conda_env

Representation of conda environment.yaml files for bioimageio specifications.

Used by:

• API Reference  spec  BioimageioCondaEnv

Classes:

Name	Description
BioimageioCondaEnv	A special CondaEnv that
CondaEnv	Represenation of the content of a conda environment.yaml file
PipDeps	Pip dependencies to include in conda dependecies

BioimageioCondaEnv pydantic-model

Bases: CondaEnv

A special CondaEnv that - automatically adds bioimageio specific dependencies - sorts dependencies

Show JSON schema:

{
  "$defs": {
    "PipDeps": {
      "description": "Pip dependencies to include in conda dependecies",
      "properties": {
        "pip": {
          "items": {
            "type": "string"
          },
          "title": "Pip",
          "type": "array"
        }
      },
      "title": "PipDeps",
      "type": "object"
    }
  },
  "description": "A special `CondaEnv` that\n- automatically adds bioimageio specific dependencies\n- sorts dependencies",
  "properties": {
    "name": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Name"
    },
    "channels": {
      "items": {
        "type": "string"
      },
      "title": "Channels",
      "type": "array"
    },
    "dependencies": {
      "items": {
        "anyOf": [
          {
            "type": "string"
          },
          {
            "$ref": "#/$defs/PipDeps"
          }
        ]
      },
      "title": "Dependencies",
      "type": "array"
    }
  },
  "title": "BioimageioCondaEnv",
  "type": "object"
}

Fields:

• name (Optional[str])
• channels (List[str])
• dependencies (List[Union[str, PipDeps]])

Validators:

• _ensure_valid_conda_env_name → name
• _normalize_bioimageio_conda_env

channels pydantic-field

channels: List[str]

dependencies pydantic-field

dependencies: List[Union[str, PipDeps]]

name pydantic-field

name: Optional[str] = None

wo_name property

wo_name

get_pip_deps

get_pip_deps() -> List[str]

Get the pip dependencies of this conda env.

Source code in src/bioimageio/spec/conda_env.py

def get_pip_deps(self) -> List[str]:
    """Get the pip dependencies of this conda env."""
    for dep in self.dependencies:
        if isinstance(dep, PipDeps):
            return dep.pip

    return []

CondaEnv pydantic-model

Bases: BaseModel

Represenation of the content of a conda environment.yaml file

Show JSON schema:

{
  "$defs": {
    "PipDeps": {
      "description": "Pip dependencies to include in conda dependecies",
      "properties": {
        "pip": {
          "items": {
            "type": "string"
          },
          "title": "Pip",
          "type": "array"
        }
      },
      "title": "PipDeps",
      "type": "object"
    }
  },
  "description": "Represenation of the content of a conda environment.yaml file",
  "properties": {
    "name": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Name"
    },
    "channels": {
      "items": {
        "type": "string"
      },
      "title": "Channels",
      "type": "array"
    },
    "dependencies": {
      "items": {
        "anyOf": [
          {
            "type": "string"
          },
          {
            "$ref": "#/$defs/PipDeps"
          }
        ]
      },
      "title": "Dependencies",
      "type": "array"
    }
  },
  "title": "CondaEnv",
  "type": "object"
}

Fields:

• name (Optional[str])
• channels (List[str])
• dependencies (List[Union[str, PipDeps]])

Validators:

• _ensure_valid_conda_env_name → name

channels pydantic-field

channels: List[str]

dependencies pydantic-field

dependencies: List[Union[str, PipDeps]]

name pydantic-field

name: Optional[str] = None

wo_name property

wo_name

get_pip_deps

get_pip_deps() -> List[str]

Get the pip dependencies of this conda env.

Source code in src/bioimageio/spec/conda_env.py

def get_pip_deps(self) -> List[str]:
    """Get the pip dependencies of this conda env."""
    for dep in self.dependencies:
        if isinstance(dep, PipDeps):
            return dep.pip

    return []

PipDeps pydantic-model

Bases: BaseModel

Pip dependencies to include in conda dependecies

Show JSON schema:

{
  "description": "Pip dependencies to include in conda dependecies",
  "properties": {
    "pip": {
      "items": {
        "type": "string"
      },
      "title": "Pip",
      "type": "array"
    }
  },
  "title": "PipDeps",
  "type": "object"
}

Fields:

• pip (List[str])

Validators:

• _remove_empty_and_sort → pip

pip pydantic-field

pip: List[str]

__gt__

__gt__(other: Any)

Source code in src/bioimageio/spec/conda_env.py

def __gt__(self, other: Any):
    if isinstance(other, PipDeps):
        return len(self.pip) > len(other.pip)
    else:
        return False

__lt__

__lt__(other: Any)

Source code in src/bioimageio/spec/conda_env.py

def __lt__(self, other: Any):
    if isinstance(other, PipDeps):
        return len(self.pip) < len(other.pip)
    else:
        return False