From 9e4b0c8bfce85f590c8dfb50ab1e4e0469661308 Mon Sep 17 00:00:00 2001
From: "Yashasvi S. Ranawat" <yashasvi.ranawat@gmail.com>
Date: Mon, 3 Mar 2025 20:57:38 +0200
Subject: [PATCH 1/6] Move to uv

---
 Pipfile        |   17 -
 Pipfile.lock   |  924 ------------------------------------------
 pyproject.toml |   30 ++
 setup.py       |   21 -
 uv.lock        | 1046 ++++++++++++++++++++++++++++++++++++++++++++++++
 5 files changed, 1076 insertions(+), 962 deletions(-)
 delete mode 100644 Pipfile
 delete mode 100644 Pipfile.lock
 create mode 100644 pyproject.toml
 delete mode 100644 setup.py
 create mode 100644 uv.lock

diff --git a/Pipfile b/Pipfile
deleted file mode 100644
index 18d95b7..0000000
--- a/Pipfile
+++ /dev/null
@@ -1,17 +0,0 @@
-[[source]]
-url = "https://pypi.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[packages]
-runner = {editable = true, path = "."}
-graphviz = "*"
-
-[dev-packages]
-sphinx = "*"
-pytest = "*"
-sphinx-rtd-theme = "*"
-black = "*"
-
-[requires]
-python_version = "3.10"
diff --git a/Pipfile.lock b/Pipfile.lock
deleted file mode 100644
index 9c52d50..0000000
--- a/Pipfile.lock
+++ /dev/null
@@ -1,924 +0,0 @@
-{
-    "_meta": {
-        "hash": {
-            "sha256": "886c4017b71e8405ed10b0999367538b240f96464ead8cbd3a6f82a7c527543d"
-        },
-        "pipfile-spec": 6,
-        "requires": {
-            "python_version": "3.10"
-        },
-        "sources": [
-            {
-                "name": "pypi",
-                "url": "https://pypi.org/simple",
-                "verify_ssl": true
-            }
-        ]
-    },
-    "default": {
-        "ase": {
-            "hashes": [
-                "sha256:004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432",
-                "sha256:66cc481e3d82bea8931d5fe677119932ea0bd1bc08b901fd84f36b37fa681c9e"
-            ],
-            "markers": "python_version >= '3.6'",
-            "version": "==3.22.1"
-        },
-        "contourpy": {
-            "hashes": [
-                "sha256:059c3d2a94b930f4dafe8105bcdc1b21de99b30b51b5bce74c753686de858cb6",
-                "sha256:0683e1ae20dc038075d92e0e0148f09ffcefab120e57f6b4c9c0f477ec171f33",
-                "sha256:07d6f11dfaf80a84c97f1a5ba50d129d9303c5b4206f776e94037332e298dda8",
-                "sha256:081f3c0880712e40effc5f4c3b08feca6d064cb8cfbb372ca548105b86fd6c3d",
-                "sha256:0e48694d6a9c5a26ee85b10130c77a011a4fedf50a7279fa0bdaf44bafb4299d",
-                "sha256:11b836b7dbfb74e049c302bbf74b4b8f6cb9d0b6ca1bf86cfa8ba144aedadd9c",
-                "sha256:19557fa407e70f20bfaba7d55b4d97b14f9480856c4fb65812e8a05fe1c6f9bf",
-                "sha256:229a25f68046c5cf8067d6d6351c8b99e40da11b04d8416bf8d2b1d75922521e",
-                "sha256:24216552104ae8f3b34120ef84825400b16eb6133af2e27a190fdc13529f023e",
-                "sha256:3b53d5769aa1f2d4ea407c65f2d1d08002952fac1d9e9d307aa2e1023554a163",
-                "sha256:3de23ca4f381c3770dee6d10ead6fff524d540c0f662e763ad1530bde5112532",
-                "sha256:407d864db716a067cc696d61fa1ef6637fedf03606e8417fe2aeed20a061e6b2",
-                "sha256:41339b24471c58dc1499e56783fedc1afa4bb018bcd035cfb0ee2ad2a7501ef8",
-                "sha256:462c59914dc6d81e0b11f37e560b8a7c2dbab6aca4f38be31519d442d6cde1a1",
-                "sha256:46e24f5412c948d81736509377e255f6040e94216bf1a9b5ea1eaa9d29f6ec1b",
-                "sha256:498e53573e8b94b1caeb9e62d7c2d053c263ebb6aa259c81050766beb50ff8d9",
-                "sha256:4ebf42695f75ee1a952f98ce9775c873e4971732a87334b099dde90b6af6a916",
-                "sha256:4f9147051cb8fdb29a51dc2482d792b3b23e50f8f57e3720ca2e3d438b7adf23",
-                "sha256:549174b0713d49871c6dee90a4b499d3f12f5e5f69641cd23c50a4542e2ca1eb",
-                "sha256:560f1d68a33e89c62da5da4077ba98137a5e4d3a271b29f2f195d0fba2adcb6a",
-                "sha256:566f0e41df06dfef2431defcfaa155f0acfa1ca4acbf8fd80895b1e7e2ada40e",
-                "sha256:56de98a2fb23025882a18b60c7f0ea2d2d70bbbcfcf878f9067234b1c4818442",
-                "sha256:66544f853bfa85c0d07a68f6c648b2ec81dafd30f272565c37ab47a33b220684",
-                "sha256:6c06e4c6e234fcc65435223c7b2a90f286b7f1b2733058bdf1345d218cc59e34",
-                "sha256:6d0a8efc258659edc5299f9ef32d8d81de8b53b45d67bf4bfa3067f31366764d",
-                "sha256:70e5a10f8093d228bb2b552beeb318b8928b8a94763ef03b858ef3612b29395d",
-                "sha256:8394e652925a18ef0091115e3cc191fef350ab6dc3cc417f06da66bf98071ae9",
-                "sha256:8636cd2fc5da0fb102a2504fa2c4bea3cbc149533b345d72cdf0e7a924decc45",
