From ac47e44f26a996183a085c5b145b418c4c093662 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 26 Nov 2024 06:48:11 +0100
Subject: [PATCH 01/12] [pre-commit.ci] pre-commit autoupdate (#510)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.7.4 → v0.8.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.4...v0.8.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f2cbf888..0d7008b6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.4
+    rev: v0.8.0
     hooks:
       - id: ruff
         name: ruff lint

From 9a8de67de314f69f2b6cf035da8362211c2a1890 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 29 Nov 2024 18:31:39 +0100
Subject: [PATCH 02/12] Bump ipython from 8.29.0 to 8.30.0 (#511)

* Bump ipython from 8.29.0 to 8.30.0

Bumps [ipython](https://github.com/ipython/ipython) from 8.29.0 to 8.30.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](https://github.com/ipython/ipython/compare/8.29.0...8.30.0)

---
updated-dependencies:
- dependency-name: ipython
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* [dependabot skip] Update environment

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pyironrunner <pyiron@mpie.de>
---
 .ci_support/environment-mpich.yml   | 2 +-
 .ci_support/environment-openmpi.yml | 2 +-
 .ci_support/environment-win.yml     | 2 +-
 binder/environment.yml              | 2 +-
 pyproject.toml                      | 4 ++--
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.ci_support/environment-mpich.yml b/.ci_support/environment-mpich.yml
index 2031c9de..07d4adb4 100644
--- a/.ci_support/environment-mpich.yml
+++ b/.ci_support/environment-mpich.yml
@@ -11,6 +11,6 @@ dependencies:
 - 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
diff --git a/.ci_support/environment-openmpi.yml b/.ci_support/environment-openmpi.yml
index e58d7df8..2f9e330a 100644
--- a/.ci_support/environment-openmpi.yml
+++ b/.ci_support/environment-openmpi.yml
@@ -12,5 +12,5 @@ dependencies:
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
-- ipython =8.29.0
+- ipython =8.30.0
 - setuptools =75.1.0
diff --git a/.ci_support/environment-win.yml b/.ci_support/environment-win.yml
index 142bb419..9abcee3f 100644
--- a/.ci_support/environment-win.yml
+++ b/.ci_support/environment-win.yml
@@ -11,5 +11,5 @@ dependencies:
 - matplotlib =3.9.2
 - networkx =3.4.2
 - pygraphviz =1.14
-- ipython =8.29.0
+- ipython =8.30.0
 - setuptools =75.1.0
diff --git a/binder/environment.yml b/binder/environment.yml
index a598ce5e..8a11e290 100644
--- a/binder/environment.yml
+++ b/binder/environment.yml
@@ -15,4 +15,4 @@ dependencies:
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
-- ipython =8.29.0
+- ipython =8.30.0
diff --git a/pyproject.toml b/pyproject.toml
index a312b9b5..bf14086e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,7 +41,7 @@ graph = [
     "pygraphviz==1.14",
     "matplotlib==3.9.2",
     "networkx==3.4.2",
-    "ipython==8.29.0",
+    "ipython==8.30.0",
 ]
 mpi = ["mpi4py==4.0.1"]
 submission = [
@@ -55,7 +55,7 @@ all = [
     "pygraphviz==1.14",
     "matplotlib==3.9.2",
     "networkx==3.4.2",
-    "ipython==8.29.0",
+    "ipython==8.30.0",
 ]
 
 [tool.setuptools.packages.find]

From 23eb02aaaa183cf2aa941ddc207f2a4b8c94bf0b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 2 Dec 2024 18:43:11 -0500
Subject: [PATCH 03/12] [pre-commit.ci] pre-commit autoupdate (#514)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.0 → v0.8.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.0...v0.8.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0d7008b6..6be1447e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.0
+    rev: v0.8.1
     hooks:
       - id: ruff
         name: ruff lint

From 8c74ce85d6d5d601289ec11704936f2ffbbe514e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Dec 2024 19:26:37 -0500
Subject: [PATCH 04/12] Bump matplotlib from 3.9.2 to 3.9.3 (#513)

* Bump matplotlib from 3.9.2 to 3.9.3

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.9.2 to 3.9.3.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](https://github.com/matplotlib/matplotlib/compare/v3.9.2...v3.9.3)

