From f5c0a14ad98c2f206867b01f1d1085d6ac1a60cc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 17 Nov 2021 13:58:41 +0000
Subject: [PATCH 01/23] Bump matplotlib from 3.4.3 to 3.5.0

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 17516db4..63398be4 100644
--- a/setup.py
+++ b/setup.py
@@ -46,7 +46,7 @@
             "pytest==6.2.5",
             "pytest-cov==3.0.0",
             "FireWorks==1.9.7",
-            "matplotlib==3.4.3",
+            "matplotlib==3.5.0",
             "pydot==1.4.2",
         ],
         "dev": ["pre-commit>=2.12.1"],

From fb36c1a85b10164dbd1b371c16cf829b5ec7bee8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 17 Nov 2021 13:59:03 +0000
Subject: [PATCH 02/23] Bump furo from 2021.11.15 to 2021.11.16

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 63398be4..8a0f4f61 100644
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,7 @@
     extras_require={
         "docs": [
             "sphinx==4.3.0",
-            "furo==2021.11.15",
+            "furo==2021.11.16",
             "m2r2==0.3.1",
             "ipython==7.29.0",
             "nbsphinx==0.8.7",

From 5a4f804e5aa872cdff16bd9acb48272dfc4adb10 Mon Sep 17 00:00:00 2001
From: David Waroquiers <david.waroquiers@matgenix.com>
Date: Thu, 18 Nov 2021 18:30:53 +0100
Subject: [PATCH 03/23] Added first implementation of a myqueue conversion
 scheme for jobflow Flows. This would allow jobflow Flows to be run within
 Myqueue.

---
 src/jobflow/managers/myqueue.py               | 110 ++++++++++++++++++
 .../managers/myqueue_scripts/workflow.py      |  26 +++++
 2 files changed, 136 insertions(+)
 create mode 100644 src/jobflow/managers/myqueue.py
 create mode 100644 src/jobflow/managers/myqueue_scripts/workflow.py

diff --git a/src/jobflow/managers/myqueue.py b/src/jobflow/managers/myqueue.py
new file mode 100644
index 00000000..8448fb0c
--- /dev/null
+++ b/src/jobflow/managers/myqueue.py
@@ -0,0 +1,110 @@
+"""Tools for running :obj:`Flow` and :obj:`Job` objects using the Myqueue package.
+
+Notes
+-----
+Myqueue heavily relies on the file system. To submit a workflow, one has to run:
+mq workflow workflow.py DIRECTORY_PATTERNS
+where workflow.py is a python script defining one workflow. For jobflow Flows, the
+workflow.py file in myqueue_scripts has to be used.
+"""
+
+from __future__ import annotations
+
+import json
+import os
+import typing
+from datetime import datetime
+from pathlib import Path
+from random import randint
+
+from monty.json import MontyDecoder, MontyEncoder
+from monty.os import cd
+
+if typing.TYPE_CHECKING:
+    from typing import List, Union
+
+    import jobflow
+
+from maggma.stores import JSONStore
+
+from jobflow import JobStore
+
+__all__ = ["flow_to_myqueue", "run_myqueue_task"]
+
+FLOW_JSON = "flow.json"
+JOB_STORE_JSON = "job_store.json"
+
+
+def flow_to_myqueue(
+    flow: Union[jobflow.Flow, jobflow.Job, List[jobflow.Job]],
+):
+    """
+    Convert a jobflow Flow to myqueue.
+
+    This is basically just dumping the jobflow Flow to a flow.json file.
+    The flow.json file is then read again when the user wants to submit
+    the workflow using myqueue.
+
+    Parameters
+    ----------
+    flow
+        A flow or job.
+
+    """
+    from jobflow.core.flow import get_flow
+
+    flow = get_flow(flow)
+    with open(FLOW_JSON, "w") as f:
+        json.dump(flow, f, cls=MontyEncoder, indent=2)
+
+
+def run_myqueue_task(uuid):
+    """
+    Run a job in myqueue.
+
+    Parameters
+    ----------
+    uuid
+        Unique identifier of the job that needs to be executed.
+    """
+    root_dir = Path.cwd()
+    # First get the jobflow Flow from the flow.json file
+    with open("flow.json", "r") as f:
+        flow = json.load(f, cls=MontyDecoder)
+
+    # Get the jobflow Job corresponding to the uuid
+    job = _get_job(flow, uuid)
+    job_dir = _get_job_dir(root_dir=root_dir)
+
+    # Initialize the store for output references
+    job_store_json_path = os.path.join(root_dir, JOB_STORE_JSON)
+    if not os.path.exists(job_store_json_path):
+        with open(job_store_json_path, "w") as f:
+            json.dump([], f)
+    store = JobStore(JSONStore(job_store_json_path, writable=True))
+    store.connect()
+
+    # Run the job
+    with cd(job_dir):
+        job.run(store=store)
+
+
+def _get_job(flow, uuid):
+    myjob = None
+    for job, _ in flow.iterflow():
+        if job.uuid == uuid:
+            if myjob is not None:
+                raise RuntimeError(f"Multiple jobs with uuid {uuid}")
+            myjob = job
+    return myjob
+
+
+def _get_job_dir(root_dir):
+    time_now = datetime.utcnow().strftime("%Y-%m-%d-%H-%M-%S-%f")
+    job_dir = root_dir / f"job_{time_now}-{randint(10000, 99999)}"
+    job_dir.mkdir()
+    return job_dir
+
+
+if __name__ == "__main__":
+    pass
diff --git a/src/jobflow/managers/myqueue_scripts/workflow.py b/src/jobflow/managers/myqueue_scripts/workflow.py
new file mode 100644
index 00000000..206c4154
--- /dev/null
+++ b/src/jobflow/managers/myqueue_scripts/workflow.py
@@ -0,0 +1,26 @@
+"""Template workflow.py file for running jobflow workflows in myqueue."""
+
+
+import json
+
+from monty.json import MontyDecoder
+from myqueue.task import task
+
+
+def create_tasks():
+    """Create tasks for myqueue."""
+    # First reconstruct the jobflow Flow object
+    with open("flow.json", "r") as f:
+        flow = json.load(f, cls=MontyDecoder)
+
+    tasks = []
+    uuid2task = {}
+    for job, parents in flow.iterflow():
+        deps = [uuid2task[parent_uuid] for parent_uuid in parents]
+        t = task(
+            "jobflow.managers.myqueue@run_myqueue_task", args=[job.uuid], deps=deps
+        )
+        uuid2task[job.uuid] = t
+        tasks.append(t)
+
+    return tasks