-                "sha256:93df44ab351119d14cd1e6b52a5063d3336f0754b72736cc63db59307dabb718",
-                "sha256:96ba37c2e24b7212a77da85004c38e7c4d155d3e72a45eeaf22c1f03f607e8ab",
-                "sha256:a10dab5ea1bd4401c9483450b5b0ba5416be799bbd50fc7a6cc5e2a15e03e8a3",
-                "sha256:a66045af6cf00e19d02191ab578a50cb93b2028c3eefed999793698e9ea768ae",
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-                "sha256:c84fdf3da00c2827d634de4fcf17e3e067490c4aea82833625c4c8e6cdea0887",
-                "sha256:ca6fab080484e419528e98624fb5c4282148b847e3602dc8dbe0cb0669469887",
-                "sha256:d0c188ae66b772d9d61d43c6030500344c13e3f73a00d1dc241da896f379bb62",
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-                "sha256:e0c02b75acfea5cab07585d25069207e478d12309557f90a61b5a3b4f77f46ce",
-                "sha256:e30aaf2b8a2bac57eb7e1650df1b3a4130e8d0c66fc2f861039d507a11760e1b",
-                "sha256:eafbef886566dc1047d7b3d4b14db0d5b7deb99638d8e1be4e23a7c7ac59ff0f",
-                "sha256:efe0fab26d598e1ec07d72cf03eaeeba8e42b4ecf6b9ccb5a356fde60ff08b85",
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-                "sha256:f1eaac5257a8f8a047248d60e8f9315c6cff58f7803971170d952555ef6344a7",
-                "sha256:f29fb0b3f1217dfe9362ec55440d0743fe868497359f2cf93293f4b2701b8251",
-                "sha256:f44d78b61740e4e8c71db1cf1fd56d9050a4747681c59ec1094750a658ceb970",
-                "sha256:f6aec19457617ef468ff091669cca01fa7ea557b12b59a7908b9474bb9674cf0",
-                "sha256:f9dc7f933975367251c1b34da882c4f0e0b2e24bb35dc906d2f598a40b72bfc7"
-            ],
-            "markers": "python_version >= '3.8'",
-            "version": "==1.1.1"
-        },
-        "cycler": {
-            "hashes": [
-                "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30",
-                "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"
-            ],
-            "markers": "python_version >= '3.8'",
-            "version": "==0.12.1"
-        },
-        "docutils": {
-            "hashes": [
-                "sha256:96f387a2c5562db4476f09f13bbab2192e764cac08ebbf3a34a95d9b1e4a59d6",
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-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==0.20.1"
-        },
-        "fonttools": {
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diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..ac327bb
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,30 @@
+[project]
+name = "Runner"
+version = "0.1.0"
+description = "Tools to easly schedule atomistic simulation workflow"
+readme = "README.md"
+authors = [
+    { name = "Yashasvi S. Ranawat", email = "yashasvi.ranawat@gmail.com" }
+]
+requires-python = ">=3.10"
+dependencies = [
+    "ase>=3.24.0",
+    "docutils>=0.3",
+    "numpy>=2.2.3",
+    "psutil>=7.0.0",
+]
+
+[project.scripts]
+runner = "runner.cli:main"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3.4",
+    "ruff>=0.9.9",
+    "sphinx>=8.1.3",
+    "sphinx-rtd-theme>=3.0.2",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 41b5f1d..0000000
--- a/setup.py
+++ /dev/null
@@ -1,21 +0,0 @@
-from setuptools import setup, find_packages
-import re
-
-
-with open("runner/__init__.py") as fd:
-    version = re.search('__version__ = "(.*)"', fd.read()).group(1)
-
-
-if __name__ == "__main__":
-    setup(
-        name="runner",
-        version=version,
-        packages=find_packages(),
-        # scripts=["say_hello.py"],
-        install_requires=["docutils>=0.3", "ase", "numpy", "psutil"],
-        entry_points={"console_scripts": ["runner=runner.cli:main"]},
-        package_data={
-            # If any package contains *.txt or *.rst files, include them:
-            "": ["*.txt", "*.rst"],
-        },
-    )
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 0000000..c193395
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,1046 @@
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+revision = 1
+requires-python = ">=3.10"
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+name = "urllib3"
+version = "2.3.0"
+source = { registry = "https://pypi.org/simple" }
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+wheels = [
+    { url = "https://files.pythonhosted.org/packages/c8/19/4ec628951a74043532ca2cf5d97b7b14863931476d117c471e8e2b1eb39f/urllib3-2.3.0-py3-none-any.whl", hash = "sha256:1cee9ad369867bfdbbb48b7dd50374c0967a0bb7710050facf0dd6911440e3df", size = 128369 },
+]

