From 4789dc6efa1f44901b3131eb3e38b205a177c737 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 11:22:33 -0400 Subject: [PATCH 01/17] remove references to pathlib2 --- exdir/core/exdir_file.py | 8 +------- exdir/core/group.py | 8 +------- exdir/plugins/git_lfs.py | 8 +------- exdir/utils/display.py | 8 +------- tests/conftest.py | 8 +------- tests/test_file.py | 9 +-------- tests/test_group.py | 8 +------- tests/test_help_functions.py | 9 +-------- tests/test_object.py | 8 +------- tests/test_raw.py | 8 +------- 10 files changed, 10 insertions(+), 72 deletions(-) diff --git a/exdir/core/exdir_file.py b/exdir/core/exdir_file.py index ebca14c..3584820 100644 --- a/exdir/core/exdir_file.py +++ b/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 diff --git a/exdir/core/group.py b/exdir/core/group.py index 44b8c31..b01d7b2 100644 --- a/exdir/core/group.py +++ b/exdir/core/group.py @@ -1,12 +1,6 @@ import os import re -try: - import pathlib -except ImportError as e: - try: - import pathlib2 as pathlib - except ImportError: - raise e +import pathlib import numpy as np import exdir try: diff --git a/exdir/plugins/git_lfs.py b/exdir/plugins/git_lfs.py index 2e4f9d8..c083d2c 100644 --- a/exdir/plugins/git_lfs.py +++ b/exdir/plugins/git_lfs.py @@ -1,12 +1,6 @@ import subprocess import exdir.plugin_interface -try: - import pathlib -except ImportError as e: - try: - import pathlib2 as pathlib - except ImportError: - raise e +import pathlib import sys class DatasetPlugin(exdir.plugin_interface.Dataset): diff --git a/exdir/utils/display.py b/exdir/utils/display.py index d4bf491..2c9299e 100644 --- a/exdir/utils/display.py +++ b/exdir/utils/display.py @@ -1,10 +1,4 @@ -try: - import pathlib -except ImportError as e: - try: - import pathlib2 as pathlib - except ImportError: - raise e +import pathlib import exdir diff --git a/tests/conftest.py b/tests/conftest.py index d2c17b9..bc7a428 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -4,13 +4,7 @@ import shutil import os import h5py -try: - import pathlib -except ImportError as e: - try: - import pathlib2 as pathlib - except ImportError: - raise e +import pathlib import time import exdir diff --git a/tests/test_file.py b/tests/test_file.py index 12d80d6..4ee1788 100644 --- a/tests/test_file.py +++ b/tests/test_file.py @@ -13,14 +13,7 @@ import pytest -import os -try: - import pathlib -except ImportError as e: - try: - import pathlib2 as pathlib - except ImportError: - raise e +import pathlib from exdir.core import File, Group from exdir.core.exdir_object import _create_object_directory, is_nonraw_object_directory, DATASET_TYPENAME, FILE_TYPENAME diff --git a/tests/test_group.py b/tests/test_group.py index 138f35d..9ec5e68 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -14,13 +14,7 @@ import os import pytest -try: - import pathlib -except ImportError as e: - try: - import pathlib2 as pathlib - except ImportError: - raise e +import pathlib import numpy as np try: from collections.abc import KeysView, ValuesView, ItemsView diff --git a/tests/test_help_functions.py b/tests/test_help_functions.py index 8297a8d..9653a1a 100644 --- a/tests/test_help_functions.py +++ b/tests/test_help_functions.py @@ -1,13 +1,6 @@ # -*- coding: utf-8 -*- -import os -try: - import pathlib -except ImportError as e: - try: - import pathlib2 as pathlib - except ImportError: - raise e +import pathlib import six import quantities as pq import numpy as np diff --git a/tests/test_object.py b/tests/test_object.py index 43abce2..f722287 100644 --- a/tests/test_object.py +++ b/tests/test_object.py @@ -14,13 +14,7 @@ import pytest import os -try: - import pathlib -except ImportError as e: - try: - import pathlib2 as pathlib - except ImportError: - raise e +import pathlib import exdir try: import ruamel_yaml as yaml diff --git a/tests/test_raw.py b/tests/test_raw.py index f3def31..8a9e068 100644 --- a/tests/test_raw.py +++ b/tests/test_raw.py @@ -1,12 +1,6 @@ import os import pytest -try: - import pathlib -except ImportError as e: - try: - import pathlib2 as pathlib - except ImportError: - raise e +import pathlib from exdir.core import Raw def test_raw_init(setup_teardown_folder): From a11e896448000ff8e6e27e90f292b3b8f7dc80db Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 11:24:52 -0400 Subject: [PATCH 02/17] remove __future__ imports --- examples/axona_to_exdir.py | 4 ---- examples/exdirio.py | 3 --- exdir/plugins/quantities.py | 3 --- tests/conftest.py | 2 -- 4 files changed, 12 deletions(-) diff --git a/examples/axona_to_exdir.py b/examples/axona_to_exdir.py index 32a71d8..579e238 100644 --- a/examples/axona_to_exdir.py +++ b/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 diff --git a/examples/exdirio.py b/examples/exdirio.py index f05c541..c08c466 100644 --- a/examples/exdirio.py +++ b/examples/exdirio.py @@ -11,9 +11,6 @@ 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 diff --git a/exdir/plugins/quantities.py b/exdir/plugins/quantities.py index a7455e6..53bbd34 100644 --- a/exdir/plugins/quantities.py +++ b/exdir/plugins/quantities.py @@ -1,6 +1,3 @@ -# Needed for quantities -from __future__ import absolute_import - import exdir import quantities as pq import numpy as np diff --git a/tests/conftest.py b/tests/conftest.py index bc7a428..b33681d 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,5 +1,3 @@ -from __future__ import print_function - import pytest import shutil import os From b418221971c27cc332ca6c8132cf9b656cdd958e Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:30:03 -0400 Subject: [PATCH 03/17] remove coding pragmas --- docs/conf.py | 1 - examples/exdirio.py | 1 - exdir/_version.py | 1 - exdir/core/__init__.py | 2 -- setup.py | 1 - tests/test_attr.py | 2 -- tests/test_dataset.py | 2 -- tests/test_file.py | 1 - tests/test_group.py | 1 - tests/test_help_functions.py | 2 -- tests/test_object.py | 1 - tests/test_plugins.py | 1 - tests/test_quantities.py | 1 - versioneer.py | 1 - 14 files changed, 18 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index e961b4a..ee35a87 100644 --- a/docs/conf.py +++ b/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. diff --git a/examples/exdirio.py b/examples/exdirio.py index c08c466..aa8b482 100644 --- a/examples/exdirio.py +++ b/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 diff --git a/exdir/_version.py b/exdir/_version.py index 6bb9041..0a07164 100644 --- a/exdir/_version.py +++ b/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 diff --git a/exdir/core/__init__.py b/exdir/core/__init__.py index 474ff48..b79694c 100644 --- a/exdir/core/__init__.py +++ b/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 diff --git a/setup.py b/setup.py index 6ee434a..c2c9b06 100644 --- a/setup.py +++ b/setup.