Remove --output-folder-path CLI flag

Removing in favour of another approach to allow the SLURM logfile
created by the DLS launcher to be put into the httomo output dir
(see #458 and #483 for more details).

docs/source/howto/run_httomo.rst

@@ -157,9 +157,6 @@ The :code:`run` command
     Options:
       --output-folder-name DIRECTORY  Define the name of the output folder created
                                       by HTTomo
-      --output-folder-path DIRECTORY  Provide path to folder in which output
-                                      should be stored. This overrides the
-                                      `out_dir` argument
       --save-all                      Save intermediate datasets for all tasks in
                                       the pipeline.
       --gpu-id INTEGER                The GPU ID of the device to use.
@@ -226,10 +223,9 @@ directory created by HTTomo would be
 Options/flags
 #############
 
-The :code:`run` command has 14 options/flags:
+The :code:`run` command has 13 options/flags:
 
 - :code:`--output-folder-name`
-- :code:`--output-folder-path`
 - :code:`--save-all`
 - :code:`--gpu-id`
 - :code:`--reslice-dir`
@@ -257,19 +253,6 @@ For example, if the :code:`OUT_DIR` path provided was :code:`/home/myuser`, and
 :code:`--output-folder-name=test-1` was given, then the absolute path of the output directory
 created by HTTomo would be :code:`/home/myuser/test-1/`.
 
-:code:`--output-folder-path`
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-If one wishes to have HTTomo *not* create an output directory, and instead for HTTomo to place
-the output in an existing directory, then the :code:`--output-folder-path` flag may be used.
-
-For example, if :code:`--output-folder-path=/home/myuser/my-output` was given, then HTTomo
-wouldn't create an output directory and would simply place the results in
-:code:`/home/myuser/my-output`.
-
-.. note:: This flag overrides the :code:`OUT_DIR` argument. Also, the given directory must
-          exist prior to running HTTomo
-
 :code:`--save-all`
 ~~~~~~~~~~~~~~~~~~
 

httomo/cli.py

@@ -67,15 +67,6 @@ def check(yaml_config: Path, in_data_file: Optional[Path] = None):
     default=None,
     help="Define the name of the output folder created by HTTomo",
 )
-@click.option(
-    "--output-folder-path",
-    type=click.Path(exists=True, file_okay=False, writable=True, path_type=Path),
-    default=None,
-    help=(
-        "Provide path to folder in which output should be stored. This overrides "
-        "the `out_dir` argument"
-    ),
-)
 @click.option(
     "--save-all",
     is_flag=True,
@@ -155,7 +146,6 @@ def run(
     yaml_config: Path,
     out_dir: Path,
     output_folder_name: Optional[Path],
-    output_folder_path: Optional[Path],
     gpu_id: int,
     save_all: bool,
     reslice_dir: Union[Path, None],
@@ -179,7 +169,6 @@ def run(
         syslog_host,
         syslog_port,
         output_folder_name,
-        output_folder_path,
     )
 
     does_contain_sweep = is_sweep_pipeline(yaml_config)
@@ -258,7 +247,6 @@ def set_global_constants(
     syslog_host: str,
     syslog_port: int,
     output_folder_name: Optional[Path],
-    output_folder_path: Optional[Path],
 ) -> None:
     if compress_intermediate:
         frames_per_chunk = 1
@@ -268,21 +256,12 @@ def set_global_constants(
     httomo.globals.SYSLOG_SERVER = syslog_host
     httomo.globals.SYSLOG_PORT = syslog_port
 
-    if output_folder_name is not None and output_folder_path is not None:
-        msg = (
-            "The flags `--output-folder-name` and `--output-folder-path` are mutually "
-            "exclusive, please use only one at most"
-        )
-        raise ValueError(msg)
-
-    if output_folder_name is None and output_folder_path is None:
+    if output_folder_name is None:
         httomo.globals.run_out_dir = out_dir.joinpath(
             f"{datetime.now().strftime('%d-%m-%Y_%H_%M_%S')}_output"
         )
-    if output_folder_name is not None:
+    else:
         httomo.globals.run_out_dir = out_dir.joinpath(output_folder_name)
-    if output_folder_path is not None:
-        httomo.globals.run_out_dir = output_folder_path
 
     if max_cpu_slices < 1:
         raise ValueError("max-cpu-slices must be greater or equal to 1")

tests/test_cli.py

@@ -93,41 +93,5 @@ def test_output_folder_name_correctly_sets_run_out_dir_global_constant(output_fo
         syslog_host="localhost",
         syslog_port=514,
         output_folder_name=Path(dir_name),
-        output_folder_path=None,
     )
     assert httomo.globals.run_out_dir == custom_output_dir
-
-
-def test_output_folder_name_and_path_flags_raise_error_if_both_provided():
-    with pytest.raises(ValueError) as e:
-        set_global_constants(
-            out_dir=Path("/"),
-            intermediate_format="hdf5",
-            compress_intermediate=False,
-            frames_per_chunk=0,
-            max_cpu_slices=1,
-            syslog_host="localhost",
-            syslog_port=514,
-            output_folder_name=Path("folder-1"),
-            output_folder_path=Path("/path/to/folder-2"),
-        )
-    assert (
-        "The flags `--output-folder-name` and `--output-folder-path` are mutually exclusive"
-        in str(e)
-    )
-
-
-def test_output_folder_path_correctly_sets_run_out_dir_global_constant():
-    output_folder_path = Path("/some/path/for/output")
-    set_global_constants(
-        out_dir=Path("/"),
-        intermediate_format="hdf5",
-        compress_intermediate=False,
-        frames_per_chunk=0,
-        max_cpu_slices=1,
-        syslog_host="localhost",
-        syslog_port=514,
-        output_folder_name=None,
-        output_folder_path=output_folder_path,
-    )
-    assert httomo.globals.run_out_dir == output_folder_path