Update Synapse formation

.github/workflows/ci.yml

@@ -20,9 +20,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.9, '3.10', '3.11']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -72,10 +72,10 @@ jobs:
     if: startsWith(github.ref, 'refs/tags')
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: '3.11'
       - name: Create a source distribution
         run: python setup.py sdist
       - name: Publish package to PyPI
@@ -93,10 +93,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v2.1.0
+        uses: docker/login-action@v3
         if: github.event_name != 'pull_request'
         with:
           registry: ghcr.io
@@ -105,12 +105,12 @@ jobs:
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@v4.1.1
+        uses: docker/metadata-action@v5
         with:
           images: ghcr.io/${{ github.repository }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v3.2.0
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: ${{ github.event_name != 'pull_request' }}

.pre-commit-config.yaml

@@ -0,0 +1,68 @@
+exclude: "^docs/conf.py|^docs/build/"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-xml
+      - id: check-yaml
+        exclude: ^mkdocs\.yml$
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer
+      - id: mixed-line-ending
+        args: ["--fix=auto"] # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+  # - repo: https://github.com/astral-sh/ruff-pre-commit
+  #   rev: "v0.0.270"
+  #   hooks:
+  #     - id: ruff
+
+  # - repo: https://github.com/pycqa/isort
+  #   rev: 5.13.2
+  #   hooks:
+  #     - id: isort
+  #       name: isort (python)
+
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        language_version: python3
+
+  # - repo: https://github.com/PyCQA/bandit
+  #   rev: 1.7.5
+  #   hooks:
+  #     - id: bandit
+  #       args: ["-c", "pyproject.toml"]
+  #       additional_dependencies: ["bandit[toml]"]
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.12.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
+# - repo: https://github.com/pre-commit/mirrors-mypy
+#   rev: 'v1.0.1'
+#   hooks:
+#   - id: mypy
+#     additional_dependencies: [pydantic~=1.10]
+
+# Checks for missing docstrings
+# - repo: https://github.com/econchick/interrogate
+#   rev: 1.5.0
+#   hooks:
+#   - id: interrogate
+#     exclude: ^(docs/conf.py|setup.py|tests)
+#     args: [--config=pyproject.toml]
+
+# finds dead python code
+# - repo: https://github.com/jendrikseipp/vulture
+#   rev: 'v2.7'
+#   hooks:
+#     - id: vulture

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.9-slim-buster
+FROM python:3.11
 
 WORKDIR /root/synapseformation
 COPY . ./

README.md

@@ -1,7 +1,11 @@
 # synapseformation
 
-[![Get synapseformation from PyPI](https://img.shields.io/pypi/v/synapseformation.svg?style=for-the-badge&logo=pypi)](https://pypi.python.org/pypi/synapseformation) [![GitHub CI](https://img.shields.io/github/workflow/status/Sage-Bionetworks/synapseformation/build.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/Sage-Bionetworks/synapseformation)
-[![Coverage Status](https://img.shields.io/coveralls/github/Sage-Bionetworks/synapseformation.svg?&style=for-the-badge&label=coverage&logo=Coveralls)](https://coveralls.io/github/Sage-Bionetworks/synapseformation)
+[![Get synapseformation from PyPI](https://img.shields.io/pypi/v/synapseformation.svg?&logo=pypi)](https://pypi.python.org/pypi/synapseformation)
+[![Coverage Status](https://img.shields.io/coveralls/github/Sage-Bionetworks/synapseformation.svg?&label=coverage&logo=Coveralls)](https://coveralls.io/github/Sage-Bionetworks/synapseformation)
+[![build](https://github.com/Sage-Bionetworks/synapseformation/actions/workflows/ci.yml/badge.svg)](https://github.com/Sage-Bionetworks/synapseformation/actions/workflows/ci.yml)
+
+> [!WARNING]
+> This package is not actively maintained and is an MVP. The functionality and dependencies may change at any time, but will follow semantic versioning guidelines. Use at your own risk.
 
