ato 2.0.4__py3-none-any.whl

ato/__init__.py

@@ -0,0 +1 @@
+__version__ = '1.12.0'

ato/adict.py

@@ -0,0 +1,582 @@
+import hashlib
+import importlib.util
+import json
+import sys
+import types
+import warnings
+from collections.abc import MutableMapping as GenericMapping
+
+import toml
+import yaml
+import os
+from copy import deepcopy as dcp
+from functools import wraps
+from types import MappingProxyType
+from typing import Mapping, MutableMapping, Callable
+
+from ato import xyz
+
+ALLOWED_EXTS = ('.yaml', '.yml', '.json', '.toml', '.xyz')
+
+
+# decorate internal methods in ADict
+def mutate_attribute(fn):
+    @wraps(fn)
+    def decorator(*args, **kwargs):
+        ctx = args[0]
+        object.__setattr__(ctx, '_mutate_attribute', True)
+        result = fn(*args, **kwargs)
+        object.__setattr__(ctx, '_mutate_attribute', False)
+        return result
+    return decorator
+
+
+class Dict(GenericMapping):
+    def __init__(self, mapping=None, /, **kwargs):
+        self._data = dict()
+        if mapping is not None:
+            self.update(mapping)
+        if kwargs:
+            self.update(kwargs)
+
+    def __len__(self):
+        return len(self._data)
+
+    def __getitem__(self, key):
+        if key in self._data:
+            return self._data[key]
+        if hasattr(self.__class__, "__missing__"):
+            return self.__class__.__missing__(self, key)
+        raise KeyError(key)
+
+    def __setitem__(self, key, item):
+        self._data[key] = item
+
+    def __delitem__(self, key):
+        del self._data[key]
+
+    def __iter__(self):
+        return iter(self._data)
+
+    # Modify __contains__ to work correctly when __missing__ is present
+    def __contains__(self, key):
+        return key in self._data
+
+    # Now, add the methods in dicts but not in MutableMapping
+    def __repr__(self):
+        return repr(self._data)
+
+    def __or__(self, other):
+        if isinstance(other, Dict):
+            return self.__class__(self._data | other._data)
+        if isinstance(other, dict):
+            return self.__class__(self._data | other)
+        return NotImplemented
+
+    def __ror__(self, other):
+        if isinstance(other, Dict):
+            return self.__class__(other._data | self._data)
+        if isinstance(other, dict):
+            return self.__class__(other | self._data)
+        return NotImplemented
+
+    def __ior__(self, other):
+        if isinstance(other, Dict):
+            self._data |= other._data
+        else:
+            self._data |= other
+        return self
+
+    def __copy__(self):
+        inst = self.__class__.__new__(self.__class__)
+        inst.__dict__.update(self.__dict__)
+        # Create a copy and avoid triggering descriptors
+        inst.__dict__["_data"] = self.__dict__["_data"].copy()
+        return inst
+
+    def copy(self):
+        if self.__class__ is Dict:
+            return Dict(self._data.copy())
+        import copy
+        data = self._data
+        try:
+            self._data = dict()
+            c = copy.copy(self)
+        finally:
+            self._data = data
+        c.update(self)
+        return c
+
+    @classmethod
+    def fromkeys(cls, iterable, value=None):
+        d = cls()
+        for key in iterable:
+            d[key] = value
+        return d
+
+
+class ADict(Dict):
+    @mutate_attribute
+    def __init__(self, *args, **kwargs):
+        if 'default' in kwargs:
+            self._default = kwargs.pop('default')
+            self._is_default_defined = True
+        else:
+            self._default = None
+            self._is_default_defined = False
+        mappings = dict()
+        for mapping in args:
+            if not isinstance(mapping, (dict, MutableMapping)):
+                try:
+                    mapping = dict(mapping)
+                except (AttributeError, TypeError, ValueError):
+                    raise TypeError(
+                        f'Any of positional arguments must be able to converted to key-value type, '
+                        f'but {mapping} is not.'
+                    )
+            mappings.update(mapping)
+        self._frozen = False
+        self._accessed_keys = set()
+        super().__init__(mappings, **kwargs)
+
+    @property
+    def frozen(self):
+        return self._frozen
+
+    @property
+    def accessed_keys(self):
+        return self._accessed_keys
+
+    def get_minimal_config(self):
+        new_config = ADict()
+        for key in self.accessed_keys:
+            value = self.__getitem__(key)
+            if isinstance(value, self.__class__):
+                new_config[key] = value.get_minimal_config()
+            else:
+                new_config[key] = value
+        return new_config
+
+    def __getitem__(self, names):
+        if isinstance(names, str):
+            if names in self._data:
+                value = self._data[names]
+            elif self._is_default_defined and not self.frozen:
+                value = self.get_default()
+                self._data[names] = value
+            else:
+                raise KeyError(f'The key "{names}" does not exist.')
