Merge branch 'develop'

.github/workflows/tests_develop.yml

@@ -10,4 +10,5 @@ on:
 
 jobs:
   test:
-    uses: whitews/FlowIO/.github/workflows/test_base.yml@develop
+    uses: whitews/FlowIO/.github/workflows/test_base.yml@develop
+    secrets: inherit

README.md

@@ -17,9 +17,10 @@ FlowIO is a Python library for reading / writing Flow Cytometry Standard (FCS)
 files, with zero external dependencies and is compatible with Python 3.7+.
 
 FlowIO retrieves event data exactly as it is encoded in the FCS file: as a 
-1-dimensional list without separating the events into channels or performing any preprocessing (e.g. applying gain). Metadata 
-stored in the FCS file is available as a dictionary via the 'text' attribute. Basic attributes
-are also available for commonly accessed properties. For example, the channel count 
+1-dimensional list without separating the events into channels or performing 
+any preprocessing (e.g. applying gain). Metadata stored in the FCS file is 
+available as a dictionary via the 'text' attribute. Basic attributes are also 
+available for commonly accessed properties. For example, the channel count 
 can be used to easily convert the event data to a multi-column NumPy array:
 
 ```
@@ -46,7 +47,7 @@ Or, if you prefer, you can install from the GitHub source:
 ```
 git clone https://github.com/whitews/flowio
 cd flowio
-python setup.py install
+pip install .
 ```
 
 ## Documentation

docs/conf.py

@@ -68,7 +68,7 @@ def __getattr__(cls, name):
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
 
 html_theme_options = {
     # 'logo': 'flowutils.png',

docs/index.rst

@@ -16,15 +16,14 @@ FlowIO Documentation
     :target: https://pypi.org/project/flowio/
 
 FlowIO is a Python library for reading / writing Flow Cytometry Standard (FCS)
-files and has zero external dependencies. FlowIO is compatible with Python 3.7+
-(FlowIO v0.9.9 was the last release supporting Python 2).
+files, with zero external dependencies and is compatible with Python 3.7+.
 
 FlowIO retrieves event data exactly as it is encoded in the FCS file: as a
 1-dimensional list without separating the events into channels or performing
-any preprocessing (e.g. applying gain). However, all the metadata stored in the
-FCS file is available as a dictionary via the 'text' attribute. Basic attributes
-are also available for commonly accessed properties. For example, the channel
-count can be used to easily convert the event data to a multi-column NumPy array:
+any preprocessing (e.g. applying gain). Metadata stored in the FCS file is
+available as a dictionary via the 'text' attribute. Basic attributes are also
+available for commonly accessed properties. For example, the channel count
+can be used to easily convert the event data to a multi-column NumPy array:
 
 .. code-block:: python
 
@@ -60,7 +59,7 @@ Or, if you prefer, you can install from the GitHub source:
 
     git clone https://github.com/whitews/flowio
     cd flowio
-    python setup.py install
+    pip install .
 
 ----
 

docs/requirements.txt

@@ -1 +1,3 @@
-Sphinx>=3
+Sphinx==6.2.1
+autoclasstoc
+sphinx_rtd_theme==1.2.1

src/flowio/_version.py

@@ -1,4 +1,4 @@
 """
 FlowIO version
 """
-__version__ = "1.2.2b2"
+__version__ = "1.2.2b3"