flowgraph 0.1.2__tar.gz → 0.1.6__tar.gz

{flowgraph-0.1.2/src/flowgraph.egg-info → flowgraph-0.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: flowgraph
-Version: 0.1.2
+Version: 0.1.6
 Summary: Headless typed workflow engine and execution runtime
 Author: Felipe Bordeu
 Maintainer: Felipe Bordeu
@@ -31,10 +31,16 @@ Requires-Dist: scipy>=1.10
 Requires-Dist: pandas
 Requires-Dist: h5py
 Requires-Dist: pillow>=10.0
+Requires-Dist: numpy>=1.24
+Requires-Dist: openpyxl>=3.1.5
+Provides-Extra: imagej
+Requires-Dist: pyimagej; extra == "imagej"
+Requires-Dist: scyjava; extra == "imagej"
 Provides-Extra: dev
 Requires-Dist: pytest>=8.0; extra == "dev"
 Requires-Dist: pytest-cov>=5.0; extra == "dev"
 Requires-Dist: ruff>=0.6; extra == "dev"
+Requires-Dist: build; extra == "dev"
 Provides-Extra: ml
 Requires-Dist: pyplaid; extra == "ml"
 Provides-Extra: cosapp
@@ -72,11 +78,32 @@ The `flowgraph` command is headless and has no GUI runtime dependency:
 
 ```bash
 uv run flowgraph inspect workflow.json
+uv run flowgraph inspect workflow.json --full
+uv run flowgraph inspect workflow.json -i name=value --override node-id.parameter=value
 uv run flowgraph run workflow.json --input name=value
+uv run flowgraph run workflow.json -i name=value
 uv run flowgraph run workflow.json --override node-id.parameter=value
 uv run flowgraph run workflow.json --json-output results.json
 ```
 
+Use `--input` or its short form `-i` for each published workflow input; repeat
+the option to provide multiple inputs.
+`flowgraph inspect` displays the resolved default to the right of each published
+input, or marks it as required or having conflicting saved values.
+Inspection is compact by default; add `--full` (or `-f`) to include the workflow
+graph. Arbitrary-code warnings remain visible in both modes.
+Inspection accepts the same `--input` / `-i` and `--override` assignments as
+execution: overrides update the displayed defaults, and explicit inputs take
+precedence and are marked `(--input)`. It never executes nodes or saves changes.
+When an input is omitted, `flowgraph run` uses its downstream node's saved
+parameter value and prints a warning to stderr identifying the input, value,
+and parameter. This also works for directly exported parameters and nested
+workflow inputs. Explicit inputs take precedence; parameter overrides are applied
+before resolving defaults. Inputs without usable saved values remain required,
+and conflicting saved values require an explicit `--input`.
+For examples and warning output, see
+[Omitted inputs and saved parameter values](doc/user-guide/workflows.md#omitted-inputs-and-saved-parameter-values).
+
 Workflows use the versioned `flowgraph-workflow` JSON format. Core validation and
 execution are UI-independent.
 
@@ -91,9 +118,15 @@ uv build --out-dir dist/
 The resulting wheel is compatible with all supported Python platforms. See
 `packaging/README.md` for release details.
 
-The initial supported publication channels are GitHub source releases and
-PyPI. Conda, Docker, operating-system package managers, and third-party mirrors
-are not supported release channels at this time. See
+The repository also includes a Conda recipe under `packaging/conda/`. FlowGraph
+is distributed through the [`flowgraph` Anaconda channel](https://anaconda.org/channels/flowgraph):
+
+```bash
+conda install -c flowgraph flowgraph
+```
+
+Docker, operating-system package managers, and third-party mirrors are not
+supported release channels at this time. See
 [`Release Channels`](docs/policies/release-channels.md) for the release policy.
 
 FlowGraph Core declares Python 3.11 or newer. CI covers Python 3.11 and 3.13 on
@@ -116,6 +149,12 @@ behavior.
 