From e95d2cda0961d1f308ea49d402617aa93684f190 Mon Sep 17 00:00:00 2001
From: "Yashasvi S. Ranawat" <yashasvi.ranawat@gmail.com>
Date: Mon, 3 Mar 2025 20:58:06 +0200
Subject: [PATCH 2/6] Apply ruff

---
 pyproject.toml             |  6 ++++++
 runner/__init__.py         |  8 +++-----
 runner/cli.py              | 24 +++++++++--------------
 runner/relay.py            | 33 ++++++++++++++-----------------
 runner/runner.py           | 40 ++++++++++++++++++++------------------
 runner/runners/__init__.py |  1 -
 runner/runners/slurm.py    | 27 +++++++++++++------------
 runner/runners/terminal.py |  7 ++++---
 runner/utils/__init__.py   |  8 ++++----
 runner/utils/run.py        |  2 +-
 runner/utils/runnerdata.py | 32 +++++++++++++-----------------
 runner/utils/utils.py      |  4 +++-
 tests/test_baserunner.py   | 15 +++++++-------
 tests/test_runnerdata.py   |  4 +++-
 14 files changed, 103 insertions(+), 108 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index ac327bb..3287f21 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,3 +28,9 @@ dev = [
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
+
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.lint]
+select = ["F", "I", "E"]
diff --git a/runner/__init__.py b/runner/__init__.py
index 38f4505..815d243 100644
--- a/runner/__init__.py
+++ b/runner/__init__.py
@@ -1,10 +1,8 @@
 """__init__ for runner"""
-from runner.runners import SlurmRunner
-from runner.runners import TerminalRunner
-from runner.relay import Relay
+
 from runner import utils
+from runner.relay import Relay
+from runner.runners import SlurmRunner, TerminalRunner
 from runner.utils.runnerdata import RunnerData
 
-
 __all__ = ["SlurmRunner", "TerminalRunner", "RunnerData", "utils", "Relay"]
-__version__ = "0.1"
diff --git a/runner/cli.py b/runner/cli.py
index b9753b6..95b32ab 100644
--- a/runner/cli.py
+++ b/runner/cli.py
@@ -7,19 +7,22 @@
 the Free Software Foundation, either version 2.1 of the License, or
 (at your option) any later version.
 """
+
 import argparse
 import textwrap
+
 from ase.db import connect
 from ase.io.formats import string2index
+
 from runner.runners.__init__ import runner_type2func
 from runner.utils import (
-    submit,
     cancel,
-    get_status,
     get_graphical_status,
     get_runner_list,
+    get_status,
     remove_runner,
     stop_runner,
+    submit,
 )
 
 
@@ -100,7 +103,7 @@ def add_arguments(parser):
 
         # stop runner
         desc = "Stop a runner from metadata."
-        add = "Runner isn't stopped immediately, but after completing spool" "process."
+        add = "Runner isn't stopped immediately, but after completing spool process."
         subparser = subparsers.add_parser(
             "stop",
             formatter_class=Formatter,
@@ -113,10 +116,7 @@ def add_arguments(parser):
 
         # submit a row
         desc = "Submit row(s) for run."
-        add = (
-            "Row ids can be int or python like"
-            " slice, eg. '1:4' gives ids 1, 2, and 3"
-        )
+        add = "Row ids can be int or python like slice, eg. '1:4' gives ids 1, 2, and 3"
         subparser = subparsers.add_parser(
             "submit",
             formatter_class=Formatter,
@@ -140,10 +140,7 @@ def add_arguments(parser):
 
         # cancel a submitted row
         desc = "Cancel row(s) for run."
-        add = (
-            "Row ids can be int or python like"
-            " slice, eg. '1:4' gives ids 1, 2, and 3"
-        )
+        add = "Row ids can be int or python like slice, eg. '1:4' gives ids 1, 2, and 3"
         subparser = subparsers.add_parser(
             "cancel",
             formatter_class=Formatter,
@@ -170,10 +167,7 @@ def add_arguments(parser):
 
         # check status of a row
         desc = "Check running status of row(s)"
-        add = (
-            "Row ids can be int or python like"
-            " slice, eg. '1:4' gives ids 1, 2, and 3"
-        )
+        add = "Row ids can be int or python like slice, eg. '1:4' gives ids 1, 2, and 3"
         subparser = subparsers.add_parser(
             "status",
             formatter_class=Formatter,
diff --git a/runner/relay.py b/runner/relay.py
index 40c9d2b..089dc26 100644
--- a/runner/relay.py
+++ b/runner/relay.py
@@ -1,15 +1,17 @@
 """
 Relay to form complex workflows
 """
-import time
+
 import json
+import time
 from copy import deepcopy
+
 import numpy as np
-from ase import Atoms
-from ase import db
-from runner.utils import submit, cancel, get_graphical_status
-from runner.utils.runnerdata import RunnerData
+from ase import Atoms, db
+
 from runner.runners import runner_types
+from runner.utils import cancel, get_graphical_status, submit
+from runner.utils.runnerdata import RunnerData
 
