Add pyproject.toml and update github actions (#277)

* add pyproject and update github actions

* fix test action

* import bioscrape in try-except

* readme update for CI and version

* setup version update

* add pypi release github action

.github/workflows/deploy.yml

@@ -0,0 +1,34 @@
+name: BioCRNpyler Deploy 
+on:
+  push:
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]  
+jobs:
+  build:
+      runs-on: ${{ matrix.os }}
+      strategy:
+        matrix:
+          os: [windows-latest, ubuntu-latest, macos-latest]
+          python-version: [3.8, 3.11, 3.12]
+      steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pytest-cov python-libsbml
+      - name: Tnstall biocrnpyler
+        run: pip install -e .[all]
+      - name: Test biocrnpyler
+        run: pytest --cov biocrnpyler
+      - uses: actions/checkout@main
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: false 
+          name: codecov-umbrella
+          token: ${{ secrets.CODECOV_TOKEN }} 
+          verbose: false

.github/workflows/pypi-release.yml

@@ -0,0 +1,30 @@
+# Manually run this action
+name: PyPI Release
+
+on:
+  workflow_dispatch:
+
+jobs:
+  pypi-publish:
+    runs-on: ubuntu-latest
+    environment: Release Deploy
+
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.12' 
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build  
+
+      - name: Build the package
+        run: |
+          python -m build
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN}}

.github/workflows/test.yml

@@ -0,0 +1,33 @@
+name: BioCRNpyler Test
+on:
+  push:
+    branches: ["*","!master"]
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 4
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.12"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pytest-cov python-libsbml
+      - name: Tnstall biocrnpyler
+        run: pip install -e .[all]
+      - name: Test biocrnpyler
+        run: pytest --cov biocrnpyler
+      - uses: actions/checkout@main
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: false 
+          name: codecov-umbrella
+          token: ${{ secrets.CODECOV_TOKEN }} 
+          verbose: false

README.md

@@ -1,7 +1,7 @@
 # BioCRNPyler — Biomolecular Chemical Reaction Network Compiler
 ## Python toolbox to create CRN models in SBML for biomolecular mechanisms
 
-[![Build Status](https://travis-ci.com/BuildACell/BioCRNPyler.svg?branch=master)](https://travis-ci.com/BuildACell/BioCRNPyler)
+[![Build Status](https://github.com/buildacell/biocrnpyler/actions/workflows/deploy.yml/badge.svg)](https://github.com/biocircuits/bioscrape/actions/workflows/deploy_bioscrape.yml)
 [![codecov](https://codecov.io/gh/BuildACell/BioCRNPyler/branch/master/graph/badge.svg)](https://codecov.io/gh/BuildACell/BioCRNPyler)
 [![PyPI version](https://badge.fury.io/py/biocrnpyler.svg)](https://badge.fury.io/py/biocrnpyler)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/BuildACell/BioCRNPyler/master?filepath=%2Fexamples%2F)
@@ -111,12 +111,13 @@ see [contribution guidelines](https://github.com/BuildACell/BioCRNPyler/blob/mas
 
 BioCRNpyler versions:
 
-* 1.0.2 (latest stable release): To install run `pip install biocrnpyler` 
+* 1.1.2 (latest stable release): To install run `pip install biocrnpyler` 
+* 1.1.1 (previous stable release, compatible only with python <= 3.10): To install run `pip install biocrnpyler==1.1.1` 
 * 0.9.0 (beta release): To install run `pip install biocrnpyler==0.9.0`
 * 0.2.1 (alpha release): To install run `pip install biocrnpyler==0.2.1`
 
 # License
 Released under the BSD 3-Clause License (see `LICENSE`)
 
-Copyright (c) 2020, Build-A-Cell. All rights reserved.
+Copyright (c) 2024, Build-A-Cell. All rights reserved.
 

pyproject.toml

@@ -0,0 +1,58 @@
+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.distutils.bdist_wheel]
+universal = true
+
+[project]
+name = "BioCRNpyler"
+version = "1.1.2"
+description = "A chemical reaction network compiler for generating large biological circuit models"
+authors = [{name='Build-A-Cell'}]
+classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: BSD License',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Topic :: Software Development',
+        'Topic :: Scientific/Engineering',
+        'Operating System :: OS Independent',
+    ]
+license = {file = "LICENSE"}
+readme = "README.md"
+keywords=["SBML", "synthetic biology", "modeling",
+          "Chemical Reaction Network", "CRN"]
+dependencies = [
+    "python-libsbml",
+    "numpy<2.0",
+    "matplotlib",
+    "networkx",
+    "bokeh>=1.4.0",
+    "fa2_modified",
+    "jupyter",
+    "pytest",
+    "pytest-cov",
+    "nbconvert"
+]
+requires-python = ">=3.7"
+
+[project.optional-dependencies]
+test = [
+  "pytest"
+]
+
+[project.urls]
+"Homepage" = "https://github.com/buildacell/biocrnpyler/"
+"Bug Tracker" = "https://github.com/buildacell/biocrnpyler/issues"
+
+[tool.setuptools]
+packages = ["biocrnpyler"]
+include-package-data = true
+package-dir = {"biocrnpyler"="biocrnpyler"}

setup.py

@@ -6,8 +6,8 @@
 
 setup(
     name='biocrnpyler',
-    version='1.1.1',
-    author='BuildACell',
+    version='1.1.2',
+    author='Build-A-Cell',
     url='https://github.com/BuildACell/biocrnpyler/',
     description='A chemical reaction network compiler for generating large biological circuit models',
     long_description=long_description,