Merge branch 'master' of github.com:joefutrelle/pyifcb into partialFileset87

Author: shravani-whoi

.github/workflows/pip-installation.yml

@@ -0,0 +1,27 @@
+name: Test Pip Install
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test-pip-install:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    
+    - name: Test pip installation
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install .
+        python -c "import ifcb"

README.md

@@ -1,40 +1,32 @@
-# pyifcb - Imaging FlowCytobot Python API, generation 2
+# pyifcb - Imaging FlowCytobot Python API
 
 ## Overview
 
-This module provides facilities for accessing and managing data generated by the Imaging FlowCytobot. It can read and write IFCB data in various formats, including the instrument's native format, and can serve as the basis of any application that uses IFCB data.
+This module provides facilities for accessing data generated by the Imaging FlowCytobot. It can read and write IFCB data in various formats, including the instrument's native format, and can serve as the basis of any application that uses IFCB data.
 
-Generation 1 of this data system was called the IFCB Data Dashboard. In this, generation 2, features of the dashboard are being broken out into smaller, independent modules that can be used together.
-
-## Authors and contributors
-
-Joe Futrelle ([email protected]) - Woods Hole Oceanographic Institution
-
-## Installation via anaconda
-
-To create a conda environment called "pyifcb":
+## Installation
 
+### With `pip`:
 ```
-conda env create -f environment.yml
-conda activate pyifcb
-python setup.py install
+pip install git+https://github.com/joefutrelle/pyifcb
 ```
+It is strongly recommended that you use a version tag when installing pyifcb. See [releases](https://github.com/joefutrelle/pyifcb/releases) for available version tags.
 
-Or to update an existing conda environment:
-
+For example to install pyifcb 1.1.1,
 ```
-conda update -n {name of existing envrionment} -f environment.yml
-conda activate {name of existing environment}
-python setup.py install
+pip install 'git+https://github.com/joefutrelle/[email protected]'
 ```
 
-If you want to update your pyifcb installation when the code is updated, use `python setup.py develop` instead.
-
-## Status
+### From the latest git commit:
+```
+git clone https://github.com/joefutrelle/pyficb
+cd pyifcb
+pip install .
+```
 
-As of 2017-04-28 pyifcb requires Python 3.
+## Documentation
 
-As of 2017-01-04 this is mostly complete and the APIs are not likely to change much, but there is no stable release yet so APIs may still change. The Wiki and code-level documentation is up to date.
+For complete documentation, see this repo's [wiki](https://github.com/joefutrelle/pyifcb/wiki).
 
 ![Build status](https://github.com/joefutrelle/pyifcb/actions/workflows/python-package.yml/badge.svg)
 

environment.yml

@@ -0,0 +1,54 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "pyifcb"
+version = "1.1.1"
+description = "Imaging FlowCytobot Python API, generation 2"
+readme = "README.md"
+authors = [{name = "Joe Futrelle", email = "[email protected]"}]
+classifiers = [
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: MIT License',
+    'Operating System :: POSIX :: Linux',
+    'Programming Language :: Python',
+    'Topic :: Scientific/Engineering',
+]
+keywords = ['FlowCytobot','Imaging','ifcb']
+dependencies = [
+    "scipy",
+    "pandas",
+    "h5py",
+    "requests",
+    "Pillow",
+    "rectpack",
+    "scikit-image",
+    "pysmb",
+    "smbprotocol",
+    "pyyaml",
+]
+
+[tool.hatch.build.targets.wheel]
+include = [
+    "ifcb/**/*",
+    "docs/**/*",
+    "auto_transfer.py",
+    "VERSION",
+    "LICENSE",
+    "README.md",
+    "transfer_config.yml.example",
+]
+
+[project.scripts]
+auto_transfer = "auto_transfer:main"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[project.urls]
+Repository = "https://github.com/joefutrelle/pyifcb"
+Documentation = "https://github.com/joefutrelle/pyifcb/wiki"
+Issues = "https://github.com/joefutrelle/pyifcb/issues"