Add ruff linting

.github/workflows/lint.yml

@@ -0,0 +1,26 @@
+name: Linting
+
+on:
+  pull_request:
+  push:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff pre-commit
+      - name: Run pre-commit on all files
+        env:
+          RUFF_OUTPUT_FORMAT: github
+        run: |
+          pre-commit run --show-diff-on-failure --color=always --all-files

.github/workflows/pypi_release.yml

@@ -25,4 +25,4 @@ jobs:
         run: |
           python -m build --sdist --outdir dist/ .
       - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks.git
+    rev: v4.6.0
+    hooks:
+      - id: no-commit-to-branch
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-xml
+      - id: check-yaml
+        exclude: "^(python/src/badger/_version.py)$"
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

README.md

@@ -55,7 +55,8 @@ or `pip`
 pip install badger-opt
 ```
 
-Currently Badger only officially support Linux. Badger on MacOS and Windows could be potentially unstable.
+Currently, Badger only officially supports Linux. Badger on MacOS and
+Windows could be potentially unstable.
 
 ## Run an optimization
 
@@ -99,6 +100,40 @@ BibTex entry:
 }
 ```
 
+Developers
+==========
+
+Clone this repository:
+```shell
+git clone https://github.com/xopt-org/badger.git
+```
+
+Create a fresh Python environment, for example using conda:
+```shell
+conda env create -n badger-env python=3.12
+```
+
+Install Badger as editable:
+```shell
+conda activate badger-env
+pip install -e ".[dev]"
+```
+
+You'll also need to install `ruff` and `pre-commit` to be able to
+pass the linting and formatting checks:
+```
+pip install ruff pre-commit
+```
+
+Then install the pre-commit hooks:
+```
+pre-commit install
+```
+
+You can also do a run at any time to check your progress:
+```
+pre-commit run --all-files
+```
 ## Issues or questions?
 
 Please check out current Badger issues [here](https://github.com/xopt-org/Badger/issues) before [opening a new one](https://github.com/xopt-org/Badger/issues/new/). Alternatively, you are welcome to [shoot us an email](mailto:[email protected]), or join our [Slack channel](https://join.slack.com/share/enQtNjI3NjY0NDk0MzUxMC0zNThjYTdmNmZlOTA3MzM2NjFjZTVmNDY5MDk4NmQ2NmQxMjE1NjBjN2VhNzYxNjBjYjgxYzMwY2ExZTIxYzkw).

pyproject.toml

@@ -64,12 +64,12 @@ where = ["src"]
 include = [ "badger", ]
 namespaces = false
 
-[tool.ruff]
-# select = []
-# ignore = []
+[tool.ruff.lint]
+extend-select = ["TID252"] # Defaults + check imports
+ignore = ["E722"] # Until bare except blocks get fixed
 
 [tool.pytest.ini_options]
-addopts = "--cov=src/badger/"
+addopts = "--cov=badger/"
 log_cli_level = "info"
 log_level = "debug"
 testpaths = ["src/badger/tests"]

src/badger/__init__.py

@@ -1,4 +1,4 @@
 try:
-    from ._version import __version__
+    from badger._version import __version__
 except ImportError:
     __version__ = "0.0.0"

src/badger/__main__.py

@@ -1,108 +1,133 @@
 import argparse
 
-from .log import config_log
-config_log()  # has to happen here to make sure the config taking effect
-from .actions import show_info
-from .actions.doctor import self_check
-from .actions.routine import show_routine
-from .actions.generator import show_generator
-from .actions.env import show_env
-from .actions.install import plugin_install
-from .actions.uninstall import plugin_remove
-from .actions.intf import show_intf
-from .actions.run import run_routine
-from .actions.config import config_settings
+from badger.actions import show_info
+from badger.actions.doctor import self_check
+from badger.actions.routine import show_routine
+from badger.actions.generator import show_generator
+from badger.actions.env import show_env
+from badger.actions.install import plugin_install
+from badger.actions.uninstall import plugin_remove
+from badger.actions.intf import show_intf
+from badger.actions.run import run_routine
+from badger.actions.config import config_settings
+from badger.log import config_log
+
+config_log()
 
 
 def main():
     # Create the top-level parser
-    parser = argparse.ArgumentParser(description='Badger the optimizer')
-    parser.add_argument('-g', '--gui', action='store_true',
-                        help='launch the GUI')
-    parser.add_argument('-ga', '--gui-acr', action='store_true',
-                        help='launch the GUI for ACR')
-    parser.add_argument('-l', '--log', choices=['CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG', 'NOTSET'],
-                        default='WARNING', const='WARNING', nargs='?',
-                        help='change the log level')
+    parser = argparse.ArgumentParser(description="Badger the optimizer")
+    parser.add_argument("-g", "--gui", action="store_true", help="launch the GUI")
+    parser.add_argument(
+        "-ga", "--gui-acr", action="store_true", help="launch the GUI for ACR"
+    )
+    parser.add_argument(
+        "-l",
+        "--log",
+        choices=["CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG", "NOTSET"],
+        default="WARNING",
+        const="WARNING",
+        nargs="?",
+        help="change the log level",
+    )
     parser.set_defaults(func=show_info)
-    subparsers = parser.add_subparsers(help='Badger commands help')
+    subparsers = parser.add_subparsers(help="Badger commands help")
 