From 5278c62cce33eba5e5b3ce10c1070b0ee92d91cb Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Nov 2021 18:20:41 +0000
Subject: [PATCH 04/23] Bump furo from 2021.11.16 to 2021.11.23

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 8a0f4f61..bf12d7ed 100644
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,7 @@
     extras_require={
         "docs": [
             "sphinx==4.3.0",
-            "furo==2021.11.16",
+            "furo==2021.11.23",
             "m2r2==0.3.1",
             "ipython==7.29.0",
             "nbsphinx==0.8.7",

From c6e1d4b5ddd86c976c7539a8415be8e8596f953f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Nov 2021 18:21:09 +0000
Subject: [PATCH 05/23] Bump maggma from 0.32.1 to 0.32.3

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 23bb4f4e..fe39b83d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 monty==2021.8.17
 networkx==2.6.3
 pydash==5.1.0
-maggma==0.32.1
+maggma==0.32.3
 pydantic==1.8.2
 PyYAML==6.0

From f31d7573f38d8d5446275e314f456087b56a37c5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Nov 2021 18:21:48 +0000
Subject: [PATCH 06/23] Bump ipython from 7.29.0 to 7.30.0

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index bf12d7ed..1b2216c5 100644
--- a/setup.py
+++ b/setup.py
@@ -36,7 +36,7 @@
             "sphinx==4.3.0",
             "furo==2021.11.23",
             "m2r2==0.3.1",
-            "ipython==7.29.0",
+            "ipython==7.30.0",
             "nbsphinx==0.8.7",
             "nbsphinx-link==1.3.0",
             "FireWorks==1.9.7",

From 96b5d6a4c31c21bdfab945f2e4a33b011286c567 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Nov 2021 18:29:04 +0000
Subject: [PATCH 07/23] Bump sphinx from 4.3.0 to 4.3.1

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 1b2216c5..a0fdce86 100644
--- a/setup.py
+++ b/setup.py
@@ -33,7 +33,7 @@
     ],
     extras_require={
         "docs": [
-            "sphinx==4.3.0",
+            "sphinx==4.3.1",
             "furo==2021.11.23",
             "m2r2==0.3.1",
             "ipython==7.30.0",

From 2178d9c0f925276db82cf936ad8c247e44577597 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Dec 2021 18:21:10 +0000
Subject: [PATCH 08/23] Bump fireworks from 1.9.7 to 1.9.8