 ## Documentation and support
 
+- [FlowGraph documentation](https://flowgraph.readthedocs.io/en/latest/)
+- [Built-in node catalog](doc/reference/adapters/index.md) and
+  [Python custom-node guide](doc/user-guide/custom-nodes.md).
+- The website documentation lives in `doc/` (outside the Python package).
+  To build the Read the Docs site locally, run
+  `uv run --with zensical zensical build -f zensical.toml` from this repository.
 - [`Architecture`](docs/architecture.md) describes the core boundaries and workflow
   model.
 - [`Support Policy`](docs/policies/support-policy.md) describes supported environments and

{flowgraph-0.1.2 → flowgraph-0.1.6}/README.md

@@ -26,11 +26,32 @@ The `flowgraph` command is headless and has no GUI runtime dependency:
 
 ```bash
 uv run flowgraph inspect workflow.json
+uv run flowgraph inspect workflow.json --full
+uv run flowgraph inspect workflow.json -i name=value --override node-id.parameter=value
 uv run flowgraph run workflow.json --input name=value
+uv run flowgraph run workflow.json -i name=value
 uv run flowgraph run workflow.json --override node-id.parameter=value
 uv run flowgraph run workflow.json --json-output results.json
 ```
 
+Use `--input` or its short form `-i` for each published workflow input; repeat
+the option to provide multiple inputs.
+`flowgraph inspect` displays the resolved default to the right of each published
+input, or marks it as required or having conflicting saved values.
+Inspection is compact by default; add `--full` (or `-f`) to include the workflow
+graph. Arbitrary-code warnings remain visible in both modes.
+Inspection accepts the same `--input` / `-i` and `--override` assignments as
+execution: overrides update the displayed defaults, and explicit inputs take
+precedence and are marked `(--input)`. It never executes nodes or saves changes.
+When an input is omitted, `flowgraph run` uses its downstream node's saved
+parameter value and prints a warning to stderr identifying the input, value,
+and parameter. This also works for directly exported parameters and nested
+workflow inputs. Explicit inputs take precedence; parameter overrides are applied
+before resolving defaults. Inputs without usable saved values remain required,
+and conflicting saved values require an explicit `--input`.
+For examples and warning output, see
+[Omitted inputs and saved parameter values](doc/user-guide/workflows.md#omitted-inputs-and-saved-parameter-values).
+
 Workflows use the versioned `flowgraph-workflow` JSON format. Core validation and
 execution are UI-independent.
 
@@ -45,9 +66,15 @@ uv build --out-dir dist/
 The resulting wheel is compatible with all supported Python platforms. See
 `packaging/README.md` for release details.
 
-The initial supported publication channels are GitHub source releases and
-PyPI. Conda, Docker, operating-system package managers, and third-party mirrors
-are not supported release channels at this time. See
+The repository also includes a Conda recipe under `packaging/conda/`. FlowGraph
+is distributed through the [`flowgraph` Anaconda channel](https://anaconda.org/channels/flowgraph):
+
+```bash
+conda install -c flowgraph flowgraph
+```
+
+Docker, operating-system package managers, and third-party mirrors are not
+supported release channels at this time. See
 [`Release Channels`](docs/policies/release-channels.md) for the release policy.
 
 FlowGraph Core declares Python 3.11 or newer. CI covers Python 3.11 and 3.13 on
@@ -70,6 +97,12 @@ behavior.
 
 ## Documentation and support
 
+- [FlowGraph documentation](https://flowgraph.readthedocs.io/en/latest/)
+- [Built-in node catalog](doc/reference/adapters/index.md) and
+  [Python custom-node guide](doc/user-guide/custom-nodes.md).
+- The website documentation lives in `doc/` (outside the Python package).
+  To build the Read the Docs site locally, run
+  `uv run --with zensical zensical build -f zensical.toml` from this repository.
 - [`Architecture`](docs/architecture.md) describes the core boundaries and workflow
   model.
 - [`Support Policy`](docs/policies/support-policy.md) describes supported environments and

{flowgraph-0.1.2 → flowgraph-0.1.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "flowgraph"
-version = "0.1.2"
+version = "0.1.6"
 description = "Headless typed workflow engine and execution runtime"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -35,13 +35,20 @@ dependencies = [
   "pandas",
   "h5py",
   "pillow>=10.0",
+  "numpy>=1.24",
+  "openpyxl>=3.1.5",
 ]
 
