Merge pull request #297 from pyiron/ruff

add ruff formatter

.ci_support/release.py

@@ -1,12 +1,19 @@
 def get_setup_version_and_pattern(setup_content):
     depend_lst, version_lst = [], []
     for l in setup_content:
-        if '==' in l:
-            lst = l.split('[')[-1].split(']')[0].replace(' ', '').replace('"', '').replace("'", '').split(',')
+        if "==" in l:
+            lst = (
+                l.split("[")[-1]
+                .split("]")[0]
+                .replace(" ", "")
+                .replace('"', "")
+                .replace("'", "")
+                .split(",")
+            )
             for dep in lst:
-                if dep != '\n':
-                    version_lst.append(dep.split('==')[1])
-                    depend_lst.append(dep.split('==')[0])
+                if dep != "\n":
+                    version_lst.append(dep.split("==")[1])
+                    depend_lst.append(dep.split("==")[0])
 
     version_high_dict = {d: v for d, v in zip(depend_lst, version_lst)}
     return version_high_dict
@@ -16,14 +23,14 @@ def get_env_version(env_content):
     read_flag = False
     depend_lst, version_lst = [], []
     for l in env_content:
-        if 'dependencies:' in l:
+        if "dependencies:" in l:
             read_flag = True
         elif read_flag:
-            lst = l.replace('-', '').replace(' ', '').replace('\n', '').split("=")
+            lst = l.replace("-", "").replace(" ", "").replace("\n", "").split("=")
             if len(lst) == 2:
                 depend_lst.append(lst[0])
                 version_lst.append(lst[1])
-    return {d:v for d, v in zip(depend_lst, version_lst)}
+    return {d: v for d, v in zip(depend_lst, version_lst)}
 
 
 def update_dependencies(setup_content, version_low_dict, version_high_dict):
@@ -35,27 +42,29 @@ def update_dependencies(setup_content, version_low_dict, version_high_dict):
             version_combo_dict[dep] = dep + "==" + ver
 
     setup_content_new = ""
-    pattern_dict = {d:d + "==" + v for d, v in version_high_dict.items()}
+    pattern_dict = {d: d + "==" + v for d, v in version_high_dict.items()}
     for l in setup_content:
         for k, v in pattern_dict.items():
             if v in l:
                 l = l.replace(v, version_combo_dict[k])
-        setup_content_new +=l
+        setup_content_new += l
     return setup_content_new
 
 
 if __name__ == "__main__":
-    with open('pyproject.toml', "r") as f:
+    with open("pyproject.toml", "r") as f:
         setup_content = f.readlines()
 
-    with open('environment.yml', "r") as f:
+    with open("environment.yml", "r") as f:
         env_content = f.readlines()
 
     setup_content_new = update_dependencies(
         setup_content=setup_content[2:],
         version_low_dict=get_env_version(env_content=env_content),
-        version_high_dict=get_setup_version_and_pattern(setup_content=setup_content[2:]),
+        version_high_dict=get_setup_version_and_pattern(
+            setup_content=setup_content[2:]
+        ),
     )
 
-    with open('pyproject.toml', "w") as f:
+    with open("pyproject.toml", "w") as f:
         f.writelines("".join(setup_content[:2]) + setup_content_new)

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        name: ruff lint
+        args: ["--fix"]
+        files: ^pysqa/
+      - id: ruff-format
+        name: ruff format

pysqa/__init__.py

@@ -2,4 +2,5 @@
 
 from ._version import get_versions
 
+__all__ = [QueueAdapter]
 __version__ = get_versions()["version"]

pysqa/executor/__init__.py

@@ -1 +1,3 @@
 from pysqa.executor.executor import Executor
+
+__all__ = [Executor]

pysqa/wrapper/lsf.py

@@ -40,8 +40,8 @@ def convert_queue_status(queue_status_output: str) -> pandas.DataFrame:
         job_id_lst, user_lst, status_lst, job_name_lst = [], [], [], []
         line_split_lst = queue_status_output.split("\n")
         if len(line_split_lst) > 1:
-            for l in line_split_lst[1:]:
-                line_segments = l.split()
+            for line in line_split_lst[1:]:
+                line_segments = line.split()
                 if len(line_segments) > 1:
                     job_id_lst.append(int(line_segments[0]))
                     user_lst.append(line_segments[1])

setup.py

@@ -5,4 +5,4 @@
 setup(
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-)
+)

tests/test_basic.py

@@ -64,7 +64,7 @@ def test_memory_string_comparison(self):
         )
         self.assertEqual(
             BasisQueueAdapter._value_in_range(
-                90000 * 1024 ** 2, value_min="1K", value_max="70G"
+                90000 * 1024**2, value_min="1K", value_max="70G"
             ),
             "70G",
         )

tests/test_cmd.py

@@ -11,12 +11,11 @@ class TestCMD(unittest.TestCase):
     def setUpClass(cls):
         cls.test_dir = os.path.abspath(os.path.dirname(__file__))
 
