Changes to classification parameters for doppio

recipes/ispyb/em-spa-bfactor-wrapper.json

@@ -65,7 +65,6 @@
       "node_creator": 2
     },
     "parameters": {
-      "picker_id": "{picker_id}",
       "refined_class_uuid": "{refined_class_uuid}",
       "refined_grp_uuid": "{refined_grp_uuid}"
     },

recipes/ispyb/em-spa-class2d-wrapper.json

@@ -13,7 +13,6 @@
       "mpi_run_command": "srun -n 5",
       "particle_diameter": "{particle_diameter}",
       "particles_file": "{particles_file}",
-      "picker_id": "{picker_id}",
       "relion_options": {},
       "threads": 8
     },

recipes/ispyb/em-spa-class3d-wrapper.json

@@ -14,7 +14,6 @@
       "mpi_run_command": "srun -n 9",
       "particle_diameter": "{particle_diameter}",
       "particles_file": "{particles_file}",
-      "picker_id": "{picker_id}",
       "relion_options": {},
       "symmetry": "{symmetry}",
       "threads": 4

recipes/ispyb/em-spa-refine-wrapper.json

@@ -22,6 +22,7 @@
   "3": {
     "job_parameters": {
       "mask_diameter": "{mask_diameter}",
+      "mpi_run_command": "srun -n 5",
       "particle_diameter": "{particle_diameter}",
       "relion_options": {},
       "symmetry": "{symmetry}"
@@ -65,7 +66,6 @@
       "refine_wrapper": 7
     },
     "parameters": {
-      "picker_id": "{picker_id}",
       "refined_class_uuid": "{refined_class_uuid}",
       "refined_grp_uuid": "{refined_grp_uuid}"
     },
@@ -92,6 +92,7 @@
   "7": {
     "job_parameters": {
       "mask_diameter": "{mask_diameter}",
+      "mpi_run_command": "srun -n 5",
       "particle_diameter": "{particle_diameter}"
     },
     "output": {
@@ -134,7 +135,6 @@
       "node_creator": 2
     },
     "parameters": {
-      "picker_id": "{picker_id}",
       "refined_class_uuid": "{symmetry_refined_class_uuid}",
       "refined_grp_uuid": "{symmetry_refined_grp_uuid}"
     },

recipes/murfey/em-spa-bfactor.json

@@ -41,7 +41,6 @@
       "node_creator": 2
     },
     "parameters": {
-      "picker_id": "{picker_id}",
       "refined_class_uuid": "{refined_class_uuid}",
       "refined_grp_uuid": "{refined_grp_uuid}"
     },

recipes/murfey/em-spa-class2d.json

@@ -17,10 +17,8 @@
       "class_uuids": "{class_uuids}",
       "do_icebreaker_jobs": "False",
       "mask_diameter": "{mask_diameter}",
-      "mpi_run_command": "srun -n 5",
       "particle_diameter": "{particle_diameter}",
       "particles_file": "{particles_file}",
-      "picker_id": "{picker_id}",
       "relion_options": {},
       "threads": 8
     },

recipes/murfey/em-spa-class3d.json

@@ -16,10 +16,8 @@
       "initial_model_file": "{initial_model_file}",
       "initial_model_iterations": "{initial_model_iterations}",
       "mask_diameter": "{mask_diameter}",
-      "mpi_run_command": "srun -n 9",
       "particle_diameter": "{particle_diameter}",
       "particles_file": "{particles_file}",
-      "picker_id": "{picker_id}",
       "relion_options": {},
       "symmetry": "{symmetry}",
       "threads": 4

recipes/murfey/em-spa-refine.json

@@ -41,7 +41,6 @@
       "refine_wrapper": 7
     },
     "parameters": {
-      "picker_id": "{picker_id}",
       "refined_class_uuid": "{refined_class_uuid}",
       "refined_grp_uuid": "{refined_grp_uuid}"
     },
@@ -83,7 +82,6 @@
       "node_creator": 2
     },
     "parameters": {
-      "picker_id": "{picker_id}",
       "refined_class_uuid": "{symmetry_refined_class_uuid}",
       "refined_grp_uuid": "{symmetry_refined_grp_uuid}"
     },

src/cryoemservices/services/postprocess.py

@@ -35,7 +35,7 @@ class PostProcessParameters(BaseModel):
     postprocess_lowres: float = 10
     symmetry: str = "C1"
     particles_file: str = ""
-    picker_id: int
+    picker_id: int | None = None
     refined_grp_uuid: int
     refined_class_uuid: int
     relion_options: RelionServiceOptions

src/cryoemservices/wrappers/class2d_wrapper.py

@@ -6,7 +6,7 @@
 import re
 import subprocess
 from pathlib import Path
-from typing import Callable, Optional
+from typing import Callable
 
 import numpy as np
 from gemmi import cif
@@ -36,7 +36,7 @@ class Class2DParameters(BaseModel):
     vdam_final_fraction: float = 0.1
     dont_combine_weights_via_disc: bool = True
     preread_images: bool = True
-    scratch_dir: Optional[str] = None
+    scratch_dir: str | None = None
     nr_pool: int = 100
     pad: int = 2
     skip_gridding: bool = False
@@ -47,7 +47,7 @@ class Class2DParameters(BaseModel):
     class2d_nr_classes: int = 50
     flatten_solvent: bool = True
     do_zero_mask: bool = True
-    highres_limit: Optional[float] = None
+    highres_limit: float | None = None
     centre_classes: bool = True
     oversampling: int = 1
     skip_align: bool = False
@@ -57,10 +57,10 @@ class Class2DParameters(BaseModel):
     allow_coarser: bool = False
     do_norm: bool = True
     do_scale: bool = True
-    mpi_run_command: str = "srun -n 5"
+    mpi_run_command: str = "mpirun -n 5"
     threads: int = 8
     gpus: str = "0"
-    picker_id: int
+    picker_id: int | None = None
     class2d_grp_uuid: int
     class_uuids: str
     do_icebreaker_jobs: bool = True

