Merge pull request #993 from qiboteam/qq_run

Replace qq auto with qq run

README.md

@@ -59,9 +59,9 @@ targets: [0]
 
 ```
 ### How to run protocols
-To run the protocols specified in the ```runcard```, Qibocal uses the `qq auto` command
+To run the protocols specified in the ```runcard```, Qibocal uses the `qq run` command
 ```sh
-qq auto <runcard> -o <output_folder>
+qq run <runcard> -o <output_folder>
 ```
 if ```<output_folder>``` is specified, the results will be saved in it, otherwise ```qq``` will automatically create a default folder containing the current date and the username.
 

doc/source/getting-started/example.rst

@@ -29,4 +29,4 @@ Run the routine
 
 .. code-block::
 
-    qq auto example.yml -o resonator_spectroscopy_routine
+    qq run example.yml -o resonator_spectroscopy_routine

doc/source/getting-started/interface.rst

@@ -60,15 +60,15 @@ regarding the protocols executed.
     qq report <output_folder>
 
 
-``qq auto``
+``qq run``
 ^^^^^^^^^^^
 
-The previous commands are put together using ``qq auto`` which will perform data acquisition, post-processing and report generation.
+The previous commands are put together using ``qq run`` which will perform data acquisition, post-processing and report generation.
 When executing multiple protocols they are executed following the actions specified in the runcard.
 
 .. code-block::
 
-    qq auto <path_to_runcard> -o <output_folder>
+    qq run <path_to_runcard> -o <output_folder>
 
 ``qq update``
 ^^^^^^^^^^^^^

doc/source/protocols/dispersive_shift.rst

@@ -55,7 +55,7 @@ It follows an example of the experiment parameters.
         freq_width: 1000000
 
 
-After running `qq auto`, the experiment is executed and the result will looks like
+After running `qq run`, the experiment is executed and the result will looks like
 the following picture.
 
 .. image:: dispersive_shift.png

doc/source/protocols/rabi/rabi.rst

@@ -60,7 +60,7 @@ It follows an example of the experiment parameters.
 To run properly this experiment it is important to set the
 `relaxation_time` higher than the qubit `T1`.
 
-After running `qq auto`, the experiment is executed and the result will looks like
+After running `qq run`, the experiment is executed and the result will looks like
 the following picture.
 
 .. image:: rabi_amplitude.png

src/qibocal/cli/_base.py

@@ -8,10 +8,10 @@
 
 from ..auto.runcard import Runcard
 from .acquisition import acquire as acquisition
-from .autocalibration import autocalibrate
 from .compare import compare_reports
 from .fit import fit as fitting
 from .report import report as reporting
+from .run import protocols_execution
 from .update import update as updating
 from .upload import upload_report
 
@@ -58,8 +58,8 @@ def command():
     default=None,
     help="Name of the Qibo backend.,",
 )
-def auto(runcard, folder, force, update, platform, backend):
-    """Autocalibration.
+def run(runcard, folder, force, update, platform, backend):
+    """Execute the qubit calibration.
 
     Arguments:
 
@@ -72,7 +72,7 @@ def auto(runcard, folder, force, update, platform, backend):
     if backend is not None:
         runcard.backend = backend
 
-    autocalibrate(runcard, folder, force, update)
+    protocols_execution(runcard, folder, force, update)
 
 
 @command.command(context_settings=CONTEXT_SETTINGS)
@@ -236,3 +236,48 @@ def upload(path, tag, author):
 )
 def compare(report_1_path, report_2_path, folder, force):
     compare_reports(folder, report_1_path, report_2_path, force)
+
+
+@command.command(context_settings=CONTEXT_SETTINGS, deprecated=True)
+@click.argument(
+    "runcard", metavar="RUNCARD", type=click.Path(exists=True, path_type=pathlib.Path)
+)
+@click.option(
+    "folder",
+    "-o",
+    type=click.Path(path_type=pathlib.Path),
+    help="Output folder. If not provided a standard name will generated.",
+)
+@click.option(
+    "force",
+    "-f",
+    is_flag=True,
+    help="Use --force option to overwrite the output folder.",
+)
+@click.option(
+    "--update/--no-update",
+    default=True,
+    help="Use --no-update option to avoid updating iteratively the platform."
+    "With this option the new runcard will not be produced.",
+)
+@click.option(
+    "--platform",
+    default=None,
+    help="Name of the Qibolab platform.",
+)
+@click.option(
+    "--backend",
+    default=None,
+    help="Name of the Qibo backend.,",
+)
+def auto(runcard, folder, force, update, platform, backend):
+    """Execute the qubit calibration.
+
+    Arguments:
+
+     - RUNCARD: runcard with declarative inputs.
+    """
+    click.echo(
+        "Warning: This command is deprecated and may be removed in a future version. Please use 'qq run' instead. ",
+        err=True,
+    )

src/qibocal/cli/autocalibration.py → src/qibocal/cli/run.py

@@ -9,7 +9,7 @@
 from .report import report
 
 
-def autocalibrate(runcard: Runcard, folder: Path, force, update):
+def protocols_execution(runcard: Runcard, folder: Path, force, update):
     """Autocalibration.
 
     Arguments:

tests/test_cli.py

@@ -19,7 +19,7 @@ def test_qq_update(update, tmp_path, monkeypatch):
     runner = CliRunner()
     runner.invoke(
         command,
-        ["auto", str(DUMMY_ACTION), "-o", str(output_folder), "-f", update],
+        ["run", str(DUMMY_ACTION), "-o", str(output_folder), "-f", update],
         catch_exceptions=False,
     )
 
@@ -85,8 +85,8 @@ def test_compare_report_dates(tmp_path):
     compare_dir = tmp_path / "compare_dir"
 
     runner = CliRunner()
-    runner.invoke(command, ["auto", str(DUMMY_COMPARE), "-o", str(report_dir_1), "-f"])
-    runner.invoke(command, ["auto", str(DUMMY_COMPARE), "-o", str(report_dir_2), "-f"])
+    runner.invoke(command, ["run", str(DUMMY_COMPARE), "-o", str(report_dir_1), "-f"])
+    runner.invoke(command, ["run", str(DUMMY_COMPARE), "-o", str(report_dir_2), "-f"])
 
     runner.invoke(
         command,

tests/test_output.py

@@ -25,7 +25,7 @@
 ACTION = Action(**action)
 
 
-# TODO: this is essentially a proto `qq auto` invocation, it should be simplified as
+# TODO: this is essentially a proto `qq run` invocation, it should be simplified as
 # much as possible in the library, and made available in conftest
 @pytest.fixture
 def fake_output(tmp_path: Path) -> tuple[Output, Path]:

tests/test_protocols.py

@@ -62,19 +62,19 @@ def locate_tomography_file(runcard):
 
 @pytest.mark.parametrize("update", ["--update", "--no-update"])
 @pytest.mark.parametrize("runcard", generate_runcard_single_protocol(), ids=idfn)
-def test_auto_command(runcard, update, tmp_path):
+def test_run_command(runcard, update, tmp_path):
     """Test auto command pipeline."""
     runcard = runcard[0]
 
     locate_tomography_file(runcard)
 
     (tmp_path / SINGLE_ACTION_RUNCARD).write_text(yaml.safe_dump(runcard))
-    outpath = tmp_path / "auto_test"
+    outpath = tmp_path / "run_test"
     runner = CliRunner()
     runner.invoke(
         command,
         [
-            "auto",
+            "run",
             str(tmp_path / SINGLE_ACTION_RUNCARD),
             "-o",
             str(outpath),