     # Parser for the 'doctor' command
-    parser_doctor = subparsers.add_parser(
-        'doctor', help='Badger status self-check')
-    parser_doctor.add_argument('-r', '--reset', action='store_true',
-                               help='reset Badger to factory settings')
+    parser_doctor = subparsers.add_parser("doctor", help="Badger status self-check")
+    parser_doctor.add_argument(
+        "-r", "--reset", action="store_true", help="reset Badger to factory settings"
+    )
     parser_doctor.set_defaults(func=self_check)
 
     # Parser for the 'routine' command
-    parser_routine = subparsers.add_parser('routine', help='Badger routines')
-    parser_routine.add_argument('routine_name',
-                                nargs='?', type=str, default=None)
-    parser_routine.add_argument('-r', '--run', action='store_true',
-                                help='run the routine')
-    parser_routine.add_argument('-y', '--yes', action='store_true',
-                                help='run the routine without confirmation')
-    parser_routine.add_argument('-v', '--verbose', type=int, choices=[0, 1, 2],
-                                default=2, const=2, nargs='?',
-                                help='verbose level of optimization progress')
+    parser_routine = subparsers.add_parser("routine", help="Badger routines")
+    parser_routine.add_argument("routine_name", nargs="?", type=str, default=None)
+    parser_routine.add_argument(
+        "-r", "--run", action="store_true", help="run the routine"
+    )
+    parser_routine.add_argument(
+        "-y", "--yes", action="store_true", help="run the routine without confirmation"
+    )
+    parser_routine.add_argument(
+        "-v",
+        "--verbose",
+        type=int,
+        choices=[0, 1, 2],
+        default=2,
+        const=2,
+        nargs="?",
+        help="verbose level of optimization progress",
+    )
     parser_routine.set_defaults(func=show_routine)
 
     # Parser for the 'generator' command
-    parser_generator = subparsers.add_parser('generator', help='Badger generators')
-    parser_generator.add_argument('generator_name', nargs='?', type=str, default=None)
+    parser_generator = subparsers.add_parser("generator", help="Badger generators")
+    parser_generator.add_argument("generator_name", nargs="?", type=str, default=None)
     parser_generator.set_defaults(func=show_generator)
 
     # Parser for the 'intf' command
-    parser_intf = subparsers.add_parser('intf', help='Badger interfaces')
-    parser_intf.add_argument('intf_name', nargs='?', type=str, default=None)
+    parser_intf = subparsers.add_parser("intf", help="Badger interfaces")
+    parser_intf.add_argument("intf_name", nargs="?", type=str, default=None)
     parser_intf.set_defaults(func=show_intf)
 
     # Parser for the 'env' command
-    parser_env = subparsers.add_parser('env', help='Badger environments')
-    parser_env.add_argument('env_name', nargs='?', type=str, default=None)
+    parser_env = subparsers.add_parser("env", help="Badger environments")
+    parser_env.add_argument("env_name", nargs="?", type=str, default=None)
     parser_env.set_defaults(func=show_env)
 
     # Parser for the 'install' command
-    parser_inst = subparsers.add_parser('install', help='Badger install plugin')
-    parser_inst.add_argument('plugin_type', nargs='?', type=str, default=None)
-    parser_inst.add_argument('plugin_specific', nargs='?', type=str, default=None)
+    parser_inst = subparsers.add_parser("install", help="Badger install plugin")
+    parser_inst.add_argument("plugin_type", nargs="?", type=str, default=None)
+    parser_inst.add_argument("plugin_specific", nargs="?", type=str, default=None)
     parser_inst.set_defaults(func=plugin_install)
 
     # Parser for the 'remove' command
-    parser_remove = subparsers.add_parser('remove', help='Badger remove plugin')
-    parser_remove.add_argument('plugin_type', nargs='?', type=str, default=None)
-    parser_remove.add_argument('plugin_specific', nargs='?', type=str, default=None)
+    parser_remove = subparsers.add_parser("remove", help="Badger remove plugin")
+    parser_remove.add_argument("plugin_type", nargs="?", type=str, default=None)
+    parser_remove.add_argument("plugin_specific", nargs="?", type=str, default=None)
     parser_remove.set_defaults(func=plugin_remove)
 