 
 class Relay:
@@ -125,17 +127,15 @@ def commit(self, database=None):
         if database is None:
             if self._database is None:
                 raise RuntimeError(
-                    f"{self.__str__()} needs a"
-                    f" database for commit. No previous"
-                    f" database commits."
+                    f"{self.__str__()} needs a database for commit. "
+                    f"No previous database commits."
                 )
             database = self._database
         elif self._database is not None:
             if self._database != database:
                 raise RuntimeError(
-                    f"{self.__str__()} already commited with"
-                    f" {self._database}, cannot commit with"
-                    f" {database}"
+                    f"{self.__str__()} already commited with {self._database}, "
+                    f"cannot commit with {database}"
                 )
 
         # recursively commit parents
@@ -153,9 +153,8 @@ def commit(self, database=None):
 
             if status in ["submit", "running", "cancel"]:
                 raise RuntimeError(
-                    f"cannot commit {self.__str__()}. It is "
-                    f"either submitted, running, or being"
-                    f" cancelled."
+                    f"cannot commit {self.__str__()}. It is either submitted, "
+                    f"running, or being cancelled."
                 )
 
         with db.connect(database) as fdb:
@@ -400,7 +399,7 @@ def get_row(self, cycle_time=10, wait=True):
 
     row = property(
         get_row,
-        doc=("Atoms row attached with the relay, awaits " "for the run to finish"),
+        doc=("Atoms row attached with the relay, awaits for the run to finish"),
     )
 
     def _to_dict(self):
@@ -586,9 +585,7 @@ def _spider(self, dict_=None, parent_call=None):
             if isinstance(parent, Relay):
                 if parent.id_ not in dict_:
                     if parent.id_ in parent_call:
-                        raise RuntimeError(
-                            "Cyclic connection detected." " Abandon ship!"
-                        )
+                        raise RuntimeError("Cyclic connection detected. Abandon ship!")
                     dict_[parent.id_] = parent
 
                     dict_ = parent._spider(dict_, parent_call)
diff --git a/runner/runner.py b/runner/runner.py
index 4e2273e..59cb7e1 100644
--- a/runner/runner.py
+++ b/runner/runner.py
@@ -2,17 +2,18 @@
 Base runner for different runnners
 """
 
-import shutil
-import pickle
 import json
 import logging
-import time
 import os
+import pickle
+import shutil
+import time
+from abc import ABC, abstractmethod
 from base64 import b64decode
 from datetime import datetime
-from abc import ABC, abstractmethod
-from ase import db
-from ase import Atoms
+
+from ase import Atoms, db
+
 from runner.utils import Cd, run
 from runner.utils.runnerdata import RunnerData
 
@@ -105,7 +106,7 @@ def to_database(self, update=False):
         if self.name in runners:
             if not update:
                 raise RuntimeError(
-                    "Runner exists, pass argument update as" " true to update"
+                    "Runner exists, pass argument update as true to update"
                 )
             if runners[self.name].get("running", False):
                 raise RuntimeError("Runner already running")
@@ -249,7 +250,7 @@ def _update_status_running(self):
                 status, atoms, log_msg = [
                     "failed",
                     None,
-                    "{}\nJob id lost\n" "".format(datetime.now()),
+                    "{}\nJob id lost\n".format(datetime.now()),
                 ]
             if status != "running":
                 # if not still running, update status and add log message
@@ -258,7 +259,7 @@ def _update_status_running(self):
         # update status for jobs that stopped running
         for id_, values in update_ids_status.items():
             status, log_msg = values
-            logger.debug("ID {} finished" "".format(id_))
+            logger.debug("ID {} finished".format(id_))
 
             if status == "done":
                 with Cd(self.run_folder, mkdir=False):
@@ -273,7 +274,7 @@ def _update_status_running(self):
                             assert isinstance(atoms, Atoms)
                         except Exception as e:
                             status = "failed"
-                            log_msg += "{}\n Unpickling failed: {}\n" "".format(
+                            log_msg += "{}\n Unpickling failed: {}\n".format(
                                 datetime.now(), e
                             )
             # run post-tasks
@@ -385,7 +386,7 @@ def _submit_run(self):
                 _ = row.data.get("runner", {})
                 _.update(
                     {
-                        "log": "{}\n{}\n" "".format(datetime.now(), err),
+                        "log": "{}\n{}\n".format(datetime.now(), err),
                         "fail_count": self.multi_fail + 1,
                     }
                 )
@@ -451,14 +452,14 @@ def _submit_run(self):
                     if status == "submit":
                         job_id, log_msg = self._submit(run_scripts, scheduler_options)
                         if job_id:
-                            logger.debug("submitting success {}" "".format(job_id))
+                            logger.debug("submitting success {}".format(job_id))
                             # update status and save job_id
                             status = "running"
                             with open("job.id", "w") as file_o:
                                 file_o.write("{}".format(job_id))
                             sent_jobs += 1
                         else:
-                            logger.debug("submitting failed {}" "".format(job_id))
+                            logger.debug("submitting failed {}".format(job_id))
                             status = "failed"
 
