WIP: workgraph

TODO remove expandvars hack, use by default local folder

TODO remove example reference from tests

Arbitrary CLI args for shell tasks (#66)

This PR adds the `_CliArgsBaseModel` class (inspired from `_WhenBaseModel`), which replaces the `command_option` and `input_arg_options` of the `ConfigShellTaskSpecs`. Validation is applied on the correctness of the keyword and positional arguments to ensure they start with `-` or `--`.

The three test YAML files are updated accordingly, leading to changes in the pretty-print test text files, which is also part of the PR.

Actually making something useful out of these arguments only happens when the WG is created, so will require #45 to be merged.

Fix svgs being created in main directory. (#67)

Create `svg` files in subdirectory under `tests/files/svgs` instead of top-level directory, and ignore them via `.gitignore`, while syncing the `svgs` directory.
Merge remote-tracking branch 'origin/main' into workgraph

---

Pass single argument string to `ShellTasks` (#72)

* Try to make current example YAML files run through.

* Update class names after rebase/merge

* Add `no_icon` config file

* First working version apart from flags.

* Try fixing argument format.

* Current state before branch-off.

* Pass one multi-line string as `cli_argument`

* Cleanup.

* Pass arguments as list.

* Remove `workgraph-dev.py` dev file.

* Fix issues from `hatch fmt`

reimplementing cli_arguments

change to unspecified inputs are added as positional cli args automatically

delete examples

add files required to run the workflow

remove old files

use rootdir from config

move files to confi folder

adapt configs to relativ to config folder

rm expandvars

fix hatch fmt

fix hatch fmt

update reference

rm comment

implement wait_on

clean up code

clean up add doc

pyproject.toml

@@ -33,7 +33,10 @@ dependencies = [
   "aiida-core>=2.5",
   "termcolor",
   "pygraphviz",
-  "lxml"
+  "lxml",
+  "aiida-core~=2.5",
+  "aiida-workgraph==0.3.14",
+  "node_graph==0.0.11",
 ]
 license = {file = "LICENSE"}
 

src/sirocco/core/graph_items.py

@@ -2,6 +2,7 @@
 
 from dataclasses import dataclass, field
 from itertools import chain, product
+from pathlib import Path
 from typing import TYPE_CHECKING, Any, ClassVar, Self
 
 from sirocco.parsing._yaml_data_models import (

src/sirocco/parsing/_yaml_data_models.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import time
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 from datetime import datetime
 from pathlib import Path
 from typing import Annotated, Any, ClassVar, Literal
@@ -82,43 +82,6 @@ def convert_datetime(cls, value) -> datetime:
         return datetime.fromisoformat(value)
 
 
-class _CliArgsBaseModel(BaseModel):
-    """Base class for cli_arguments specifications"""
-
-    # TODO: Even allow for `str`, or always require list?
-    positional: str | list[str] | None = None
-    # Field needed for child class doing pydantic parsing
-    keyword: dict[str, str] | None = Field(default_factory=dict)
-    flags: str | list[str] | None = None
-    source_file: str | list[str] | None = None
-
-    # TODO: Should we allow users to pass it without the hyphen(s), and prepend them automatically?
-    # TODO: While convenient, it could be a bad idea, if users put in wrong things. Better to be explicit.
-    @field_validator("keyword", mode="before")
-    @classmethod
-    def validate_keyword_args(cls, value):
-        """Ensure keyword arguments start with '-' or '--'."""
-        if value is not None:
-            invalid_keys = [key for key in value if not key.startswith(("-", "--"))]
-            if invalid_keys:
-                invalid_kwarg_exc = f"Invalid keyword arguments: {', '.join(invalid_keys)}"
-                raise ValueError(invalid_kwarg_exc)
-        return value
-
-    @field_validator("flags", mode="before")
-    @classmethod
-    def validate_flag_args(cls, value):
-        """Ensure positional arguments start with '-' or '--'."""
-        if value is not None:
-            if isinstance(value, str):
-                value = [value]
-            invalid_flags = [arg for arg in value if not arg.startswith(("-", "--"))]
-            if invalid_flags:
-                invalid_flags_exc = f"Invalid positional arguments: {', '.join(invalid_flags)}"
-                raise ValueError(invalid_flags_exc)
-        return value
-
-
 class TargetNodesBaseModel(_NamedBaseModel):
     """class for targeting other task or data nodes in the graph
 
@@ -310,12 +273,14 @@ class ConfigRootTask(ConfigBaseTask):
 class ConfigShellTaskSpecs:
     plugin: ClassVar[Literal["shell"]] = "shell"
     command: str = ""
-    cli_arguments: _CliArgsBaseModel | None = None
+    cli_arguments: str = ""
+    env_source_files: str | list[str] = field(default_factory=list)
     src: str | None = None
 
 
 class ConfigShellTask(ConfigBaseTask, ConfigShellTaskSpecs):
-    pass
+    command: str = ""
+    env_source_files: str | list[str] = Field(default_factory=list)
 
 
 @dataclass
@@ -341,6 +306,9 @@ class ConfigBaseData(_NamedBaseModel, ConfigBaseDataSpecs):
     """
 
     parameters: list[str] = []
+    type: str | None = None
+    src: str | None = None
+    format: str | None = None
 
     @field_validator("type")
     @classmethod