 [project.optional-dependencies]
+imagej = [
+  "pyimagej",
+  "scyjava",
+]
 dev = [
   "pytest>=8.0",
   "pytest-cov>=5.0",
   "ruff>=0.6",
+  "build",
 ]
 ml = [
   "pyplaid",
@@ -81,3 +88,16 @@ pythonpath = [".", "src"]
 target-version = "py311"
 line-length = 100
 
+#[tool.uv.sources]
+#muscat = { git = "https://gitlab.com/drti/muscat.git", rev = "ParMmg" }
+##micromamba install -n uv_muscat_build_packages scotch mmgsuite=*=h* kokkos=*=h*
+## uv pip install ipywidgets
+## uv pip install jupyterlab
+##export OMP_PROC_BIND=spread
+##export OMP_PLACES=threads
+##LD_LIBRARY_PATH=/home/fbw/.local/share/mamba/envs/uv_muscat_build_packages/lib/ uv run jupyter lab
+
+#[tool.uv]
+#config-settings-package = {muscat = {"cmake.args" = ["-DCMAKE_PREFIX_PATH=/home/fbw/.local/share/mamba/envs/uv_muscat_build_packages/lib/cmake/",
+#"-DSCOTCH_ROOT=/home/fbw/.local/share/mamba/envs/uv_muscat_build_packages/"
+#]}}

{flowgraph-0.1.2 → flowgraph-0.1.6}/src/flowgraph/adapters/__init__.py

@@ -17,6 +17,7 @@ from flowgraph.adapters.filters import (
     FILTER_MESH_WITH_MUSCAT,
 )
 from flowgraph.adapters.image_tools import AVAILABLE_NODES as IMAGE_TOOLS_AVAILABLE_NODES
+from flowgraph.adapters.imagej import AVAILABLE_NODES as IMAGEJ_AVAILABLE_NODES
 from flowgraph.adapters.mesh_creation_tools import AVAILABLE_NODES as MESH_CREATION_AVAILABLE_NODES
 from flowgraph.adapters.mesh_generations import CSV_TO_MESH
 from flowgraph.adapters.mesh_ops import AVAILABLE_NODES as MESH_OPS_AVAILABLE_NODES
@@ -26,24 +27,29 @@ from flowgraph.adapters.readers import (
     LOAD_MESHIO,
     LOAD_MESHLANE,
     LOAD_MUSCAT,
+    READ_TABLE,
 )
 from flowgraph.adapters.remote_files import DOWNLOAD_URL
 from flowgraph.adapters.simple_sources import (
+    SET_BOOLEAN,
     SET_FLOAT,
     SET_INT,
     SET_LIST_FLOAT,
     SET_LIST_INT,
     SET_LIST_STR,
     SET_STRING,
+    SET_VEC2D,
+    SET_VEC2DI,
     SET_VEC3D,
 )
 from flowgraph.adapters.sinks import AVAILABLE_NODES as SINKS_AVAILABLE_NODES
+from flowgraph.adapters.table_tools import AVAILABLE_NODES as TABLE_TOOLS_AVAILABLE_NODES
 from flowgraph.adapters.user_code import AVAILABLE_NODES as USER_CODE_AVAILABLE_NODES
 from flowgraph.adapters.workflow import AVAILABLE_NODES as WORKFLOW_AVAILABLE_NODES
 from flowgraph.adapters.workflow_interfaces import (
     AVAILABLE_NODES as WORKFLOW_INTERFACE_AVAILABLE_NODES,
 )
-from flowgraph.adapters.writers import WRITE_MESHIO, WRITE_MESHLANE, WRITE_MUSCAT
+from flowgraph.adapters.writers import WRITE_MESHIO, WRITE_MESHLANE, WRITE_MUSCAT, WRITE_TABLE
 from flowgraph.application.workflow_core import NodeDefinition
 