-    @unittest.mock.patch('sys.stdout', new_callable=io.StringIO)
-    def assert_stdout_command_line(self, cmd_args, execute_command, expected_output, mock_stdout):
-        command_line(
-            arguments_lst=cmd_args,
-            execute_command=execute_command
-        )
+    @unittest.mock.patch("sys.stdout", new_callable=io.StringIO)
+    def assert_stdout_command_line(
+        self, cmd_args, execute_command, expected_output, mock_stdout
+    ):
+        command_line(arguments_lst=cmd_args, execute_command=execute_command)
         self.assertEqual(mock_stdout.getvalue(), expected_output)
 
     def test_help(self):
@@ -45,33 +44,41 @@ def execute_command(
 
         self.assert_stdout_command_line(
             [
-                "--config_directory", os.path.join(self.test_dir, "config", "slurm"),
+                "--config_directory",
+                os.path.join(self.test_dir, "config", "slurm"),
                 "--submit",
-                "--queue", "slurm",
-                "--job_name", "test",
-                "--working_directory", ".",
-                "--cores", "2",
-                "--memory", "1GB",
-                "--run_time", "10",
-                "--command", "echo hello"
+                "--queue",
+                "slurm",
+                "--job_name",
+                "test",
+                "--working_directory",
+                ".",
+                "--cores",
+                "2",
+                "--memory",
+                "1GB",
+                "--run_time",
+                "10",
+                "--command",
+                "echo hello",
             ],
             execute_command,
             "1\n",
         )
         with open("run_queue.sh") as f:
             output = f.readlines()
         content = [
-            '#!/bin/bash\n',
-            '#SBATCH --output=time.out\n',
-            '#SBATCH --job-name=test\n',
-            '#SBATCH --chdir=.\n',
-            '#SBATCH --get-user-env=L\n',
-            '#SBATCH --partition=slurm\n',
-            '#SBATCH --time=4320\n',
-            '#SBATCH --mem=1GBG\n',
-            '#SBATCH --cpus-per-task=10\n',
-            '\n',
-            'echo hello'
+            "#!/bin/bash\n",
+            "#SBATCH --output=time.out\n",
+            "#SBATCH --job-name=test\n",
+            "#SBATCH --chdir=.\n",
+            "#SBATCH --get-user-env=L\n",
+            "#SBATCH --partition=slurm\n",
+            "#SBATCH --time=4320\n",
+            "#SBATCH --mem=1GBG\n",
+            "#SBATCH --cpus-per-task=10\n",
+            "\n",
+            "echo hello",
         ]
         self.assertEqual(output, content)
         os.remove("run_queue.sh")
@@ -88,12 +95,14 @@ def execute_command(
 
         self.assert_stdout_command_line(
             [
-                "--config_directory", os.path.join(self.test_dir, "config", "slurm"),
+                "--config_directory",
+                os.path.join(self.test_dir, "config", "slurm"),
                 "--delete",
-                "--id", "1"
+                "--id",
+                "1",
             ],
             execute_command,
-            "S\n"
+            "S\n",
         )
 
     def test_status(self):
@@ -104,27 +113,40 @@ def execute_command(
             shell=False,
             error_filename="pysqa.err",
         ):
-            with open(os.path.join(self.test_dir, "config", "slurm", "squeue_output")) as f:
+            with open(
+                os.path.join(self.test_dir, "config", "slurm", "squeue_output")
+            ) as f:
                 return f.read()
 
