Merge pull request #187 from berquist/remove-more-python2

Remove remaining Python 2 support

.git-blame-ignore-revs

@@ -0,0 +1,15 @@
+# pyupgrade
+d2a29a2c36b92d1e77ac291a42ece5d8a455a69b
+0f081e455c6082b8f43bdc1ce8d03359e13cf5be
+fec69ce479a84bac8270b5f1c95ae6344c9f797a
+59dc3c129b40a7992b5d1fab5e5f04705662f71a
+2d7173ec9277da9eb59982c03c7a6e4e06a49759
+7cfe37c6e20df0417248451dd919aeabaed1349a
+b8563af7487d4ea9cda48d5beb49b7354feda5db
+26b7b0c40d317341168090353f85e87e1d9b9f51
+c2ffbb7204424f6af32bb8f150e86c8f51bd9eb9
+55f776114a9b5ef96d2504e1118ee74d75f34cc0
+160475c6680a33a0c57535e7275cc6dad473c4ef
+0419e92e29ecb98eec10cbd2534022563dbf44e5
+6048a44d34a9398bda910563f5f85f1a43714319
+328b8843108c427c6153d2e3e2bf32ce41682433

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+---
+fail_fast: false
+repos:
+  - repo: meta
+    hooks:
+      - id: check-hooks-apply
+      - id: check-useless-excludes
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      - id: check-yaml
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.16.0
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]
+  - repo: https://github.com/Mateusz-Grzelinski/actionlint-py
+    rev: "v1.7.1.15"
+    hooks:
+      - id: actionlint

docs/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # exdir documentation build configuration file, created by
 # sphinx-quickstart on Fri Feb  3 09:52:17 2017.

environment.yml

@@ -13,5 +13,4 @@ dependencies:
     - pytest
     - pytest-benchmark
     - h5py
-    - six
     - pandas

examples/axona_to_exdir.py

@@ -1,7 +1,3 @@
-from __future__ import division
-from __future__ import print_function
-from __future__ import with_statement
-
 import sys
 import quantities as pq
 import os
@@ -43,7 +39,7 @@ def parse_header_and_leave_cursor(file_handle):
         header += str(byte, 'latin-1')
 
         if not byte:
-            raise IOError("Hit end of file '" + eeg_filename + "'' before '" + search_string + "' found.")
+            raise OSError("Hit end of file '" + eeg_filename + "'' before '" + search_string + "' found.")
 
         if header[-len(search_string):] == search_string:
             break
@@ -88,7 +84,7 @@ def __init__(self, filename):
         if extension != ".set":
             raise ValueError("file extension must be '.set'")
 
-        with open(self._absolute_filename, "r") as f:
+        with open(self._absolute_filename) as f:
             text = f.read()
 
         params = parse_params(text)
@@ -118,7 +114,7 @@ def __init__(self, filename):
                 for i in range(num_chans):
                     channel_id = self._channel_count + i
                     channel_ids.append(channel_id)
-                    channel_names.append("channel_{}_group_{}_internal_{}".format(channel_id, group_id, i))
+                    channel_names.append(f"channel_{channel_id}_group_{group_id}_internal_{i}")
 
                 channel_index = {"group_id": group_id,
                                  "channel_names": np.array(channel_names, dtype="S"),
@@ -143,7 +139,7 @@ def __init__(self, filename):
     def _channel_gain(self, channel_group_index, channel_index):
         # TODO split into two functions, one for mapping and one for gain lookup
         global_channel_index = channel_group_index * 4 + channel_index
-        param_name = "gain_ch_{}".format(global_channel_index)
+        param_name = f"gain_ch_{global_channel_index}"
         return float(self._params[param_name])
 
     def read_epoch():
@@ -217,7 +213,7 @@ def read_tracking(self):
         # TODO store attributes, such as pixels_per_metre
         pos_filename = os.path.join(self._path, self._base_filename+".pos")
         if not os.path.exists(pos_filename):
-            raise IOError("'.pos' file not found:" + pos_filename)
+            raise OSError("'.pos' file not found:" + pos_filename)
 
         with open(pos_filename, "rb") as f:
             params = parse_header_and_leave_cursor(f)
@@ -296,7 +292,7 @@ def read_analogsignal(self,
                 elif file_type == "egf":
                     sample_count = int(params["num_EGF_samples"])
                 else:
-                    raise IOError("Unknown file type. Should be .eeg or .efg.")
+                    raise OSError("Unknown file type. Should be .eeg or .efg.")
 