 
@@ -93,9 +99,10 @@ ADAPTERS = AdapterCatalog(
         AdapterGroup(
             "Inputs",
             subgroups=(
-                AdapterGroup("Scalars", (SET_STRING, SET_INT, SET_FLOAT)),
+                AdapterGroup("Scalars", (SET_STRING, SET_BOOLEAN, SET_INT, SET_FLOAT)),
                 AdapterGroup(
-                    "Lists/Vectors", (SET_LIST_STR, SET_LIST_INT, SET_LIST_FLOAT, SET_VEC3D)
+                    "Lists/Vectors",
+                    (SET_LIST_STR, SET_LIST_INT, SET_LIST_FLOAT, SET_VEC2D, SET_VEC2DI, SET_VEC3D),
                 ),
                 AdapterGroup(
                     "Files",
@@ -108,7 +115,7 @@ ADAPTERS = AdapterCatalog(
             subgroups=(
                 AdapterGroup(
                     "Readers",
-                    (LOAD_MUSCAT, LOAD_MESHIO, LOAD_MESHLANE, LOAD_CSV),
+                    (LOAD_MUSCAT, LOAD_MESHIO, LOAD_MESHLANE, LOAD_CSV, READ_TABLE),
                 ),
                 AdapterGroup("Mesh Gens", (CSV_TO_MESH,)),
                 AdapterGroup("Mesh Creation", MESH_CREATION_AVAILABLE_NODES),
@@ -119,12 +126,13 @@ ADAPTERS = AdapterCatalog(
                 AdapterGroup("Mesh Ops", MESH_OPS_AVAILABLE_NODES),
                 AdapterGroup("Field Ops", FIELD_OPS_AVAILABLE_NODES),
                 AdapterGroup("File Conversion", (MESH_FILE_CONVERSION,)),
-                AdapterGroup("Writers", (WRITE_MUSCAT, WRITE_MESHLANE, WRITE_MESHIO)),
+                AdapterGroup("Writers", (WRITE_MUSCAT, WRITE_MESHLANE, WRITE_MESHIO, WRITE_TABLE)),
             ),
         ),
         AdapterGroup("Controls", CONTROL_AVAILABLE_NODES),
         AdapterGroup("Image Tools", IMAGE_TOOLS_AVAILABLE_NODES),
-        AdapterGroup("Code", USER_CODE_AVAILABLE_NODES),
+        AdapterGroup("Table Tools", TABLE_TOOLS_AVAILABLE_NODES),
+        AdapterGroup("Code", USER_CODE_AVAILABLE_NODES + IMAGEJ_AVAILABLE_NODES),
         AdapterGroup("Workflow", WORKFLOW_INTERFACE_AVAILABLE_NODES + WORKFLOW_AVAILABLE_NODES),
         AdapterGroup("Sinks", SINKS_AVAILABLE_NODES),
         AdapterGroup("Doc", DOCUMENTATION_AVAILABLE_NODES),

{flowgraph-0.1.2 → flowgraph-0.1.6}/src/flowgraph/adapters/controls.py

@@ -5,6 +5,7 @@ from collections.abc import Mapping
 from typing import Any
 
 from flowgraph.application.workflow_core import (
+    ExecContext,
     NodeDefinition,
     ParameterDefinition,
     PortDefinition,
@@ -51,13 +52,18 @@ def _slider_bounds(
     return minimum, maximum, value
 
 
-def _float_slider(_inputs: Mapping[str, Any], parameters: Mapping[str, Any]) -> Mapping[str, Any]:
+def _float_slider(
+    _inputs: Mapping[str, Any],
+    parameters: Mapping[str, Any],
+    _exec_context: ExecContext | None = None,
+) -> Mapping[str, Any]:
     """Output the current finite floating-point slider value."""
     return {"value": _slider_bounds(parameters, integer=False)[2]}
 
 
 FLOAT_SLIDER = NodeDefinition(
     id="float-slider",
+    requirements=(),
     icon="mdi-tune-vertical",
     label="Float Slider",
     description="Outputs a floating-point value selected with a slider.",
@@ -72,13 +78,18 @@ FLOAT_SLIDER = NodeDefinition(
 )
 
 
-def _int_slider(_inputs: Mapping[str, Any], parameters: Mapping[str, Any]) -> Mapping[str, Any]:
+def _int_slider(
+    _inputs: Mapping[str, Any],
+    parameters: Mapping[str, Any],
+    _exec_context: ExecContext | None = None,
+) -> Mapping[str, Any]:
     """Output the current integer slider value."""
     return {"value": _slider_bounds(parameters, integer=True)[2]}
 
