Updated Metadata and Dependencies (#41)

* Dev (#32)

* Modified bumpversion

* Added code formatting, linting

* Fixed documentation, modified bumpversion

* Modified bump2version and readme

* Fixed bumpversion for README

* Removed buggy precommit hooks

* Removed bumpversion sign option

* Changed bumpversion fields

* Bump version: 2.1.9 → 2.2.0-dev0

* Fixed bug in bumpversion dev builds

* Bump version: 2.2.0-dev0 → 2.2.0-dev1

* Upgrade/bioformats (#20)

* Migration from loci_tools.jar to bioformats_package.jar

* Changed setup.py

* Fixed bug associated with initializing a BioWriter without metadata parameter (#21)

* Feat/ci (#22)

* Added code format and lint git actions

* fix: Fixed format gitaction, disabled zarr tests

* Added dev dependencies and test workflow

* Started docker ci build

* Docker build base

* Black formatting

* Updated git actions

* Changed bumpversion config

* Finished Docker configs

* Added PyPi publishing action

* Bump version: 2.2.0-dev1 → 2.2.0-dev2

* Fixed docker and pypi workflows

* Reverted version

* Changed pypi workflow

* Fixed twine username

* Feat/ometypes (#23)

* Replaced OmeXml.py with ome_types

* Resolved uncaught OmeXml references

* Bump version: 2.2.0-dev1 → 2.2.0-dev2

* Bump version: 2.2.0-dev2 → 2.2.0-dev3

* Fix/metadata (#24)

* Added additional metadata reformatting

* Fixed repeated values in metadata replacement dictionary

* Fixed unresolved merge conflict in README

* Fixed additional README conflict

* Fix/rgb (#26)

* Fixed versioning in docs

* Fix czi rgb image bug

* Fix czi rgb image bug

* Special catch for Zeiss CZI rgb images

* Fix/biowriter (#27)

* Fixed metadata issues with BioWriter

* fix: JavaWriter backend exports correct results on any XYZCT data

* Removed debug code

* Fixed error in unittest from missing dependency

* Feat/bioreader (#28)

* Bump version: 2.2.0 → 2.2.1-dev0

* re-added support for CT dimensions, improved performance

* Added pickle support for PythonReader

* Bump version: 2.2.1-dev0 → 2.2.1-dev1

* Feat/biowriter: Scalability and Extended Writing Ability (#29)

* Updated Python BioWriter to use newer version of tifffile

* Prototype of scalable scatter tile format

* Removed debug print statements

* added support for multi-channel/timepoint writing

* Added unittest, fix abstract class error

* Updated reader and biowriter metadata

* Bump version: 2.2.1-dev1 → 2.3.0-dev0

* Bioformats (#30)

* Removed bioformats_package.jar, added optional install of bioformats_jar

* Updated documentation and install options

* fixed README typo

* Update/docs (#31)

* Updated docs and tests. Changed java backend name to bioformats

* Updated examples to use new backend names

* Bump version: 2.3.0-dev0 → 2.3.0

* Updated dependency range for tifffile, changed metadata saving

* Added no verify to bump2version config

* Upgraded ome-types

* Bump version: 2.3.0 → 2.3.1-dev0

.bumpversion.cfg

@@ -1,7 +1,8 @@
 [bumpversion]
-current_version = 2.3.0
+current_version = 2.3.1-dev0
 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}

.gitignore

@@ -1,5 +1,6 @@
 __pycache__
-,vscode
+.vscode
+.venv
 docs/build
 dist
 build

.pre-commit-config.yaml

@@ -1,15 +1,15 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.1.0
+    rev: 23.3.0
     hooks:
       - id: black
         args: ["--check", "--color"]
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 6.0.0
     hooks:
       - id: flake8
         additional_dependencies: [flake8-typing-imports==1.7.0]
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v1.20.0
+    rev: v2.2.0
     hooks:
       - id: setup-cfg-fmt

README.md

@@ -1,4 +1,4 @@
-# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.3.0)
+# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.3.1-dev0)
 
 [![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/filepattern/)
@@ -53,15 +53,15 @@ Additionally, `bfio` with other dependencies can be installed:
 
 ## Docker
 
-### labshare/polus-bfio-util:2.3.0
+### labshare/polus-bfio-util:2.3.1-dev0
 
 Ubuntu based container with bfio and all dependencies (including Java).
 
-### labshare/polus-bfio-util:2.3.0-imagej
+### labshare/polus-bfio-util:2.3.1-dev0-imagej
 
 Same as above, except comes with ImageJ and PyImageJ.
 
-### labshare/polus-bfio-util:2.3.0-tensorflow
+### labshare/polus-bfio-util:2.3.1-dev0-tensorflow
 
 Tensorflow container with bfio isntalled.
 

VERSION

@@ -1 +1 @@
-2.3.0
+2.3.1-dev0