fix: 🐛 Fix predict_worker

janelia-cellmap · Mar 20, 2024 · 14c42db · 14c42db
1 parent 2400b1e
commit 14c42db
Show file tree

Hide file tree

Showing 3 changed files with 510 additions and 68 deletions.
diff --git a/dacapo/blockwise/predict_worker.py b/dacapo/blockwise/predict_worker.py
@@ -46,7 +46,7 @@ def cli(log_level):
 @click.option(
     "-i",
     "--iteration",
-    type=Optional[int],
+    type=int,
     help="The training iteration of the model to use for prediction.",
     default=None,
 )

diff --git a/dacapo/examples/distance_task/cosem_finetune_example.ipynb b/dacapo/examples/distance_task/cosem_finetune_example.ipynb
@@ -10,8 +10,7 @@
     "from dacapo.store.create_store import create_config_store\n",
     "\n",
     "config_store = create_config_store()\n",
-    "\n",
-    ""
+    "\n"
    ]
   },
   {
@@ -43,8 +42,7 @@
     "\n",
     "datasplit = datasplit_config.datasplit_type(datasplit_config)\n",
     "viewer = datasplit._neuroglancer()\n",
-    "config_store.store_datasplit_config(datasplit_config)\n",
-    ""
+    "config_store.store_datasplit_config(datasplit_config)\n"
    ]
   },
   {
@@ -73,8 +71,7 @@
     "    tol_distance=40.0,\n",
     "    scale_factor=80.0,\n",
     ")\n",
-    "config_store.store_task_config(task_config)\n",
-    ""
+    "config_store.store_task_config(task_config)\n"
    ]
   },
   {
@@ -106,8 +103,7 @@
     "    constant_upsample=True,\n",
     "    upsample_factors=[(2, 2, 2)],\n",
     ")\n",
-    "config_store.store_architecture_config(architecture_config)\n",
-    ""
+    "config_store.store_architecture_config(architecture_config)\n"
    ]
   },
   {
@@ -154,8 +150,7 @@
     "    min_masked=0.05,\n",
     "    clip_raw=True,\n",
     ")\n",
-    "config_store.store_trainer_config(trainer_config)\n",
-    ""
+    "config_store.store_trainer_config(trainer_config)\n"
    ]
   },
   {
@@ -173,7 +168,6 @@
    "outputs": [],
    "source": [
     "from dacapo.experiments import RunConfig\n",
-    "from dacapo.experiments.run import Run\n",
     "\n",
     "from dacapo.experiments.starts import CosemStartConfig\n",
     "\n",
@@ -199,8 +193,7 @@
     "    )\n",
     "\n",
     "    print(run_config.name)\n",
-    "    config_store.store_run_config(run_config)\n",
-    ""
+    "    config_store.store_run_config(run_config)\n"
    ]
   },
   {
@@ -225,8 +218,7 @@
     "config_store = create_config_store()\n",
     "\n",
     "run = Run(config_store.retrieve_run_config(\"cosem_distance_run_4nm_finetune\"))\n",
-    "train_run(run)\n",
-    ""
+    "train_run(run)\n"
    ]
   },
   {
@@ -237,8 +229,6 @@
    ]
   }
  ],
- "nbformat": 4,
- "nbformat_minor": 2,
  "metadata": {
   "language_info": {
    "codemirror_mode": {
@@ -252,5 +242,7 @@
    "pygments_lexer": "ipython3",
    "version": 3
   }
- }
-}
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}