Update developer install to modern package toml

.github/workflows/conda.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Install dependencies
         run: conda install -y python conda-build "grpcio-tools<1.62" conda-verify
       - name: Compiling the prototypes
-        run: python python-libraries/nanover-core/setup.py compile_proto --proto-dir=protocol
+        run: python ./python-libraries/compile_proto.py --proto-dir=./protocol --python-dir=./python-libraries/nanover-core/src
       - name: Building the Conda packages
         run: |
           $build_command \

.github/workflows/tests.yml

@@ -44,8 +44,8 @@ jobs:
         run: conda install -y mpi4py openmm
       - name: Install tests dependancies
         run: python -m pip install -r python-libraries/requirements.test
-      - name: Compile
-        run: ./compile.sh --no-dotnet
+      - name: Compile (mypy requires --no-edit)
+        run: ./compile.sh --no-dotnet --no-edit
       - name: mypy
         run: |
           # Mypy accepts paths, modules or packages as inputs. However, only

compile.sh

@@ -63,13 +63,13 @@ if [[ $with_python == true ]]; then
 	python -m pip install -r ./python-libraries/requirements.test ${user_option}
 
 	announce "Compiling proto files to python"
-	python ./python-libraries/nanover-core/setup.py compile_proto
+	python ./python-libraries/compile_proto.py --proto-dir=./protocol --python-dir=./python-libraries/nanover-core/src
 
 	announce "Installing the python packages"
 	python -m pip install ${edit_option} ${nanover_user_option} ./python-libraries/nanover-core/
 
 	for package in python-libraries/nanover-*/; do
-		if [[ -f "${package}/setup.py" ]]; then
+		if [[ -f "${package}/pyproject.toml" ]]; then
 			python -m pip install ${edit_option} ${nanover_user_option} ${package}
 		fi
 	done

python-libraries/compile_proto.py

@@ -0,0 +1,130 @@
+import argparse
+import os
+import textwrap
+from contextlib import contextmanager
+from importlib import resources
+from pathlib import Path
+
+
+def handle_user_arguments(args=None) -> argparse.Namespace:
+    """
+    Parse the arguments from the command line.
+
+    :return: The namespace of arguments read from the command line.
+    """
+    description = textwrap.dedent(
+        """\
+    Compile the gRPC protocol files to python.
+    """
+    )
+    parser = argparse.ArgumentParser(description=description)
+
+    parser.add_argument(
+        "--proto-dir",
+        required=True,
+        dest="proto_dir",
+        metavar="PATH",
+        help="The path to the directory containing the proto files",
+    )
+
+    parser.add_argument(
+        "--python-dir",
+        required=True,
+        dest="python_dir",
+        metavar="PATH",
+        help="The path to the directory where to generate the python files",
+    )
+
+    arguments = parser.parse_args(args)
+    return arguments
+
+
+def compile_protocol(proto_dir, python_dir):
+    """
+    Compile the protocol files to python.
+
+    :param proto_dir: The path to the directory containing the proto files.
+    :param python_dir: The path to the directory where to generate the python files.
+    """
+    from grpc_tools import protoc
+
+    try:
+        os.makedirs(python_dir)
+    except OSError:
+        pass
+
+    # Note on calling grpc_tools.protoc as a python function:
+    # grpc_tools.protoc.main is called by the command line with sys.argv and
+    # the include path for the default protobuf proto files. sys.argv is a list of
+    # the arguments passed to the command line, the first element of that list is
+    # the command itself; what is passed as a command does not matter, but the actual
+    # arguments must start at sys.argv[1] (hence "protoc" as first argument passed
+    # to the function).
+    proto_include = resources.files("grpc_tools") / "_proto"
+    with move_in_directory(proto_dir):
+        for protocol_file in Path(".").glob("**/*.proto"):
+            print(f"Compiling {protocol_file}")
+            protoc.main(
+                (
+                    "protoc",
+                    "--proto_path=.",
+                    f"--python_out={python_dir}",
+                    f"--grpc_python_out={python_dir}",
+                    str(protocol_file),
+                    f"--proto_path={proto_include}",
+                )
+            )
+    generated_protocol_directories = (
+        path for path in (python_dir / "nanover/protocol").glob("**/*") if path.is_dir()
+    )
+    for directory in generated_protocol_directories:
+        (directory / "__init__.py").touch()
+        contained_files = (file for file in directory.glob("*_pb2*.py"))
+        with open(directory / "__init__.py", "w+") as init_py:
+            for contained_file in contained_files:
+                file_name = os.path.splitext(os.path.split(contained_file)[1])[0]
+                init_py.write("from .%s import *\n" % file_name)
+
+
+@contextmanager
+def move_in_directory(destination):
+    """
+    Context manager that moves in the given directory.
+
+    When the interpreter enters the context manager, the working directory becomes
+    the given destination. When the interpreter exists the context manager, the
+    working directory is restored to where the working directory was before entering.
+
+    Example:
+    ========
+
+    >>> with move_in_directory("bar"):
+    >>>    # working directory is "bar"
+    >>>    pass
+    >>> # working directory is "foo" again
+
+    :param destination: The directory to use as working directory.
+    """
+    destination = Path(destination)
+    directory_to_restore = Path.cwd()
+    try:
+        os.chdir(str(destination))
+        yield
+    finally:
+        os.chdir(str(directory_to_restore))
+
+
+def main():
+    """
+    Entry point for the command line.
+    """
+    arguments = handle_user_arguments()
+
+    compile_protocol(
+        Path(arguments.proto_dir).resolve(),
+        Path(arguments.python_dir).resolve(),
+    )
+
+
+if __name__ == "__main__":
+    main()

python-libraries/nanover-ase/pyproject.toml

@@ -0,0 +1,24 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover-ase"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "ASE integration for NanoVer"
+readme = "README.md"
+requires-python = ">=3.11"
+dependencies = [
+    "nanover",
+    "ase >= 3.21",
+]
+dynamic = ["version"]
+
+[project.scripts]
+nanover-omm-ase = "nanover.ase.openmm.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*"]  # package names should match these glob patterns (["*"] by default)

python-libraries/nanover-core/pyproject.toml

@@ -0,0 +1,29 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "NanoVer python framework"
+requires-python = ">=3.11"
+dependencies = [
+    "setuptools>=40.1.1",
+    "grpcio>=1.63.0",
+    "grpcio-tools>=1.63.0",
+    "pytest",
+    "aiogrpc",
+    "numpy",
+    "hypothesis",
+    "typing_extensions",
+]
+dynamic = ["version"]
+
+[project.scripts]
+nanover-multiplayer = "nanover.multiplayer.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*", "nanover.protocol"]  # package names should match these glob patterns (["*"] by default)