             # updating database
@@ -469,8 +470,9 @@ def _submit_run(self):
             # adds status, name of calculation, and data
             self.fdb.update(id_, status=status, run_name=name, data=data)
             logger.info(
-                "ID {} submission: "
-                "{}".format(id_, (status if status == "failed" else "successful"))
+                "ID {} submission: {}".format(
+                    id_, (status if status == "failed" else "successful")
+                )
             )
 
     def _write_run_data(self, atoms, tasks, files, status, log_msg):
@@ -555,16 +557,16 @@ def _cancel_run(self):
                 self._cancel(job_id)
                 status, log_msg = [
                     "failed",
-                    "{}\nCancelled by user\n" "".format(datetime.now()),
+                    "{}\nCancelled by user\n".format(datetime.now()),
                 ]
             else:
                 logger.debug("lost {}".format(id_))
                 # no job_id but still cancel, eg when pending
                 status, log_msg = [
                     "failed",
-                    "{}\nCancelled by user, "
-                    "no job was running\n"
-                    "".format(datetime.now()),
+                    "{}\nCancelled by user, no job was running\n".format(
+                        datetime.now()
+                    ),
                 ]
             # updating status and log
             data = row.data
diff --git a/runner/runners/__init__.py b/runner/runners/__init__.py
index 9a49f50..883758d 100644
--- a/runner/runners/__init__.py
+++ b/runner/runners/__init__.py
@@ -1,7 +1,6 @@
 from runner.runners.slurm import SlurmRunner
 from runner.runners.terminal import TerminalRunner
 
-
 __all__ = ["SlurmRunner", "TerminalRunner"]
 
 runner_list = ["SlurmRunner", "TerminalRunner"]
diff --git a/runner/runners/slurm.py b/runner/runners/slurm.py
index e55be78..6ed9414 100644
--- a/runner/runners/slurm.py
+++ b/runner/runners/slurm.py
@@ -1,7 +1,7 @@
-from runner.runner import BaseRunner
 import subprocess as sb
-from _datetime import datetime
+from datetime import datetime
 
+from runner.runner import BaseRunner
 
 # List of states from the man page of squeue
 # states are mapped to status and log message
@@ -15,29 +15,28 @@
     "COMPLETED": ["done", "Job has terminated all processes on all nodes."],
     "CONFIGURING": [
         "running",
-        "Job  has  been allocated resources, but are "
-        "waiting for them to become ready for use "
-        "(e.g. booting).",
+        "Job  has  been allocated resources, but are waiting for them to become ready "
+        "for use (e.g. booting).",
     ],
     "COMPLETING": [
         "running",
-        "Job is in the process of completing. Some "
-        "processes on some nodes may still be active.",
+        "Job is in the process of completing. Some processes on some nodes may still "
+        "be active.",
     ],
     "FAILED": [
         "failed",
-        "Job  terminated  with  non-zero  exit code or other " "failure condition.",
+        "Job  terminated  with  non-zero  exit code or other failure condition.",
     ],
     "NODE_FAIL": [
         "failed",
-        "Job terminated due to failure of one or more " "allocated resources",
+        "Job terminated due to failure of one or more allocated resources",
     ],
     "PENDING": ["running", "Job is awaiting resource allocation."],
     "PREEMPTED": ["failed", "Job terminated due to preemption."],
     "RUNNING": ["running", "Job currently has an allocation."],
     "SUSPENDED": [
         "running",
-        "Job  has an allocation, but execution has been " "suspended",
+        "Job  has an allocation, but execution has been suspended",
     ],
     "TIMEOUT": ["failed", "Job terminated upon reaching its time limit."],
 }
@@ -107,7 +106,7 @@ def _submit(self, tasks, scheduler_options):
         # default values
         job_id = None
 
-        log_msg = "{}\nSubmission using {} scheduler\n" "".format(
+        log_msg = "{}\nSubmission using {} scheduler\n".format(
             datetime.now(), self.name
         )
         # add interpreter
@@ -115,7 +114,7 @@ def _submit(self, tasks, scheduler_options):
 
         # add SBATCH options
         for key, value in scheduler_options.items():
-            run_script += "#SBATCH {}{}{}\n" "".format(
+            run_script += "#SBATCH {}{}{}\n".format(
                 key, "=" if key.startswith("--") else " ", value
             )
 
@@ -137,7 +136,7 @@ def _submit(self, tasks, scheduler_options):
             log_msg += "Submitted batch job {}\n".format(job_id)
         else:
             # failed
-            log_msg += "Submission failed: {}" "\n".format(out.stderr.decode("utf-8"))
+            log_msg += "Submission failed: {}\n".format(out.stderr.decode("utf-8"))
         return job_id, log_msg
 
     def _cancel(self, job_id):
@@ -203,7 +202,7 @@ def _status(self, job_id):
                 status_list.append(_slurm_map[state][0])
             except KeyError:
                 status = "failed"
-                log_msg += "{}\n Undefined slurm state:{}\n" "".format(end_time, state)
+                log_msg += "{}\n Undefined slurm state:{}\n".format(end_time, state)
                 return status, log_msg
 
         if "failed" in status_list:
diff --git a/runner/runners/terminal.py b/runner/runners/terminal.py
index 2935c18..027bf56 100644
--- a/runner/runners/terminal.py
+++ b/runner/runners/terminal.py
@@ -1,7 +1,8 @@
-from runner.runner import BaseRunner
 import subprocess as sb
 from _datetime import datetime
 
