Merge from eyurtsev/fcsparser

.github/workflows/release.yml

@@ -0,0 +1,38 @@
+name: release
+
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - 'pyproject.toml'
+  workflow_dispatch:
+
+env:
+  POETRY_VERSION: "1.3.1"
+
+jobs:
+  if_release:
+    # Disallow publishing from branches that aren't `master`.
+    if: github.ref == 'refs/heads/master'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install poetry
+        run: pipx install poetry==$POETRY_VERSION
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "poetry"
+      - name: Build project for distribution
+        run: poetry build
+      - name: Check Version
+        id: check-version
+        run: |
+          echo version=$(poetry version --short) >> $GITHUB_OUTPUT
+      - name: Publish to PyPI
+        env:
+          POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_API_TOKEN }}
+        run: | 
+          poetry publish

.github/workflows/test.yml

@@ -0,0 +1,33 @@
+name: test
+on:
+  push:
+    branches: [master]
+  pull_request:
+
+env:
+  POETRY_VERSION: "1.3.1"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install poetry
+        run: pipx install poetry==$POETRY_VERSION
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "poetry"
+      - name: Install dependencies
+        run: poetry install --with test
+      - name: Run unit tests
+        run: |
+          poetry run poe pytest

.gitignore

@@ -0,0 +1,10 @@
+.idea
+**/*.pyc
+.cache
+/venv
+/.vscode
+/build
+/dist
+versioneer.py
+/fcsparser.egg-info
+setup.cfg

.travis.yml

@@ -1,9 +1,47 @@
 language: python
+
+sudo: false
+
+
+cache:
+  directories:
+    - ~/.cache/pip
+
 env:
-    - TOXENV=py27
-    - TOXENV=py33
-    - TOXENV=py34
+  global:
+    - PIP_WHEEL_DIR=$HOME/.cache/pip/wheels
+    - PIP_FIND_LINKS=file://$HOME/.cache/pip/wheels
+
+matrix:
+  include:
+    - python: 2.7
+      env: PANDAS=0.16.2
+    - python: 2.7
+      env: PANDAS=0.17.1
+    - python: 2.7
+      env: PANDAS=0.18.1
+    - python: 3.5
+      env: PANDAS=0.16.2
+    - python: 3.5
+      env: PANDAS=0.17.1
+    - python: 3.5
+      env: PANDAS=0.18.1
+
+before_install:
+  - pip install -U pip
+  - pip install wheel
+
+
 install:
-    - pip install tox
-script:
-    - tox
+  - pip wheel numpy
+  - pip wheel -r requirements.test.txt
+
+  - pip install numpy
+  - pip install -r requirements.test.txt
+  - pip install pandas==$PANDAS
+
+script: 
+  - py.test fcsparser/ --cov fcsparser -v --cov-report term-missing
+
+after_success:
+  - coveralls

AUTHORS

@@ -5,4 +5,7 @@ Here is the list of the primary authors & contributors:
     Aymeric Duclert
     Ben Roth
     Jaime X. Ramos
-    Vanessa Jonsson
+    Vanessa Jonsson
+    Oskari Mantere
+    Augustine (Gus) Dunn
+    Nathanael Lampe

CHANGE_LOG

@@ -1,2 +1,41 @@
-v0.1.2: 2015-12-28: Bug fix for unicode issues
-v0.1.0: 2015-09-03 Repository separated from FlowCytometryTools
+v0.2.3 (2021-10-07): Support for parsing more types of FCS files
+
+PR from Brian Teague to support FCS files generated by Cytek xP5 which
+involve 3-byte fields.
+
+v0.2.2 (2021-08-13): Bug fixes
+
+Author: Brian Teague <bpteague@gmail.com>
+Date:   Fri Aug 13 13:42:19 2021 -0400
+
+    parse TEXT segments that don't end with a delimiter (#27)
+
+
+v0.2.1 (2020-05-13): Bug fixes
+
+Max Zhao (2):
+      Adding encoding option setting for reading fcs files
+      Add bitmask to mask bits outside of specified data range (#22)
+
+cericson (1):
+      Bugfix: Handle repeated TEXT delimiter (#18)
+
+monchin (1):
+      To avoid 'text end' equals 'data start' (#20)
+
+
+v0.2.0 (2018-02-19):
+
+- python2/3 compatibility fix 
+
+*Breaking changes*
+
+- pandas is required
+- removed (output_datatype) kwarg in parse
+- data is automatically converted to float32 to protect the user from making 
+  mistakes when the data type is mixed (but the user can choose to turn
+  conversion off).
+
+v0.1.2 (2015-12-28): Bug fix for unicode issues
+
+v0.1.0 (2015-09-03): Repository separated from FlowCytometryTools

