Release version 3.3.0 (#588)

* Update changelog, bump version

* Bump changelog version

AxonDeepSeg/__init__.py

@@ -1 +1 @@
-__version__ = "3.2.0"
+__version__ = "3.3.0"

CHANGELOG.md

@@ -1,6 +1,76 @@
 Changelog
 ===============================================================================
 
+## Version 3.3.0 - 2022-01-14
+[View detailed changelog](https://github.com/neuropoly/axondeepseg/compare/v3.2.0...v3.3.0)
+
+**BUG**
+
+ - Fix morphometrics error with ellipse axon shape [View pull request](https://github.com/neuropoly/axondeepseg/pull/558)
+ - Fix patches2im_overlap when width = height  [View pull request](https://github.com/neuropoly/axondeepseg/pull/510)
+ - Patch myelin thickness calculation [View pull request](https://github.com/neuropoly/axondeepseg/pull/449)
+ - Bug fix due to h5py package version in fsleyes [View pull request](https://github.com/neuropoly/axondeepseg/pull/392)
+ - Pin h5py~=2.10.0 as a workaround for upstream Keras/TensorFlow issues [View pull request](https://github.com/neuropoly/axondeepseg/pull/382)
+ - Resolve bug that makes TEM data not segment well with multiple files [View pull request](https://github.com/neuropoly/axondeepseg/pull/370)
+
+**ENHANCEMENT**
+
+ - Added the axon shape selection in the GUI (take two) [View pull request](https://github.com/neuropoly/axondeepseg/pull/541)
+ - Generate numbers image with CLI  [View pull request](https://github.com/neuropoly/axondeepseg/pull/519)
+ - Refactor the code for the settings menu [View pull request](https://github.com/neuropoly/axondeepseg/pull/507)
+ - Add Optical Microscopy model in notebooks [View pull request](https://github.com/neuropoly/axondeepseg/pull/530)
+ - Add perimeter to morphometrics[View pull request](https://github.com/neuropoly/axondeepseg/pull/501)
+ - Add CLI support to generate morphometrics file. [View pull request](https://github.com/neuropoly/axondeepseg/pull/434)
+ - Replaced rcParams with font_manager to find the font [View pull request](https://github.com/neuropoly/axondeepseg/pull/491)
+ - Remove wildcard imports [View pull request](https://github.com/neuropoly/axondeepseg/pull/487)
+ - Migration to GitHub Actions [View pull request](https://github.com/neuropoly/axondeepseg/pull/479)
+ - Change the name of -o flag to -overlap flag  [View pull request](https://github.com/neuropoly/axondeepseg/pull/474)
+ - Add a model to .gitignore [View pull request](https://github.com/neuropoly/axondeepseg/pull/471)
+ - Change the default name for saving the morphometrics file [View pull request](https://github.com/neuropoly/axondeepseg/pull/472)
+ - Use pathlib in the ads_plugin instead of os.path [View pull request](https://github.com/neuropoly/axondeepseg/pull/448)
+ - Integrate Simeon's model with FSLeyes and CLI [View pull request](https://github.com/neuropoly/axondeepseg/pull/457)
+ - Fix Naming Convention [View pull request](https://github.com/neuropoly/axondeepseg/pull/441)
+ -  Fixed Notebooks and Binder links in doc[View pull request](https://github.com/neuropoly/axondeepseg/pull/413)
+ - Move test files to OSF, add download functionality [View pull request](https://github.com/neuropoly/axondeepseg/pull/373)
+ - Add postprocessing tests [View pull request](https://github.com/neuropoly/axondeepseg/pull/365)
+
+
+**FEATURE**
+
+ - Implement Batch morphometrics for images present in directory/directories [View pull request](https://github.com/neuropoly/axondeepseg/pull/518)
+ - Implement Ellipse Minor Axis as Diameter [View pull request](https://github.com/neuropoly/axondeepseg/pull/399)
+ - Add a settings menu to the FSLeyes plugin  [View pull request](https://github.com/neuropoly/axondeepseg/pull/462)
+ - Add Axon mask simulator [View pull request](https://github.com/neuropoly/axondeepseg/pull/179)
+
+**DOCUMENTATION**
+
+ - Update Youtube video links [View pull request](https://github.com/neuropoly/axondeepseg/pull/574)
+ - Apply RTD fix to make builds pass again  [View pull request](https://github.com/neuropoly/axondeepseg/pull/578)
+ - Update figure link  [View pull request](https://github.com/neuropoly/axondeepseg/pull/575)
+ - Migrate images to new repo [View pull request](https://github.com/neuropoly/axondeepseg/pull/543)
+ - Change link [View pull request](https://github.com/neuropoly/axondeepseg/pull/535)
+ - Add description of morphometrics columns headings [View pull request](https://github.com/neuropoly/axondeepseg/pull/516)
+ - Add a reference to Readme.md [View pull request](https://github.com/neuropoly/axondeepseg/pull/500)
+ - Update the documentation for installing the GPU compatible version of ADS [View pull request](https://github.com/neuropoly/axondeepseg/pull/490)
+ - Add tutorial video link in RTD  [View pull request](https://github.com/neuropoly/axondeepseg/pull/493)
+ - Fix docs for optical microscopy model [View pull request](https://github.com/neuropoly/axondeepseg/pull/485)
+ - Documentation updates  [View pull request](https://github.com/neuropoly/axondeepseg/pull/433)
+ - Fix new changelog display in RTD  [View pull request](https://github.com/neuropoly/axondeepseg/pull/388)
+ - Add zoomed window on masks examples in RTD  [View pull request](https://github.com/neuropoly/axondeepseg/pull/386)
+ - Remove PyPI install instructions from RTD [View pull request](https://github.com/neuropoly/axondeepseg/pull/376)
+ - Fix youtube video link in RTD [View pull request](https://github.com/neuropoly/axondeepseg/pull/379)
+
+**INSTALLATION**
+
+ - Link the test_files to GitHub [View pull request](https://github.com/neuropoly/axondeepseg/pull/534)
+ - Download models from Github repo [View pull request](https://github.com/neuropoly/axondeepseg/pull/533)
+ - Generate images synthetically in tests [View pull request](https://github.com/neuropoly/axondeepseg/pull/520)
+ - Change install to one env file & update docs  [View pull request](https://github.com/neuropoly/axondeepseg/pull/484)
+ - Refactor AxonDeepSeg/models directory and update .gitignore [View pull request](https://github.com/neuropoly/axondeepseg/pull/476)
+ - Change how ADS dependencies are installed [View pull request](https://github.com/neuropoly/axondeepseg/pull/452)
+ - Add PR template [View pull request](https://github.com/neuropoly/axondeepseg/pull/467)
+ - Remove old config file (set_config) [View pull request](https://github.com/neuropoly/axondeepseg/pull/456)
+
 ## Version 3.2.0 - 2020-10-16
 [View detailed changelog](https://github.com/neuropoly/axondeepseg/compare/v3.0...v3.2.0)