 
 INT_SLIDER = NodeDefinition(
     id="int-slider",
+    requirements=(),
     icon="mdi-tune-vertical",
     label="Integer Slider",
     description="Outputs an integer value selected with a slider.",

{flowgraph-0.1.2 → flowgraph-0.1.6}/src/flowgraph/adapters/cosapp.py

@@ -9,13 +9,14 @@ from pathlib import Path
 from typing import Any
 
 from flowgraph.application.workflow_core import (
+    ExecContext,
     NodeDefinition,
     ParameterDefinition,
     PortDefinition,
     PortDirection,
 )
 
-from .data_types import ANY, FILE, STRING
+from .data_types import ANY, FILE, STRING, FilePath
 
 COSAPP_RESULT_PORT = PortDefinition("result", PortDirection.OUTPUT, ANY, "CoSApp system")
 
@@ -69,8 +70,11 @@ def _validate_output_paths(output_paths: Mapping[str, str]) -> None:
 
 def _load_model(module_path: object, factory_name: object) -> Any:
     """Load and construct a root CoSApp ``System`` from a trusted Python file."""
-    if not isinstance(module_path, str) or not module_path.strip():
+    if isinstance(module_path, FilePath):
+        module_path = str(module_path)
+    if not module_path.strip():
         raise ValueError("The CoSApp model file must be a non-empty Python file path")
+
     if not isinstance(factory_name, str) or not factory_name.strip():
         raise ValueError("The CoSApp factory name must be a non-empty attribute name")
 
@@ -130,7 +134,11 @@ def _get_path(model: object, path: str) -> Any:
         raise ValueError(f"CoSApp output path {path!r} does not exist") from error
 
 
-def _execute_cosapp(inputs: Mapping[str, Any], parameters: Mapping[str, Any]) -> Mapping[str, Any]:
+def _execute_cosapp(
+    inputs: Mapping[str, Any],
+    parameters: Mapping[str, Any],
+    _exec_context: ExecContext | None = None,
+) -> Mapping[str, Any]:
     """Construct, configure, execute, and export one CoSApp model instance."""
     input_paths = _path_mapping(parameters.get("inputs", "{}"), "inputs")
     output_paths = _path_mapping(parameters.get("outputs", "{}"), "outputs")
@@ -147,6 +155,7 @@ def _execute_cosapp(inputs: Mapping[str, Any], parameters: Mapping[str, Any]) ->
 
 COSAPP_WORKFLOW = NodeDefinition(
     id="cosapp-workflow",
+    requirements=("py:cosapp",),
     icon="mdi-play-network-outline",
     label="CoSApp Workflow",
     description="Executes a trusted external CoSApp System and exports declared result paths.",

{flowgraph-0.1.2 → flowgraph-0.1.6}/src/flowgraph/adapters/data_types.py

@@ -1,9 +1,13 @@
+from pathlib import Path
+
+import numpy as np
 from Muscat.LinAlg.Transform import Transform
 from Muscat.MeshContainers.Filters.FilterObjects import ElementFilter
 from Muscat.MeshContainers.Filters.FilterOperators import FilterOperatorBase
 from PIL.Image import Image
 
 from flowgraph.application.workflow_core import DataType
+from flowgraph.domain.filepath import FilePath
 from flowgraph.domain.mesh_document import MeshDocument
 
 ANY = DataType("any", "Any", object)
@@ -16,11 +20,14 @@ LIST_STR = DataType("list[str]", "List Text", list[str])
 LIST_INT = DataType("list[int]", "List Ints", list[int])
 LIST_FLOAT = DataType("list[float]", "List Floats", list[float])
 LIST_ANY = DataType("list[any]", "List Any", list)
-FILE = DataType("filename", "Path", str)
+FILE = DataType("filename", "FilePath", FilePath)
+
+DIRECTORY = DataType("dirname", "Path", Path)
 
 MESH_DOCUMENT = DataType("mesh-document", "Mesh document", MeshDocument)
 TABLE_DOCUMENT = DataType("table-document", "Table", dict)
 IMAGE = DataType("image", "Image", Image)
+IMAGEJ = DataType("imagej", "ImageJ NumPy", np.ndarray)
 MUSCAT_ELEMENT_FILTER = DataType(
     "filter-like",
     "Selector",
@@ -30,8 +37,8 @@ VEC3D = DataType("VEC3D", "3D Vector", list[float])
 VEC2D = DataType("VEC2D", "2D Vector", list[float])
 VEC3DSTR = DataType("VEC3DSTR", "3D Text Vector", list[str])
 