+from runner.runner import BaseRunner
+
 
 class TerminalRunner(BaseRunner):
     """
@@ -67,7 +68,7 @@ def _submit(self, tasks, scheduler_options):
         # default values
         job_id = None
 
-        log_msg = "{}\nSubmission using {} scheduler\n" "".format(
+        log_msg = "{}\nSubmission using {} scheduler\n".format(
             datetime.now(), self.name
         )
         # add start status file
@@ -97,7 +98,7 @@ def _submit(self, tasks, scheduler_options):
             log_msg += "Submitted batch job {}\n".format(job_id)
         else:
             # failed
-            log_msg += "Submission failed: {}" "\n".format(out.stderr.decode("utf-8"))
+            log_msg += "Submission failed: {}\n".format(out.stderr.decode("utf-8"))
         return job_id, log_msg
 
     def _cancel(self, job_id):
diff --git a/runner/utils/__init__.py b/runner/utils/__init__.py
index 8ae7ea9..5dae07b 100644
--- a/runner/utils/__init__.py
+++ b/runner/utils/__init__.py
@@ -1,17 +1,17 @@
 """__init__ for utils"""
+
 from runner.utils.utils import (
     Cd,
-    json_keys2int,
-    get_status,
-    submit,
     cancel,
     get_graphical_status,
     get_runner_list,
+    get_status,
+    json_keys2int,
     remove_runner,
     stop_runner,
+    submit,
 )
 
-
 __all__ = [
     "Cd",
     "json_keys2int",
diff --git a/runner/utils/run.py b/runner/utils/run.py
index 0f94765..d68a162 100644
--- a/runner/utils/run.py
+++ b/runner/utils/run.py
@@ -2,9 +2,9 @@
 python file to run python tasks
 """
 
+import argparse
 import json
 import pickle
-import argparse
 
 
 def main():
diff --git a/runner/utils/runnerdata.py b/runner/utils/runnerdata.py
index 5059cf6..1b47cad 100644
--- a/runner/utils/runnerdata.py
+++ b/runner/utils/runnerdata.py
@@ -1,11 +1,11 @@
-""" Utility to handle runner data"""
+"""Utility to handle runner data"""
+
 import json
 import os
 from base64 import b64encode
 from copy import copy
 
-from runner.utils.utils import json_keys2int, get_db_connect
-
+from runner.utils.utils import get_db_connect, json_keys2int
 
 default_files = ["run.sh", "batch.slrm", "atoms.pkl", "run.py", "status.txt", "job.id"]
 
@@ -183,9 +183,7 @@ def add_files(self, filenames, add_as=None):
             if not isinstance(add_as, (tuple, list)):
                 add_as = [add_as]
             if len(add_as) != len(filenames):
-                raise RuntimeError(
-                    "Length of filenames and add_as should" " be the same"
-                )
+                raise RuntimeError("Length of filenames and add_as should be the same")
         else:
             add_as = filenames
 
@@ -366,7 +364,7 @@ def _test_parents(parents, log_msg=""):
         raise RuntimeError(err)
     for i in parents:
         if not isinstance(i, int):
-            err = log_msg + "Runner: parents should be a list of" "int\n"
+            err = log_msg + "Runner: parents should be a list ofint\n"
             raise RuntimeError(err)
 
 
@@ -381,7 +379,7 @@ def _test_files(files, log_msg=""):
             err = log_msg + "Runner: filenames should be str\n"
             raise RuntimeError(err)
         if not isinstance(content, (str, bytes)):
-            err = log_msg + "Runner: file contents should be str" " or bytes\n"
+            err = log_msg + "Runner: file contents should be str or bytes\n"
             raise RuntimeError(err)
 
 
@@ -401,14 +399,12 @@ def _test_tasks(tasks, files=None, log_msg="", _skip_empty_task_test=True):
             raise RuntimeError(err)
         if len(task) < 2:
             err = (
-                log_msg + "Runner: each task sould have a name"
-                " and command or filename\n"
+                log_msg
+                + "Runner: each task sould have a name and command or filename\n"
             )
             raise RuntimeError(err)
         if not isinstance(task[1], str):
-            err = (
-                log_msg + "Runner: shell command or python filename" " should be str\n"
-            )
+            err = log_msg + "Runner: shell command or python filename should be str\n"
             raise RuntimeError(err)
         if task[0] == "python":
             # testing filename in files
@@ -417,20 +413,20 @@ def _test_tasks(tasks, files=None, log_msg="", _skip_empty_task_test=True):
                 filename += ".py"
             if filename not in files:
                 err = (
-                    log_msg + "Runner: python filename {} should"
-                    " be in files\n".format(filename)
+                    log_msg
+                    + "Runner: python filename {} should be in files\n".format(filename)
                 )
                 raise RuntimeError(err)
             if len(task) > 2:
                 if not isinstance(task[2], dict):
-                    err = log_msg + "Runner: python parameters " "should be dict\n"
+                    err = log_msg + "Runner: python parameters should be dict\n"
                     raise RuntimeError(err)
             if len(task) > 3:
                 if not isinstance(task[3], str):
-                    err = log_msg + "Runner: python command should" "be str\n"
+                    err = log_msg + "Runner: python command shouldbe str\n"
                     raise RuntimeError(err)
         elif task[0] != "shell":
-            raise RuntimeError("Runner: task should either be 'shell'" " or 'python'\n")
+            raise RuntimeError("Runner: task should either be 'shell' or 'python'\n")
 
