Merge branch 'staging' into staging

.ci/steps/setup_step.yml

@@ -14,6 +14,7 @@ steps:
 
     # make sure we have the latest and greatest
     conda env create -f environment/anaconda/local/environment.yml python=3.6 --force
+    conda init bash
     source activate ${{parameters.conda}}
     pip install -e interpretation
     pip install -e cv_lib

examples/interpretation/notebooks/HRNet_Penobscot_demo_notebook.ipynb

@@ -166,12 +166,16 @@
    },
    "outputs": [],
    "source": [
-    "max_iterations = None  # The number of iterations you want to run in training or validation\n",
+    "# The number of datapoints you want to run in training or validation per batch \n",
     "# Setting to None will run whole dataset\n",
+    "# useful for integration tests with a setting of something like 3\n",
     "# Use only if you want to check things are running and don't want to run\n",
     "# through whole dataset\n",
-    "max_epochs = config.TRAIN.END_EPOCH  # The number of epochs to run in training\n",
-    "max_snapshots = config.TRAIN.SNAPSHOTS"
+    "max_iterations = None  \n",
+    "# The number of epochs to run in training\n",
+    "max_epochs = config.TRAIN.END_EPOCH  \n",
+    "max_snapshots = config.TRAIN.SNAPSHOTS\n",
+    "dataset_root = config.DATASET.ROOT"
    ]
   },
   {
@@ -199,8 +203,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "image_dir = os.path.join(config.DATASET.ROOT, \"inlines\")\n",
-    "mask_dir = os.path.join(config.DATASET.ROOT, \"masks\")\n",
+    "image_dir = os.path.join(dataset_root, \"inlines\")\n",
+    "mask_dir = os.path.join(dataset_root, \"masks\")\n",
     "\n",
     "image_iter = pipe(os.path.join(image_dir, \"*.tiff\"), glob.iglob,)\n",
     "\n",
@@ -360,7 +364,7 @@
    "outputs": [],
    "source": [
     "train_set = PenobscotInlinePatchDataset(\n",
-    "    config.DATASET.ROOT,\n",
+    "    dataset_root,\n",
     "    config.TRAIN.PATCH_SIZE,\n",
     "    config.TRAIN.STRIDE,\n",
     "    split=\"train\",\n",
@@ -370,7 +374,7 @@
     ")\n",
     "\n",
     "val_set = PenobscotInlinePatchDataset(\n",
-    "    config.DATASET.ROOT,\n",
+    "    dataset_root,\n",
     "    config.TRAIN.PATCH_SIZE,\n",
     "    config.TRAIN.STRIDE,\n",
     "    split=\"val\",\n",
@@ -593,7 +597,7 @@
    "outputs": [],
    "source": [
     "logger.info(\"Starting training\")\n",
-    "trainer.run(train_loader, max_epochs=config.TRAIN.END_EPOCH)"
+    "trainer.run(train_loader, max_epochs=max_epochs)"
    ]
   },
   {
@@ -610,7 +614,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%load_ext tensorboard"
+    "if max_epochs>1:\n",
+    "    %load_ext tensorboard"
    ]
   },
   {
@@ -619,7 +624,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%tensorboard --logdir outputs --port 6007 --host 0.0.0.0"
+    "if max_epochs>1:\n",
+    "    %tensorboard --logdir outputs --port 6007 --host 0.0.0.0"
    ]
   }
  ],