-VEC3DI = DataType("VEC3D", "3D Vector", list[int])
-VEC2DI = DataType("VEC2D", "2D Vector", list[int])
+VEC3DI = DataType("VEC3DI", "3D Integer Vector", list[int])
+VEC2DI = DataType("VEC2DI", "2D Integer Vector", list[int])
 
 
 MULTI_SELECT = DataType("list[bool]", "List bool", list[bool])

{flowgraph-0.1.2 → flowgraph-0.1.6}/src/flowgraph/adapters/documentation.py

@@ -5,11 +5,12 @@ from flowgraph.application.workflow_core import NodeDefinition, ParameterDefinit
 
 DOC_TITLE = NodeDefinition(
     id="title-doc",
+    requirements=(),
     icon="",
     label="Title",
     description="Just a Title",
     ports=(),
-    executor=lambda x, y: None,
+    executor=lambda x, y, _exec_context: None,
     parameters=(
         ParameterDefinition(
             name="title",
@@ -24,11 +25,12 @@ DOC_TITLE = NodeDefinition(
 
 DOC_PARAGRAPH = NodeDefinition(
     id="paragraph-doc",
+    requirements=(),
     icon="",
     label="Paragraph",
     description="Long-form documentation text",
     ports=(),
-    executor=lambda x, y: None,
+    executor=lambda x, y, _exec_context: None,
     parameters=(
         ParameterDefinition(
             name="text",

{flowgraph-0.1.2 → flowgraph-0.1.6}/src/flowgraph/adapters/field_ops.py

@@ -14,6 +14,7 @@ from Muscat.MeshTools.MeshTools import GetElementsCenters
 
 from flowgraph.adapters.data_types import MESH_DOCUMENT
 from flowgraph.application.workflow_core import (
+    ExecContext,
     NodeDefinition,
     ParameterDefinition,
     PortDefinition,
@@ -25,7 +26,9 @@ from .data_types import ParameterKind
 
 
 def _transfer_fields(
-    inputs: Mapping[str, Any], _parameters: Mapping[str, Any]
+    inputs: Mapping[str, Any],
+    _parameters: Mapping[str, Any],
+    _exec_context: ExecContext | None = None,
 ) -> Mapping[str, Any]:
     """Transfer all nodal fields from ``source_data`` onto ``target``."""
     source_mesh: Mesh = inputs["source_data"].mesh
@@ -87,6 +90,7 @@ def _transfer_fields(
 
 
 TRANSFER_FIELDS_NODE = NodeDefinition(
+    requirements=("py:muscat", "py:numpy"),
     id="transfer-fields",
     icon="mdi-swap-horizontal-bold",
     label="Transfer Fields",

{flowgraph-0.1.2 → flowgraph-0.1.6}/src/flowgraph/adapters/file_conversion.py

@@ -5,6 +5,7 @@ from pathlib import Path
 from typing import Any, ClassVar
 
 from flowgraph.application.workflow_core import (
+    ExecContext,
     NodeDefinition,
     ParameterDefinition,
     ParameterOption,
@@ -221,7 +222,9 @@ except ImportError:
 
 
 def mesh_file_conversion(
-    inputs: Mapping[str, Any], parameters: Mapping[str, Any]
+    inputs: Mapping[str, Any],
+    parameters: Mapping[str, Any],
+    _exec_context: ExecContext | None = None,
 ) -> Mapping[str, Any]:
     """Convert a mesh while preserving the explicit reader/writer algorithm.
 
@@ -340,7 +343,8 @@ def mesh_file_conversion(
 
 MESH_FILE_CONVERSION = NodeDefinition(
     id="convert-mesh-file-format",
-    icon="mdi--file-swap",
+    requirements=("py:muscat", "py:meshio"),
+    icon="mdi-file-swap",
     label="Convert Mesh File Format",
     description="Read and write a mesh (and solutions if supported) to a new format file",
     ports=(PortDefinition("converted_filename", PortDirection.OUTPUT, FILE, "Output Filename"),),