Merge pull request #178 from pyiron/cmd_update

Move command line interface from python -m pysqa.cmd to python -m pysqa
pyiron · May 4, 2023 · 908ed91 · 908ed91
2 parents 43cb5ff + c719d56
commit 908ed91
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Showing 4 changed files with 91 additions and 65 deletions.
diff --git a/pysqa/cmd.py b/pysqa/cmd.py
@@ -48,8 +48,7 @@ def command_line(argv, execute_command=execute_command):
             ],
         )
     except getopt.GetoptError:
-        print("cmd.py help")
-        sys.exit()
+        print("python -m pysqa --help")
     else:
         mode_submit = False
         mode_delete = False
@@ -92,9 +91,6 @@ def command_line(argv, execute_command=execute_command):
                     dependency_list = [arg]
                 else:
                     dependency_list.append(arg)
-            elif opt in ("-h", "--help"):
-                print("cmd.py help ... coming soon.")
-                sys.exit()
         if mode_submit or mode_delete or mode_reservation or mode_status:
             qa = QueueAdapter(directory=directory, execute_command=execute_command)
             if mode_submit:
@@ -122,9 +118,8 @@ def command_line(argv, execute_command=execute_command):
             for p, folder, files in os.walk(working_directory):
                 remote_dirs.append(p)
                 remote_files += [os.path.join(p, f) for f in files]
-            print(json.dumps({"dirs": remote_dirs, "files": remote_files}))
-        sys.exit()
-
-
-if __name__ == "__main__":
-    command_line(sys.argv[1:])
+            print(
+                json.dumps({"dirs": sorted(remote_dirs), "files": sorted(remote_files)})
+            )
+        else:
+            print("python -m pysqa --help ... coming soon.")
diff --git a/pysqa/ext/remote.py b/pysqa/ext/remote.py
@@ -117,7 +117,7 @@ def get_job_from_remote(self, working_directory):
         )
         remote_dict = json.loads(
             self._execute_remote_command(
-                command="python -m pysqa.cmd --list --working_directory "
+                command="python -m pysqa --list --working_directory "
                 + remote_working_directory
             )
         )
@@ -191,11 +191,7 @@ def _open_ssh_connection(self):
         return ssh
 
     def _remote_command(self):
-        return (
-            "python -m pysqa.cmd --config_directory "
-            + self._ssh_remote_config_dir
-            + " "
-        )
+        return "python -m pysqa --config_directory " + self._ssh_remote_config_dir + " "
 
     def _get_queue_status_command(self):
         return self._remote_command() + "--status"

diff --git a/tests/test_cmd.py b/tests/test_cmd.py
@@ -1,5 +1,8 @@
 import os
+import io
+import json
 import unittest
+import unittest.mock
 from pysqa.cmd import command_line
 
 
@@ -8,13 +11,27 @@ 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(
+            argv=cmd_args,
+            execute_command=execute_command
+        )
+        self.assertEqual(mock_stdout.getvalue(), expected_output)
+
     def test_help(self):
-        with self.assertRaises(SystemExit):
-            command_line(["--help"])
+        self.assert_stdout_command_line(
+            ["--help"],
+            None,
+            "python -m pysqa --help ... coming soon.\n",
+        )
 
     def test_wrong_option(self):
-        with self.assertRaises(SystemExit):
-            command_line(["--error"])
+        self.assert_stdout_command_line(
+            ["--error"],
+            None,
+            "python -m pysqa --help\n",
+        )
 
     def test_submit(self):
         def execute_command(
@@ -26,21 +43,21 @@ def execute_command(
         ):
             return "1\n"
 
-        with self.assertRaises(SystemExit):
-            command_line(
-                [
-                    "--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"
-                ],
-                execute_command=execute_command
-            )
+        self.assert_stdout_command_line(
+            [
+                "--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"
+            ],
+            execute_command,
+            "1\n",
+        )
         with open("run_queue.sh") as f:
             output = f.readlines()
         content = [
@@ -69,18 +86,17 @@ def execute_command(
         ):
             return "Success\n"
 
-        with self.assertRaises(SystemExit):
-            command_line(
-                [
-                    "--config_directory", os.path.join(self.test_dir, "config", "slurm"),
-                    "--delete",
-                    "--id", "1",
-                ],
-                execute_command=execute_command
-            )
+        self.assert_stdout_command_line(
+            [
+                "--config_directory", os.path.join(self.test_dir, "config", "slurm"),
+                "--delete",
+                "--id", "1"
+            ],
+            execute_command,
+            "S\n"
+        )
 
     def test_status(self):
-
         def execute_command(
             commands,
             working_directory=None,
@@ -91,14 +107,25 @@ def execute_command(
             with open(os.path.join(self.test_dir, "config", "slurm", "squeue_output")) as f:
                 return f.read()
 
-        with self.assertRaises(SystemExit):
-            command_line(
-                [
-                    "--config_directory", os.path.join(self.test_dir, "config", "slurm"),
-                    "--status"
-                ],
-                execute_command=execute_command
-            )
+        self.assert_stdout_command_line(
+            [
+                "--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"
+        )
 
     def test_list(self):
         def execute_command(
@@ -110,13 +137,21 @@ def execute_command(
         ):
             pass
 
-        with self.assertRaises(SystemExit):
-            command_line(
-                [
-                    "--config_directory", os.path.join(self.test_dir, "config", "slurm"),
-                    "--list",
-                    "--working_directory", os.path.join(self.test_dir, "config", "slurm"),
+        self.assert_stdout_command_line(
+            [
+                "--config_directory", os.path.join(self.test_dir, "config", "slurm"),
+                "--list",
+                "--working_directory", os.path.join(self.test_dir, "config", "slurm"),
 
-                ],
-                execute_command=execute_command
-            )
+            ],
+            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"
+        )
diff --git a/tests/test_remote.py b/tests/test_remote.py
@@ -43,13 +43,13 @@ def test_convert_path_to_remote(self):
 
     def test_delete_command(self):
         self.assertEqual(
-            "python -m pysqa.cmd --config_directory /u/share/pysqa/resources/queues/ --delete --id 123",
+            "python -m pysqa --config_directory /u/share/pysqa/resources/queues/ --delete --id 123",
             self.remote._adapter._delete_command(job_id=123)
         )
 
     def test_reservation_command(self):
         self.assertEqual(
-            "python -m pysqa.cmd --config_directory /u/share/pysqa/resources/queues/ --reservation --id 123",
+            "python -m pysqa --config_directory /u/share/pysqa/resources/queues/ --reservation --id 123",
             self.remote._adapter._reservation_command(job_id=123)
         )