+            self._accessed_keys.add(names)
+        else:
+            value = [self.__getitem__(name) for name in names]
+            self._accessed_keys.update(names)
+        if self.frozen:
+            value = dcp(value)
+        return value
+
+    def __setitem__(self, names, values):
+        if not self.frozen:
+            if isinstance(names, str):
+                if isinstance(values, Mapping):
+                    values = self.__class__(**values)
+                elif isinstance(values, (list, tuple)):
+                    values = [self.__class__(**value) if isinstance(value, Mapping) else value for value in values]
+                super().__setitem__(names, values)
+            elif isinstance(values, (list, tuple)):
+                for name, value in zip(names, values):
+                    self.__setitem__(name, value)
+            else:
+                for name in names:
+                    self.__setitem__(name, values)
+
+    def __getattr__(self, name):
+        try:
+            return object.__getattribute__(self, name)
+        except AttributeError:
+            try:
+                return self.__getitem__(name)
+            except KeyError:
+                raise AttributeError(name)
+
+    def __setattr__(self, name, value):
+        if self._mutate_attribute:
+            object.__setattr__(self, name, value)
+        else:
+            self.__setitem__(name, value)
+
+    def __delattr__(self, names):
+        if self._mutate_attribute:
+            object.__delattr__(self, names)
+        elif isinstance(names, str):
+            self.__delitem__(names)
+        else:
+            for name in names:
+                self.__delitem__(name)
+
+    def __deepcopy__(self, memo=None):
+        mappings = dcp(self._data)
+        kwargs = dict()
+        if self._is_default_defined:
+            kwargs.update(default=self._default)
+        return self.__class__(mappings, **kwargs)
+
+    def __getstate__(self):
+        state = dcp(self.__dict__)
+        state.pop('_mutate_attribute')
+        return state
+
+    @mutate_attribute
+    def __setstate__(self, state):
+        self._data = state.pop('_data')
+        for k, v in state.items():
+            object.__setattr__(self, k, v)
+
+    def set_default(self, default=None):
+        self._default = default
+
+    def remove_default(self):
+        self._is_default_defined = False
+        self._default = None
+
+    def get_default(self):
+        if self._is_default_defined:
+            _default = object.__getattribute__(self, '_default')
+            if callable(_default):
+                return _default()
+            else:
+                return dcp(_default)
+        else:
+            raise ValueError('Default value is not defined.')
+
+    def get(self, name, default=None):
+        if name in self:
+            return self.__getitem__(name)
+        elif self._is_default_defined:
+            if self._frozen:
+                raise KeyError(f'The key "{name}" does not exist.')
+            return self.get_default()
+        else:
+            return default
+
+    def __delitem__(self, key):
+        if not self.frozen:
+            super().__delitem__(key)
+
+    def pop(self, name, default=None):
+        value = self.get(name, default)
+        if name in self:
+            self.__delitem__(name)
+        return value
+
+    def raw(self, name, default=None):
+        value = self.get(name, default)
+        item = self.__class__(key=name, value=value)
+        return item
+
+    @mutate_attribute
+    def filter(self, fn: Callable):
+        data = dict()
+        for key, value in self.items():
+            if fn(key, value):
+                data[key] = value
+        self._data = data
+
+    def get_value_by_name(self, name):
+        keys = name.split('.')