---
updated-dependencies:
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* [dependabot skip] Update environment

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pyironrunner <pyiron@mpie.de>
---
 .ci_support/environment-mpich.yml   | 2 +-
 .ci_support/environment-openmpi.yml | 2 +-
 .ci_support/environment-win.yml     | 2 +-
 binder/environment.yml              | 2 +-
 pyproject.toml                      | 4 ++--
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.ci_support/environment-mpich.yml b/.ci_support/environment-mpich.yml
index 07d4adb4..534f273e 100644
--- a/.ci_support/environment-mpich.yml
+++ b/.ci_support/environment-mpich.yml
@@ -8,7 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.2
+- matplotlib =3.9.3
 - networkx =3.4.2
 - pygraphviz =1.14
 - ipython =8.30.0
diff --git a/.ci_support/environment-openmpi.yml b/.ci_support/environment-openmpi.yml
index 2f9e330a..c6d3dee4 100644
--- a/.ci_support/environment-openmpi.yml
+++ b/.ci_support/environment-openmpi.yml
@@ -8,7 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.2
+- matplotlib =3.9.3
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
diff --git a/.ci_support/environment-win.yml b/.ci_support/environment-win.yml
index 9abcee3f..cbf51a66 100644
--- a/.ci_support/environment-win.yml
+++ b/.ci_support/environment-win.yml
@@ -8,7 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.2
+- matplotlib =3.9.3
 - networkx =3.4.2
 - pygraphviz =1.14
 - ipython =8.30.0
diff --git a/binder/environment.yml b/binder/environment.yml
index 8a11e290..6c7a4fa5 100644
--- a/binder/environment.yml
+++ b/binder/environment.yml
@@ -11,7 +11,7 @@ dependencies:
 - flux-pmix =0.5.0
 - versioneer =0.28
 - h5py =3.12.1
-- matplotlib =3.9.2
+- matplotlib =3.9.3
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
diff --git a/pyproject.toml b/pyproject.toml
index bf14086e..69076846 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ Repository = "https://github.com/pyiron/executorlib"
 cache = ["h5py==3.12.1"]
 graph = [
     "pygraphviz==1.14",
-    "matplotlib==3.9.2",
+    "matplotlib==3.9.3",
     "networkx==3.4.2",
     "ipython==8.30.0",
 ]
@@ -53,7 +53,7 @@ all = [
     "pysqa==0.2.2",
     "h5py==3.12.1",
     "pygraphviz==1.14",
-    "matplotlib==3.9.2",
+    "matplotlib==3.9.3",
     "networkx==3.4.2",
     "ipython==8.30.0",
 ]

From 32864a3951b595e6e3ea0050ee16b7fe3a925efb Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Dec 2024 14:07:50 -0800
Subject: [PATCH 05/12] [pre-commit.ci] pre-commit autoupdate (#515)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.1 → v0.8.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.1...v0.8.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6be1447e..6b467002 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.8.2
     hooks:
       - id: ruff
         name: ruff lint

From 27207d87abd73d4cc3ae35e69c9cc598c919851d Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Mon, 9 Dec 2024 14:39:39 -0800
Subject: [PATCH 06/12] Create automerge.yml (#516)

---
 .github/workflows/automerge.yml | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 .github/workflows/automerge.yml

diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
new file mode 100644
index 00000000..95fce378
--- /dev/null
+++ b/.github/workflows/automerge.yml
@@ -0,0 +1,17 @@
+name: Bot auto-merge
+on: pull_request  # yamllint disable-line rule:truthy
+
+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.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}}

From d6a0268697e058a8c1615715d8b68f242bb2d996 Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Thu, 12 Dec 2024 08:54:06 -0800
Subject: [PATCH 07/12] Update automerge.yml

---
 .github/workflows/automerge.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
index 95fce378..73689b4b 100644
--- a/.github/workflows/automerge.yml
+++ b/.github/workflows/automerge.yml
@@ -8,7 +8,7 @@ permissions:
 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.repository == 'pyiron/executorlib'
+    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"

From f1c4ffa9cfb5c81edf427f2573174459d4bc8789 Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Thu, 12 Dec 2024 09:24:27 -0800
Subject: [PATCH 08/12] Update automerge.yml

