Remove code migrated into Hoplite repository.

agile_modeling.ipynb

@@ -59,16 +59,15 @@
     "\n",
     "from chirp import audio_utils\n",
     "from chirp.inference import baw_utils\n",
-    "from chirp.inference import tf_examples\n",
     "from chirp.models import metrics\n",
-    "from chirp.taxonomy import namespace\n",
+    "from hoplite.taxonomy import namespace\n",
     "from chirp.inference.search import bootstrap\n",
     "from chirp.inference.search import search\n",
     "from chirp.inference.search import display\n",
     "from chirp.inference.classify import classify\n",
     "from chirp.inference.classify import data_lib\n",
-    "from chirp.projects.zoo import model_configs\n",
-    "from chirp.projects.zoo import zoo_interface\n"
+    "from hoplite.zoo import model_configs\n",
+    "from hoplite.zoo import zoo_interface\n"
    ]
   },
   {

analysis.ipynb

@@ -56,7 +56,7 @@
     "from chirp.inference.search import search\n",
     "from chirp.inference.search import display\n",
     "from chirp.inference.classify import classify\n",
-    "from chirp.projects.zoo import zoo_interface\n"
+    "from hoplite.zoo import zoo_interface\n"
    ]
   },
   {

chirp/configs/config_globals.py

@@ -14,6 +14,7 @@
 # limitations under the License.
 
 """Define the globals that can be used in configuration files."""
+
 from typing import Any
 
 from chirp import audio_utils

chirp/data/bird_taxonomy/bird_taxonomy.py

@@ -26,8 +26,8 @@
 from chirp.data import filter_scrub_utils as fsu
 from chirp.data import tfds_features
 from chirp.data.bird_taxonomy import premade_queries
-from chirp.taxonomy import namespace_db
 from etils import epath
+from hoplite.taxonomy import namespace_db
 import jax
 from jax import numpy as jnp
 import numpy as np

chirp/data/bird_taxonomy/premade_queries.py

@@ -16,7 +16,7 @@
 """A set of premade queries to generate stable data configs."""
 
 from chirp.data import filter_scrub_utils as fsu
-from chirp.taxonomy import namespace_db
+from hoplite.taxonomy import namespace_db
 
 # SSW_STATS_PATH contains useful statistics for SSW species, used to guide our
 # DFS search in chirp.data.sampling_utils.sample_recordings_under_constraints.

chirp/data/filter_scrub_utils.py

@@ -19,7 +19,7 @@
 from typing import Any, Dict, NamedTuple, Sequence, Union
 
 from chirp.data import sampling_utils as su
-from chirp.taxonomy import namespace_db
+from hoplite.taxonomy import namespace_db
 import numpy as np
 import pandas as pd
 

chirp/data/soundevents/soundevents.py

@@ -24,8 +24,8 @@
 from chirp import audio_utils
 from chirp.data import filter_scrub_utils as fsu
 from chirp.data import tfds_features
-from chirp.taxonomy import namespace_db
 from etils import epath
+from hoplite.taxonomy import namespace_db
 from jax import numpy as jnp
 import numpy as np
 import pandas as pd

chirp/data/soundscapes/soundscapes.py

@@ -25,8 +25,8 @@
 from chirp.data import tfds_features
 from chirp.data.bird_taxonomy import bird_taxonomy
 from chirp.data.soundscapes import soundscapes_lib
-from chirp.taxonomy import annotations_fns
 from etils import epath
+from hoplite.taxonomy import annotations_fns
 import numpy as np
 import pandas as pd
 import tensorflow as tf

chirp/data/soundscapes/soundscapes_lib.py

@@ -20,9 +20,9 @@
 from typing import Any, Callable, Iterator, Set
 
 from absl import logging
-from chirp.taxonomy import namespace
-from chirp.taxonomy import namespace_db
 from etils import epath
+from hoplite.taxonomy import namespace
+from hoplite.taxonomy import namespace_db
 from jax import numpy as jnp
 import numpy as np
 import pandas as pd

chirp/eval/callbacks.py

@@ -20,15 +20,15 @@
 
 from absl import logging
 from chirp.eval import eval_lib
-from chirp.projects.zoo import model_configs
-from chirp.projects.zoo import zoo_interface
-from chirp.taxonomy import namespace
-from chirp.taxonomy import namespace_db
 from chirp.train import classifier
 from chirp.train import hubert
 from chirp.train import separator
 from clu import checkpoint
 from etils import epath
+from hoplite.taxonomy import namespace
+from hoplite.taxonomy import namespace_db
+from hoplite.zoo import model_configs
+from hoplite.zoo import zoo_interface
 import jax
 from jax import numpy as jnp
 import ml_collections
@@ -142,13 +142,11 @@ def fprop(inputs):
 
       head_index = list(model_bundle.model.num_classes.keys()).index('label')
       output_weights = train_state.params[f'Dense_{head_index}']['kernel'].T
-      self.learned_representations.update(
-          {
-              n: w
-              for n, w in zip(class_list.classes, output_weights)
-              if n not in self.learned_representation_blocklist
-          }
-      )
+      self.learned_representations.update({
+          n: w
+          for n, w in zip(class_list.classes, output_weights)
+          if n not in self.learned_representation_blocklist
+      })
 
