confit 0.2.1__tar.gz

confit-0.2.1/LICENSE

@@ -0,0 +1,11 @@
+Copyright 2023 Assistance Publique - Hôpitaux de Paris
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

confit-0.2.1/PKG-INFO

@@ -0,0 +1,150 @@
+Metadata-Version: 2.1
+Name: confit
+Version: 0.2.1
+Summary: Smart configuration framework
+Author-email: Perceval Wajsburt <perceval.wajsburt-ext@aphp.fr>, Thomas Petit-Jean <thomas.petitjean@aphp.fr>, Adam Remaki <adam.remaki@aphp.fr>, Alice Calliger <alice.calliger@aphp.fr>
+License: Copyright 2023 Assistance Publique - Hôpitaux de Paris
+        
+        Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Requires-Python: <4.0,>=3.7.1
+Description-Content-Type: text/markdown
+Provides-Extra: dev
+License-File: LICENSE
+
+![Tests](https://img.shields.io/github/actions/workflow/status/aphp/confit/tests.yml?branch=main&label=tests&style=flat-square)
+[![Documentation](https://img.shields.io/github/actions/workflow/status/aphp/confit/documentation.yml?branch=main&label=docs&style=flat-square)](https://aphp.github.io/confit/latest/)
+[![PyPI](https://img.shields.io/pypi/v/confit?color=blue&style=flat-square)](https://pypi.org/project/confit/)
+[![Codecov](https://img.shields.io/codecov/c/github/aphp/confit?logo=codecov&style=flat-square)](https://codecov.io/gh/aphp/confit)
+
+
+# Confit
+
+Confit is a complete and easy-to-use configuration framework aimed at improving the reproducibility
+of experiments by relying on the Python typing system, minimal configuration files and
+command line interfaces.
+
+## Getting started
+
+Install the library with pip:
+
+<div class="termy">
+
+```bash
+pip install confit
+```
+
+</div>
+
+Confit only abstracts the boilerplate code related to configuration and
+leaves the rest of your code unchanged.
+
+Here is an example:
+
+<h5 a><strong><code>script.py</code></strong></h5>
+
+```diff
++ from confit import Cli, Registry, RegistryCollection
+  
++ class registry(RegistryCollection):
++     factory = Registry(("test_cli", "factory"), entry_points=True)
+ 
++ @registry.factory.register("submodel")
+class SubModel:
+    # Type hinting is optional but recommended !
+    def __init__(self, value: float, desc: str = ""):
+        self.value = value
+        self.desc = desc
+ 
+ 
++ @registry.factory.register("bigmodel")
+class BigModel:
+    def __init__(self, date: datetime.date, submodel: SubModel):
+        self.date = date
+        self.submodel = submodel
+ 
++ app = Cli(pretty_exceptions_show_locals=False)
+ 
++ @app.command(name="script", registry=registry)
+def func(modelA: BigModel, modelB: BigModel, other: int, seed: int):
+    assert modelA.submodel is modelB.submodel
+    assert modelA.date == datetime.date(2010, 10, 10)
+    print("Other:", other)
+ 
++ if __name__ == "__main__":
++     app()
+```
+
+
+Create a new config file
+
+<h5 a><strong><code>config.cfg</code></strong></h5>
+
+```ini
+# CLI sections
+[script]
+modelA = ${modelA}
+modelB = ${modelB}
+
+# CLI common parameters
+[modelA]
+@factory = "bigmodel"
+date = "2003-02-01"
+
+[modelA.submodel]
+@factory = "submodel"
+value = 12
+
+[modelB]
+date = "2003-04-05"
+submodel = ${modelA.submodel}
+```
+
+and run the following command from the terminal
+
+<div class="termy">
+
+```bash
+python script.py --config config.cfg --seed 42
+```
+
+</div>
+
+You can still call the `function` method from your code, but now also benefit from
+argument validation !
+
+```python
+from script import func, BigModel, SubModel
+
+# To seed before creating the models
+from confit.utils.random import set_seed
+
+seed = 42
+set_seed(seed)
+
+submodel = SubModel(value=12)
+# BigModel will cast date strings as datetime.date objects
+modelA = BigModel(date="2003-02-01", submodel=submodel)
+modelB = BigModel(date="2003-04-05", submodel=submodel)
+func(
+    modelA=modelA,
+    modelB=modelA,
+    seed=seed,
+)
+```
+
+
+Visit the [documentation](https://aphp.github.io/confit/) for more information!
+
+## Acknowledgement
+
+We would like to thank [Assistance Publique – Hôpitaux de Paris](https://www.aphp.fr/)
+and [AP-HP Foundation](https://fondationrechercheaphp.fr/) for funding this project.

