.github/workflows/test_base.yml

@@ -0,0 +1,40 @@
+name: Test
+
+on:
+  workflow_call:
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install
+        run: |
+          pip install --upgrade pip
+          pip install coverage
+          pip install -e .[test]
+
+      - name: Run tests with coverage
+        run: |
+          coverage run --source flowio run_tests.py
+          coverage xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: coverage.xml
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

.github/workflows/test_flowkit_develop.yml

@@ -0,0 +1,45 @@
+name: Test FlowKit downstream (develop)
+
+on:
+  push:
+    branches:
+      - develop
+
+jobs:
+  test-develop:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Checkout FlowIO
+        uses: actions/checkout@v4
+        with:
+          ref: develop
+          path: flowio
+
+      - name: Checkout FlowKit (develop)
+        uses: actions/checkout@v4
+        with:
+          repository: whitews/FlowKit
+          ref: develop
+          path: flowkit
+
+      - name: Install FlowKit
+        working-directory: flowkit
+        run: |
+          pip install --upgrade pip
+          pip install .
+          pip install ../flowio
+
+      - name: Run FlowKit tests
+        working-directory: flowkit
+        run: |
+          python3 ./run_tests.py

.github/workflows/test_flowkit_master.yml

@@ -0,0 +1,45 @@
+name: Test FlowKit downstream (master)
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  test-master:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Checkout FlowIO
+        uses: actions/checkout@v4
+        with:
+          ref: master
+          path: flowio
+
+      - name: Checkout FlowKit (master)
+        uses: actions/checkout@v4
+        with:
+          repository: whitews/FlowKit
+          ref: master
+          path: flowkit
+
+      - name: Install FlowKit
+        working-directory: flowkit
+        run: |
+          pip install --upgrade pip
+          pip install .
+          pip install ../flowio
+
+      - name: Run FlowKit tests
+        working-directory: flowkit
+        run: |
+          python3 ./run_tests.py

.github/workflows/tests_develop.yml

@@ -0,0 +1,14 @@
+name: Test (develop)
+
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+jobs:
+  test:
+    uses: whitews/FlowIO/.github/workflows/test_base.yml@develop
+    secrets: inherit

.github/workflows/tests_master.yml

@@ -0,0 +1,14 @@
+name: Test (master)
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    uses: whitews/FlowIO/.github/workflows/test_base.yml@master
+    secrets: inherit

.gitignore

@@ -4,6 +4,8 @@
 .DS_Store
 build/
 dist/
+scratch/
 *.egg
 *.fcs
 *.egg-info
+/docs/_build/*

.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+   configuration: docs/conf.py

MANIFEST.in

@@ -0,0 +1,2 @@
+include LICENSE
+prune tests/

README.md

@@ -3,15 +3,34 @@
 [![PyPI license](https://img.shields.io/pypi/l/flowio.svg?colorB=dodgerblue)](https://pypi.python.org/pypi/flowio/)
 [![PyPI pyversions](https://img.shields.io/pypi/pyversions/flowio.svg)](https://pypi.python.org/pypi/flowio/)
 [![PyPI version](https://img.shields.io/pypi/v/flowio.svg?colorB=blue)](https://pypi.python.org/pypi/flowio/)
+[![DOI](https://zenodo.org/badge/14634514.svg)](https://zenodo.org/badge/latestdoi/14634514)
 
-[![Build Status](https://travis-ci.com/whitews/FlowIO.svg?branch=master)](https://travis-ci.com/whitews/FlowIO)
+
+[![Test (master)](https://github.com/whitews/FlowIO/actions/workflows/tests_master.yml/badge.svg)](https://github.com/whitews/FlowIO/actions/workflows/tests_master.yml)
+[![Test (develop)](https://github.com/whitews/FlowIO/actions/workflows/tests_develop.yml/badge.svg)](https://github.com/whitews/FlowIO/actions/workflows/tests_develop.yml)
 [![Coverage](https://codecov.io/gh/whitews/FlowIO/branch/master/graph/badge.svg)](https://codecov.io/gh/whitews/flowio)
 [![Documentation Status](https://readthedocs.org/projects/flowio/badge/?version=latest)](https://flowio.readthedocs.io/en/latest/?badge=latest)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/flowio)
 
 ## Overview
 
 FlowIO is a Python library for reading / writing Flow Cytometry Standard (FCS) 
-files and has zero external dependencies. FlowIO is compatible with Python 3 (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). 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.
@@ -29,21 +48,14 @@ 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 .
 ```
 
-## Usage
+## Documentation
 
-FlowIO retrieves event data exactly as it is encoded in the FCS file: as a 
-1-dimensional list without separating the events into channels. However, all the metadata 
-found within 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:
+The FlowIO API documentation is available [on ReadTheDocs here](https://flowio.readthedocs.io/en/latest/?badge=latest). If you have any questions about FlowIO or find any bugs [please submit an issue to the GitHub repository here](https://github.com/whitews/FlowIO/issues/new/).
 
-```
-import flowio
-import numpy
+### Changelogs
+
+[Changelogs for versions are available here](https://github.com/whitews/FlowIO/releases)
 
-fcs_data = flowio.FlowData('example.fcs')
-npy_data = numpy.reshape(fcs_data.events, (-1, fcs_data.channel_count))
-```

docs/_static/css/custom.css

@@ -10,4 +10,12 @@ dl.method {
 dl.function {
     margin-top: 27px;
     margin-left: 17px;
+}
+
+dt.field-even {
+    padding-top: 27px;
+}
+
+dd.field-even {
+    padding-top: 27px;
 }

docs/api.rst

@@ -1,17 +1,27 @@
+.. currentmodule:: flowio
+
 FlowIO API
 ===================================
 
-FlowIO includes a single FlowData class for reading existing FCS files and
-a :code:`create_fcs` function for creating new FCS files.
-
 FlowData Class
 --------------
 
-.. autoclass:: flowio.FlowData
+.. autoclass:: FlowData
     :members:
 
+
+Reading FCS Files with Multiple Data Sets
+-----------------------------------------
+
+.. autofunction:: read_multiple_data_sets
+
 Creating New FCS Files
 ----------------------
 
-.. automodule:: flowio.create_fcs
-   :members:
+.. autofunction:: create_fcs
+
+FlowIO Exceptions
+-----------------
+
+.. automodule:: flowio.exceptions
+   :members:

docs/conf.py

@@ -10,9 +10,9 @@
 
 on_rtd = os.environ.get('READTHEDOCS') == 'True'
 if on_rtd:
-    sys.path.insert(0, os.path.abspath('..'))
+    sys.path.insert(0, os.path.abspath('../src'))
 else:
-    sys.path.insert(0, os.path.abspath('../..'))
+    sys.path.insert(0, os.path.abspath('../src'))
 
 
 class Mock(MagicMock):
@@ -68,13 +68,13 @@ 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',
-    'github_user': 'whitews',
-    'github_repo': 'flowio',
-    'github_banner': True
+    # 'logo': 'logo.png',
+    # 'github_user': 'whitews',
+    # 'github_repo': 'flowio',
+    # 'github_banner': True
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,