Use uv for python

.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

.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

README.md

@@ -13,8 +13,10 @@ 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
-pip install . --upgrade
+uv sync
 ```

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
@@ -23,15 +23,15 @@ 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
-    $ 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

pyproject.toml

@@ -0,0 +1,36 @@
+[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==3.22.1",
+    "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"
+
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.lint]
+select = ["F", "I", "E"]

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"

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,

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)