[Release] Update for release 0.2.0

Author: kevin931

CytofDR/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "0.1.0"
+__version__ = "0.2.0"
 
 from CytofDR import dr, evaluation

README.md

@@ -6,7 +6,7 @@
 
 | Branch | Release | CI/CD | Documentation | Code Coverage |
 | --- | --- | --- | --- | --- |
-| dev | ![Badge1](https://img.shields.io/badge/Version-0.1.0-success) |![Tests](https://github.com/kevin931/CytofDR/actions/workflows/ci.yml/badge.svg?branch=dev) | [![Documentation Status](https://readthedocs.org/projects/cytofdr/badge/?version=latest)](https://cytofdr.readthedocs.io/en/latest/?badge=latest) | [![codecov](https://codecov.io/gh/kevin931/CytofDR/branch/dev/graph/badge.svg?token=K9AJQLYU8N)](https://codecov.io/gh/kevin931/CytofDR) |
+| dev | ![Badge1](https://img.shields.io/badge/Version-0.2.0-success) |![Tests](https://github.com/kevin931/CytofDR/actions/workflows/ci.yml/badge.svg?branch=dev) | [![Documentation Status](https://readthedocs.org/projects/cytofdr/badge/?version=latest)](https://cytofdr.readthedocs.io/en/latest/?badge=latest) | [![codecov](https://codecov.io/gh/kevin931/CytofDR/branch/dev/graph/badge.svg?token=K9AJQLYU8N)](https://codecov.io/gh/kevin931/CytofDR) |
 
 
 ## About
@@ -42,7 +42,7 @@ The core dependencies should automatically install!
 Our dependencies are broken down core dependencies and optional dependencies. Below is a list of core dependencies:
 
 - scikit-learn
-- numpy (<=1.21)
+- numpy
 - scipy
 - umap-learn
 - openTSNE
@@ -131,17 +131,21 @@ Of course, there are many more customizations and ways you can use ``CytofDR``.
 
 There you will find ways to install our package and get started! Also, we offer tutorials on customizations, working with DR methods, and finally our detailed evaluation framework. We hope that you can find what you need over there!
 
-## Latest Release: v0.1.0
+## Latest Release: v0.2.0
+
+This releases adds some new features along with some minor improvements and fixes.
 
-This is the first official release of ``CytofDR`` with LTS.
 
 ### Changes and New Features
 
-- Support for magic methods: ``print`` and ``[]`` for ``Reductions`` class
-- Add ``names`` attributes to ``Reductions`` class
-- Add custom DR evaluation
-- Add functions to save DR embeddings and evaluations
-- Improve documentation and docstrings
+- Add `pairwise_downsample` option for pairwise distance optimization in `Reductions.evaluate` method.
+- Add example datasets for the GitHub repo.
+- Improve docstrings for documentations.
+- Improve unit tests for coverage.
+
+### Deprecations
+
+- The `comparison_classes` parameter of the `EvaluationMetrics.embedding_concordance` method will no longer accept `str` input.
 
 ## Issues and Contributions
 

docs/source/change/index.rst

@@ -9,19 +9,24 @@ doing!
 ------------------------
 
 ************************
-Latest Release: v0.1.0
+Latest Release: v0.2.0
 ************************
 
-This is the first official release of ``CytofDR`` with LTS.
+This releases adds some new features along with some minor improvements and fixes.
+
 
 Changes and New Features
 --------------------------
 
-- Support for magic methods: ``print`` and ``[]`` for ``Reductions`` class
-- Add ``names`` attributes to ``Reductions`` class
-- Add custom DR evaluation
-- Add functions to save DR embeddings and evaluations
-- Improve documentation and docstrings
+- Add `pairwise_downsample` option for pairwise distance optimization in `Reductions.evaluate` method.
+- Add example datasets for the GitHub repo.
+- Improve docstrings for documentations.
+- Improve unit tests for coverage.
+
+Deprecations
+----------------
+
+- The `comparison_classes` parameter of the `EvaluationMetrics.embedding_concordance` method will no longer accept `str` input.
 
 
 .. toctree::

docs/source/change/releases.rst

@@ -6,6 +6,27 @@ Here we include our release notes for past releases in sequential order.
 
 --------------------
 
+********
+v0.2.0
+********
+
+This releases adds some new features along with some minor improvements and fixes.
+
+
+Changes and New Features
+--------------------------
+
+- Add `pairwise_downsample` option for pairwise distance optimization in `Reductions.evaluate` method.
+- Add example datasets for the GitHub repo.
+- Improve docstrings for documentations.
+- Improve unit tests for coverage.
+
+Deprecations
+----------------
+
+- The `comparison_classes` parameter of the `EvaluationMetrics.embedding_concordance` method will no longer accept `str` input.
+
+
 ********
 v0.1.0
 ********

docs/source/conf.py

@@ -20,7 +20,7 @@
 project = 'CytofDR'
 copyright = '2022, Kevin Wang'
 author = 'Kevin Wang'
-release = '0.1.0'
+release = '0.2.0'
 
 extensions = [
     "sphinx_rtd_theme",

meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "CytofDR" %}
-{% set version = "0.1.0" %}
+{% set version = "0.2.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 7880f5b23d8b6554732f7ead73c07642d7e2eae080434e18953829603aee9bd3
+  sha256: 437a892d497aebdb166b0962aad612daec026072c506bb86a7c0d02a6800f5bc
 
 build:
   noarch: python
@@ -23,7 +23,7 @@ requirements:
   run:
     - python >=3.7
     - scikit-learn
-    - numpy <=1.21
+    - numpy
     - scipy
     - umap-learn
     - openTSNE

setup.py

@@ -4,7 +4,7 @@
 import shutil
 import distutils.cmd
 
-VERSION = "0.1.0"
+VERSION = "0.2.0"
 
 class PypiCommand(distutils.cmd.Command):