                 sample_rate_split = params["sample_rate"].split(" ")
                 bytes_per_sample = params["bytes_per_sample"]
@@ -323,7 +319,7 @@ def read_analogsignal(self,
 
                     params["channel_id"] = eeg_original_channel_id
 
-                    gain = self._params["gain_ch_{}".format(eeg_final_channel_id)]
+                    gain = self._params[f"gain_ch_{eeg_final_channel_id}"]
 
                     signal = scale_analog_signal(data,
                                                  gain,
@@ -402,12 +398,12 @@ def set_subject_attrs():
     # TODO for each channel_group, create LFP
 
     for channel_index in axona_folder._channel_indexes:
-        channel_group = processing.create_group("channel_group_{}".format(channel_index["group_id"]))
+        channel_group = processing.create_group(f"channel_group_{channel_index['group_id']}")
         if len(channel_index["analogsignals"]) > 0:
             lfp = channel_group.create_group("LFP")
 
             for index, analog_signal in enumerate(channel_index["analogsignals"]):
-                lfp_timeseries = lfp.require_group("LFP_timeseries_{}".format(index))
+                lfp_timeseries = lfp.require_group(f"LFP_timeseries_{index}")
                 lfp_timeseries.attrs["num_samples"] = 1  # TODO
                 lfp_timeseries.attrs["starting_time"] = {
                     "value": 0.0,  # TODO
@@ -421,7 +417,7 @@ def set_subject_attrs():
             event_waveform = channel_group.create_group("EventWaveform")
 
             for index, spiketrain in enumerate(channel_index["spiketrains"]):
-                waveform_timeseries = event_waveform.create_group("waveform_timeseries_{}".format(index))
+                waveform_timeseries = event_waveform.create_group(f"waveform_timeseries_{index}")
                 waveform_timeseries.attrs["num_samples"] = spiketrain["num_spikes"]
                 waveform_timeseries.attrs["sample_length"] = spiketrain["samples_per_spike"]
                 waveform_timeseries.attrs["electrode_idx"] = channel_index["channel_ids"]

examples/exdirio.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 This is the implementation of the NEO IO for the exdir format.
 Depends on: scipy
@@ -11,9 +10,6 @@
          Mikkel E. Lepperød @CINPLA
 """
 
-from __future__ import division
-from __future__ import print_function
-from __future__ import with_statement
 
 import sys
 from neo.io.baseio import BaseIO

examples/usecase_exdir.py

@@ -42,7 +42,7 @@
         print(f[experiment]["voltage"])
         print("First voltage:", f[experiment]["voltage"][0])
     else:
-        print("No voltage values for: {}".format(experiment))
+        print(f"No voltage values for: {experiment}")
 
 
 

examples/usecase_h5py.py

@@ -47,7 +47,7 @@
         print(f[experiment]["voltage"])
         print("First voltage:", f[experiment]["voltage"][0])
     else:
-        print("No voltage values for: {}".format(experiment))
+        print(f"No voltage values for: {experiment}")
 
 
 

exdir/_version.py

@@ -1,4 +1,3 @@
-
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -114,7 +113,7 @@ def run_command(
             return None, None
     else:
         if verbose:
-            print("unable to find command, tried %s" % (commands,))
+            print(f"unable to find command, tried {commands}")
         return None, None
     stdout = process.communicate()[0].strip().decode()
     if process.returncode != 0:
@@ -162,7 +161,7 @@ def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
     # _version.py.
     keywords: Dict[str, str] = {}
     try:
-        with open(versionfile_abs, "r") as fobj:
+        with open(versionfile_abs) as fobj:
             for line in fobj:
                 if line.strip().startswith("git_refnames ="):
                     mo = re.search(r'=\s*"(.*)"', line)

exdir/core/__init__.py

@@ -1,5 +1,3 @@
- # -*- coding: utf-8 -*-
-
 """
 .. module:: exdir.core
 .. moduleauthor:: Svenn-Arne Dragly, Milad H. Mobarhan, Mikkel E. Lepperød, Simen Tennøe

exdir/core/attribute.py

@@ -179,8 +179,7 @@ def _open_or_create(self):
         return attrs
 
     def __iter__(self):
-        for key in self.keys():
-            yield key
+        yield from self.keys()
 
     @property
     def filename(self):
@@ -212,8 +211,8 @@ def __str__(self):
             return "<Attributes of closed Exdir object>"
         string = ""
         for key in self:
-            string += "{}: {},".format(key, self[key])
-        return "Attribute({}, {{{}}})".format(self.parent.name, string)
+            string += f"{key}: {self[key]},"
+        return f"Attribute({self.parent.name}, {{{string}}})"
 
     def _repr_html_(self):
         if self.file.io_mode == OpenMode.FILE_CLOSED:
@@ -223,5 +222,4 @@ def _repr_html_(self):
     def __repr__(self):
         if self.file.io_mode == OpenMode.FILE_CLOSED:
             return "<Attributes of closed Exdir object>"
-        return "Attributes of Exdir object '{}' at '{}'".format(
-            self.parent.name, id(self))
+        return f"Attributes of Exdir object '{self.parent.name}' at '{id(self)}'"

