,
 """
-__all__ = ["fileDialog"]
+__all__ = ["file_dialog"]
 import pathlib
 from typing import Any, Dict, Optional, Type, Union
 
@@ -253,4 +253,4 @@ def keypress(self, event):
                 p.update({"color": col, "facecolor": col})
 
 
-fileDialog: Type[App] = App()
+file_dialog: Type[App] = App()

scripts/VSManalysis_v2.py

@@ -102,7 +102,7 @@ def diamag_background_rem(data, N):
     min_harg = int(np.argmin(data[:, 1]))
 
     # linear fit to saturated data (+- N points from max/min field)
-    highFit = np.polyfit(
+    high_fit = np.polyfit(
         data[max_harg - N : max_harg + N, 1],
         data[max_harg - N : max_harg + N, 2],
         1,
@@ -113,7 +113,7 @@ def diamag_background_rem(data, N):
         1,
     )
     # Average grad
-    fit_grad = (highFit[0] + low_fit[0]) / 2
+    fit_grad = (high_fit[0] + low_fit[0]) / 2
     # Delete linear grad from all data
     data[:, 2] = data[:, 2] - (fit_grad * data[:, 1])
     return data
@@ -128,7 +128,7 @@ def invert(data):
     return data
 
 
-def makeTruem(data):
+def make_true_m(data):
     """VSM takes m from lock in X, this takes m from lock in R, useful if theta!=0."""
     vsm_calibration = (
         data.data[5, data.find_col("m (emu)")]
@@ -141,7 +141,7 @@ def makeTruem(data):
     return data
 
 
-def plotmH(data):
+def plot_m_h(data):
     """Take a stoner type data source."""
     plot.clf()
     plot.xlabel("H(T)")
@@ -157,9 +157,9 @@ def split_filename(my_filename):
     """
     for i in range(len(my_filename) - 1, -1, -1):
         if my_filename[i] == ".":
-            fileName = my_filename[:i]
-            fileExt = my_filename[i:]
-            return [fileName, fileExt]
+            filename = my_filename[:i]
+            file_ext = my_filename[i:]
+            return [filename, file_ext]
     return [my_filename, ""]
 
 
@@ -169,7 +169,7 @@ def edit_data(data, operations):
         return data
     N = int(input("Input the number of saturated data points on each arm:   "))
     if 1 in operations:
-        data = makeTruem(data)
+        data = make_true_m(data)
     if 2 in operations:
         data.data = drift_eliminator(data.data, N)
     if 3 in operations:
@@ -234,7 +234,7 @@ def edit_data(data, operations):
                         break
         fw.close()
         while True:
-            plotmH(data)
+            plot_m_h(data)
             if "Original m (emu)" not in data.column_headers:
                 data.add_column(data.column("m (emu)"), "Original m (emu)")
             print(
@@ -250,13 +250,13 @@ def edit_data(data, operations):
                 "5.  Reflect graph in y axis \n",
             )
 
-            strOp = input("")
+            str_op = input("")
             operations = []  # array of options selected
-            for i in range(len(strOp.strip())):
-                operations.append(int(strOp[i]))
+            for i in range(len(str_op.strip())):
+                operations.append(int(str_op[i]))
             t = data.clone  # edit a copied array.
             t = edit_data(t, operations)
-            plotmH(t)
+            plot_m_h(t)
             what_next = input(
                 "Press enter to save changes, r to restart or q to quit the program:  "
             )

scripts/XMCD_Reduction.py

@@ -1,6 +1,6 @@
 """Simple XMCD Data reduction example."""
 
-# pylint: disable=invalid-name, redefined-outer-name
+# pylint: disable=invalid-name, redefined-outer-name,no-member
 import re
 
 import numpy as np
@@ -141,7 +141,7 @@ def collate(grp, trail, **kwargs):
 
 # Read the directory of data files and sort by run number
 fldr = DataFolder(directory, pattern=pattern, read_means=True)
-fldr.sort("run")
+fldr.sort("run")  # pylint: disable=no-member
 # Remove files outside of the run number range
 fldr.filterout(lambda f: f["run"] > endrun or f["run"] < startrun)
 # group the files by position, temperatures and polarisations

tests/Stoner/tools/test_widgets.py

@@ -60,14 +60,14 @@ def dummy(mode="getOpenFileName"):
     app = getattr(widgets, "App")
     setattr(app, "modes", modes)
 
-    assert widgets.fileDialog.open_dialog() == ret_pth
-    assert widgets.fileDialog.open_dialog(title="Test", start=".") == ret_pth
-    assert widgets.fileDialog.open_dialog(patterns={"*.bad": "Very bad files"}) == ret_pth
-    assert widgets.fileDialog.open_dialog(mode="OpenFiles") == [ret_pth]
-    assert widgets.fileDialog.open_dialog(mode="SaveFile") is None
-    assert widgets.fileDialog.open_dialog(mode="SelectDirectory") == ret_pth.parent
+    assert widgets.file_dialog.open_dialog() == ret_pth
+    assert widgets.file_dialog.open_dialog(title="Test", start=".") == ret_pth
+    assert widgets.file_dialog.open_dialog(patterns={"*.bad": "Very bad files"}) == ret_pth
+    assert widgets.file_dialog.open_dialog(mode="OpenFiles") == [ret_pth]
+    assert widgets.file_dialog.open_dialog(mode="SaveFile") is None
+    assert widgets.file_dialog.open_dialog(mode="SelectDirectory") == ret_pth.parent
     with pytest.raises(ValueError):
-        widgets.fileDialog.open_dialog(mode="Whateve")
+        widgets.file_dialog.open_dialog(mode="Whateve")
 
 
 def test_loader():