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- from setuptools import setup import os diff --git a/tests/test_attr.py b/tests/test_attr.py index fb1f41b..7512de7 100644 --- a/tests/test_attr.py +++ b/tests/test_attr.py @@ -1,5 +1,3 @@ -# -*- coding: utf-8 -*- - # This file is part of Exdir, the Experimental Directory Structure. # # Copyright 2017 Simen Tennøe diff --git a/tests/test_dataset.py b/tests/test_dataset.py index 16ddedd..3a43310 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -1,5 +1,3 @@ -# -*- coding: utf-8 -*- - # This file is part of Exdir, the Experimental Directory Structure. # # Copyright 2017 Simen Tennøe diff --git a/tests/test_file.py b/tests/test_file.py index 4ee1788..0b42cba 100644 --- a/tests/test_file.py +++ b/tests/test_file.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # # This file is part of Exdir, the Experimental Directory Structure. # diff --git a/tests/test_group.py b/tests/test_group.py index 9ec5e68..e4df2a0 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # # This file is part of Exdir, the Experimental Directory Structure. # diff --git a/tests/test_help_functions.py b/tests/test_help_functions.py index 9653a1a..f32d797 100644 --- a/tests/test_help_functions.py +++ b/tests/test_help_functions.py @@ -1,5 +1,3 @@ -# -*- coding: utf-8 -*- - import pathlib import six import quantities as pq diff --git a/tests/test_object.py b/tests/test_object.py index f722287..7b80489 100644 --- a/tests/test_object.py +++ b/tests/test_object.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # # This file is part of Exdir, the Experimental Directory Structure. # diff --git a/tests/test_plugins.py b/tests/test_plugins.py index b9b3ea8..199d49c 100644 --- a/tests/test_plugins.py +++ b/tests/test_plugins.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # # This file is part of Exdir, the Experimental Directory Structure. # diff --git a/tests/test_quantities.py b/tests/test_quantities.py index d2e0878..3fb0273 100644 --- a/tests/test_quantities.py +++ b/tests/test_quantities.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # # This file is part of Exdir, the Experimental Directory Structure. # diff --git a/versioneer.py b/versioneer.py index 1e3753e..5fe1f4d 100644 --- a/versioneer.py +++ b/versioneer.py @@ -1,4 +1,3 @@ - # Version: 0.29 """The Versioneer - like a rocketeer, but for versions. From e1d0fde51d263c1d3679eb2bc7c2acd8a1e04068 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 11:31:04 -0400 Subject: [PATCH 04/17] remove redundant open modes --- examples/axona_to_exdir.py | 2 +- exdir/_version.py | 2 +- exdir/core/dataset.py | 2 +- tests/test_numpy_attributes.py | 6 +++--- versioneer.py | 8 ++++---- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/examples/axona_to_exdir.py b/examples/axona_to_exdir.py index 579e238..ed79e34 100644 --- a/examples/axona_to_exdir.py +++ b/examples/axona_to_exdir.py @@ -84,7 +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) diff --git a/exdir/_version.py b/exdir/_version.py index 0a07164..d305b28 100644 --- a/exdir/_version.py +++ b/exdir/_version.py @@ -161,7 +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) diff --git a/exdir/core/dataset.py b/exdir/core/dataset.py index 7f5e6ca..d5040ac 100644 --- a/exdir/core/dataset.py +++ b/exdir/core/dataset.py @@ -113,7 +113,7 @@ 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: diff --git a/tests/test_numpy_attributes.py b/tests/test_numpy_attributes.py index b9df35a..47872c2 100644 --- a/tests/test_numpy_attributes.py +++ b/tests/test_numpy_attributes.py @@ -12,7 +12,7 @@ def test_simple(setup_teardown_folder): f.attrs["array"] = np.array([1, 2, 3]) f.close() - with open(str(setup_teardown_folder[1] / "attributes.yaml"), "r", encoding="utf-8") as f: + with open(str(setup_teardown_folder[1] / "attributes.yaml"), encoding="utf-8") as f: content = "array:\n- 1\n- 2\n- 3\n" assert content == f.read() @@ -23,7 +23,7 @@ def test_with_quantities(setup_teardown_folder): f.attrs["array"] = np.array([1, 2, 3]) * pq.m f.close() - with open(str(setup_teardown_folder[1] / "attributes.yaml"), "r", encoding="utf-8") as f: + with open(str(setup_teardown_folder[1] / "attributes.yaml"), encoding="utf-8") as f: content = 'array:\n value:\n - 1.0\n - 2.0\n - 3.0\n unit: "m"\n' # NOTE split and conversion to set is just because the order of the items is not important @@ -35,7 +35,7 @@ def test_with_quantities_reverse_order(setup_teardown_folder): f.attrs["array"] = np.array([1, 2, 3]) * pq.m f.close() - with open(str(setup_teardown_folder[1] / "attributes.yaml"), "r") as f: + with open(str(setup_teardown_folder[1] / "attributes.yaml")) as f: content = 'array:\n value:\n - 1.0\n - 2.0\n - 3.0\n unit: "m"\n' # NOTE split and conversion to set is just because the order of the items is not important diff --git a/versioneer.py b/versioneer.py index 5fe1f4d..6ab1bc7 100644 --- a/versioneer.py +++ b/versioneer.py @@ -1199,7 +1199,7 @@ 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) @@ -1447,7 +1447,7 @@ def do_vcs_install(versionfile_source: str, ipy: Optional[str]) -> None: files.append(versioneer_file) present = False try: - with open(".gitattributes", "r") as fobj: + with open(".gitattributes") as fobj: for line in fobj: if line.strip().startswith(versionfile_source): if "export-subst" in line.strip().split()[1:]: @@ -2199,7 +2199,7 @@ def do_setup() -> int: maybe_ipy: Optional[str] = ipy if os.path.exists(ipy): try: - with open(ipy, "r") as f: + with open(ipy) as f: old = f.read() except OSError: old = "" @@ -2231,7 +2231,7 @@ def scan_setup_py() -> int: found = set() setters = False errors = 0 - with open("setup.py", "r") as f: + with open("setup.py") as f: for line in f.readlines(): if "import versioneer" in line: found.add("import") From 26a2b6412296323fe09f435d6516a4d65c33ca96 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 11:41:57 -0400 Subject: [PATCH 05/17] remove dependence on six --- environment.yml | 1 - setup.py | 1 - tests/test_attr.py | 10 +++++----- tests/test_help_functions.py | 7 +++---- 4 files changed, 8 insertions(+), 11 deletions(-) diff --git a/environment.yml b/environment.yml index b77bd4b..fd7348e 100644 --- a/environment.yml +++ b/environment.yml @@ -13,5 +13,4 @@ dependencies: - pytest - pytest-benchmark - h5py - - six - pandas diff --git a/setup.py b/setup.py index c2c9b06..c6e21af 100644 --- a/setup.py +++ b/setup.py @@ -37,7 +37,6 @@ install_requires=[ "numpy>=1.20", "ruamel.yaml==0.17.21", - "six>=1.15", ], zip_safe=False, ) diff --git a/tests/test_attr.py b/tests/test_attr.py index 7512de7..d015b3f 100644 --- a/tests/test_attr.py +++ b/tests/test_attr.py @@ -18,7 +18,7 @@ import ruamel.yaml as yaml from exdir.core import Attribute, File -import six + def test_attr_init(): attribute = Attribute("parent", "mode", "file") @@ -212,7 +212,7 @@ def test_unicode(setup_teardown_file): """Access via Unicode string with non-ascii characters.""" f = setup_teardown_file[3] - name = six.u("Omega") + six.unichr(0x03A9) + name = "Omega" + chr(0x03A9) f.attrs[name] = 42 out = f.attrs[name] assert out == 42 @@ -250,10 +250,10 @@ def test_unicode_scalar(setup_teardown_file): """Storage of variable-length unicode strings (auto-creation).""" f = setup_teardown_file[3] - f.attrs["x"] = six.u("Hello") + six.unichr(0x2340) + six.u("!!") + f.attrs["x"] = "Hello" + chr(0x2340) + "!!" out = f.attrs["x"] - assert out == six.u("Hello") + six.unichr(0x2340) + six.u("!!") - assert type(out) == six.text_type + assert isinstance(out, str) + assert out == "Hello" + chr(0x2340) + "!!" def test_attrs(setup_teardown_file): diff --git a/tests/test_help_functions.py b/tests/test_help_functions.py index f32d797..f7b54c6 100644 --- a/tests/test_help_functions.py +++ b/tests/test_help_functions.py @@ -1,5 +1,4 @@ import pathlib -import six import quantities as pq import numpy as np import pytest @@ -27,7 +26,7 @@ def test_assert_valid_name_minimal(setup_teardown_folder): with pytest.raises(NameError): exob._assert_valid_name("\n", f) - exob._assert_valid_name(six.unichr(0x4500), f) + exob._assert_valid_name(chr(0x4500), f) with pytest.raises(NameError): exob._assert_valid_name(exob.META_FILENAME, f) @@ -51,7 +50,7 @@ def test_assert_valid_name_thorough(setup_teardown_folder): exob._assert_valid_name("\n", f) with pytest.raises(NameError): - exob._assert_valid_name(six.unichr(0x4500), f) + exob._assert_valid_name(chr(0x4500), f) with pytest.raises(NameError): exob._assert_valid_name(exob.META_FILENAME, f) @@ -78,7 +77,7 @@ def test_assert_valid_name_none(setup_teardown_folder): invalid_name = "\n" exob._assert_valid_name(invalid_name, f) - invalid_name = six.unichr(0x4500) + invalid_name = chr(0x4500) exob._assert_valid_name(invalid_name, f) exob._assert_valid_name(exob.META_FILENAME, f) From d6edd0b44320ba62e27059c5aa9194e246e8c678 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 11:48:48 -0400 Subject: [PATCH 06/17] IOError is now just an alias for OSError --- examples/axona_to_exdir.py | 6 +++--- exdir/core/dataset.py | 2 +- exdir/core/exdir_object.py | 4 ++-- exdir/core/group.py | 2 +- exdir/core/mode.py | 6 +++--- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/examples/axona_to_exdir.py b/examples/axona_to_exdir.py index ed79e34..376b29b 100644 --- a/examples/axona_to_exdir.py +++ b/examples/axona_to_exdir.py @@ -39,7 +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 @@ -213,7 +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) @@ -292,7 +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"] diff --git a/exdir/core/dataset.py b/exdir/core/dataset.py index d5040ac..dac8be5 100644 --- a/exdir/core/dataset.py +++ b/exdir/core/dataset.py @@ -117,7 +117,7 @@ def _reload_data(self): 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("The file '{}' 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)) else: diff --git a/exdir/core/exdir_object.py b/exdir/core/exdir_object.py index 41a768e..d3d2dd5 100644 --- a/exdir/core/exdir_object.py +++ b/exdir/core/exdir_object.py @@ -28,7 +28,7 @@ def _create_object_directory(directory, metadata): don't already exist. """ if directory.exists(): - raise IOError("The directory '" + str(directory) + "' already exists") + raise OSError("The directory '" + str(directory) + "' already exists") valid_types = [DATASET_TYPENAME, FILE_TYPENAME, GROUP_TYPENAME] typename = metadata[EXDIR_METANAME][TYPE_METANAME] if typename not in valid_types: @@ -67,7 +67,7 @@ def _remove_object_directory(directory): Remove object directory and meta file if directory exist. """ if not directory.exists(): - raise IOError("The directory '" + str(directory) + "' does not exist") + raise OSError("The directory '" + str(directory) + "' does not exist") assert is_inside_exdir(directory) shutil.rmtree(directory) diff --git a/exdir/core/group.py b/exdir/core/group.py index b01d7b2..58114a3 100644 --- a/exdir/core/group.py +++ b/exdir/core/group.py @@ -389,7 +389,7 @@ def __getitem__(self, name): ) if not exob.is_nonraw_object_directory(directory): - raise IOError( + raise OSError( "Directory '" + directory + "' is not a valid exdir object." ) diff --git a/exdir/core/mode.py b/exdir/core/mode.py index c86cd1f..24b277c 100644 --- a/exdir/core/mode.py +++ b/exdir/core/mode.py @@ -12,7 +12,7 @@ def assert_file_open(file_object): Decorator to check if the file is not closed. """ if file_object.io_mode == OpenMode.FILE_CLOSED: - raise IOError("Unable to operate on closed File instance.") + raise OSError("Unable to operate on closed File instance.") def assert_file_writable(file_object): @@ -21,6 +21,6 @@ def assert_file_writable(file_object): and that it is not in read only mode. """ if file_object.io_mode == OpenMode.FILE_CLOSED: - raise IOError("Unable to operate on closed File instance.") + raise OSError("Unable to operate on closed File instance.") if file_object.io_mode == OpenMode.READ_ONLY: - raise IOError("Cannot change data on file in read only 'r' mode") + raise OSError("Cannot change data on file in read only 'r' mode") From 61be04681f84c28e83e5af7e6b598f43af08d7e9 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 11:49:53 -0400 Subject: [PATCH 07/17] update super calls --- exdir/core/dataset.py | 2 +- exdir/core/group.py | 2 +- exdir/core/raw.py | 2 +- exdir/plugins/git_lfs.