diff --git a/README.md b/README.md index 38c0a23..4f0810e 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.4.10) +# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.5.0) [![Documentation Status](https://readthedocs.org/projects/bfio/badge/?version=latest)](https://bfio.readthedocs.io/en/latest/?badge=latest) [![PyPI](https://img.shields.io/pypi/v/bfio)](https://pypi.org/project/bfio/) @@ -31,7 +31,7 @@ Docker containers with all necessary components are available (see ### Setting up Java -**Note:** `bfio` can be used without Java, but only the `python` and `zarr` +**Note:** `bfio` can be used without Java, but only the `python`, `zarr`, `zarr3`, and `tensorstore` backends will be usable. This means only files in tiled OME Tiff or OME Zarr format can be read/written. @@ -50,15 +50,15 @@ be installed using pip: ## Docker -### polusai/bfio:2.4.10 +### polusai/bfio:2.5.0 Ubuntu based container with bfio and all dependencies (including Java). -### polusai/bfio:2.4.10-imagej +### polusai/bfio:2.5.0-imagej Same as above, except comes with ImageJ and PyImageJ. -### polusai/bfio:2.4.10-tensorflow +### polusai/bfio:2.5.0-tensorflow Tensorflow container with bfio installed. diff --git a/docker/base/Dockerfile b/docker/base/Dockerfile index 0975ce8..301dc12 100644 --- a/docker/base/Dockerfile +++ b/docker/base/Dockerfile @@ -49,11 +49,6 @@ RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch # Install using the new Python RUN python${PYTHON_VERSION} -m pip install /bfio_src --no-cache-dir -# Apply jgo copy patch -RUN git apply \ - --directory=usr/local/lib/python${PYTHON_VERSION}/dist-packages \ - /bfio_src/docker/jgo_copy.patch - # clean up RUN rm -rf /bfio_src diff --git a/docker/imagej/Dockerfile b/docker/imagej/Dockerfile index a99b872..4432744 100644 --- a/docker/imagej/Dockerfile +++ b/docker/imagej/Dockerfile @@ -44,11 +44,6 @@ RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch # Install RUN python3 -m pip install /bfio_src --no-cache-dir -#Apply jgo copy patch -RUN git apply \ - --directory=usr/local/lib/python${PYTHON_VERSION}/site-packages \ - /bfio_src/docker/jgo_copy.patch - # Install packages ENV LIBRARY_PATH=/lib:/usr/lib diff --git a/docker/tensorflow/Dockerfile b/docker/tensorflow/Dockerfile index 4327d92..4214c20 100644 --- a/docker/tensorflow/Dockerfile +++ b/docker/tensorflow/Dockerfile @@ -37,9 +37,6 @@ RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch # Install RUN pip3 install /bfio_src --no-cache-dir -#Apply jgo copy patch -RUN git apply --directory=usr/local/lib/python${PYTHON_VERSION}/dist-packages /bfio_src/docker/jgo_copy.patch - # clean up RUN rm -rf /bfio_src diff --git a/docs/source/Examples/Converter.rst b/docs/source/Examples/Converter.rst index 044151f..28fa2d0 100644 --- a/docs/source/Examples/Converter.rst +++ b/docs/source/Examples/Converter.rst @@ -8,7 +8,7 @@ Introduction The bfio package is designed to make it easy to process arbitrarily sized images in a fast, scalable way. The two core classes, :doc:`/Reference/BioReader` and -:doc:`/Reference/BioWriter`, can use one of three different backends depending +:doc:`/Reference/BioWriter`, can use one of five different backends depending on the file type that will be read. Usually, the proper backend will be selected when opening a file. For cases where bfio fails to select the proper backend, the ``backend`` parameter can be passed to the constructor. The following backends @@ -20,10 +20,14 @@ are available in ``bfio``. 2. ``backend="bioformats"`` can be used to read any `any format supported by Bio-Formats `_. The BioWriter with java backend will only save images as OME tiled tiff. -3. ``backend="zarr"`` can be used to read/write a subset of Zarr files following +3. ``backend="zarr"`` can be used to read/write a subset of Zarr v2 files following the `OME Zarr spec `_. +4. ``backend="zarr3"`` can be used to read/write Zarr v3 files following + the `OME Zarr spec `_. +5. ``backend="tensorstore"`` provides optimized reading/writing for both OME Tiff + and OME Zarr (v2 and v3) files with enhanced performance. -The advantage to using the ``python`` and ``zarr`` backends are speed and +The advantage to using the ``python``, ``zarr``, ``zarr3``, and ``tensorstore`` backends are speed and scalability at the expense of a rigid file structure, while the ``bioformats`` backend provides broad access to a wide array of file types but is considerably slower. diff --git a/docs/source/Installation.rst b/docs/source/Installation.rst index 347266f..78ab744 100644 --- a/docs/source/Installation.rst +++ b/docs/source/Installation.rst @@ -13,7 +13,7 @@ A conda distribution is also available in the conda-forge channel. To install it Java and Bio-Formats ------------------- -``bfio`` can be used without Java, but only the ``python`` and ``zarr`` +``bfio`` can be used without Java, but only the ``python``, ``zarr``, ``zarr3``, and ``tensorstore`` backends will be usable. This means only files in tiled OME Tiff or OME Zarr format can be read/written. diff --git a/pyproject.toml b/pyproject.toml index 461fc92..2b97948 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -87,7 +87,7 @@ namespaces = false [tool.bumpversion] -current_version = "2.4.10" +current_version = "2.5.0" commit = true tag = true commit_args = "--no-verify" diff --git a/requirements/requirements-base.txt b/requirements/requirements-base.txt index 1d93466..1ce2768 100644 --- a/requirements/requirements-base.txt +++ b/requirements/requirements-base.txt @@ -1 +1 @@ -bfio==2.4.10 +bfio==2.5.0 diff --git a/src/bfio/VERSION b/src/bfio/VERSION index b0f6bf0..437459c 100644 --- a/src/bfio/VERSION +++ b/src/bfio/VERSION @@ -1 +1 @@ -2.4.10 +2.5.0