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index a0fdce86..d2804f00 100644
--- a/setup.py
+++ b/setup.py
@@ -39,13 +39,13 @@
             "ipython==7.30.0",
             "nbsphinx==0.8.7",
             "nbsphinx-link==1.3.0",
-            "FireWorks==1.9.7",
+            "FireWorks==1.9.8",
             "autodoc_pydantic==1.5.1",
         ],
         "tests": [
             "pytest==6.2.5",
             "pytest-cov==3.0.0",
-            "FireWorks==1.9.7",
+            "FireWorks==1.9.8",
             "matplotlib==3.5.0",
             "pydot==1.4.2",
         ],

From cd0c260753f1aba41e11c479a91d51712ebe7b7c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Dec 2021 18:25:46 +0000
Subject: [PATCH 09/23] Bump ipython from 7.30.0 to 7.30.1

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index d2804f00..0156a7b6 100644
--- a/setup.py
+++ b/setup.py
@@ -36,7 +36,7 @@
             "sphinx==4.3.1",
             "furo==2021.11.23",
             "m2r2==0.3.1",
-            "ipython==7.30.0",
+            "ipython==7.30.1",
             "nbsphinx==0.8.7",
             "nbsphinx-link==1.3.0",
             "FireWorks==1.9.8",

From aa2be5b39aa957bb060804047dd963fa8df3d7cb Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Dec 2021 18:26:25 +0000
Subject: [PATCH 10/23] Bump matplotlib from 3.5.0 to 3.5.1

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 0156a7b6..bbe3cb8f 100644
--- a/setup.py
+++ b/setup.py
@@ -46,7 +46,7 @@
             "pytest==6.2.5",
             "pytest-cov==3.0.0",
             "FireWorks==1.9.8",
-            "matplotlib==3.5.0",
+            "matplotlib==3.5.1",
             "pydot==1.4.2",
         ],
         "dev": ["pre-commit>=2.12.1"],

From 312b86b5592576d59c7619a3450fb58f25587c1d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Dec 2021 18:30:16 +0000
Subject: [PATCH 11/23] Bump m2r2 from 0.3.1 to 0.3.2

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index bbe3cb8f..e5880ae1 100644
--- a/setup.py
+++ b/setup.py
@@ -35,7 +35,7 @@
         "docs": [
             "sphinx==4.3.1",
             "furo==2021.11.23",
-            "m2r2==0.3.1",
+            "m2r2==0.3.2",
             "ipython==7.30.1",
             "nbsphinx==0.8.7",
             "nbsphinx-link==1.3.0",

From 9ed307fa5f044e16c0c1fbe1223750beb7fa4b1f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 20 Dec 2021 18:23:18 +0000
Subject: [PATCH 12/23] Bump sphinx from 4.3.1 to 4.3.2

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index e5880ae1..219fa50e 100644
--- a/setup.py
+++ b/setup.py
@@ -33,7 +33,7 @@
     ],
     extras_require={
         "docs": [
-            "sphinx==4.3.1",
+            "sphinx==4.3.2",
             "furo==2021.11.23",
             "m2r2==0.3.2",
             "ipython==7.30.1",

From 02102a908c2e20b5eaec81518659915e9ea28d58 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 3 Jan 2022 18:18:10 +0000
Subject: [PATCH 13/23] Bump nbsphinx from 0.8.7 to 0.8.8

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 219fa50e..b2b8971f 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@
             "furo==2021.11.23",
             "m2r2==0.3.2",
             "ipython==7.30.1",
-            "nbsphinx==0.8.7",
+            "nbsphinx==0.8.8",
             "nbsphinx-link==1.3.0",
             "FireWorks==1.9.8",
             "autodoc_pydantic==1.5.1",

From b0350acc611f5f8a2a354abca735c83512aec279 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 3 Jan 2022 18:18:12 +0000
Subject: [PATCH 14/23] Bump pydantic from 1.8.2 to 1.9.0

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index fe39b83d..79af6a42 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,5 +2,5 @@ monty==2021.8.17
 networkx==2.6.3
 pydash==5.1.0
 maggma==0.32.3
-pydantic==1.8.2
+pydantic==1.9.0
 PyYAML==6.0

From d8747aa0be3f53ac7a0d831fe84875cb061a60ed Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 3 Jan 2022 18:18:23 +0000
Subject: [PATCH 15/23] Bump furo from 2021.11.23 to 2022.1.2