         self.assert_stdout_command_line(
             [
-                "--config_directory", os.path.join(self.test_dir, "config", "slurm"),
-                "--status"
+                "--config_directory",
+                os.path.join(self.test_dir, "config", "slurm"),
+                "--status",
             ],
             execute_command,
-            json.dumps({
-                "jobid": [5322019, 5322016, 5322017, 5322018, 5322013], "user": ["janj", "janj", "janj", "janj", "maxi"],
-                "jobname": ["pi_19576488", "pi_19576485", "pi_19576486", "pi_19576487", "pi_19576482"],
-                "status": ["running", "running", "running", "running", "running"],
-                "working_directory": [
-                    "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_1",
-                    "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_2",
-                    "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_3",
-                    "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_4",
-                    "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_5"
-                ]
-            }) +"\n"
+            json.dumps(
+                {
+                    "jobid": [5322019, 5322016, 5322017, 5322018, 5322013],
+                    "user": ["janj", "janj", "janj", "janj", "maxi"],
+                    "jobname": [
+                        "pi_19576488",
+                        "pi_19576485",
+                        "pi_19576486",
+                        "pi_19576487",
+                        "pi_19576482",
+                    ],
+                    "status": ["running", "running", "running", "running", "running"],
+                    "working_directory": [
+                        "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_1",
+                        "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_2",
+                        "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_3",
+                        "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_4",
+                        "/cmmc/u/janj/pyiron/projects/2023/2023-04-19-dft-test/job_5",
+                    ],
+                }
+            )
+            + "\n",
         )
 
     def test_list(self):
@@ -139,19 +161,31 @@ def execute_command(
 
         self.assert_stdout_command_line(
             [
-                "--config_directory", os.path.join(self.test_dir, "config", "slurm"),
+                "--config_directory",
+                os.path.join(self.test_dir, "config", "slurm"),
                 "--list",
-                "--working_directory", os.path.join(self.test_dir, "config", "slurm"),
-
+                "--working_directory",
+                os.path.join(self.test_dir, "config", "slurm"),
             ],
             execute_command,
-            json.dumps({
-                "dirs": [os.path.join(self.test_dir, "config", "slurm")],
-                "files": sorted([
-                    os.path.join(self.test_dir, "config", "slurm", "squeue_output"),
-                    os.path.join(self.test_dir, "config", "slurm", "slurm_extra.sh"),
-                    os.path.join(self.test_dir, "config", "slurm", "slurm.sh"),
-                    os.path.join(self.test_dir, "config", "slurm", "queue.yaml"),
-                ])
-            }) + "\n"
+            json.dumps(
+                {
+                    "dirs": [os.path.join(self.test_dir, "config", "slurm")],
+                    "files": sorted(
+                        [
+                            os.path.join(
+                                self.test_dir, "config", "slurm", "squeue_output"
+                            ),
+                            os.path.join(
+                                self.test_dir, "config", "slurm", "slurm_extra.sh"
+                            ),
+                            os.path.join(self.test_dir, "config", "slurm", "slurm.sh"),
+                            os.path.join(
+                                self.test_dir, "config", "slurm", "queue.yaml"
+                            ),
+                        ]
+                    ),
+                }
+            )
+            + "\n",
         )

tests/test_execute_command.py

@@ -10,47 +10,47 @@ def test_commands_as_lst(self):
             working_directory=".",
             split_output=True,
             shell=False,
-            error_filename="pysqa.err"
+            error_filename="pysqa.err",
         )
-        self.assertEqual(output, ['hello', ''])
+        self.assertEqual(output, ["hello", ""])
 
     def test_commands_as_lst_no_split(self):
         output = execute_command(
             commands=["echo", "hello"],
             working_directory=".",
             split_output=False,
             shell=False,
-            error_filename="pysqa.err"
+            error_filename="pysqa.err",
         )
-        self.assertEqual(output, 'hello\n')
+        self.assertEqual(output, "hello\n")
 
     def test_commands_as_lst_shell_true(self):
         output = execute_command(
             commands=["echo", "hello"],
             working_directory=".",
             split_output=True,
             shell=True,
-            error_filename="pysqa.err"
+            error_filename="pysqa.err",
         )
-        self.assertEqual(output, ['hello', ''])
+        self.assertEqual(output, ["hello", ""])
 
     def test_commands_as_str(self):
         output = execute_command(
             commands="echo hello",
             working_directory=".",
             split_output=True,
             shell=False,
-            error_filename="pysqa.err"
+            error_filename="pysqa.err",
         )
-        self.assertEqual(output, ['hello', ''])
+        self.assertEqual(output, ["hello", ""])
 
     def test_commands_fails(self):
         output = execute_command(
             commands="exit 1",
             working_directory=".",
             split_output=True,
             shell=False,
-            error_filename="pysqa_fails.err"
+            error_filename="pysqa_fails.err",
         )
         self.assertIsNone(output)
         with open("pysqa_fails.err") as f: