Merge remote-tracking branch 'origin/main' into flux_log_files

.ci_support/environment-mpich.yml

@@ -8,9 +8,8 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.2
 - networkx =3.4.2
 - pygraphviz =1.14
-- ipython =8.29.0
+- ipython =8.30.0
 - pysqa =0.2.2
 - setuptools =75.1.0

.ci_support/environment-old.yml

@@ -8,7 +8,6 @@ dependencies:
 - mpi4py =3.1.4
 - pyzmq =25.0.0
 - h5py =3.6.0
-- matplotlib =3.5.3
 - networkx =2.8.8
 - ipython =7.33.0
 - pygraphviz =1.10

.ci_support/environment-openmpi.yml

@@ -8,9 +8,8 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.2
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
-- ipython =8.29.0
+- ipython =8.30.0
 - setuptools =75.1.0

.ci_support/environment-win.yml

@@ -8,8 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.2
 - networkx =3.4.2
 - pygraphviz =1.14
-- ipython =8.29.0
+- ipython =8.30.0
 - setuptools =75.1.0

.github/workflows/automerge.yml

@@ -0,0 +1,21 @@
+name: Bot auto-merge
+on:
+  pull_request:  # yamllint disable-line rule:truthy
+  workflow_run:
+    workflows: ["Benchmark", "Black", "Unittests-minimal", "Notebooks", "Pip check", "Unittests-flux-mpich", "Unittests-flux-openmpi", "Unittests-mpich", "Unittests-openmpi", "Unittests-msmpi", "Unittest Lower Bound"]
+    types: [completed]
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  autobot:
+    runs-on: ubuntu-latest
+    if: (github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]') && github.event.pull_request.conclusion == 'success' && github.repository == 'pyiron/executorlib'
+    steps:
+      - name: Enable auto-merge for bot PRs
+        run: gh pr merge --auto --squash "$PR_URL"
+        env:
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GH_TOKEN: ${{secrets.GITHUB_TOKEN}}

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.4
+    rev: v0.8.3
     hooks:
       - id: ruff
         name: ruff lint

binder/environment.yml

@@ -11,8 +11,8 @@ dependencies:
 - flux-pmix =0.5.0
 - versioneer =0.28
 - h5py =3.12.1
-- matplotlib =3.9.2
+- matplotlib =3.10.0
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
-- ipython =8.29.0
+- ipython =8.30.0

executorlib/__init__.py

@@ -63,6 +63,7 @@ class Executor:
         refresh_rate (float): Set the refresh rate in seconds, how frequently the input queue is checked.
         plot_dependency_graph (bool): Plot the dependencies of multiple future objects without executing them. For
                                       debugging purposes and to get an overview of the specified dependencies.
+        plot_dependency_graph_filename (str): Name of the file to store the plotted graph in.
 
     Examples:
         ```
@@ -103,6 +104,7 @@ def __init__(
         disable_dependencies: bool = False,
         refresh_rate: float = 0.01,
         plot_dependency_graph: bool = False,
+        plot_dependency_graph_filename: Optional[str] = None,
     ):
         # Use __new__() instead of __init__(). This function is only implemented to enable auto-completion.
         pass
@@ -125,6 +127,7 @@ def __new__(
         disable_dependencies: bool = False,
         refresh_rate: float = 0.01,
         plot_dependency_graph: bool = False,
+        plot_dependency_graph_filename: Optional[str] = None,
     ):
         """
         Instead of returning a executorlib.Executor object this function returns either a executorlib.mpi.PyMPIExecutor,
@@ -171,6 +174,7 @@ def __new__(
             refresh_rate (float): Set the refresh rate in seconds, how frequently the input queue is checked.
             plot_dependency_graph (bool): Plot the dependencies of multiple future objects without executing them. For
                                           debugging purposes and to get an overview of the specified dependencies.
+            plot_dependency_graph_filename (str): Name of the file to store the plotted graph in.
 
         """
         default_resource_dict = {
@@ -222,6 +226,7 @@ def __new__(
                 init_function=init_function,
                 refresh_rate=refresh_rate,
                 plot_dependency_graph=plot_dependency_graph,
+                plot_dependency_graph_filename=plot_dependency_graph_filename,
             )
         else:
             _check_pysqa_config_directory(pysqa_config_directory=pysqa_config_directory)

executorlib/interactive/executor.py

@@ -43,13 +43,15 @@ class ExecutorWithDependencies(ExecutorBase):
     Args:
         refresh_rate (float, optional): The refresh rate for updating the executor queue. Defaults to 0.01.
         plot_dependency_graph (bool, optional): Whether to generate and plot the dependency graph. Defaults to False.
+        plot_dependency_graph_filename (str): Name of the file to store the plotted graph in.
         *args: Variable length argument list.
         **kwargs: Arbitrary keyword arguments.
 
     Attributes:
         _future_hash_dict (Dict[str, Future]): A dictionary mapping task hash to future object.
         _task_hash_dict (Dict[str, Dict]): A dictionary mapping task hash to task dictionary.
         _generate_dependency_graph (bool): Whether to generate the dependency graph.
+        _generate_dependency_graph (str): Name of the file to store the plotted graph in.
 