---
 .github/workflows/automerge.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
index 73689b4b..8c0039b2 100644
--- a/.github/workflows/automerge.yml
+++ b/.github/workflows/automerge.yml
@@ -1,5 +1,9 @@
 name: Bot auto-merge
-on: pull_request  # yamllint disable-line rule:truthy
+on:
+  pull_request:  # yamllint disable-line rule:truthy
+  workflow_run:
+    workflows: ["Benchmark", "Black", "Coverage", "Unittests-minimal", "Notebooks", "Pip check", "Unittest", "Unittests-flux-mpich", "Unittests-flux-openmpi", "Unittests-mpich", "Unittests-openmpi", "Unittests-msmpi", "Unittest Lower Bound"]
+    types: [completed]
 
 permissions:
   contents: write

From 171a9794fda05db75edf536926fe0cf4a715d9c5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 13 Dec 2024 23:18:26 -0700
Subject: [PATCH 09/12] Bump matplotlib from 3.9.3 to 3.9.4 (#520)

* Bump matplotlib from 3.9.3 to 3.9.4

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.9.3 to 3.9.4.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](https://github.com/matplotlib/matplotlib/compare/v3.9.3...v3.9.4)

---
updated-dependencies:
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* [dependabot skip] Update environment

* Update automerge.yml

* Update automerge.yml

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pyironrunner <pyiron@mpie.de>
Co-authored-by: Jan Janssen <jan-janssen@users.noreply.github.com>
---
 .ci_support/environment-mpich.yml   | 2 +-
 .ci_support/environment-openmpi.yml | 2 +-
 .ci_support/environment-win.yml     | 2 +-
 .github/workflows/automerge.yml     | 2 +-
 binder/environment.yml              | 2 +-
 pyproject.toml                      | 4 ++--
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.ci_support/environment-mpich.yml b/.ci_support/environment-mpich.yml
index 534f273e..bb82319c 100644
--- a/.ci_support/environment-mpich.yml
+++ b/.ci_support/environment-mpich.yml
@@ -8,7 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.3
+- matplotlib =3.9.4
 - networkx =3.4.2
 - pygraphviz =1.14
 - ipython =8.30.0
diff --git a/.ci_support/environment-openmpi.yml b/.ci_support/environment-openmpi.yml
index c6d3dee4..8f687701 100644
--- a/.ci_support/environment-openmpi.yml
+++ b/.ci_support/environment-openmpi.yml
@@ -8,7 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.3
+- matplotlib =3.9.4
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
diff --git a/.ci_support/environment-win.yml b/.ci_support/environment-win.yml
index cbf51a66..b772f12a 100644
--- a/.ci_support/environment-win.yml
+++ b/.ci_support/environment-win.yml
@@ -8,7 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.3
+- matplotlib =3.9.4
 - networkx =3.4.2
 - pygraphviz =1.14
 - ipython =8.30.0
diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
index 8c0039b2..f5a034d9 100644
--- a/.github/workflows/automerge.yml
+++ b/.github/workflows/automerge.yml
@@ -2,7 +2,7 @@ name: Bot auto-merge
 on:
   pull_request:  # yamllint disable-line rule:truthy
   workflow_run:
-    workflows: ["Benchmark", "Black", "Coverage", "Unittests-minimal", "Notebooks", "Pip check", "Unittest", "Unittests-flux-mpich", "Unittests-flux-openmpi", "Unittests-mpich", "Unittests-openmpi", "Unittests-msmpi", "Unittest Lower Bound"]
+    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:
diff --git a/binder/environment.yml b/binder/environment.yml
index 6c7a4fa5..d84b9464 100644
--- a/binder/environment.yml
+++ b/binder/environment.yml
@@ -11,7 +11,7 @@ dependencies:
 - flux-pmix =0.5.0
 - versioneer =0.28
 - h5py =3.12.1
-- matplotlib =3.9.3
+- matplotlib =3.9.4
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
diff --git a/pyproject.toml b/pyproject.toml
index 69076846..1263232c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ Repository = "https://github.com/pyiron/executorlib"
 cache = ["h5py==3.12.1"]
 graph = [
     "pygraphviz==1.14",
-    "matplotlib==3.9.3",
+    "matplotlib==3.9.4",
     "networkx==3.4.2",
     "ipython==8.30.0",
 ]
@@ -53,7 +53,7 @@ all = [
     "pysqa==0.2.2",
     "h5py==3.12.1",
     "pygraphviz==1.14",
-    "matplotlib==3.9.3",
+    "matplotlib==3.9.4",
     "networkx==3.4.2",
     "ipython==8.30.0",
 ]