 
 def _test_scheduler_options(scheduler_options, log_msg=""):
diff --git a/runner/utils/utils.py b/runner/utils/utils.py
index dfefe4a..77a3a05 100644
--- a/runner/utils/utils.py
+++ b/runner/utils/utils.py
@@ -1,7 +1,9 @@
 """
 Utility tools for runners
 """
+
 import os
+
 import ase.db as db
 
 
@@ -125,7 +127,7 @@ def get_graphical_status(
         from graphviz import Digraph
     except ModuleNotFoundError:
         raise ModuleNotFoundError(
-            "get_graphical_status needs graphviz, " "run: pip install graphviz"
+            "get_graphical_status needs graphviz, run: pip install graphviz"
         )
 
     def add_task_graph(name, tasks, dot):
diff --git a/tests/test_baserunner.py b/tests/test_baserunner.py
index 542d6b3..befe8dd 100644
--- a/tests/test_baserunner.py
+++ b/tests/test_baserunner.py
@@ -1,13 +1,12 @@
+import os
 import time
 from copy import copy
-import os
 
 import ase.db as db
 from ase.atoms import Atoms
 
 from runner import TerminalRunner
 
-
 energy = """\
 from ase.atoms import Atoms
 
@@ -72,9 +71,9 @@ def test_successful_run():
     run.spool(_endless=False)
     assert fdb.get(id_3).status == "done"
 
-    assert not str(id_) in os.listdir(), "no cleanup after done"
-    assert not str(id_1) in os.listdir(), "no cleanup after done"
-    assert not str(id_2) in os.listdir(), "no cleanup after done"
+    assert str(id_) not in os.listdir(), "no cleanup after done"
+    assert str(id_1) not in os.listdir(), "no cleanup after done"
+    assert str(id_2) not in os.listdir(), "no cleanup after done"
     assert str(id_3) in os.listdir(), "keep_run failed"
 
 
@@ -111,6 +110,6 @@ def test_failed_run():
         assert fdb.get(i).status == "failed", i
         if i == id_[0]:
             assert str(i) in os.listdir(), "failed run folder cleaned"
-            assert (
-                fdb.get(i).data["runner"]["fail_count"] == 1
-            ), "fail count not updated"
+            assert fdb.get(i).data["runner"]["fail_count"] == 1, (
+                "fail count not updated"
+            )
diff --git a/tests/test_runnerdata.py b/tests/test_runnerdata.py
index 2b1a8d5..733f31d 100644
--- a/tests/test_runnerdata.py
+++ b/tests/test_runnerdata.py
@@ -1,7 +1,9 @@
-import pytest
 import os
+
 import ase.db as db
+import pytest
 from ase.atoms import Atoms
+
 from runner.utils.runnerdata import RunnerData
 
 

From aa0f5a07e75204e7e434ff4baa3744c203fbb81c Mon Sep 17 00:00:00 2001
From: "Yashasvi S. Ranawat" <yashasvi.ranawat@gmail.com>
Date: Mon, 3 Mar 2025 21:45:42 +0200
Subject: [PATCH 3/6] Downgrade ASE to have calculator in db

---
 pyproject.toml             | 2 +-
 runner/runners/terminal.py | 2 +-
 uv.lock                    | 8 ++++----
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3287f21..8d84025 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ authors = [
 ]
 requires-python = ">=3.10"
 dependencies = [
-    "ase>=3.24.0",
+    "ase==3.22.1",
     "docutils>=0.3",
     "numpy>=2.2.3",
     "psutil>=7.0.0",
diff --git a/runner/runners/terminal.py b/runner/runners/terminal.py
index 027bf56..c1f9a79 100644
--- a/runner/runners/terminal.py
+++ b/runner/runners/terminal.py
@@ -1,5 +1,5 @@
 import subprocess as sb
-from _datetime import datetime
+from datetime import datetime
 
 from runner.runner import BaseRunner
 
diff --git a/uv.lock b/uv.lock
index c193395..a2b8a5c 100644
--- a/uv.lock
+++ b/uv.lock
@@ -17,16 +17,16 @@ wheels = [
 
