Move to using pyproject.toml exclusively for dependency management

.github/workflows/main.yml

@@ -21,14 +21,13 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.12"
+          python-version-file: "pyproject.toml"
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          pip install -e .[dev]
           make
-          pip install -e .
 
       - name: Run tests with pytest
         run: |
@@ -47,19 +46,20 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.12"
+          python-version-file: "pyproject.toml"
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          make
           pip install -e .
-
+          make
+
+      - name: Run examples
+        run: |
           synapse-sim --iface-ip 127.0.0.1 --rpc-port 50051 &
 
           sleep 2
 
           python synapse/examples/stream_out.py 127.0.0.1:50051
 
-          kill $(jobs -p)
+          kill $(jobs -p)

.gitignore

@@ -97,7 +97,7 @@ ipython_config.py
 # pyenv
 #   For a library or package, you might want to ignore these files since the code is
 #   intended to run in multiple environments; otherwise, check them in:
-# .python-version
+.python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.

README.md

@@ -158,14 +158,16 @@ For an example, see the [Blackrock Neurotech CerePlex driver](https://github.com
 Dependencies:
 
     git submodule update --init
-    pip install -r requirements.txt
+    pip install .
     ./setup.sh all
     # or
     make all
 
 To build and install in development mode:
 
-    pip install -e .
+    git submodule update --init
+    pip install -e .[dev]
+    make
 
 To build and install a wheel:
 
@@ -176,6 +178,13 @@ To build and install a wheel:
 
 ## Development
 
+It is highly recommened setting up a [virtual python environment](https://docs.python.org/3/library/venv.html) if you are actively developing this repo:
+```bash
+python -m venv .venv
+
+source .venv/bin/activate
+```
+
 If you want to catch linting errors before pushing, you can install a pre-commit hook.
 
 ```bash

pyproject.toml

@@ -1,3 +1,47 @@
+[project]
+name = "science-synapse"
+version = "2.0.0"
+description = "Client library and CLI for the Synapse API"
+authors = [{name = "Science Team", email = "team@science.xyz"}]
+readme = "README.md"
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+
+requires-python = ">=3.9"
+dependencies = [
+    "build>=1.2.2.post1",
+    "coolname>=2.2.0",
+    "crcmod>=1.7",
+    "dearpygui>=2.0.0",
+    "grpcio>=1.71.0",
+    "grpcio-tools>=1.71.0",
+    "numpy>=2.0.0",
+    "pandas>=2.2.0",
+    "paramiko >=3.5.1",
+    "protobuf>=5.29",
+    "protoletariat>=3.3.9",
+    "pyqt5>=5.15.11",
+    "pyqtgraph>=0.13.7",
+    "pyserial>=3.5",
+    "pyyaml>=6.0",
+    "pyzmq>=26.3.0",
+    "rich>=13.9.4",
+    "scipy>=1.13.1",
+]
+
+[project.optional-dependencies]
+dev = [
+    "ruff>=0.9.10",
+    "pre-commit>=4.1.0",
+    "pytest>=8.3.5",
+    "pytest-asyncio>=0.25.3",
+]
+
 [build-system]
-requires = ["setuptools", "wheel", "Cython", "crcmod"]
+requires = ["setuptools", "wheel", "Cython"]
 build-backend = "setuptools.build_meta"
+
+
+[project.scripts]
+synapsectl = "synapse.cli:main"
+synapse-sim = "synapse.simulator:main"

setup.py

@@ -1,6 +1,5 @@
-from setuptools import setup, find_packages, Extension
+from setuptools import setup, Extension
 from Cython.Build import cythonize
-from pathlib import Path
 import os
 
 extra_compile_args = []
@@ -13,9 +12,6 @@
         "-O3",
     ]
 
-this_directory = Path(__file__).parent
-long_description = (this_directory / "README.md").read_text()
-
 extensions = [
     Extension(
         "synapse.utils.ndtp",
@@ -25,40 +21,8 @@
 ]
 
 setup(
-    name="science-synapse",
-    version="2.0.0",
-    description="Client library and CLI for the Synapse API",
-    author="Science Team",
-    author_email="team@science.xyz",
-    packages=find_packages(include=["synapse", "synapse.*"]),
-    long_description=long_description,
-    long_description_content_type="text/markdown",
     ext_modules=cythonize(
         extensions,
         compiler_directives={"language_level": "3"},
     ),
-    python_requires=">=3.9",
-    install_requires=[
-        "coolname",
-        "grpcio-tools",
-        "protoletariat",
-        "numpy >=2.0.0",
-        "pyserial",
-        "scipy",
-        "crcmod",
-        "rich",
-        "pyqtgraph",
-        "pyqt5",
-        "pandas >=2.2.0",
-        "dearpygui",
-        "pyzmq",
-        "pyyaml",
-        "paramiko >=3.5.1"
-    ],
-    entry_points={
-        "console_scripts": [
-            "synapsectl = synapse.cli:main",
-            "synapse-sim = synapse.simulator:main",
-        ],
-    },
 )