confit-0.2.1/README.md

@@ -0,0 +1,128 @@
+![Tests](https://img.shields.io/github/actions/workflow/status/aphp/confit/tests.yml?branch=main&label=tests&style=flat-square)
+[![Documentation](https://img.shields.io/github/actions/workflow/status/aphp/confit/documentation.yml?branch=main&label=docs&style=flat-square)](https://aphp.github.io/confit/latest/)
+[![PyPI](https://img.shields.io/pypi/v/confit?color=blue&style=flat-square)](https://pypi.org/project/confit/)
+[![Codecov](https://img.shields.io/codecov/c/github/aphp/confit?logo=codecov&style=flat-square)](https://codecov.io/gh/aphp/confit)
+
+
+# Confit
+
+Confit is a complete and easy-to-use configuration framework aimed at improving the reproducibility
+of experiments by relying on the Python typing system, minimal configuration files and
+command line interfaces.
+
+## Getting started
+
+Install the library with pip:
+
+<div class="termy">
+
+```bash
+pip install confit
+```
+
+</div>
+
+Confit only abstracts the boilerplate code related to configuration and
+leaves the rest of your code unchanged.
+
+Here is an example:
+
+<h5 a><strong><code>script.py</code></strong></h5>
+
+```diff
++ from confit import Cli, Registry, RegistryCollection
+  
++ class registry(RegistryCollection):
++     factory = Registry(("test_cli", "factory"), entry_points=True)
+ 
++ @registry.factory.register("submodel")
+class SubModel:
+    # Type hinting is optional but recommended !
+    def __init__(self, value: float, desc: str = ""):
+        self.value = value
+        self.desc = desc
+ 
+ 
++ @registry.factory.register("bigmodel")
+class BigModel:
+    def __init__(self, date: datetime.date, submodel: SubModel):
+        self.date = date
+        self.submodel = submodel
+ 
++ app = Cli(pretty_exceptions_show_locals=False)
+ 
++ @app.command(name="script", registry=registry)
+def func(modelA: BigModel, modelB: BigModel, other: int, seed: int):
+    assert modelA.submodel is modelB.submodel
+    assert modelA.date == datetime.date(2010, 10, 10)
+    print("Other:", other)
+ 
++ if __name__ == "__main__":
++     app()
+```
+
+
+Create a new config file
+
+<h5 a><strong><code>config.cfg</code></strong></h5>
+
+```ini
+# CLI sections
+[script]
+modelA = ${modelA}
+modelB = ${modelB}
+
+# CLI common parameters
+[modelA]
+@factory = "bigmodel"
+date = "2003-02-01"
+
+[modelA.submodel]
+@factory = "submodel"
+value = 12
+
+[modelB]
+date = "2003-04-05"
+submodel = ${modelA.submodel}
+```
+
+and run the following command from the terminal
+
+<div class="termy">
+
+```bash
+python script.py --config config.cfg --seed 42
+```
+
+</div>
+
+You can still call the `function` method from your code, but now also benefit from
+argument validation !
+
+```python
+from script import func, BigModel, SubModel
+
+# To seed before creating the models
+from confit.utils.random import set_seed
+
+seed = 42
+set_seed(seed)
+
+submodel = SubModel(value=12)
+# BigModel will cast date strings as datetime.date objects
+modelA = BigModel(date="2003-02-01", submodel=submodel)
+modelB = BigModel(date="2003-04-05", submodel=submodel)
+func(
+    modelA=modelA,
+    modelB=modelA,
+    seed=seed,
+)
+```
+
+
+Visit the [documentation](https://aphp.github.io/confit/) for more information!
+
+## Acknowledgement
+
+We would like to thank [Assistance Publique – Hôpitaux de Paris](https://www.aphp.fr/)
+and [AP-HP Foundation](https://fondationrechercheaphp.fr/) for funding this project.

