Merge branch 'develop'

Author: whitews

.github/workflows/test_base.yml

@@ -7,7 +7,7 @@ jobs:
   test:
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     runs-on: ubuntu-latest
 

.github/workflows/test_flowkit_develop.yml

@@ -11,33 +11,52 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.12"]
 
     steps:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Upgrade pip
+        run:
+          pip install --upgrade pip
+
       - name: Checkout FlowIO
         uses: actions/checkout@v4
         with:
           ref: develop
           path: flowio
 
+      - name: Checkout FlowUtils
+        uses: actions/checkout@v4
+        with:
+          repository: whitews/FlowUtils
+          ref: develop
+          path: flowutils
+
       - name: Checkout FlowKit (develop)
         uses: actions/checkout@v4
         with:
           repository: whitews/FlowKit
           ref: develop
           path: flowkit
 
+      - name: Install FlowIO
+        working-directory: flowio
+        run: |
+          pip install .
+
+      - name: Install FlowUtils
+        working-directory: flowutils
+        run: |
+          pip install .
+
       - name: Install FlowKit
         working-directory: flowkit
         run: |
-          pip install --upgrade pip
           pip install .
-          pip install ../flowio
 
       - name: Run FlowKit tests
         working-directory: flowkit

.github/workflows/test_flowkit_master.yml

@@ -11,7 +11,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.12"]
 
     steps:
       - name: Setup Python

.readthedocs.yaml

@@ -8,6 +8,10 @@ build:
 python:
   install:
     - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
 
 sphinx:
    configuration: docs/conf.py

README.md

@@ -14,26 +14,18 @@
 
 ## Overview
 
-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 
-can be used to easily convert the event data to a multi-column NumPy array:
-
-```
-import flowio
-import numpy
-
-fcs_data = flowio.FlowData('example.fcs')
-npy_data = numpy.reshape(fcs_data.events, (-1, fcs_data.channel_count))
-```
-
-For higher level interaction with flow cytometry data, including GatingML and FlowJo 10 support, 
-see the related [FlowKit](https://github.com/whitews/FlowKit) project.
+FlowIO is a Python library for reading and writing Flow Cytometry Standard (FCS)
+files, with minimal dependencies and is compatible with Python 3.9+. It is intended 
+as a lightweight library, suitable for parsing FCS data sets (e.g. as a web server 
+backend, for simple metadata extraction, etc.). It is **highly recommended** that 
+one be familiar with the various FCS file standards (2.0, 3.0, 3,1) before using 
+FlowIO for downstream analysis. For higher level cytometry analysis, please see the 
+related [FlowKit](https://github.com/whitews/FlowKit) library which offers a much 
+wider set of analysis options such as compensation, transformation, and gating 
+support (including support for importing FlowJo 10 workspaces).
+
+If you have any questions about FlowIO, find any bugs, or feel something is missing 
+from the documentation [please submit an issue to the GitHub repository here](https://github.com/whitews/FlowIO/issues/new/).
 
 ## Installation