Change preset to db[-_]preset.

run_af2/bin/submit-af2

@@ -27,7 +27,7 @@
 # handle command line arguments
 if test $# -lt 2; then
     echo "usage: submit-af2 [--use-gpu]"
-    echo "                  [--preset {reduced_dbs,full_dbs}]"
+    echo "                  [--db-preset {reduced_dbs,full_dbs}]"
     echo "                  [--max-template-date YYYY-MM-DD]"
     echo "                  <OUTPUT DIR> <FASTA FILE> [<FASTA FILE> ...]"
     exit 1
@@ -41,9 +41,9 @@ for i in 1 2 3; do
         shift
         SLURM_AF_PARAMS="--partition=a100,rtx8000 --gres=gpu:1"
         AF_PIPELINE_PARAM="${AF_PIPELINE_PARAM} --use-gpu"
-    else if test x"${1}" = x"--preset"; then
+    else if test x"${1}" = x"--db-preset"; then
              shift
-             AF_PIPELINE_PARAM="${AF_PIPELINE_PARAM} --preset ${1}"
+             AF_PIPELINE_PARAM="${AF_PIPELINE_PARAM} --db-preset ${1}"
              shift
          else if test x"${1}" = x"--max-template-date"; then
                   shift

run_af2/src/run_af2/_shared.py

@@ -58,7 +58,7 @@ def parse_af2_arguments(parser):
     :returns: :class:`argparse.Namespace` object from
               `argparse.ArgumentParser.parse_args`.
     """
-    preset_choices = {
+    db_preset_choices = {
         "reduced_dbs": ["bfd_database_path", "uniclust30_database_path"],
         "full_dbs": ["small_bfd_database_path"],
     }
@@ -102,8 +102,8 @@ def parse_af2_arguments(parser):
     )
     af2_group.add_argument(
         "-p",
-        "--preset",
-        choices=preset_choices.keys(),
+        "--db-preset",
+        choices=db_preset_choices.keys(),
         help="Choose model configuration - no ensembling and smaller genetic "
         + "databases (reduced_dbs), no ensembling and full genetic databases "
         + "configuration (full_dbs), the casp14 preset is not available right "
@@ -113,7 +113,7 @@ def parse_af2_arguments(parser):
     af2_group.add_argument(
         "--version",
         action="version",
-        version="%(prog)s {}".format(get_version()),
+        version=f"{get_version()}",
         help="Show the version number and exit.",
     )
     af2_group.add_argument(
@@ -149,7 +149,7 @@ def parse_af2_arguments(parser):
         "--small-bfd-database-path",
         type=str,
         help="Path to the small version of the BFD database, used with "
-        + "'--preset reduced_dbs'.",
+        + "'--db-preset reduced_dbs'.",
         metavar="<PATH/ PREFIX>",
         default=None,
     )
@@ -190,11 +190,11 @@ def parse_af2_arguments(parser):
     )
     opts = parser.parse_args()
 
-    # check that the preset setting makes sense
-    for arg in preset_choices[opts.preset]:
+    # check that the db_preset setting makes sense
+    for arg in db_preset_choices[opts.db_preset]:
         if getattr(opts, arg) is not None:
             print(
-                f"WARNING: '--preset {opts.preset}' disables use of "
+                f"WARNING: '--db-preset {opts.db_preset}' disables use of "
                 + f"'--{(arg).replace('_', '-')}'.",
                 file=sys.stderr,
                 flush=True,

run_af2/src/run_af2/run_singularity.py

@@ -115,7 +115,7 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
     tmpdir,
     binds,
     use_gpu,
-    preset,
+    db_preset,
     data_paths,
 ):
     """Assemble the command to run AF2 from the Singularity image."""
@@ -147,7 +147,7 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
             f"--output_dir={snglrty_out}",
             f"--model_names={','.join(model_names)}",
             f"--max_template_date={max_template_date}",
-            f"--preset={preset}",
+            f"--db_preset={db_preset}",
             "--logtostderr",
         ]
     )
@@ -188,7 +188,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     max_template_date=None,
     model_names=None,
     use_gpu=False,
-    preset="full_dbs",
+    db_preset="full_dbs",
     af2_image_file=None,
     # "/export/soft/singularity-containers/alphafold",
     af2_image_dir="/scicore/home/schwede/GROUP/alphafold_data/",
@@ -236,11 +236,11 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     :type model_names: :class:`list` of :class:`str`
     :param use_gpu: Run the AF2 pipeline using GPUs or not.
     :type use_gpu: :class:`bool`
-    :param preset: Model configuration - no ensembling and smaller genetic
-                   databases (reduced_dbs), no ensembling and full genetic
-                   databases configuration (full_dbs). Corresponds to the preset
-                   parameter in AF2.
-    :type preset: :class:`str`
+    :param db_preset: Model configuration - no ensembling and smaller genetic
+                      databases (reduced_dbs), no ensembling and full genetic
+                      databases configuration (full_dbs). Corresponds to the
+                      preset parameter in AF2.
+    :type db_preset: :class:`str`
     :param af2_image_file: Declare a Singularity image to run the AF2 pipeline
                            from. If None, an image from af2_image_dir will be
                            used.
@@ -269,9 +269,10 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
                               bfd_database_path in AF2.
     :type bfd_database_path: :class:`str`
     :param small_bfd_database_path: Small BFD database path, used with
-                                    preset="reduced_dbs", not a HHblits prefix
-                                    as for the large BFD database. Corresponds to
-                                    small_bfd_database_path in AF2.
+                                    db_preset="reduced_dbs", not a HHblits
+                                    prefix as for the large BFD database.
+                                    Corresponds to small_bfd_database_path in
+                                    AF2.
     :type small_bfd_database_path: :class:`str`
     :param uniclust30_database_path: Uniclust30 database prefix. Corresponds to
                                      uniclust30_database_path in AF2.
@@ -298,9 +299,9 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     tmpdir = os.getenv(tmpdir_var)
     if tmpdir is None:
         raise ValueError(f"tmpdir_var {tmpdir_var} must not be empty.")
-    if preset not in ["full_dbs", "reduced_dbs"]:
+    if db_preset not in ["full_dbs", "reduced_dbs"]:
         raise ValueError(
-            f"preset {preset} not allowed, known values: "
+            f"db_preset {db_preset} not allowed, known values: "
             + "'full_dbs', 'reduced_dbs'"
         )
 
@@ -313,10 +314,10 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         "template_mmcif_dir": template_mmcif_dir,
         "obsolete_pdbs_path": obsolete_pdbs_path,
     }
-    if preset == "full_dbs":
+    if db_preset == "full_dbs":
         data_paths["bfd_database_path"] = bfd_database_path
         data_paths["uniclust30_database_path"] = uniclust30_database_path
-    elif preset == "reduced_dbs":
+    elif db_preset == "reduced_dbs":
         data_paths["small_bfd_database_path"] = small_bfd_database_path
 
     # Collect bind mountpoints for singularity, mountpoints for input data plus
@@ -344,7 +345,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         tmpdir,
         binds,
         use_gpu,
-        preset,
+        db_preset,
         data_paths,
     )
 
@@ -369,7 +370,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         if proc.returncode:
             raise RuntimeError(
                 "Singularity/ AF2 did not finish successfully, "
-                + "exit code: %d" % proc.returncode,
+                + f"exit code: {proc.returncode}",
                 proc.returncode,
             )
 
@@ -407,7 +408,7 @@ def main():
             opts.max_template_date,
             opts.model_names,
             opts.use_gpu,
-            opts.preset,
+            opts.db_preset,
             af2_image_file=opts.singularity_image,
             **data_paths,
         )