Merge branch 'v2.3.2-update' into 'develop'

remove --no-run-relax

See merge request schwede/af2-at-scicore!1

run_af2/src/run_af2/_shared.py

@@ -116,14 +116,6 @@ def parse_af2_arguments(parser):
         help="Use existing MSAs from current working directory.",
         default=False,
     )
-    af2_group.add_argument(
-        "--no-run-relax",
-        action="store_true",
-        help="Don't Run relaxation on models after prediction. That is "
-        + "inverted of alphafold's own --run_relax, and meant to replace "
-        + "'--run_relax=False'",
-        default=False,
-    )
     af2_group.add_argument(
         "--use-gpu-relax",
         action="store_true",

run_af2/src/run_af2/run_singularity.py

@@ -117,7 +117,6 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
     db_preset,
     model_preset,
     use_precomputed_msas,
-    no_run_relax,
     use_gpu_relax,
     num_multimer_predictions_per_model,
     data_paths,
@@ -161,7 +160,6 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
 
     bool_args = {
         "use_precomputed_msas": use_precomputed_msas,
-        "run_relax": not no_run_relax,
         "use_gpu_relax": use_gpu_relax,
     }
     for arg, val in bool_args.items():
@@ -213,7 +211,6 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     db_preset="full_dbs",
     model_preset="monomer",
     use_precomputed_msas=False,
-    no_run_relax=False,
     use_gpu_relax=False,
     num_multimer_predictions_per_model=5,
     af2_image_file=None,
@@ -276,11 +273,6 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     :param use_precomputed_msas: Use existing MSAs from cwd. Corresponds to the
                                  use_precomputed_msas parameter in AF2.
     :type use_precomputed_msas: :class:`bool`
-    :param no_run_relax: Disable relaxation at the end of modelling.
-                         Corresponds to AF2's no_run_relax parameter but works
-                         oppositely, True means no relaxation, False means
-                         relaxation.
-    :type no_run_relax: :class:`bool`
     :param use_gpu_relax: Run relaxation on GPU. Corresponds to the
                           use_gpu_relax parameter in AF2.
     :type use_gpu_relax: :class:`bool`
@@ -418,7 +410,6 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         db_preset,
         model_preset,
         use_precomputed_msas,
-        no_run_relax,
         use_gpu_relax,
         num_multimer_predictions_per_model,
         data_paths,
@@ -490,7 +481,6 @@ def main():
             opts.db_preset,
             opts.model_preset,
             opts.use_precomputed_msas,
-            opts.no_run_relax,
             opts.use_gpu_relax,
             opts.num_multimer_predictions_per_model,
             opts.singularity_image,