From 4d7120e997121d7a424187fced70c42ac64c806b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Dec 2024 17:03:42 -0700
Subject: [PATCH 10/12] [pre-commit.ci] pre-commit autoupdate (#522)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.2 → v0.8.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.2...v0.8.3)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6b467002..cb6cca04 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.2
+    rev: v0.8.3
     hooks:
       - id: ruff
         name: ruff lint

From baec2a123785eb76bf9c37c78fa4d02070233709 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Dec 2024 17:34:48 -0700
Subject: [PATCH 11/12] Bump matplotlib from 3.9.4 to 3.10.0 (#521)

* Bump matplotlib from 3.9.4 to 3.10.0

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.9.4 to 3.10.0.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](https://github.com/matplotlib/matplotlib/compare/v3.9.4...v3.10.0)

---
updated-dependencies:
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* [dependabot skip] Update environment

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pyironrunner <pyiron@mpie.de>
Co-authored-by: Jan Janssen <jan-janssen@users.noreply.github.com>
---
 .ci_support/environment-mpich.yml   | 2 +-
 .ci_support/environment-openmpi.yml | 2 +-
 .ci_support/environment-win.yml     | 2 +-
 binder/environment.yml              | 2 +-
 pyproject.toml                      | 4 ++--
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.ci_support/environment-mpich.yml b/.ci_support/environment-mpich.yml
index bb82319c..cb9eece3 100644
--- a/.ci_support/environment-mpich.yml
+++ b/.ci_support/environment-mpich.yml
@@ -8,7 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.4
+- matplotlib =3.10.0
 - networkx =3.4.2
 - pygraphviz =1.14
 - ipython =8.30.0
diff --git a/.ci_support/environment-openmpi.yml b/.ci_support/environment-openmpi.yml
index 8f687701..8d33c18a 100644
--- a/.ci_support/environment-openmpi.yml
+++ b/.ci_support/environment-openmpi.yml
@@ -8,7 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.4
+- matplotlib =3.10.0
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
diff --git a/.ci_support/environment-win.yml b/.ci_support/environment-win.yml
index b772f12a..8608bfaa 100644
--- a/.ci_support/environment-win.yml
+++ b/.ci_support/environment-win.yml
@@ -8,7 +8,7 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.9.4
+- matplotlib =3.10.0
 - networkx =3.4.2
 - pygraphviz =1.14
 - ipython =8.30.0
diff --git a/binder/environment.yml b/binder/environment.yml
index d84b9464..ada84da0 100644
--- a/binder/environment.yml
+++ b/binder/environment.yml
@@ -11,7 +11,7 @@ dependencies:
 - flux-pmix =0.5.0
 - versioneer =0.28
 - h5py =3.12.1
-- matplotlib =3.9.4
+- matplotlib =3.10.0
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
diff --git a/pyproject.toml b/pyproject.toml
index 1263232c..032fc74c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ Repository = "https://github.com/pyiron/executorlib"
 cache = ["h5py==3.12.1"]
 graph = [
     "pygraphviz==1.14",
-    "matplotlib==3.9.4",
+    "matplotlib==3.10.0",
     "networkx==3.4.2",
     "ipython==8.30.0",
 ]
@@ -53,7 +53,7 @@ all = [
     "pysqa==0.2.2",
     "h5py==3.12.1",
     "pygraphviz==1.14",
-    "matplotlib==3.9.4",
+    "matplotlib==3.10.0",
     "networkx==3.4.2",
     "ipython==8.30.0",
 ]

From c3a0ae7279f65ad321538b4fff430ee7c0f81307 Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Mon, 16 Dec 2024 20:20:09 -0700
Subject: [PATCH 12/12] Add option to save graph as PNG (#523)

* Add option to save graph as PNG

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fixes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove file after test

