Merge branch 'maintenance/v0.1.x' into dev

kevin931 · Aug 10, 2023 · 9027524 · 9027524
2 parents 13fdd76 + 523cd0c
commit 9027524
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diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright 2022 PyCytoData Authors
+Copyright 2022-2023 PyCytoData Authors
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),

diff --git a/PyCytoData/__init__.py b/PyCytoData/__init__.py
@@ -1,4 +1,4 @@
 from PyCytoData.data import DataLoader, PyCytoData, FileIO
 from PyCytoData import exceptions, preprocess
 
-__VERSION__ = "0.1.1"
+__VERSION__ = "0.1.2"
diff --git a/PyCytoData/data.py b/PyCytoData/data.py
diff --git a/README.md b/README.md
@@ -161,23 +161,22 @@ For detailed documentation along with tutorials and API Reference, please visit
 
 If you prefer to build documentation on your own, refer to [this guide](https://pycytodata.readthedocs.io/en/latest/change/build.html) for more details.
 
-## Latest Release: 0.1.1
+## Latest Release: 0.1.2
 
-This is a minor release with various bug fixes and documentation improvents.
+This is a minor release that fixes a critical bug that affects all previous releases.
+Update is strongly recommended.
 
 ### Bug Fixes
 
-- Fixed a potential issue with loading benchmark datasets' samples out of order (This behavior is not guaranteed, but a implementation detail)
-- Fixed an issue with ``DataLoader.load_dataset`` not recognizing downloaded datasets
-- Fixed an issue with ``preprocess.bead_normalization`` having uninitialized array (#9)
+- Fixed a critical issue with ``PyCytoData.load_dataset()`` not working due to old web source down ([#3](https://github.com/kevin931/PyCytoData/issues/3))
+    - This issue stems from upstream web source, thus affecting all previous releases.
+    - This update fixes the issue with a different implementation.
+    - There is no implementation change.
 
-### Changes and New Features
 
-- No new feature added
-- Improved documentations with streamlined front page and updated links
-- Added docstrings for `+` and `+=` operators
-- Updated references for CytofDR paper publication in Nature Communications
+### Changes and New Features
 
+- No new feature added.
 
 ## References
 

diff --git a/docs/source/change/index.rst b/docs/source/change/index.rst
@@ -9,26 +9,25 @@ doing!
 -------------------
 
 *************************
-Latest Release: v0.1.1
+Latest Release: v0.1.2
 *************************
 
-This is a minor release with various bug fixes and documentation improvents.
+This is a minor release that fixes a critical bug that affects all previous releases.
+Update is strongly recommended.
 
 Bug Fixes
 -----------
 
-- Fixed a potential issue with loading benchmark datasets' samples out of order (This behavior is not guaranteed, but a implementation detail)
-- Fixed an issue with ``DataLoader.load_dataset`` not recognizing downloaded datasets
-- Fixed an issue with ``preprocess.bead_normalization`` having uninitialized array (#9)
+- Fixed a critical issue with ``PyCytoData.load_dataset()`` not working due to old web source down (`#3 <https://github.com/kevin931/PyCytoData/issues/3>`_)
+    - This issue stems from upstream web source, thus affecting all previous releases.
+    - This update fixes the issue with a different implementation.
+    - There is no implementation change.
 
 
 Changes and New Features
 --------------------------
 
-- No new feature added
-- Improved documentations with streamlined front page and updated links
-- Added docstrings for `+` and `+=` operators
-- Updated references for CytofDR paper publication in Nature Communications
+- No new feature added.
 
 -------------------------
 

diff --git a/docs/source/change/releases.rst b/docs/source/change/releases.rst
@@ -6,6 +6,30 @@ Here we include our release notes for past releases in sequential order.
 
 ------------------
 
+********
+v0.1.2
+********
+
+This is a minor release that fixes a critical bug that affects all previous releases.
+Update is strongly recommended.
+
+Bug Fixes
+-----------
+
+- Fixed a critical issue with ``PyCytoData.load_dataset()`` not working due to old web source down (`#3 <https://github.com/kevin931/PyCytoData/issues/3>`_)
+    - This issue stems from upstream web source, thus affecting all previous releases.
+    - This update fixes the issue with a different implementation.
+    - There is no implementation change.
+
+
+Changes and New Features
+--------------------------
+
+- No new feature added.
+
+-------------------
+
+
 ********
 v0.1.1
 ********

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -6,11 +6,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'PyCytoData'
-copyright = '2022, PyCytoData Authors'
+copyright = '2022-2023, PyCytoData Authors'
 author = 'PyCytoData Authors'
 
 # The full version, including alpha/beta/rc tags
-release = '0.1.1'
+release = '0.1.2'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/tutorial/fileio.rst b/docs/source/tutorial/fileio.rst
@@ -211,8 +211,8 @@ Load Multiple Datasets at Once
 ------------------------------------
 
 If you have multiple samples in the same format (i.e. The columns are in the same
-configuration), you can load multiple samples at once into one single ``PyCytoData``
-object: 
+configuration after accounting for dropped columns as seen in the next section),
+you can load multiple samples at once into one single ``PyCytoData`` object: 
 
 .. code-block:: python
 
@@ -221,6 +221,9 @@ object:
     2
 
 All samples will be stored in a single object, but sample indices will be preserved.
+In the cases that channels are misaligned or mismatched, preprocessing on the users'
+side is needed to ensure that they are the same. Otherwise, a `ValueError` will be
+thrown. 
 
 Specifying Columns
 -------------------

diff --git a/meta.yaml b/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "PyCytoData" %}
-{% set version = "0.1.1" %}
+{% set version = "0.1.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: aad643a1a82162c3e9ee2072b57cdbef3493cf71ece106c31bba8798a4627c44
+  sha256: 54b6e8bb244653e9cf58efd2d7c11ae829f5de0b9cea569d27376d7e41e98829
 
 build:
   noarch: python

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 from typing import List
 
-VERSION = "0.1.1"
+VERSION = "0.1.2"
 
 class PypiCommand(distutils.cmd.Command):