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/exdir/core/dataset.py b/exdir/core/dataset.py index dac8be5..b803740 100644 --- a/exdir/core/dataset.py +++ b/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, diff --git a/exdir/core/group.py b/exdir/core/group.py index 58114a3..5606b9d 100644 --- a/exdir/core/group.py +++ b/exdir/core/group.py @@ -56,7 +56,7 @@ def __init__(self, root_directory, parent_path, object_name, file): """ WARNING: Internal. Should only be called from require_group. """ - super(Group, self).__init__( + super().__init__( root_directory=root_directory, parent_path=parent_path, object_name=object_name, diff --git a/exdir/core/raw.py b/exdir/core/raw.py index f60aee3..42821cc 100644 --- a/exdir/core/raw.py +++ b/exdir/core/raw.py @@ -8,7 +8,7 @@ class Raw(exob.Object): Raw objects currently have no features apart from showing their path. """ def __init__(self, root_directory, parent_path, object_name, file): - super(Raw, self).__init__( + super().__init__( root_directory=root_directory, parent_path=parent_path, object_name=object_name, diff --git a/exdir/plugins/git_lfs.py b/exdir/plugins/git_lfs.py index c083d2c..d73268c 100644 --- a/exdir/plugins/git_lfs.py +++ b/exdir/plugins/git_lfs.py @@ -37,7 +37,7 @@ def before_load(self, dataset_path): class Plugin(exdir.plugin_interface.Plugin): def __init__(self, verbose=False): - super(Plugin, self).__init__("git_lfs", dataset_plugins=[DatasetPlugin(verbose)]) + super().__init__("git_lfs", dataset_plugins=[DatasetPlugin(verbose)]) def plugins(): return _plugins(verbose=False) From 01f54236a9f2184978f7bff013e200f9b64b5e51 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 11:54:56 -0400 Subject: [PATCH 08/17] use f-strings --- examples/axona_to_exdir.py | 10 +++++----- examples/usecase_exdir.py | 2 +- examples/usecase_h5py.py | 2 +- exdir/_version.py | 2 +- exdir/core/attribute.py | 4 ++-- exdir/core/exdir_file.py | 2 +- exdir/core/exdir_object.py | 6 +++--- exdir/core/group.py | 4 ++-- exdir/core/validation.py | 6 +++--- exdir/plugins/git_lfs.py | 2 +- exdir/utils/display.py | 12 ++++++------ tests/benchmarks/benchmarks.py | 6 +++--- tests/benchmarks/profiling.py | 2 +- tests/test_dataset.py | 4 ++-- versioneer.py | 6 +++--- 15 files changed, 35 insertions(+), 35 deletions(-) diff --git a/examples/axona_to_exdir.py b/examples/axona_to_exdir.py index 376b29b..4770818 100644 --- a/examples/axona_to_exdir.py +++ b/examples/axona_to_exdir.py @@ -114,7 +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"), @@ -139,7 +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(): @@ -319,7 +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, @@ -403,7 +403,7 @@ def set_subject_attrs(): 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 @@ -417,7 +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"] diff --git a/examples/usecase_exdir.py b/examples/usecase_exdir.py index 386623d..f2899a3 100644 --- a/examples/usecase_exdir.py +++ b/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}") diff --git a/examples/usecase_h5py.py b/examples/usecase_h5py.py index 9c2d302..50bd608 100644 --- a/examples/usecase_h5py.py +++ b/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}") diff --git a/exdir/_version.py b/exdir/_version.py index d305b28..a0e92bf 100644 --- a/exdir/_version.py +++ b/exdir/_version.py @@ -113,7 +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: diff --git a/exdir/core/attribute.py b/exdir/core/attribute.py index 8febf40..76bd636 100644 --- a/exdir/core/attribute.py +++ b/exdir/core/attribute.py @@ -212,8 +212,8 @@ def __str__(self): return "" 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: diff --git a/exdir/core/exdir_file.py b/exdir/core/exdir_file.py index 3584820..0ca7542 100644 --- a/exdir/core/exdir_file.py +++ b/exdir/core/exdir_file.py @@ -120,7 +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 diff --git a/exdir/core/exdir_object.py b/exdir/core/exdir_object.py index d3d2dd5..bd41eb4 100644 --- a/exdir/core/exdir_object.py +++ b/exdir/core/exdir_object.py @@ -32,7 +32,7 @@ def _create_object_directory(directory, metadata): valid_types = [DATASET_TYPENAME, FILE_TYPENAME, GROUP_TYPENAME] typename = metadata[EXDIR_METANAME][TYPE_METANAME] if typename not in valid_types: - raise ValueError("{typename} is not a valid typename".format(typename=typename)) + raise ValueError(f"{typename} is not a valid typename") directory.mkdir() meta_filename = directory / META_FILENAME with meta_filename.open("w", encoding="utf-8") as meta_file: @@ -229,7 +229,7 @@ def create_raw(self, name): _assert_valid_name(name, self) directory_name = self.directory / name if directory_name.exists(): - raise FileExistsError("'{}' already exists in '{}'".format(name, self)) + raise FileExistsError(f"'{name}' already exists in '{self}'") directory_name.mkdir() return Raw( root_directory=self.root_directory, @@ -245,7 +245,7 @@ def require_raw(self, name): if directory_name.exists(): if is_nonraw_object_directory(directory_name): raise FileExistsError( - "Directory '{}' already exists, but is not raw.".format(directory_name) + f"Directory '{directory_name}' already exists, but is not raw." ) return Raw( root_directory=self.root_directory, diff --git a/exdir/core/group.py b/exdir/core/group.py index 5606b9d..f8566bd 100644 --- a/exdir/core/group.py +++ b/exdir/core/group.py @@ -181,7 +181,7 @@ def create_group(self, name): if name in self: raise FileExistsError( - "'{}' already exists in '{}'".format(name, self.name) + f"'{name}' already exists in '{self.name}'" ) group_directory = self.directory / path @@ -443,7 +443,7 @@ def __setitem__(self, name, value): if not isinstance(self[name], ds.Dataset): raise RuntimeError( - "Unable to assign value, {} already exists".format(name) + f"Unable to assign value, {name} already exists" ) self[name].value = value diff --git a/exdir/core/validation.py b/exdir/core/validation.py index 2b4b850..8bdd325 100644 --- a/exdir/core/validation.py +++ b/exdir/core/validation.py @@ -42,7 +42,7 @@ def _assert_unique(parent_path, name): if (parent_path / name).exists(): raise RuntimeError( - "'{}' already exists in '{}'".format(name, parent_path) + f"'{name}' already exists in '{parent_path}'" ) @@ -71,12 +71,12 @@ def _assert_nonreserved(name): if name_str in reserved_names: raise NameError( - "Name cannot be '{}' because it is a reserved filename in Exdir.".format(name_str) + f"Name cannot be '{name_str}' because it is a reserved filename in Exdir." ) if _is_reserved(name_str): raise NameError( - "Name cannot be '{}' because it is a reserved filename in Windows.".format(name_str) + f"Name cannot be '{name_str}' because it is a reserved filename in Windows." ) def _assert_valid_characters(name): diff --git a/exdir/plugins/git_lfs.py b/exdir/plugins/git_lfs.py index d73268c..0cd5657 100644 --- a/exdir/plugins/git_lfs.py +++ b/exdir/plugins/git_lfs.py @@ -19,7 +19,7 @@ def before_load(self, dataset_path): git_path = pathlib.Path(git_path.decode('utf-8').rstrip()) relative_path = path.relative_to(git_path) if self.verbose: - print("Fetching Git LFS object for {}".format(relative_path)) + print(f"Fetching Git LFS object for {relative_path}") command = ['git', '-c', 'lfs.fetchexclude=""', 'lfs', 'pull', '-I', str(relative_path)] process = subprocess.Popen(command, cwd=str(git_path), stdout=subprocess.PIPE, stderr=subprocess.PIPE) if self.verbose: diff --git a/exdir/utils/display.py b/exdir/utils/display.py index 2c9299e..8124d32 100644 --- a/exdir/utils/display.py +++ b/exdir/utils/display.py @@ -9,9 +9,9 @@ def _build_tree(o): else: name = o.object_name - contents += "{} ({})".format(name, o.__class__.__name__) + contents += f"{name} ({o.__class__.__name__})" if isinstance(o, exdir.core.Dataset): - contents += "
  • Shape: {}
  • Type: {}
".format(o.shape, o.dtype) + contents += f"
  • Shape: {o.shape}
  • Type: {o.dtype}
" else: try: keys = o.keys() @@ -19,7 +19,7 @@ def _build_tree(o): for a in keys: inner_contents += _build_tree(o[a]) if inner_contents != "": - contents += "
    {}
".format(inner_contents) + contents += f"
    {inner_contents}
" except AttributeError: pass @@ -65,16 +65,16 @@ def html_tree(obj): def _build_attrs_tree(key, value): contents = "
  • " - contents += "{}: ".format(key) + contents += f"{key}: " try: items = value.items() inner_contents = "" for subkey, subvalue in items: inner_contents += _build_attrs_tree(subkey, subvalue) if inner_contents != "": - contents += "
      {}
    ".format(inner_contents) + contents += f"
      {inner_contents}
    " except AttributeError: - contents += "{}".format(value) + contents += f"{value}" contents += "
    • " diff --git a/tests/benchmarks/benchmarks.py b/tests/benchmarks/benchmarks.py index a03e709..caebeee 100644 --- a/tests/benchmarks/benchmarks.py +++ b/tests/benchmarks/benchmarks.py @@ -139,7 +139,7 @@ def add_large_dataset(obj): def create_many_objects(obj): for i in range(5000): - group = obj.create_group("group{}".format(i)) + group = obj.create_group(f"group{i}") # data = np.zeros((10, 10, 10)) # group.create_dataset("dataset{}".format(i), data=data) @@ -155,9 +155,9 @@ def create_large_tree(obj, level=0): if level > 4: return for i in range(3): - group = obj.create_group("group_{}_{}".format(i, level)) + group = obj.create_group(f"group_{i}_{level}") data = np.zeros((10, 10, 10)) - group.create_dataset("dataset_{}_{}".format(i, level), data=data) + group.create_dataset(f"dataset_{i}_{level}", data=data) create_large_tree(group, level + 1) diff --git a/tests/benchmarks/profiling.py b/tests/benchmarks/profiling.py index 7e10f18..b789118 100644 --- a/tests/benchmarks/profiling.py +++ b/tests/benchmarks/profiling.py @@ -18,4 +18,4 @@ def setup_exdir(): obj = setup_exdir()[0] for i in range(5000): - group = obj.create_group("group{}".format(i)) + group = obj.create_group(f"group{i}") diff --git a/tests/test_dataset.py b/tests/test_dataset.py index 3a43310..ffadee2 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -568,7 +568,7 @@ def test_slice_zero_length_dimension(setup_teardown_file): f = setup_teardown_file[3] for i, shape in enumerate([(0,), (0, 3), (0, 2, 1)]): - dset = f.create_dataset('x%d'%i, shape, dtype=np.int32) + dset = f.create_dataset(f"x{i}", shape, dtype=np.int32) assert dset.shape == shape out = dset[...] assert isinstance(out, np.ndarray) @@ -587,7 +587,7 @@ def test_slice_other_dimension(setup_teardown_file): f = setup_teardown_file[3] for i, shape in enumerate([(3, 0), (1, 2, 0), (2, 0, 1)]): - dset = f.create_dataset('x%d'%i, shape, dtype=np.int32) + dset = f.create_dataset(f"x{i}", shape, dtype=np.int32) assert dset.shape == shape out = dset[:1] assert isinstance(out, np.ndarray) diff --git a/versioneer.py b/versioneer.py index 6ab1bc7..8d7359c 100644 --- a/versioneer.py +++ b/versioneer.py @@ -493,7 +493,7 @@ 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: @@ -1532,7 +1532,7 @@ def write_to_version_file(filename: str, versions: Dict[str, Any]) -> None: with open(filename, "w") as f: f.write(SHORT_VERSION_PY % contents) - print("set %s to '%s'" % (filename, versions["version"])) + print("set {} to '{}'".format(filename, versions["version"])) def plus_or_dot(pieces: Dict[str, Any]) -> str: @@ -1832,7 +1832,7 @@ def get_versions(verbose: bool = False) -> Dict[str, Any]: try: ver = versions_from_file(versionfile_abs) if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) + print(f"got version from file {versionfile_abs} {ver}") return ver except NotThisMethod: pass From 49b7914d31248be723b9f6cfebdd607184307ecc Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:11:45 -0400 Subject: [PATCH 09/17] use f-strings --- examples/axona_to_exdir.py | 2 +- exdir/core/attribute.py | 3 +-- exdir/core/dataset.py | 11 +++++----- exdir/core/exdir_file.py | 15 ++++++------- exdir/core/exdir_object.py | 23 +++++-------------- exdir/core/group.py | 40 +++++++++++----------------------- exdir/core/validation.py | 8 +++---- exdir/utils/display.py | 14 ++++++------ tests/benchmarks/benchmarks.py | 20 ++++++----------- 9 files changed, 51 insertions(+), 85 deletions(-) diff --git a/examples/axona_to_exdir.py b/examples/axona_to_exdir.py index 4770818..b12dd3a 100644 --- a/examples/axona_to_exdir.py +++ b/examples/axona_to_exdir.py @@ -398,7 +398,7 @@ 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") diff --git a/exdir/core/attribute.py b/exdir/core/attribute.py index 76bd636..046f6e0 100644 --- a/exdir/core/attribute.py +++ b/exdir/core/attribute.py @@ -223,5 +223,4 @@ def _repr_html_(self): def __repr__(self): if self.file.io_mode == OpenMode.FILE_CLOSED: return "" - return "Attributes of Exdir object '{}' at '{}'".format( - self.parent.name, id(self)) + return f"Attributes of Exdir object '{self.parent.name}' at '{id(self)}'" diff --git a/exdir/core/dataset.py b/exdir/core/dataset.py index b803740..c977f3f 100644 --- a/exdir/core/dataset.py +++ b/exdir/core/dataset.py @@ -65,9 +65,9 @@ def __getitem__(self, args): and self.meta["plugins"][plugin_name]["required"] == True and plugin_name not in enabled_plugins): raise Exception(( - "Plugin '{}' was used to write '{}', " + 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 @@ -117,9 +117,9 @@ def _reload_data(self): test_string = "version https://git-lfs.github.com/spec/v1" contents = f.read(len(test_string)) if contents == test_string: - raise OSError("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 "" - return "".format( - self.name, self.shape, self.dtype) + return f"" @property def _data(self): diff --git a/exdir/core/exdir_file.py b/exdir/core/exdir_file.py index 0ca7542..1fb7e58 100644 --- a/exdir/core/exdir_file.py +++ b/exdir/core/exdir_file.py @@ -72,8 +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) @@ -91,9 +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( @@ -137,8 +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": @@ -221,5 +221,4 @@ def __contains__(self, name): def __repr__(self): if self.io_mode == OpenMode.FILE_CLOSED: return "" - return "".format( - self.directory, self.user_mode) + return f"" diff --git a/exdir/core/exdir_object.py b/exdir/core/exdir_object.py index bd41eb4..2970b4b 100644 --- a/exdir/core/exdir_object.py +++ b/exdir/core/exdir_object.py @@ -39,27 +39,17 @@ def _create_object_directory(directory, metadata): if metadata == _default_metadata(typename): # if it is the default, we know how to print it fast metadata_string = ('' - '{exdir_meta}:\n' - ' {type_meta}: "{typename}"\n' - ' {version_meta}: {version}\n' - '').format( - exdir_meta=EXDIR_METANAME, - type_meta=TYPE_METANAME, - typename=typename, - version_meta=VERSION_METANAME, - version=1 - ) + f'{EXDIR_METANAME}:\n' + f' {TYPE_METANAME}: "{typename}"\n' + f' {VERSION_METANAME}: 1\n' + '') else: from io import StringIO with StringIO() as buf: yaml.YAML(typ="safe", pure=True).dump(metadata, buf) metadata_string = buf.getvalue() - try: - meta_file.write(metadata_string) - except TypeError: - # NOTE workaround for Python 2.7 - meta_file.write(metadata_string.decode('utf8')) + meta_file.write(metadata_string) def _remove_object_directory(directory): @@ -294,5 +284,4 @@ def _repr_html_(self): def __repr__(self): if self.file.io_mode == OpenMode.FILE_CLOSED: return "" - return "".format( - self.directory, self.file.user_mode) + return f"" diff --git a/exdir/core/group.py b/exdir/core/group.py index f8566bd..b2b0d46 100644 --- a/exdir/core/group.py +++ b/exdir/core/group.py @@ -34,16 +34,12 @@ def _assert_data_shape_dtype_match(data, shape, dtype): if data is not None: if shape is not None and np.prod(shape) != np.prod(data.shape): raise ValueError( - "Provided shape and data.shape do not match: {} vs {}".format( - shape, data.shape - ) + f"Provided shape and data.shape do not match: {shape} vs {data.shape}" ) if dtype is not None and not data.dtype == dtype: raise ValueError( - "Provided dtype and data.dtype do not match: {} vs {}".format( - dtype, data.dtype - ) + f"Provided dtype and data.dtype do not match: {dtype} vs {data.dtype}" ) return @@ -228,8 +224,8 @@ def require_group(self, name): return current_object else: raise TypeError( - "An object with name '{}' already " - "exists, but it is not a Group.".format(name) + f"An object with name '{name}' already " + "exists, but it is not a Group." ) elif group_directory.exists(): raise FileExistsError( @@ -290,9 +286,7 @@ def require_dataset(self, name, shape=None, dtype=None, exact=False, if not isinstance(current_object, ds.Dataset): raise TypeError( - "Incompatible object already exists: {}".format( - current_object.__class__.__name__ - ) + f"Incompatible object already exists: {current_object.__class__.__name__}" ) data, attrs, meta = ds._prepare_write( @@ -302,31 +296,28 @@ def require_dataset(self, name, shape=None, dtype=None, exact=False, meta={} ) - # TODO verify proper attributes _assert_data_shape_dtype_match(data, shape, dtype) shape, dtype = _data_to_shape_and_dtype(data, shape, dtype) + print(f"shape: {shape} current_object.shape: {current_object.shape}") if not np.array_equal(shape, current_object.shape): raise TypeError( - "Shapes do not match (existing {} vs " - "new {})".format(current_object.shape, shape) + f"Shapes do not match (existing {current_object.shape} vs " + f"new {shape})" ) if dtype != current_object.dtype: if exact: raise TypeError( "Datatypes do not exactly match " - "existing {} vs new {})".format(current_object.dtype, dtype) + f"existing {current_object.dtype} vs new {dtype})" ) if not np.can_cast(dtype, current_object.dtype): raise TypeError( - "Cannot safely cast from {} to {}".format( - dtype, - current_object.dtype - ) + f"Cannot safely cast from {dtype} to {current_object.dtype}" ) return current_object @@ -372,11 +363,9 @@ def __getitem__(self, name): return self[top_directory][sub_name] if name not in self: - error_message = "No such object: '{name}' in path '{path}'".format( - name=name, - path=str(self.directory) + raise KeyError( + f"No such object: '{name}' in path '{str(self.directory)}'" ) - raise KeyError(error_message) directory = self.directory / path @@ -403,11 +392,8 @@ def __getitem__(self, name): return self._group(name) else: error_string = ( - "Object {name} has data type {type}.