confit-0.2.1/confit/__init__.py

@@ -0,0 +1,10 @@
+from .cli import Cli  # noqa F401
+from .config import Config  # noqa F401
+from .registry import (
+    Registry,  # noqa F401
+    get_default_registry,  # noqa F401
+    set_default_registry,  # noqa F401
+    RegistryCollection,  # noqa F401
+)
+
+__version__ = "0.2.1"

confit-0.2.1/confit/cli.py

@@ -0,0 +1,158 @@
+import inspect
+import sys
+from pathlib import Path
+from typing import Any, Callable, Dict, List, Optional, Type, Union
+
+from pydantic import ValidationError
+from typer import Context, Typer, colors, secho
+from typer.core import TyperCommand
+from typer.models import CommandFunctionType, Default
+
+from .config import Config, merge_from_disk
+from .registry import validate_arguments
+from .utils.random import set_seed
+from .utils.xjson import loads
+
+
+def parse_overrides(args: List[str]) -> Dict[str, Any]:
+    """
+    Parse the overrides from the command line into a dictionary
+    of key-value pairs.
+
+    Parameters
+    ----------
+    args: List[str]
+        The arguments to parse
+
+    Returns
+    -------
+    Dict[str, Any]
+        The parsed overrides as a dictionary
+    """
+    result = {}
+    while args:
+        opt = args.pop(0)
+        err = f"Invalid config override '{opt}'"
+        if opt.startswith("--"):  # new argument
+            opt = opt.replace("--", "")
+            if "=" in opt:  # we have --opt=value
+                opt, value = opt.split("=", 1)
+            else:
+                if not args or args[0].startswith("--"):  # flag with no value
+                    value = "true"
+                else:
+                    value = args.pop(0)
+            opt = opt.replace("-", "_")
+            result[opt] = loads(value)
+        else:
+            secho(f"{err}: doesn't support shorthands", fg=colors.RED)
+            exit(1)
+    return result
+
+
+class Cli(Typer):
+    """
+    Custom Typer object that:
+
+    - validates a command parameters before executing it
+    - accepts a configuration file describing the parameters
+    - automatically instantiates parameters given a dictionary when type hinted
+    """
+
+    def command(  # noqa
+        self,
+        name,
+        *,
+        cls: Optional[Type[TyperCommand]] = None,
+        context_settings: Optional[Dict[Any, Any]] = None,
+        help: Optional[str] = None,
+        epilog: Optional[str] = None,
+        short_help: Optional[str] = None,
+        options_metavar: str = "[OPTIONS]",
+        add_help_option: bool = True,
+        no_args_is_help: bool = False,
+        hidden: bool = False,
+        deprecated: bool = False,
+        # Rich settings
+        rich_help_panel: Union[str, None] = Default(None),
+        registry: Any = None,
+    ) -> Callable[[CommandFunctionType], CommandFunctionType]:
+        typer_command = super().command(
+            name=name,
+            cls=cls,
+            help=help,
+            epilog=epilog,
+            short_help=short_help,
+            options_metavar=options_metavar,
+            add_help_option=add_help_option,
+            no_args_is_help=no_args_is_help,
+            hidden=hidden,
+            deprecated=deprecated,
+            rich_help_panel=rich_help_panel,
+            context_settings={
+                **(context_settings or {}),
+                "ignore_unknown_options": True,
+                "allow_extra_args": True,
+            },
+        )
+
+        def wrapper(fn):
+            validated = validate_arguments(fn)
+
+            @typer_command
+            def command(ctx: Context, config: Optional[List[Path]] = None):
+                config_path = config
+
+                has_meta = _fn_has_meta(fn)
+                if config_path:
+                    config, name_from_file = merge_from_disk(config_path)
+                else:
+                    config = Config({name: {}})
+                for k, v in parse_overrides(ctx.args).items():
+                    if "." not in k:
+                        parts = (name, k)
+                    else:
+                        parts = k.split(".")
+                        if (
+                            parts[0] in validated.model.__fields__
+                            and parts[0] not in config
+                        ):
+                            parts = (name, *parts)
+                    current = config
+                    if parts[0] not in current:
+                        raise Exception(
+                            f"{k} does not match any existing section in config"
+                        )
+                    for part in parts[:-1]:
+                        current = current.setdefault(part, Config())
+                    current[parts[-1]] = v
+                try:
+                    resolved_config = config.resolve(registry=registry)
+                    default_seed = validated.model.__fields__.get("seed")
+                    seed = config.get(name, {}).get("seed", default_seed)
+                    if seed is not None:
+                        set_seed(seed)
+                    if has_meta:
+                        config_meta = dict(
+                            config_path=config_path,
+                            resolved_config=resolved_config,
+                            unresolved_config=config,
+                        )
+                        return validated(
+                            **resolved_config.get(name, {}),
+                            config_meta=config_meta,
+                        )
+                    else:
+                        return validated(**resolved_config.get(name, {}))
+                except ValidationError as e:
+                    print("\x1b[{}m{}\x1b[0m".format("38;5;1", "Validation error"))
+                    print(str(e))
+                    sys.exit(1)
+
+            return validated
+
+        return wrapper
+
+
+def _fn_has_meta(fn):
+    return "config_meta" in inspect.signature(fn).parameters