+        value = self._data
+        for key in keys:
+            value = value[key]
+        return value
+
+    @mutate_attribute
+    def freeze(self):
+        self._frozen = True
+        return self
+
+    @mutate_attribute
+    def defrost(self):
+        self._frozen = False
+        return self
+
+    @mutate_attribute
+    def update(self, __m=None, recurrent=False, **kwargs):
+        if not self.frozen:
+            if __m is not None:
+                self.update(**__m, recurrent=recurrent)
+            if recurrent:
+                children = self.__class__()
+                for k, v in kwargs.items():
+                    if k in self and isinstance(v, Mapping):
+                        self.__getitem__(k).update(**v, recurrent=True)
+                    else:
+                        children[k] = v
+                super().update(**children)
+            else:
+                super().update(**kwargs)
+        return self
+
+    @mutate_attribute
+    def update_if_absent(self, __m=None, recurrent=False, **kwargs):
+        if not self.frozen:
+            if __m is not None:
+                self.update_if_absent(**__m, recurrent=recurrent)
+            children = self.__class__()
+            for k, v in kwargs.items():
+                if k in self and isinstance(v, Mapping):
+                    self.__getitem__(k).update_if_absent(**v, recurrent=True)
+                elif k not in self:
+                    children[k] = v
+            super().update(**children)
+        return self
+
+    def get_structural_mapping(self, key, value):
+        if key is None:
+            key = ""
+        items = []
+        if isinstance(value, (MutableMapping, dict)):
+            for k, v in value.items():
+                concat = k if key == '' else f'{key}.{k}'
+                items += self.get_structural_mapping(concat, v)
+        else:
+            return [(key, type(value).__name__)]
+        return items
+
+    def get_structural_repr(self):
+        structural_repr = self.__class__()
+        for k, v in self.get_structural_mapping("", self):
+            structural_repr[k] = v
+        return structural_repr
+
+    def get_structural_hash(self):
+        structural_repr = self.get_structural_repr()
+        structural_repr = list(structural_repr.items())
+        structural_repr.sort(key=lambda x: x[0])
+        structural_hash = ''
+        for k, v in structural_repr:
+            structural_hash += f'[{k}:{v}]'
+        return str(dcp(hashlib.sha1(structural_hash.encode('utf-8')).hexdigest()))
+
+    @mutate_attribute
+    def convert_to_immutable(self):
+        self._data = MappingProxyType(self._data)
+
+    @mutate_attribute
+    def json(self):
+        return json.dumps(self.to_dict())
+
+    def clone(self):
+        return dcp(self)
+
+    def to_dict(self):
+        data = dict()
+        for key, value in self.items():
+            if isinstance(value, Mapping):
+                data[key] = self.__class__(**value).to_dict()
+            elif isinstance(value, (list, tuple)):
+                data[key] = [self.__class__(**item).to_dict() if isinstance(item, Mapping) else item for item in value]
+            else:
+                data[key] = value
+        return data
+
+    def to_xyz(self, format_dict=None):
+        return xyz.dumps(self.to_dict(), format_dict=format_dict)
+
+    @classmethod
+    def from_file(cls, path):
+        if os.path.exists(path):
+            ext = os.path.splitext(path)[1].lower()
+            if ext in ('.yml', '.yaml'):
+                with open(path, 'rb') as f:
+                    return cls(yaml.load(f, Loader=yaml.FullLoader))
+            elif ext == '.toml':
+                with open(path, 'r') as f:
+                    return cls(toml.load(f))
+            elif ext == '.json':
+                with open(path, 'r') as f:
+                    obj = json.load(f)
+                    if isinstance(obj, list):
+                        return [cls(item) for item in obj]
+                    else:
+                        return cls(obj)
+            elif ext == '.jsonl':
+                with open(path, 'r') as f:
+                    dict_list = json.load(f)
+                    return [cls(item) for item in dict_list]
+            elif ext == '.xyz':
+                obj = xyz.load(path)
+                if isinstance(obj, list):
+                    return [cls(item) for item in obj]
+                else:
+                    return cls(obj)
+            elif ext == '.py':
+                obj = cls.compile_from_file(path)
+                if isinstance(obj, list):
+                    return [cls(item) for item in obj]
+                else:
+                    return cls(obj)
+            else:
+                raise ValueError(f'{ext} is not a valid file extension.')
+        else:
+            raise FileNotFoundError(f'{path} does not exist.')
+
+    @classmethod
+    def compile_from_file(cls, path):
+        config_name = os.path.splitext(os.path.basename(path))[0]
+        spec = importlib.util.spec_from_file_location(config_name, path)
+        config_module = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(config_module)
+        sys.modules[config_name] = config_module
+        config = {
+            name: value
+            for name, value in config_module.__dict__.items()
+            if not name.startswith('__') and not isinstance(value, (types.ModuleType, types.FunctionType))
+        }
+        del sys.modules[config_name]
+        return cls(**config)
+
+    def mm_like_update(self, **kwargs):
+        for key, value in kwargs.items():
+            if isinstance(value, MutableMapping):
+                recurrent = '_delete_' not in value
+                if not recurrent:
+                    del value['_delete_']
+                if key in self and isinstance(self[key], MutableMapping) and recurrent:
+                    self[key].mm_like_update(**value)
+                else:
+                    self[key] = value
+            else:
+                self[key] = value
+
+    @classmethod
+    def from_mm_config(cls, path):
+        config = cls.from_file(path)
+        mm_like_config = cls()
+        if '_base_' in config:
+            base_paths = config.pop('_base_')
+            if isinstance(base_paths, str):
+                base_paths = [base_paths]
+            base_paths = [
+                os.path.join(os.path.dirname(os.path.realpath(path)), base_path)
+                if not os.path.exists(base_path) else base_path
+                for base_path in base_paths
+            ]
+            base_configs = [cls.from_mm_config(path) for path in base_paths]
+        else:
+            base_configs = []
+        for base_config in base_configs:
+            mm_like_config.mm_like_update(**base_config)
+        mm_like_config.mm_like_update(**config)
+        return mm_like_config
+
+    @mutate_attribute
+    def load(self, path, **kwargs):
+        if os.path.exists(path):
+            ext = os.path.splitext(path)[1].lower()
+            if ext in ('.yml', '.yaml'):
+                with open(path, 'rb') as f:
+                    self._data = yaml.load(f, Loader=yaml.FullLoader)
+            elif ext == '.json':
+                with open(path, 'r') as f:
+                    self._data = json.load(f, **kwargs)
+            elif ext == '.xyz':
+                self._data = xyz.load(path)
+            elif ext == '.py':
+                self._data = self.compile_from_file(path).to_dict()
+            else:
+                raise ValueError(f'{ext} is not a valid file extension.')