 [[package]]
 name = "ase"
-version = "3.24.0"
+version = "3.22.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "matplotlib" },
     { name = "numpy" },
     { name = "scipy" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/5c/c9/9adb9bc641bd7222367886e4e6c753b4c64da4ff2d9565ab39aee1e34734/ase-3.24.0.tar.gz", hash = "sha256:9acc93d6daaf48cd27b844c56f8bf49428b9db0542faa3cc30d9d5b8e1842195", size = 2383264 }
+sdist = { url = "https://files.pythonhosted.org/packages/69/64/096410b2e0b58aee082b40a37cdd61e708ed722a7471d7cf0e2dcb01cade/ase-3.22.1.tar.gz", hash = "sha256:004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432", size = 2807134 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/1f/cd/b1253035a1da90e89f31947e052c558cd83df3bcaff34aa199e5e806d773/ase-3.24.0-py3-none-any.whl", hash = "sha256:974922df87ef4ec8cf1140359a55ab4c4dc55c38e26876bdd9c00968da1f463c", size = 2928893 },
+    { url = "https://files.pythonhosted.org/packages/38/b0/3c0a7afaf66274588216c251376ac2bea0269eb7a5e1da77521811060553/ase-3.22.1-py3-none-any.whl", hash = "sha256:66cc481e3d82bea8931d5fe677119932ea0bd1bc08b901fd84f36b37fa681c9e", size = 2192122 },
 ]
 
 [[package]]
@@ -765,7 +765,7 @@ dev = [
 
 [package.metadata]
 requires-dist = [
-    { name = "ase", specifier = ">=3.24.0" },
+    { name = "ase", specifier = "==3.22.1" },
     { name = "docutils", specifier = ">=0.3" },
     { name = "numpy", specifier = ">=2.2.3" },
     { name = "psutil", specifier = ">=7.0.0" },

From 2d814f5ee39daf13c7fdee838355570bd7c6172a Mon Sep 17 00:00:00 2001
From: "Yashasvi S. Ranawat" <yashasvi.ranawat@gmail.com>
Date: Mon, 3 Mar 2025 21:58:04 +0200
Subject: [PATCH 4/6] Change workflow

---
 .github/workflows/lint.yml           | 13 +++++++++----
 .github/workflows/python-package.yml | 28 +++++++++++++---------------
 2 files changed, 22 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index f194116..ece15de 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -7,8 +7,13 @@ jobs:
     name: Check coding style
     runs-on: ubuntu-latest
     steps:
-      # clone repo and check out
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Check that all Python code is linted with black
-        run: pip install black && black . --check
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Lint the project
+        run: uv run ruff check && uv run ruff format --check
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 5ac3188..5c2805c 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -15,20 +15,18 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, "3.10", 3.11]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install . --upgrade
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v4
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Test with pytest
+        run: uv run pytest

From af400891eba22d38ec8fc41d71043d886ad9c188 Mon Sep 17 00:00:00 2001
From: "Yashasvi S. Ranawat" <yashasvi.ranawat@gmail.com>
Date: Mon, 3 Mar 2025 22:51:31 +0200
Subject: [PATCH 5/6] update the docs

---
 README.md        |  2 +-
 docs/install.rst | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 112d3d6..3559a07 100644
--- a/README.md
+++ b/README.md
@@ -16,5 +16,5 @@ Tools to easly schedule atomistic simulation workflow. Docs available at [readth
 ```sh
 git clone https://github.com/SINGROUP/Runner.git
 cd Runner
-pip install . --upgrade
+uv sync
 ```
diff --git a/docs/install.rst b/docs/install.rst
index b5ec8d4..4e02d84 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -5,8 +5,8 @@ Installation
 Requirements
 ====================
 
-* Python_ 3.6 or newer
-* ASE_ 3.19 or newer
+* Python_ 3.10 or newer
+* ASE_ 3.22.1 or older
 
 .. _Python: https://www.python.org/
 .. _ASE: https://wiki.fysik.dtu.dk/ase/index.html
@@ -27,11 +27,11 @@ which can be installed as::
 
     $ git clone https://github.com/SINGROUP/Runner.git
     $ cd Runner
-    $ pip install . --upgrade
+    $ uv sync
 
 
-To update the installation::
+To use familiar `pip` workflow::
 
     $ cd Runner
     $ git pull
-    $ pip install . --upgrade
+    $ uv pip install . --upgrade

From ae2ac043cd6e336ec24027258b88035476b82007 Mon Sep 17 00:00:00 2001
From: "Yashasvi S. Ranawat" <yashasvi.ranawat@gmail.com>
Date: Mon, 3 Mar 2025 22:55:42 +0200
Subject: [PATCH 6/6] Add link to uv

---
 README.md        | 2 ++
 docs/install.rst | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3559a07..1d0d7a6 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,8 @@ Tools to easly schedule atomistic simulation workflow. Docs available at [readth
 
 ## Installation
 
+The package can be installed with [uv](https://docs.astral.sh/uv/):
+
 ```sh
 git clone https://github.com/SINGROUP/Runner.git
 cd Runner
diff --git a/docs/install.rst b/docs/install.rst
index 4e02d84..3a4ed65 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -23,7 +23,7 @@ installed during setup.
 :git:
 
 The source is available on `github <https://github.com/SINGROUP/Runner>`_,
-which can be installed as::
+which can be installed using `uv <https://docs.astral.sh/uv/>`_ as::
 
     $ git clone https://github.com/SINGROUP/Runner.git
     $ cd Runner