src/cryoemservices/wrappers/class3d_wrapper.py

@@ -6,7 +6,7 @@
 import re
 import subprocess
 from pathlib import Path
-from typing import Callable, Optional, Tuple
+from typing import Callable, Tuple
 
 import numpy as np
 from gemmi import cif
@@ -50,14 +50,14 @@ class Class3DParameters(BaseModel):
     particle_diameter: float = 0
     mask_diameter: float = 190
     do_initial_model: bool = False
-    initial_model_file: Optional[str] = None
+    initial_model_file: str | None = None
     initial_model_iterations: int = 200
     initial_model_offset_range: float = 6
     initial_model_offset_step: float = 2
     start_initial_model_C1: bool = True
     dont_combine_weights_via_disc: bool = True
     preread_images: bool = True
-    scratch_dir: Optional[str] = None
+    scratch_dir: str | None = None
     nr_pool: int = 10
     pad: int = 2
     skip_gridding: bool = False
@@ -71,8 +71,8 @@ class Class3DParameters(BaseModel):
     class3d_nr_classes: int = 4
     flatten_solvent: bool = True
     do_zero_mask: bool = True
-    highres_limit: Optional[float] = None
-    fn_mask: Optional[str] = None
+    highres_limit: float | None = None
+    fn_mask: str | None = None
     oversampling: int = 1
     skip_align: bool = False
     healpix_order: int = 2
@@ -82,11 +82,11 @@ class Class3DParameters(BaseModel):
     symmetry: str = "C1"
     do_norm: bool = True
     do_scale: bool = True
-    mpi_run_command: str = "srun -n 5"
-    threads: int = 8
+    mpi_run_command: str = "mpirun -n 9"
+    threads: int = 4
     gpus: str = "0:1:2:3"
     initial_model_gpus: str = "0,1,2,3"
-    picker_id: int
+    picker_id: int | None = None
     class3d_grp_uuid: int
     class_uuids: str
     relion_options: RelionServiceOptions

src/cryoemservices/wrappers/refine3d_wrapper.py

@@ -68,7 +68,7 @@ class RefineParameters(BaseModel):
     mask_lowpass: float = 15
     mask_extend: int = 3
     mask_soft_edge: int = 3
-    mpi_run_command: str = "srun -n 5"
+    mpi_run_command: str = "mpirun -n 5"
     dont_correct_greyscale: bool = True
     initial_lowpass: float = 20.0
     dont_combine_weights_via_disc: bool = True

tests/services/test_class2d.py

@@ -330,7 +330,7 @@ def test_class2d_service_complete_batch(mock_subprocess, offline_transport, tmp_
 
     # Check the expected command was run
     class2d_command = [
-        "srun",
+        "mpirun",
         "-n",
         "5",
         "relion_refine_mpi",

tests/services/test_class3d.py

@@ -103,9 +103,9 @@ def test_class3d_service_has_initial_model(
     # Check the expected 3D classifcation command was run
     assert mock_subprocess.call_count == 4
     class3d_command = [
-        "srun",
+        "mpirun",
         "-n",
-        "5",
+        "9",
         "relion_refine_mpi",
         "--i",
         "Select/job013/particles_100000.star",
@@ -146,7 +146,7 @@ def test_class3d_service_has_initial_model(
         "--norm",
         "--scale",
         "--j",
-        "8",
+        "4",
         "--gpu",
         "0:1:2:3",
         "--pipeline_control",
@@ -282,6 +282,7 @@ def test_class3d_service_rerun(
                     "do_initial_model": False,
                     "initial_model_file": f"{tmp_path}/initial_model.mrc",
                     "mask_diameter": "190.0",
+                    "mpi_run_command": "srun -n 5",
                     "particle_diameter": "180",
                     "particles_file": f"{tmp_path}/Select/job013/particles_100000.star",
                     "picker_id": "6",
@@ -376,7 +377,7 @@ def test_class3d_service_rerun(
         "--norm",
         "--scale",
         "--j",
-        "8",
+        "4",
         "--gpu",
         "0:1:2:3",
         "--pipeline_control",

tests/wrappers/test_class2d_wrapper.py

@@ -352,7 +352,7 @@ def test_class2d_wrapper_complete_batch(
 
     # Check the expected command was run
     class2d_command = [
-        "srun",
+        "mpirun",
         "-n",
         "5",
         "relion_refine_mpi",

tests/wrappers/test_class3d_wrapper.py

@@ -499,9 +499,9 @@ def test_class3d_wrapper_has_initial_model(
     # Check the expected 3D classifcation command was run
     assert mock_subprocess.call_count == 4
     class3d_command = [
-        "srun",
+        "mpirun",
         "-n",
-        "5",
+        "9",
         "relion_refine_mpi",
         "--i",
         "Select/job013/particles_100000.star",
@@ -542,7 +542,7 @@ def test_class3d_wrapper_has_initial_model(
         "--norm",
         "--scale",
         "--j",
-        "8",
+        "4",
         "--gpu",
         "0:1:2:3",
         "--pipeline_control",

tests/wrappers/test_refine3d_wrapper.py

@@ -350,7 +350,7 @@ def test_refine3d_wrapper_no_mask(
     )
 
     refine3d_command = [
-        "srun",
+        "mpirun",
         "-n",
         "5",
         "relion_refine_mpi",