update bioformats to 7.1.0

.flake8

@@ -1,6 +1,6 @@
 [flake8]
 docstring-convention=google
 max-line-length=88
-exclude=noxfile.py,docs/*,tests/*,examples/*,.nox/*,build/*,bfio/OmeXml.py,setup.py
+exclude=noxfile.py,docs/*,tests/*,examples/*,.nox/*,build/*
 ignore=D105, W503, D100, D104, AZ100
 extend-ignore = E203

.github/workflows/format.yml

@@ -20,4 +20,4 @@ jobs:
       - uses: psf/black@stable
         with:
           options: "--check --color --verbose"
-          src: "./bfio"
+          src: "./src"

.gitignore

@@ -1,6 +1,6 @@
 __pycache__
 .vscode
-.venv
+venv
 docs/build
 dist
 build

pyproject.toml

@@ -0,0 +1,123 @@
+[build-system]
+ # Run dependencies are also considered as build dependencies
+ # due to cascading import situation in src/bfio/__init__.py
+requires = [
+  "setuptools", 
+  "wheel",
+  "imagecodecs>=2021.2.26",
+  "numpy",
+  "ome-types>=0.4.2",
+  "zarr>=2.6.1",
+  "scyjava",
+  "jpype1",
+  "tifffile>=2022.8.12"
+]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "bfio"
+dynamic = ["version"]
+dependencies = [
+    "imagecodecs>=2021.2.26",
+    "numpy",
+    "ome-types>=0.4.2",
+    "zarr>=2.6.1",
+    "scyjava",
+    "jpype1",
+    "tifffile>=2022.8.12"
+]
+
+description = "Simple reading and writing classes for tiled tiffs using Bioformats."
+readme = "README.md"
+license = {file = "LICENSE"}
+
+authors = [
+  {name = "Nick Schaub", email = "nick.schaub@nih.gov"},
+  {name = "Sameeul Bashir Samee", email = "sameeul.samee@axleinfo.com"},
+]
+
+maintainers = [
+  {name = "Sameeul Bashir Samee", email = "sameeul.samee@axleinfo.com"},
+]
+
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+] 
+
+requires-python = ">=3.8"
+
+
+[project.optional-dependencies]
+dev = [
+    "ome_zarr",
+    "requests>=2.26.0"
+]
+
+
+[project.urls]
+Documentation = "https://bfio.readthedocs.io/en/latest/"
+Repository = "https://github.com/PolusAI/bfio"
+
+
+[tool.setuptools.dynamic]
+version = {attr = "bfio.__version__"}
+
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+include-package-data = true
+
+
+[tool.setuptools.packages.find]
+where = ["src"]
+namespaces = false
+
+
+[tool.setuptools.package-data]
+"*" = [
+    "VERSION"
+]
+
+
+[tool.bumpversion]
+current_version = "2.3.3"
+commit = true
+tag = true
+commit_args = "--no-verify"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(\\-(?P<release>[a-z]+)(?P<build>\\d+))?"
+serialize = [
+    "{major}.{minor}.{patch}-{release}{build}",
+    "{major}.{minor}.{patch}"
+]
+
+[tool.bumpversion.parts.release]
+optional_value = "_"
+first_value = "dev"
+values = [
+    "dev",
+    "_"
+]
+
+[[tool.bumpversion.files]]
+filename = "src/bfio/VERSION"
+search = "{current_version}"
+replace = "{new_version}"
+
+[[tool.bumpversion.files]]
+filename = "requirements/requirements-base.txt"
+search = "bfio[all]=={current_version}"
+replace = "bfio[all]=={new_version}"
+
+[[tool.bumpversion.files]]
+filename = "README.md"
+search = "{current_version}"
+replace = "{new_version}"
+
+
+[tool.codespell]
+skip = "*.svg,*.html"
+ignore-words-list = "utput"

src/bfio/__init__.py

@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+from __future__ import absolute_import, unicode_literals
+
+import logging
+import pathlib
+
+JAR_VERSION = None
+
+logging.basicConfig(
+    format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
+    datefmt="%d-%b-%y %H:%M:%S",
+)
+logger = logging.getLogger("bfio.init")
+
+log_level = logging.WARNING
+
+try:
+    with open(pathlib.Path(__file__).parent.joinpath("VERSION"), "r") as fh:
+        __version__ = fh.read()
+except FileNotFoundError:
+    logger.info(
+        "Could not find VERSION. "
+        + "This is likely due to using a local/cloned version of bfio."
+    )
+    __version__ = "0.0.0"
+logger.info("VERSION = {}".format(__version__))
+
+
+from .bfio import BioReader, BioWriter, start  # NOQA: F401, E402

bfio/backends.py → src/bfio/backends.py

@@ -937,9 +937,9 @@ def _init_writer(self):
 
         self._tags = []
 
-        self.frontend._metadata.images[
-            0
-        ].id = f"Image:{Path(self.frontend._file_path).name}"
+        self.frontend._metadata.images[0].id = (
+            f"Image:{Path(self.frontend._file_path).name}"
+        )
 
         if self.frontend.X * self.frontend.Y * self.frontend.bpp > 2**31:
             big_tiff = True

bfio/bfio.py → src/bfio/bfio.py

@@ -5,18 +5,16 @@
 import typing
 from concurrent.futures import ThreadPoolExecutor
 from pathlib import Path
-from platform import processor, system
 
 import numpy
 import ome_types
 import tifffile
+import jpype
+import scyjava
 
 from bfio import backends
 from bfio.base_classes import BioBase
 
-import jpype
-import scyjava
-
 try:
 
     def start() -> str:
@@ -30,10 +28,7 @@ def start() -> str:
         """
 
         global JAR_VERSION
-        if system() == "Darwin" and processor() == "arm":
-            scyjava.config.endpoints.append("ome:formats-gpl:7.0.0")
-        else:
-            scyjava.config.endpoints.append("ome:formats-gpl:7.0.1")
+        scyjava.config.endpoints.append("ome:formats-gpl:7.1.0")
         scyjava.start_jvm()
         loci = jpype.JPackage("loci")
         loci.common.DebugTools.setRootLevel("ERROR")
@@ -1009,9 +1004,9 @@ class if specified. *Defaults to None.*
             self._metadata = metadata.model_copy(deep=True)
 
             self._metadata.images[0].name = self._file_path.name
-            self._metadata.images[
-                0
-            ].pixels.dimension_order = ome_types.model.Pixels_DimensionOrder.XYZCT
+            self._metadata.images[0].pixels.dimension_order = (
+                ome_types.model.Pixels_DimensionOrder.XYZCT
+            )
         else:
             self._metadata = self._minimal_xml()
 

tests/test_read.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 import unittest
-import requests, io, pathlib, shutil, logging, sys
+import requests, pathlib, shutil, logging, sys
 import bfio
 import numpy as np
 import random
@@ -43,6 +43,8 @@ def setUpModule():
             with open(TEST_DIR.joinpath(file), "wb") as fw:
                 fw.write(r.content)
         else:
+            if TEST_DIR.joinpath(file).exists():
+                shutil.rmtree(TEST_DIR.joinpath(file))
             zarr_download(url, str(TEST_DIR))
 
     """Load the czi image, and save as a npy file for further testing."""