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .ci_support/environment-mpich.yml   |  1 -
 .ci_support/environment-old.yml     |  1 -
 .ci_support/environment-openmpi.yml |  1 -
 .ci_support/environment-win.yml     |  1 -
 executorlib/__init__.py             |  5 +++++
 executorlib/interactive/executor.py | 15 +++++++++++++--
 executorlib/standalone/plot.py      | 19 ++++++++++++-------
 pyproject.toml                      |  6 ++++--
 tests/test_dependencies_executor.py | 21 +++++++++++++++++++++
 9 files changed, 55 insertions(+), 15 deletions(-)

diff --git a/.ci_support/environment-mpich.yml b/.ci_support/environment-mpich.yml
index cb9eece3..4fc6c1a0 100644
--- a/.ci_support/environment-mpich.yml
+++ b/.ci_support/environment-mpich.yml
@@ -8,7 +8,6 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.10.0
 - networkx =3.4.2
 - pygraphviz =1.14
 - ipython =8.30.0
diff --git a/.ci_support/environment-old.yml b/.ci_support/environment-old.yml
index 0d6d5097..031d8291 100644
--- a/.ci_support/environment-old.yml
+++ b/.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
diff --git a/.ci_support/environment-openmpi.yml b/.ci_support/environment-openmpi.yml
index 8d33c18a..08788672 100644
--- a/.ci_support/environment-openmpi.yml
+++ b/.ci_support/environment-openmpi.yml
@@ -8,7 +8,6 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.10.0
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.2.2
diff --git a/.ci_support/environment-win.yml b/.ci_support/environment-win.yml
index 8608bfaa..1314027d 100644
--- a/.ci_support/environment-win.yml
+++ b/.ci_support/environment-win.yml
@@ -8,7 +8,6 @@ dependencies:
 - mpi4py =4.0.1
 - pyzmq =26.2.0
 - h5py =3.12.1
-- matplotlib =3.10.0
 - networkx =3.4.2
 - pygraphviz =1.14
 - ipython =8.30.0
diff --git a/executorlib/__init__.py b/executorlib/__init__.py
index 5e0a1c94..3409eb09 100644
--- a/executorlib/__init__.py
+++ b/executorlib/__init__.py
@@ -62,6 +62,7 @@ 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:
         ```
@@ -101,6 +102,7 @@ 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
@@ -122,6 +124,7 @@ 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,
@@ -167,6 +170,7 @@ 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 = {
@@ -216,6 +220,7 @@ 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)
diff --git a/executorlib/interactive/executor.py b/executorlib/interactive/executor.py
index 5a31f1e6..ed32d31f 100644
--- a/executorlib/interactive/executor.py
+++ b/executorlib/interactive/executor.py
@@ -42,6 +42,7 @@ 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.
 
@@ -49,6 +50,7 @@ class ExecutorWithDependencies(ExecutorBase):
         _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.
 
     """
 
@@ -57,6 +59,7 @@ 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))
@@ -75,7 +78,11 @@ 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,
@@ -142,7 +149,11 @@ 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(
diff --git a/executorlib/standalone/plot.py b/executorlib/standalone/plot.py
index 84fa2eb5..3c5cc252 100644
--- a/executorlib/standalone/plot.py
+++ b/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
 
@@ -106,16 +107,15 @@ 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()
@@ -123,6 +123,11 @@ def draw(node_lst: list, edge_lst: list):
         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")))
diff --git a/pyproject.toml b/pyproject.toml
index 032fc74c..588d668a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,10 @@ Repository = "https://github.com/pyiron/executorlib"
 cache = ["h5py==3.12.1"]
 graph = [
     "pygraphviz==1.14",
-    "matplotlib==3.10.0",
+    "networkx==3.4.2",
+]
+graphnotebook = [
+    "pygraphviz==1.14",
     "networkx==3.4.2",
     "ipython==8.30.0",
 ]
@@ -53,7 +56,6 @@ all = [
     "pysqa==0.2.2",
     "h5py==3.12.1",
     "pygraphviz==1.14",
-    "matplotlib==3.10.0",
     "networkx==3.4.2",
     "ipython==8.30.0",
 ]
diff --git a/tests/test_dependencies_executor.py b/tests/test_dependencies_executor.py
index d3ddeb9a..5c03b49a 100644
--- a/tests/test_dependencies_executor.py
+++ b/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})