diff --git a/cellprofiler_core/__init__.py b/cellprofiler_core/__init__.py index 6e96fc64..213df64a 100644 --- a/cellprofiler_core/__init__.py +++ b/cellprofiler_core/__init__.py @@ -1 +1 @@ -__version__ = "4.2.7" +__version__ = "4.2.8" diff --git a/cellprofiler_core/__main__.py b/cellprofiler_core/__main__.py index e2d6fe32..e69de29b 100644 --- a/cellprofiler_core/__main__.py +++ b/cellprofiler_core/__main__.py @@ -1,55 +0,0 @@ -import os -import pathlib - -import click - -import cellprofiler_core.commands - -CONTEXT_SETTINGS = dict(auto_envvar_prefix="COMPLEX") - - -class Command(click.MultiCommand): - def get_command(self, context, name): - try: - name = f"cellprofiler_core.commands._{name}_command" - - imported_module = __import__(name, None, None, ["command"]) - except ImportError: - return - - return imported_module.command - - def list_commands(self, context): - command_names = [] - - commands_pathname = cellprofiler_core.commands.__file__ - - commands_directory = pathlib.Path(commands_pathname).parent - - for filename in os.listdir(commands_directory): - if filename.endswith("_command.py") and filename.startswith("_"): - command_name = filename[1:-11] - - command_names += [command_name] - - command_names.sort() - - return command_names - - -class Environment: - def __init__(self): - pass - - -pass_environment = click.make_pass_decorator(Environment, ensure=True) - - -@click.command(cls=Command, context_settings=CONTEXT_SETTINGS) -@pass_environment -def main(context): - pass - - -if __name__ == "__main__": - main({}) diff --git a/cellprofiler_core/commands/__init__.py b/cellprofiler_core/commands/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/cellprofiler_core/commands/_pipeline_command.py b/cellprofiler_core/commands/_pipeline_command.py deleted file mode 100644 index 4a5d3d78..00000000 --- a/cellprofiler_core/commands/_pipeline_command.py +++ /dev/null @@ -1,40 +0,0 @@ -import click - -from ..__main__ import pass_environment - - -@click.group("pipeline") -@pass_environment -def command(context): - pass - - -@command.command("measurements", help="returns measurements extracted by the pipeline") -@pass_environment -def measurements(context): - pass - - -@command.command("run", help="executes the pipeline") -@click.argument("pipeline", type=click.File("r")) -@click.option("--batch-size", type=int) -@click.option("--data", type=click.Path()) -@click.option("--default-images-directory", type=click.Path()) -@click.option("--default-output-directory", type=click.Path()) -@click.option("--images", multiple=True, type=click.Path()) -@click.option("--beginning", default=1, type=int) -@click.option("--end", type=int) -@click.option("--group", type=str) -@pass_environment -def run( - context, - batch_size, - data, - images_directory, - output_directory, - images, - beginning, - end, - grouping, -): - pass diff --git a/cellprofiler_core/commands/_worker_command.py b/cellprofiler_core/commands/_worker_command.py deleted file mode 100644 index b2298f77..00000000 --- a/cellprofiler_core/commands/_worker_command.py +++ /dev/null @@ -1,15 +0,0 @@ -import click - -from ..__main__ import pass_environment - - -@click.group("worker") -@pass_environment -def command(context): - pass - - -@command.command("start") -@pass_environment -def start(context): - pass diff --git a/docs/conf.py b/docs/conf.py index 3f7911ab..aff4ad8f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -12,6 +12,6 @@ project = "CellProfiler-core" -release = "4.2.7" +release = "4.2.8" templates_path = ["_templates"] diff --git a/setup.cfg b/setup.cfg index 90ece8ce..4441e861 100644 --- a/setup.cfg +++ b/setup.cfg @@ -3,6 +3,6 @@ filterwarnings = ignore::DeprecationWarning ignore::FutureWarning minversion = - 4.2.7 + 4.2.8 testpaths = ./tests/ diff --git a/setup.py b/setup.py index e3cef28b..a3461f70 100644 --- a/setup.py +++ b/setup.py @@ -8,16 +8,14 @@ "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", ], extras_require={ "dev": [ - "black==19.10b0", - "click>=7.1.2", - "pre-commit==2.2.0", "sphinx==3.1.2", "twine==3.1.1", ], - "test": ["pytest==5.4.1"], + "test": ["pytest~=7.4.1"], "wx": ["wxPython==4.1.0"], }, install_requires=[ @@ -29,8 +27,8 @@ "numpy>=1.18.2", "prokaryote==2.4.4", "psutil>=5.7.0", - "python-bioformats==4.0.7", - "python-javabridge==4.0.3", + "python-bioformats>=4.0.7,<5", + "python-javabridge>=4.0.3,<5", "pyzmq~=22.3", "scikit-image==0.18.3", "scipy>=1.4.1", @@ -41,6 +39,6 @@ packages=setuptools.find_packages(exclude=["tests"]), python_requires=">=3.8", url="https://github.com/CellProfiler/core", - version="4.2.7", + version="4.2.8", zip_safe=False, )