\n" + f"Object {name} has data type {meta_data[exob.EXDIR_METANAME][exob.TYPE_METANAME]}.\n" "We cannot open objects of this type." - ).format( - name=name, - type=meta_data[exob.EXDIR_METANAME][exob.TYPE_METANAME] ) raise NotImplementedError(error_string) diff --git a/exdir/core/validation.py b/exdir/core/validation.py index 8bdd325..ef63355 100644 --- a/exdir/core/validation.py +++ b/exdir/core/validation.py @@ -88,8 +88,8 @@ def _assert_valid_characters(name): for char in name_str: if char not in VALID_CHARACTERS: raise NameError( - "Name '{}' contains invalid character '{}'.\n" - "Valid characters are:\n{}".format(name_str, char, VALID_CHARACTERS) + f"Name '{name_str}' contains invalid character '{char}'.\n" + f"Valid characters are:\n{VALID_CHARACTERS}" ) def unique(parent_path, name): @@ -128,8 +128,8 @@ def thorough(parent_path, name): for item in os.listdir(str(parent_path)): if name_lower == item.lower(): raise RuntimeError( - "A directory with name (case independent) '{}' already exists " - " and cannot be made according to the naming rule 'thorough'.".format(name) + f"A directory with name (case independent) '{name}' already exists " + " and cannot be made according to the naming rule 'thorough'." ) diff --git a/exdir/utils/display.py b/exdir/utils/display.py index 8124d32..bdd567a 100644 --- a/exdir/utils/display.py +++ b/exdir/utils/display.py @@ -50,15 +50,15 @@ def html_tree(obj): } """ - script = """ + script = f""" var node = document.getElementById('{ulid}'); exdir.CollapsibleLists.applyTo(node); - """.format(ulid=ulid) + """ - result = ("" - "
      {contents}
    " - "" - "").format(style=style, ulid=ulid, contents=_build_tree(obj), script=script) + result = (f"" + f"
      {_build_tree(obj)}
    " + f"" + "") return result @@ -82,4 +82,4 @@ def _build_attrs_tree(key, value): def html_attrs(attributes): - return "
      {}
    ".format(_build_attrs_tree("Attributes", attributes)) + return f"
      {_build_attrs_tree('Attributes', attributes)}
    " diff --git a/tests/benchmarks/benchmarks.py b/tests/benchmarks/benchmarks.py index caebeee..5502e41 100644 --- a/tests/benchmarks/benchmarks.py +++ b/tests/benchmarks/benchmarks.py @@ -11,7 +11,7 @@ one_hundred_attributes["hello" + str(i)] = "world" def benchmark(name, target, setup=None, teardown=None, iterations=1): - print(("Running {name}...").format(name=name)) + print(f"Running {name}...") total_time = 0 setup_teardown_start = time.time() @@ -29,18 +29,12 @@ def benchmark(name, target, setup=None, teardown=None, iterations=1): total_setup_teardown = setup_teardown_end - setup_teardown_start output = ( - "{name}\n" + + f"{name}\n" + ("-" * len(name)) + "\n" + - "Iterations:\n{iterations}\n" + - "Total time:\n{total_time}\n" + - "Total time (iterations + setup/teardown):\n{total_setup_teardown}\n" + - "Mean:\n{mean}\n" - ).format( - name=name, - iterations=iterations, - total_time=total_time, - total_setup_teardown=total_setup_teardown, - mean=total_time / iterations + f"Iterations:\n{iterations}\n" + + f"Total time:\n{total_time}\n" + + f"Total time (iterations + setup/teardown):\n{total_setup_teardown}\n" + + f"Mean:\n{total_time / iterations}\n" ) print(output) @@ -141,7 +135,7 @@ def create_many_objects(obj): for i in range(5000): group = obj.create_group(f"group{i}") # data = np.zeros((10, 10, 10)) - # group.create_dataset("dataset{}".format(i), data=data) + # group.create_dataset(f"dataset{i}", data=data) def iterate_objects(obj): From a3ab5aedb0730dae1426e1a8beec6d2be757ffd4 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:15:15 -0400 Subject: [PATCH 10/17] clean up comprehensions --- exdir/core/attribute.py | 3 +-- exdir/core/group.py | 3 +-- exdir/plugin_interface/plugin_interface.py | 12 ++++++------ 3 files changed, 8 insertions(+), 10 deletions(-) diff --git a/exdir/core/attribute.py b/exdir/core/attribute.py index 046f6e0..98c6c50 100644 --- a/exdir/core/attribute.py +++ b/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): diff --git a/exdir/core/group.py b/exdir/core/group.py index b2b0d46..a1d5d5f 100644 --- a/exdir/core/group.py +++ b/exdir/core/group.py @@ -483,8 +483,7 @@ def __iter__(self): assert_file_open(self.file) # NOTE os.walk is way faster than os.listdir + os.path.isdir directories = next(os.walk(str(self.directory)))[1] - for name in sorted(directories): - yield name + yield from sorted(directories) def __len__(self): """ diff --git a/exdir/plugin_interface/plugin_interface.py b/exdir/plugin_interface/plugin_interface.py index 7c32c0d..f62512e 100644 --- a/exdir/plugin_interface/plugin_interface.py +++ b/exdir/plugin_interface/plugin_interface.py @@ -228,16 +228,16 @@ def solve_plugin_order(plugins, read_mode=False): queue = new_queue # remove missing plugins from maps - plugin_map = dict( - (name, v) + plugin_map = { + name: v for name, v in plugin_map.items() if name in needed_plugins - ) - dependency_map = dict( - (name, v) + } + dependency_map = { + name: v for name, v in dependency_map.items() if name in needed_plugins - ) + } ordered_plugins = [] while dependency_map: From 6aff7b25bee7b51008e31e4e4c12449ae87f6f56 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:15:41 -0400 Subject: [PATCH 11/17] use f-strings --- exdir/core/dataset.py | 4 ++-- tests/test_dataset.