     # Parser for the 'run' command
-    parser_run = subparsers.add_parser('run', help='run routines')
-    parser_run.add_argument('-a', '--generator', required=True,
-                            help='generator to use')
-    parser_run.add_argument('-ap', '--generator_params',
-                            help='parameters for the generator')
-    parser_run.add_argument('-e', '--env', required=True,
-                            help='environment to use')
-    parser_run.add_argument('-ep', '--env_params',
-                            help='parameters for the environment')
-    parser_run.add_argument('-c', '--config', required=True,
-                            help='config for the routine')
-    parser_run.add_argument('-s', '--save', nargs='?', const='',
-                            help='the routine name to be saved')
-    parser_run.add_argument('-y', '--yes', action='store_true',
-                            help='run the routine without confirmation')
-    parser_run.add_argument('-v', '--verbose', type=int, choices=[0, 1, 2],
-                            default=2, const=2, nargs='?',
-                            help='verbose level of optimization progress')
+    parser_run = subparsers.add_parser("run", help="run routines")
+    parser_run.add_argument("-a", "--generator", required=True, help="generator to use")
+    parser_run.add_argument(
+        "-ap", "--generator_params", help="parameters for the generator"
+    )
+    parser_run.add_argument("-e", "--env", required=True, help="environment to use")
+    parser_run.add_argument(
+        "-ep", "--env_params", help="parameters for the environment"
+    )
+    parser_run.add_argument(
+        "-c", "--config", required=True, help="config for the routine"
+    )
+    parser_run.add_argument(
+        "-s", "--save", nargs="?", const="", help="the routine name to be saved"
+    )
+    parser_run.add_argument(
+        "-y", "--yes", action="store_true", help="run the routine without confirmation"
+    )
+    parser_run.add_argument(
+        "-v",
+        "--verbose",
+        type=int,
+        choices=[0, 1, 2],
+        default=2,
+        const=2,
+        nargs="?",
+        help="verbose level of optimization progress",
+    )
     parser_run.set_defaults(func=run_routine)
 
     # Parser for the 'config' command
-    parser_config = subparsers.add_parser('config', help='Badger configurations')
-    parser_config.add_argument('key', nargs='?', type=str, default=None)
+    parser_config = subparsers.add_parser("config", help="Badger configurations")
+    parser_config.add_argument("key", nargs="?", type=str, default=None)
     parser_config.set_defaults(func=config_settings)
 
     args = parser.parse_args()
     args.func(args)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

src/badger/actions/__init__.py

@@ -1,7 +1,7 @@
 from importlib import metadata
-from .doctor import check_n_config_paths
-from ..utils import yprint
-from ..log import set_log_level
+from badger.actions.doctor import check_n_config_paths
+from badger.utils import yprint
+from badger.log import set_log_level
 
 
 def show_info(args):
@@ -10,15 +10,15 @@ def show_info(args):
 
     if args.gui:
         if check_n_config_paths():
-            from ..gui.default import launch_gui
+            from badger.gui.default import launch_gui
 
             launch_gui()
 
         return
 
     if args.gui_acr:
         if check_n_config_paths():
-            from ..gui.default import launch_gui
+            from badger.gui.default import launch_gui
 
             launch_gui()
 
@@ -27,7 +27,7 @@ def show_info(args):
     if not check_n_config_paths():
         return
 
-    from ..settings import init_settings
+    from badger.settings import init_settings
 
     config_singleton = init_settings()
     BADGER_PLUGIN_ROOT = config_singleton.read_value("BADGER_PLUGIN_ROOT")
@@ -36,12 +36,12 @@ def show_info(args):
     BADGER_ARCHIVE_ROOT = config_singleton.read_value("BADGER_ARCHIVE_ROOT")
 
     info = {
-        'name': 'Badger the optimizer',
-        'version': metadata.version('badger-opt'),
-        'plugin root': BADGER_PLUGIN_ROOT,
-        'database root': BADGER_DB_ROOT,
-        'logbook root': BADGER_LOGBOOK_ROOT,
-        'archive root': BADGER_ARCHIVE_ROOT,
+        "name": "Badger the optimizer",
+        "version": metadata.version("badger-opt"),
+        "plugin root": BADGER_PLUGIN_ROOT,
+        "database root": BADGER_DB_ROOT,
+        "logbook root": BADGER_LOGBOOK_ROOT,
+        "archive root": BADGER_ARCHIVE_ROOT,
         # 'plugin installation url': read_value('BADGER_PLUGINS_URL')
     }