+        else:
+            raise FileNotFoundError(f'{path} does not exist.')
+
+    @mutate_attribute
+    def load_mm_config(self, path):
+        self.update(self.from_mm_config(path).to_dict())
+
+    @classmethod
+    def compose_hierarchy(
+        cls,
+        root,
+        config_filename='config',
+        select=None,
+        overrides=None,
+        on_missing='error',
+        required=None
+    ):
+        select = select or {}
+        loaded_paths = []
+        config = cls()
+
+        def _load_first(_base_path, *, label):
+            _is_missing = True
+            for _ext in ALLOWED_EXTS:
+                _config_path = os.path.join(root, _base_path+_ext)
+                if os.path.exists(_config_path):
+                    config.update(cls.from_file(_config_path))
+                    loaded_paths.append((label, _config_path))
+                    _is_missing = False
+            return _is_missing
+
+        if not _load_first(config_filename, label='base') and on_missing == 'error':
+            raise FileNotFoundError(f'{config_filename}.[yaml|yml|json|toml|xyz] not found in {root}')
+        for group, options in select.items():
+            options = options if isinstance(options, (list, tuple)) else [options]
+            for option in options:
+                is_missing = _load_first(os.path.join(group, str(option)), label=f'{group}:{option}')
+                if is_missing:
+                    if on_missing == 'error':
+                        raise FileNotFoundError(f'{group}/{option} not found')
+                    elif on_missing == 'warn':
+                        warnings.warn(f'missing: {group}/{option}')
+        for key, value in (overrides or {}).items():
+            if isinstance(value, Mapping):
+                value = ADict(**value)
+            current_config = config
+            sub_keys = key.split('.')
+            for sub_key in sub_keys[:-1]:
+                if sub_key not in current_config or not isinstance(current_config[sub_key], ADict):
+                    current_config[sub_key] = ADict()
+                current_config = current_config[sub_key]
+            current_config[sub_keys[-1]] = value
+        for is_required in (required or []):
+            current_config = config
+            is_missing = False
+            for key in is_required.split('.'):
+                if key not in current_config:
+                    is_missing = True
+                    break
+                current_config = current_config[key]
+            if is_missing:
+                raise KeyError(f"Missing required key: {is_required}")
+        return config
+
+    def dump(self, path, **kwargs):
+        dir_path = os.path.dirname(os.path.realpath(path))
+        os.makedirs(dir_path, exist_ok=True)
+        ext = os.path.splitext(path)[1].lower()
+        if ext in ('.yml', '.yaml'):
+            with open(path, 'w') as f:
+                return yaml.dump(self.to_dict(), f, Dumper=yaml.Dumper, **kwargs)
+        elif ext == '.toml':
+            with open(path, 'w') as f:
+                return toml.dump(self.to_dict(), f, **kwargs)
+        elif ext == '.json':
+            with open(path, 'w') as f:
+                return json.dump(self.to_dict(), f, **kwargs)
+        elif ext == '.xyz':
+            return xyz.dump(self.to_dict(), path, **kwargs)
+        else:
+            raise ValueError(f'{ext} is not a valid file extension.')
+
+    def replace_keys(self, src_keys, tgt_keys):
+        if len(src_keys) != len(tgt_keys):
+            raise IndexError(f'Source and target keys cannot be mapped: {len(src_keys)} != {len(tgt_keys)}')
+        for src_key in src_keys:
+            if src_key not in self._data:
+                raise KeyError(f'The key {src_key} does not exist.')
+        self.__setitem__(tgt_keys, [self._data.pop(src_key) for src_key in src_keys])
+
+    @classmethod
+    def auto(cls):
+        return cls(default=lambda: cls.auto())
+
+
+

ato/db_routers/__init__.py

@@ -0,0 +1,8 @@
+class BaseLogger:
+    def __init__(self, config):
+        self.config = config
+
+
+class BaseFinder:
+    def __init__(self, config):
+        self.config = config