     """
 
@@ -58,6 +60,7 @@ def __init__(
         *args: Any,
         refresh_rate: float = 0.01,
         plot_dependency_graph: bool = False,
+        plot_dependency_graph_filename: Optional[str] = None,
         **kwargs: Any,
     ) -> None:
         super().__init__(max_cores=kwargs.get("max_cores", None))
@@ -76,7 +79,11 @@ def __init__(
         )
         self._future_hash_dict = {}
         self._task_hash_dict = {}
-        self._generate_dependency_graph = plot_dependency_graph
+        self._plot_dependency_graph_filename = plot_dependency_graph_filename
+        if plot_dependency_graph_filename is None:
+            self._generate_dependency_graph = plot_dependency_graph
+        else:
+            self._generate_dependency_graph = True
 
     def submit(
         self,
@@ -143,7 +150,11 @@ def __exit__(
                     v: k for k, v in self._future_hash_dict.items()
                 },
             )
-            return draw(node_lst=node_lst, edge_lst=edge_lst)
+            return draw(
+                node_lst=node_lst,
+                edge_lst=edge_lst,
+                filename=self._plot_dependency_graph_filename,
+            )
 
 
 def create_executor(

executorlib/standalone/plot.py

@@ -1,5 +1,6 @@
+import os.path
 from concurrent.futures import Future
-from typing import Tuple
+from typing import Optional, Tuple
 
 import cloudpickle
 
@@ -106,23 +107,27 @@ def convert_arg(arg, future_hash_inverse_dict):
     )
 
 
-def draw(node_lst: list, edge_lst: list):
+def draw(node_lst: list, edge_lst: list, filename: Optional[str] = None):
     """
     Draw the graph visualization of nodes and edges.
 
     Args:
         node_lst (list): List of nodes.
         edge_lst (list): List of edges.
+        filename (str): Name of the file to store the plotted graph in.
     """
-    from IPython.display import SVG, display  # noqa
-    import matplotlib.pyplot as plt  # noqa
     import networkx as nx  # noqa
 
     graph = nx.DiGraph()
     for node in node_lst:
         graph.add_node(node["id"], label=node["name"], shape=node["shape"])
     for edge in edge_lst:
         graph.add_edge(edge["start"], edge["end"], label=edge["label"])
-    svg = nx.nx_agraph.to_agraph(graph).draw(prog="dot", format="svg")
-    display(SVG(svg))
-    plt.show()
+    if filename is not None:
+        file_format = os.path.splitext(filename)[-1][1:]
+        with open(filename, "wb") as f:
+            f.write(nx.nx_agraph.to_agraph(graph).draw(prog="dot", format=file_format))
+    else:
+        from IPython.display import SVG, display  # noqa
+
+        display(SVG(nx.nx_agraph.to_agraph(graph).draw(prog="dot", format="svg")))

pyproject.toml

@@ -39,9 +39,12 @@ Repository = "https://github.com/pyiron/executorlib"
 cache = ["h5py==3.12.1"]
 graph = [
     "pygraphviz==1.14",
-    "matplotlib==3.9.2",
     "networkx==3.4.2",
-    "ipython==8.29.0",
+]
+graphnotebook = [
+    "pygraphviz==1.14",
+    "networkx==3.4.2",
+    "ipython==8.30.0",
 ]
 mpi = ["mpi4py==4.0.1"]
 submission = [
@@ -53,9 +56,8 @@ all = [
     "pysqa==0.2.2",
     "h5py==3.12.1",
     "pygraphviz==1.14",
-    "matplotlib==3.9.2",
     "networkx==3.4.2",
-    "ipython==8.29.0",
+    "ipython==8.30.0",
 ]
 
 [tool.setuptools.packages.find]

tests/test_dependencies_executor.py

@@ -1,4 +1,5 @@
 from concurrent.futures import Future
+import os
 import unittest
 from time import sleep
 from queue import Queue
@@ -73,6 +74,26 @@ def test_executor_dependency_plot(self):
             self.assertEqual(len(nodes), 5)
             self.assertEqual(len(edges), 4)
 
+    @unittest.skipIf(
+        skip_graphviz_test,
+        "graphviz is not installed, so the plot_dependency_graph tests are skipped.",
+    )
+    def test_executor_dependency_plot_filename(self):
+        graph_file = os.path.join(os.path.dirname(__file__), "test.png")
+        with Executor(
+            max_cores=1,
+            backend="local",
+            plot_dependency_graph=False,
+            plot_dependency_graph_filename=graph_file,
+        ) as exe:
+            cloudpickle_register(ind=1)
+            future_1 = exe.submit(add_function, 1, parameter_2=2)
+            future_2 = exe.submit(add_function, 1, parameter_2=future_1)
+            self.assertTrue(future_1.done())
+            self.assertTrue(future_2.done())
+        self.assertTrue(os.path.exists(graph_file))
+        os.remove(graph_file)
+
     def test_create_executor_error(self):
         with self.assertRaises(ValueError):
             create_executor(backend="toast", resource_dict={"cores": 1})