 
 Client for using [Synapse Formation Templates](templates). Given one of these templates, `synapseformation` will be able to create all the components required in a Synapse Project.  Currently the implementation does one of these two scenarios.

setup.cfg

@@ -0,0 +1,44 @@
+[metadata]
+name = synapseformation
+version = attr: synapseformation.__version__.__version__
+description = Client for using Synapse Formation templates.
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/Sage-Bionetworks/synapseformation
+author = Thomas Yu
+license = Apache-2.0
+license_files = LICENSE
+classifiers =
+    Development Status :: 5 - Production/Stable
+    Programming Language :: Python
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Operating System :: MacOS
+    Operating System :: Microsoft :: Windows
+    Operating System :: Unix
+    Operating System :: POSIX :: Linux
+    Intended Audience :: Developers
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: Apache Software License
+    Topic :: Software Development :: Libraries
+    Topic :: Scientific/Engineering
+    Topic :: Scientific/Engineering :: Bio-Informatics
+
+project_urls =
+    Documentation = https://github.com/Sage-Bionetworks/synapseformation
+    Source Code = https://github.com/Sage-Bionetworks/synapseformation
+    Bug Tracker = https://github.com/Sage-Bionetworks/synapseformation/issues
+
+[options]
+packages = find:
+python_requires = >=3.9, <3.12
+zip_safe = False
+install_requires =
+    click
+    synapseclient>=4.0.0
+    pyyaml
+
+[options.entry_points]
+console_scripts =
+    synapseformation = synapseformation.__main__:cli

setup.py

@@ -1,53 +1,3 @@
-"""Setup"""
-import os
-from setuptools import setup, find_packages
+from setuptools import setup
 
-# figure out the version
-about = {}
-here = os.path.abspath(os.path.dirname(__file__))
-with open(os.path.join(here, "synapseformation", "__version__.py")) as f:
-    exec(f.read(), about)
-
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-setup(
-    name='synapseformation',
-    version=about["__version__"],
-    description='Client for using Synapse Formation templates.',
-    url='https://github.com/Sage-Bionetworks/synapseformation',
-    author='Kenneth Daily,Thomas Yu,Kelsey Montgomery',
-    license='Apache',
-    packages=find_packages(),
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    zip_safe=False,
-    python_requires='>=3.6',
-    entry_points={'console_scripts': ['synapseformation = synapseformation.__main__:cli']},
-    install_requires=['click',
-                      'synapseclient>=2.4.0',
-                      'pyyaml'],
-    project_urls={
-        "Documentation": "https://github.com/Sage-Bionetworks/synapseformation",
-        "Source Code": "https://github.com/Sage-Bionetworks/synapseformation",
-        "Bug Tracker": "https://github.com/Sage-Bionetworks/synapseformation/issues",
-    },
-    classifiers=[
-        'Development Status :: 5 - Production/Stable',
-        'Programming Language :: Python',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-        'Operating System :: MacOS',
-        'Operating System :: Microsoft :: Windows',
-        'Operating System :: Unix',
-        'Operating System :: POSIX :: Linux',
-        'Intended Audience :: Developers',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: Apache Software License',
-        'Topic :: Software Development :: Libraries',
-        'Topic :: Scientific/Engineering',
-        'Topic :: Scientific/Engineering :: Bio-Informatics'
-    ],
-)
+setup()

synapseformation/__main__.py

@@ -1,11 +1,10 @@
 """synapseformation command line client"""
 import click
-
 import synapseclient
 
+from .__version__ import __version__
 from .client import create_synapse_resources
 from .utils import synapse_login
-from .__version__ import __version__
 
 
 def add_version(f):
@@ -38,10 +37,15 @@ def cli():
 
 
 @cli.command()
-@click.option('--template_path', help='Template path', type=click.Path())
-@click.option('-c', '--config_path', help='Synapse configuration file',
-              type=click.Path(), show_default=True,
-              default=synapseclient.client.CONFIG_FILE)
+@click.option("--template_path", help="Template path", type=click.Path())
+@click.option(
+    "-c",
+    "--config_path",
+    help="Synapse configuration file",
+    type=click.Path(),
+    show_default=True,
+    default=synapseclient.client.CONFIG_FILE,
+)
 def create(template_path, config_path):
     """Creates Synapse Resources given a yaml or json"""
     syn = synapse_login(synapse_config=config_path)

synapseformation/__version__.py

@@ -1 +1 @@
-__version__ = "0.0.3"
+__version__ = "0.0.3"