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index b2b8971f..b1899c70 100644
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,7 @@
     extras_require={
         "docs": [
             "sphinx==4.3.2",
-            "furo==2021.11.23",
+            "furo==2022.1.2",
             "m2r2==0.3.2",
             "ipython==7.30.1",
             "nbsphinx==0.8.8",

From 13813fa97d7b2358bf9462d4a4b8ebe02d82183b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 3 Jan 2022 18:25:04 +0000
Subject: [PATCH 16/23] Bump monty from 2021.8.17 to 2021.12.1

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 79af6a42..1efb1a2f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-monty==2021.8.17
+monty==2021.12.1
 networkx==2.6.3
 pydash==5.1.0
 maggma==0.32.3

From 52b073ac90a98655af3e7e816c9a8d12b715e231 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 10 Jan 2022 18:24:26 +0000
Subject: [PATCH 17/23] Bump autodoc-pydantic from 1.5.1 to 1.6.0

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index b1899c70..2ca0e34d 100644
--- a/setup.py
+++ b/setup.py
@@ -40,7 +40,7 @@
             "nbsphinx==0.8.8",
             "nbsphinx-link==1.3.0",
             "FireWorks==1.9.8",
-            "autodoc_pydantic==1.5.1",
+            "autodoc_pydantic==1.6.0",
         ],
         "tests": [
             "pytest==6.2.5",

From 461589ac6d666b7fa0273b513441b1fedab5af2a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 10 Jan 2022 18:24:32 +0000
Subject: [PATCH 18/23] Bump ipython from 7.30.1 to 7.31.0

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 2ca0e34d..db4e3202 100644
--- a/setup.py
+++ b/setup.py
@@ -36,7 +36,7 @@
             "sphinx==4.3.2",
             "furo==2022.1.2",
             "m2r2==0.3.2",
-            "ipython==7.30.1",
+            "ipython==7.31.0",
             "nbsphinx==0.8.8",
             "nbsphinx-link==1.3.0",
             "FireWorks==1.9.8",

From fc0880c72bdadd958d1950b8566c45aea97af3d6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 17 Jan 2022 18:14:02 +0000
Subject: [PATCH 19/23] Bump sphinx from 4.3.2 to 4.4.0

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index db4e3202..1a828183 100644
--- a/setup.py
+++ b/setup.py
@@ -33,7 +33,7 @@
     ],
     extras_require={
         "docs": [
-            "sphinx==4.3.2",
+            "sphinx==4.4.0",
             "furo==2022.1.2",
             "m2r2==0.3.2",
             "ipython==7.31.0",

From 80e17a0c5191b38f68fa346faa770d6a15af7613 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 17 Jan 2022 18:14:10 +0000
Subject: [PATCH 20/23] Bump ipython from 7.31.0 to 8.0.0

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 1a828183..cfa9d717 100644
--- a/setup.py
+++ b/setup.py
@@ -36,7 +36,7 @@
             "sphinx==4.4.0",
             "furo==2022.1.2",
             "m2r2==0.3.2",
-            "ipython==7.31.0",
+            "ipython==8.0.0",
             "nbsphinx==0.8.8",
             "nbsphinx-link==1.3.0",
             "FireWorks==1.9.8",

From 3eaf8bd8d283b230fbecdd418871fc3cf34af9d2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 17 Jan 2022 18:14:24 +0000
Subject: [PATCH 21/23] Bump monty from 2021.12.1 to 2022.1.12.1

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 1efb1a2f..551ab9be 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-monty==2021.12.1
+monty==2022.1.12.1
 networkx==2.6.3
 pydash==5.1.0
 maggma==0.32.3

From 23baaf342074395fd7573789cfc796a902f9b4cd Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 24 Jan 2022 18:15:22 +0000
Subject: [PATCH 22/23] Bump ipython from 8.0.0 to 8.0.1

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index cfa9d717..78f45982 100644
--- a/setup.py
+++ b/setup.py
@@ -36,7 +36,7 @@
             "sphinx==4.4.0",
             "furo==2022.1.2",
             "m2r2==0.3.2",
-            "ipython==8.0.0",
+            "ipython==8.0.1",
             "nbsphinx==0.8.8",
             "nbsphinx-link==1.3.0",
             "FireWorks==1.9.8",

From 467584369b378f5e071823ddd76ba534c79a5222 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 24 Jan 2022 18:15:25 +0000
Subject: [PATCH 23/23] Bump monty from 2022.1.12.1 to 2022.1.19

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 551ab9be..de0f4bc5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-monty==2022.1.12.1
+monty==2022.1.19
 networkx==2.6.3
 pydash==5.1.0
 maggma==0.32.3