exdir/core/dataset.py

@@ -38,7 +38,7 @@ class Dataset(exob.Object):
         an existing dataset, which is different from the behavior in h5py.
     """
     def __init__(self, root_directory, parent_path, object_name, file):
-        super(Dataset, self).__init__(
+        super().__init__(
             root_directory=root_directory,
             parent_path=parent_path,
             object_name=object_name,
@@ -64,10 +64,10 @@ def __getitem__(self, args):
                 if ("required" in self.meta["plugins"][plugin_name]
                     and self.meta["plugins"][plugin_name]["required"] == True
                     and plugin_name not in enabled_plugins):
-                    raise Exception((
-                        "Plugin '{}' was used to write '{}', "
+                    raise Exception(
+                        f"Plugin '{plugin_name}' was used to write '{self.name}', "
                         "but is not enabled."
-                    ).format(plugin_name, self.name))
+                    )
 
         plugins = self.plugin_manager.dataset_plugins.read_order
 
@@ -113,13 +113,13 @@ def _reload_data(self):
             self.file._open_datasets[self.name] = self
         except ValueError as e:
             # Could be that it is a Git LFS file. Let's see if that is the case and warn if so.
-            with open(self.data_filename, "r", encoding="utf-8") as f:
+            with open(self.data_filename, encoding="utf-8") as f:
                 test_string = "version https://git-lfs.github.com/spec/v1"
                 contents = f.read(len(test_string))
                 if contents == test_string:
-                    raise IOError("The file '{}' is a Git LFS placeholder. "
+                    raise OSError(f"The file '{self.data_filename}' is a Git LFS placeholder. "
                         "Open the the Exdir File with the Git LFS plugin or run "
-                        "`git lfs fetch` first. ".format(self.data_filename))
+                        "`git lfs fetch` first. ")
                 else:
                     raise e
 
@@ -265,8 +265,7 @@ def __str__(self):
     def __repr__(self):
         if self.file.io_mode == OpenMode.FILE_CLOSED:
             return "<Closed Exdir Dataset>"
-        return "<Exdir Dataset {} shape {} dtype {}>".format(
-            self.name, self.shape, self.dtype)
+        return f"<Exdir Dataset {self.name} shape {self.shape} dtype {self.dtype}>"
 
     @property
     def _data(self):

exdir/core/exdir_file.py

@@ -1,13 +1,7 @@
 import os
 import shutil
 import weakref
-try:
-    import pathlib
-except ImportError as e:
-    try:
-        import pathlib2 as pathlib
-    except ImportError:
-        raise e
+import pathlib
 import warnings
 
 import exdir
@@ -78,8 +72,8 @@ def __init__(self, directory, mode=None, allow_remove=False,
         recognized_modes = ['a', 'r', 'r+', 'w', 'w-', 'x']
         if mode not in recognized_modes:
             raise ValueError(
-                "IO mode {} not recognized, "
-                "mode must be one of {}".format(mode, recognized_modes)
+                f"IO mode {mode} not recognized, "
+                f"mode must be one of {recognized_modes}"
             )
 
         self.plugin_manager = exdir.plugin_interface.plugin_interface.Manager(plugins)
@@ -97,9 +91,9 @@ def __init__(self, directory, mode=None, allow_remove=False,
                 name_validation = validation.none
             else:
                 raise ValueError(
-                    'IO name rule "{}" not recognized, '
+                    f'IO name rule "{name_validation}" not recognized, '
                     'name rule must be one of "strict", "simple", '
-                    '"thorough", "none"'.format(name_validation)
+                    '"thorough", "none"'
                 )
 
             warnings.warn(
@@ -126,7 +120,7 @@ def __init__(self, directory, mode=None, allow_remove=False,
         if already_exists:
             if not exob.is_nonraw_object_directory(directory):
                 raise RuntimeError(
-                    "Path '{}' already exists, but is not a valid exdir file.".format(directory)
+                    f"Path '{directory}' already exists, but is not a valid exdir file."
                 )
 
         should_create_directory = False
@@ -143,8 +137,8 @@ def __init__(self, directory, mode=None, allow_remove=False,
                     shutil.rmtree(str(directory))  # NOTE str needed for Python 3.5
                 else:
                     raise RuntimeError(
-                        "File {} already exists. We won't delete the entire tree "
-                        "by default. Add allow_remove=True to override.".format(directory)
+                        f"File {directory} already exists. We won't delete the entire tree "
+                        "by default. Add allow_remove=True to override."
                     )
             should_create_directory = True
         elif mode == "w-" or mode == "x":
@@ -227,5 +221,4 @@ def __contains__(self, name):
     def __repr__(self):
         if self.io_mode == OpenMode.FILE_CLOSED:
             return "<Closed Exdir File>"
-        return "<Exdir File '{}' (mode {})>".format(
-            self.directory, self.user_mode)
+        return f"<Exdir File '{self.directory}' (mode {self.user_mode})>"