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/exdir/core/dataset.py b/exdir/core/dataset.py index c977f3f..d84989f 100644 --- a/exdir/core/dataset.py +++ b/exdir/core/dataset.py @@ -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(( + raise Exception( f"Plugin '{plugin_name}' was used to write '{self.name}', " "but is not enabled." - )) + ) plugins = self.plugin_manager.dataset_plugins.read_order diff --git a/tests/test_dataset.py b/tests/test_dataset.py index ffadee2..911fa79 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -598,7 +598,7 @@ def test_slice_of_length_zero(setup_teardown_file): f = setup_teardown_file[3] for i, shape in enumerate([(3, ), (2, 2, ), (2, 1, 5)]): - dset = f.create_dataset('x%d'%i, data=np.zeros(shape, np.int32)) + dset = f.create_dataset(f"x{i}", data=np.zeros(shape, np.int32)) assert dset.shape == shape out = dset[1:1] assert isinstance(out, np.ndarray) From 751e8c5dc744796abfee7535541c5ec3457c37a8 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:19:06 -0400 Subject: [PATCH 12/17] fix test names --- tests/test_attr.py | 2 +- tests/test_dataset.py | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/test_attr.py b/tests/test_attr.py index d015b3f..6cf2656 100644 --- a/tests/test_attr.py +++ b/tests/test_attr.py @@ -209,7 +209,7 @@ def test_ascii(setup_teardown_file): def test_unicode(setup_teardown_file): - """Access via Unicode string with non-ascii characters.""" + """Access via Unicode string with non-ASCII characters.""" f = setup_teardown_file[3] name = "Omega" + chr(0x03A9) diff --git a/tests/test_dataset.py b/tests/test_dataset.py index 911fa79..2decea9 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -217,7 +217,7 @@ def test_create_fillval(setup_teardown_file): -def test_compound(setup_teardown_file): +def test_compound_fill(setup_teardown_file): """Fill value works with compound types.""" f = setup_teardown_file[3] grp = f.create_group("test") @@ -237,8 +237,8 @@ def test_exc(setup_teardown_file): def test_string(setup_teardown_file): - """Assignement of fixed-length byte string produces a fixed-length - ascii dataset """ + """Assignment of fixed-length byte string produces a fixed-length + ASCII dataset""" f = setup_teardown_file[3] grp = f.create_group("test") @@ -311,7 +311,7 @@ def test_trailing_slash(setup_teardown_file): # Feature: Compound types correctly round-trip -def test_compund(setup_teardown_file): +def test_compound(setup_teardown_file): """Compound types are read back in correct order.""" f = setup_teardown_file[3] grp = f.create_group("test") @@ -504,7 +504,7 @@ def test_read(setup_teardown_file): assert out.shape == (3, 3) def test_write_broadcast(setup_teardown_file): - """Array fill from constant is supported.""" + """Array fill from constant is supported.""" f = setup_teardown_file[3] dt = np.dtype('(3,)i') From 82d65b437315a807120e6986f5f830bd4854de7a Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:19:36 -0400 Subject: [PATCH 13/17] enable test that requires Python 3+ --- tests/test_attr.py | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/tests/test_attr.py b/tests/test_attr.py index 6cf2656..5c0551e 100644 --- a/tests/test_attr.py +++ b/tests/test_attr.py @@ -197,15 +197,14 @@ def test_ascii(setup_teardown_file): assert out == 42 # TODO verify that we don't want to support non-ASCII byte strings -# NOTE fails with Python 2.7 -# def test_raw(setup_teardown_file): - # """Access via non-ASCII byte string.""" - # f = setup_teardown_file[3] - - # name = b"non-ascii\xfe" - # f.attrs[name] = 42 - # out = f.attrs[name] - # assert out == 42 +def test_raw(setup_teardown_file): + """Access via non-ASCII byte string.""" + f = setup_teardown_file[3] + + name = b"non-ascii\xfe" + f.attrs[name] = 42 + out = f.attrs[name] + assert out == 42 def test_unicode(setup_teardown_file): From 26a285d3dfe951e571e6bcec6adbad71b8de2a3f Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:30:27 -0400 Subject: [PATCH 14/17] fix collections import --- tests/test_group.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_group.py b/tests/test_group.py index e4df2a0..e21f6d2 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -18,7 +18,7 @@ try: from collections.abc import KeysView, ValuesView, ItemsView except: - from collections import KeysView, ValuesView, ItemsView + from collections.abc import KeysView, ValuesView, ItemsView from exdir.core import Group, File, Dataset from exdir import validation as fv From 0ad9bbae89006ea516253196499288679e55860f Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:25:20 -0400 Subject: [PATCH 15/17] .git-blame-ignore-revs for ignoring non-functional changes --- .git-blame-ignore-revs | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 .git-blame-ignore-revs diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs new file mode 100644 index 0000000..e6c261b --- /dev/null +++ b/.git-blame-ignore-revs @@ -0,0 +1,15 @@ +# pyupgrade +d2a29a2c36b92d1e77ac291a42ece5d8a455a69b +0f081e455c6082b8f43bdc1ce8d03359e13cf5be +fec69ce479a84bac8270b5f1c95ae6344c9f797a +59dc3c129b40a7992b5d1fab5e5f04705662f71a +2d7173ec9277da9eb59982c03c7a6e4e06a49759 +7cfe37c6e20df0417248451dd919aeabaed1349a +b8563af7487d4ea9cda48d5beb49b7354feda5db +26b7b0c40d317341168090353f85e87e1d9b9f51 +c2ffbb7204424f6af32bb8f150e86c8f51bd9eb9 +55f776114a9b5ef96d2504e1118ee74d75f34cc0 +160475c6680a33a0c57535e7275cc6dad473c4ef +0419e92e29ecb98eec10cbd2534022563dbf44e5 +6048a44d34a9398bda910563f5f85f1a43714319 +328b8843108c427c6153d2e3e2bf32ce41682433 From 671a00759cb59f588daef96890f07b187282d182 Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:37:30 -0400 Subject: [PATCH 16/17] add pre-commit configuration --- .pre-commit-config.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 .pre-commit-config.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..d6e8f0a --- /dev/null +++ b/.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 From 0eee2c7308aaf0e888ca79c329f88c059726276d Mon Sep 17 00:00:00 2001 From: Eric Berquist Date: Wed, 19 Jun 2024 12:41:21 -0400 Subject: [PATCH 17/17] set minimum required Python version to 3.7 --- setup.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/setup.py b/setup.py index c6e21af..6c59268 100644 --- a/setup.py +++ b/setup.py @@ -1,13 +1,9 @@ -from setuptools import setup -import os - from setuptools import setup, find_packages import versioneer -long_description = open("README.md", encoding="utf-8").read() - -install_requires = [] +with open("README.md", encoding="utf-8") as handle: + long_description = handle.read() setup( name="exdir", @@ -38,5 +34,6 @@ "numpy>=1.20", "ruamel.yaml==0.17.21", ], + python_requires=">=3.7", zip_safe=False, )