CONTRIBUTING.md

@@ -0,0 +1,39 @@
+# Contributing
+
+Thanks for your interest in contributing to the parser!
+
+I no longer work on flow cytometry, so I will not personally develop any
+new features; howevever, PRs are welcome. 
+
+Be aware that I may comandeer the PRs and refactor them a bit.
+
+## Setting up for development
+
+The package uses [poetry](https://python-poetry.org/) together with
+[poethepoet](https://github.com/nat-n/poethepoet).
+
+### Install dependencies
+
+```shell
+
+poetry install --with dev,test
+```
+
+### List tasks
+
+```shell
+poe
+```
+
+### autoformat
+
+```shell
+poe autoformat
+```
+
+### unit tests 
+
+```shell
+poe pytest
+```
+

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015 Eugene Yurtsev
+Copyright (c) 2018 Eugene Yurtsev
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -1,2 +1,3 @@
 include *.txt
 global-include *.fcs
+include fcsparser/_version.py

README.rst

@@ -1,17 +1,21 @@
 FCSParser
 =================
 
-fcsparser is a python package for reading fcs files. 
 
-.. image:: https://travis-ci.org/eyurtsev/fcsparser.svg?branch=master
-   :target: http://travis-ci.org/eyurtsev/fcsparser
-   :alt: Build Status
+fcsparser is a python package for reading fcs files. 
 
+.. image:: https://github.com/eyurtsev/kor/actions/workflows/test.yml/badge.svg?branch=main&event=push   
+   :target: https://github.com/eyurtsev/kor/actions/workflows/test.yml
+   :alt: Unit Tests
 
 Install
 ==================
 
     $ pip install fcsparser
+
+or
+
+    $ conda install -c conda-forge fcsparser
 
 Using
 ==================
@@ -20,15 +24,14 @@ Using
     >>> path = fcsparser.test_sample_path
     >>> meta, data = fcsparser.parse(path, reformat_meta=True)
 
-A more detailed example can be found here: http://nbviewer.ipython.org/github/eyurtsev/fcsparser/blob/master/doc/fcsparser_example.ipynb
-
+A more detailed example can be found here: https://github.com/eyurtsev/fcsparser/blob/master/doc/fcsparser_example.ipynb
 
 Features
 ===================
 
-- **python**: 2.7, 3.3, 3.4
+- **python**: 3.8, 3.9, 3.10, 3.11
 - **FCS Formats**: Supports FCS 2.0, 3.0, and 3.1
-- **FCS Machines**: BD FACSCalibur, BD LSRFortessa, BD LSR-II, MiltenyiBiotec MACSQuant VYB
+- **FCS Machines**: BD FACSCalibur, BD LSRFortessa, BD LSR-II, MiltenyiBiotec MACSQuant VYB, Sony SH800
 
 Contributing
 =================
@@ -52,7 +55,7 @@ LICENSE
 
 The MIT License (MIT)
 
-Copyright (c) 2013-2015 Eugene Yurtsev
+Copyright (c) 2013-2023 Eugene Yurtsev
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

fcsparser/__init__.py

@@ -1,8 +1,20 @@
 import os
 
-from fcsparser._version import version as __version__
-from fcsparser.api import parse
+from .api import parse
+from .version import __version__
 
-test_sample_path = os.path.join(os.path.abspath(os.path.dirname(__file__)),
-    'tests', 'data', 'FlowCytometers', 'HTS_BD_LSR-II', 'HTS_BD_LSR_II_Mixed_Specimen_001_D6_D06.fcs')
+test_sample_path = os.path.join(
+    os.path.abspath(os.path.dirname(__file__)),
+    "tests",
+    "data",
+    "FlowCytometers",
+    "HTS_BD_LSR-II",
+    "HTS_BD_LSR_II_Mixed_Specimen_001_D6_D06.fcs",
+)
 
+
+__all__ = [
+    "parse",
+    "__version__",
+    "test_sample_path",
+]