   def __call__(self, inputs: np.ndarray) -> np.ndarray:
     return np.asarray(self.model_callback(inputs))
@@ -200,13 +198,11 @@ def _load_learned_representations(self):
     else:
       output_weights = tf.train.load_variable(variables_path, candidates[0])
       output_weights = np.squeeze(output_weights)
-    self.learned_representations.update(
-        {
-            n: w
-            for n, w in zip(class_list.classes, output_weights)
-            if n not in self.learned_representation_blocklist
-        }
-    )
+    self.learned_representations.update({
+        n: w
+        for n, w in zip(class_list.classes, output_weights)
+        if n not in self.learned_representation_blocklist
+    })
 
   def __post_init__(self):
     logging.info('Loading separation model...')
@@ -273,7 +269,7 @@ class EmbeddingModelCallback:
 
   def __post_init__(self):
     logging.info('Loading separation model...')
-    model_class = model_configs.MODEL_CLASS_MAP[self.model_key]
+    model_class = model_configs.get_model_class(self.model_key)
     self.loaded_model = model_class(**self.model_config)
     # Set the object's call method as the model_callback.
     self.model_callback = self.__call__

chirp/eval/eval_lib.py

@@ -23,7 +23,7 @@
 from absl import logging
 from chirp.data import utils as data_utils
 from chirp.models import metrics
-from chirp.taxonomy import namespace_db
+from hoplite.taxonomy import namespace_db
 import jax
 import ml_collections
 import numpy as np

chirp/export_utils.py

@@ -19,7 +19,7 @@
 from typing import Sequence
 
 from absl import logging
-from chirp.taxonomy import namespace
+from hoplite.taxonomy import namespace
 from jax.experimental import jax2tf
 import tensorflow as tf
 

chirp/inference/classify/classify.py

@@ -21,7 +21,7 @@
 from chirp.inference import tf_examples
 from chirp.inference.classify import data_lib
 from chirp.models import metrics
-from chirp.projects.zoo import zoo_interface
+from hoplite.zoo import zoo_interface
 import numpy as np
 import tensorflow as tf
 import tqdm

chirp/inference/classify/data_lib.py

@@ -34,8 +34,8 @@
 
 from chirp import audio_utils
 from chirp.inference import tf_examples
-from chirp.projects.zoo import zoo_interface
 from etils import epath
+from hoplite.zoo import zoo_interface
 import numpy as np
 import tensorflow as tf
 import tqdm

chirp/inference/embed_lib.py

@@ -27,9 +27,9 @@
 from chirp import audio_utils
 from chirp import path_utils
 from chirp.inference import tf_examples
-from chirp.projects.zoo import model_configs
-from chirp.projects.zoo import zoo_interface
 from etils import epath
+from hoplite.zoo import model_configs
+from hoplite.zoo import zoo_interface
 from ml_collections import config_dict
 import numpy as np
 import soundfile
@@ -223,7 +223,7 @@ def __init__(
 
   def setup(self):
     if self.embedding_model is None:
-      model_class = model_configs.MODEL_CLASS_MAP[self.model_key]
+      model_class = model_configs.get_model_class(self.model_key)
       self.embedding_model = model_class.from_config(self.model_config)
     if hasattr(self, 'model_key'):
       del self.model_key

chirp/inference/scann_search_lib.py

@@ -22,8 +22,8 @@
 from chirp import audio_utils
 from chirp.inference import embed_lib
 from chirp.inference import tf_examples
-from chirp.projects.zoo import taxonomy_model_tf
 from etils import epath
+from hoplite.zoo import taxonomy_model_tf
 from ml_collections import config_dict
 import numpy as np
 import tensorflow as tf

chirp/inference/search/bootstrap.py

@@ -25,9 +25,9 @@
 from chirp.inference import embed_lib
 from chirp.inference import tf_examples
 from chirp.inference.search import search
-from chirp.projects.zoo import model_configs
-from chirp.projects.zoo import zoo_interface
 from etils import epath
+from hoplite.zoo import model_configs
+from hoplite.zoo import zoo_interface
 from ml_collections import config_dict
 import tensorflow as tf
 
@@ -52,9 +52,9 @@ class BootstrapState:
 
   def __post_init__(self):
     if self.embedding_model is None:
-      self.embedding_model = model_configs.MODEL_CLASS_MAP[
+      self.embedding_model = model_configs.get_model_class(
           self.config.model_key
-      ].from_config(self.config.model_config)
+      ).from_config(self.config.model_config)
     self.create_embeddings_dataset()
     if self.source_map is None:
       if self.baw_auth_token:

chirp/inference/search/search.py

@@ -22,8 +22,8 @@
 from typing import Any, Callable, List, Sequence
 
 from chirp.inference import tf_examples
-from chirp.projects.zoo import zoo_interface
 from etils import epath
+from hoplite.zoo import zoo_interface
 import numpy as np
 from scipy.io import wavfile
 import tensorflow as tf

chirp/inference/tests/classify_test.py

@@ -19,8 +19,8 @@
 
 from chirp.inference.classify import classify
 from chirp.inference.classify import data_lib
-from chirp.projects.zoo import zoo_interface
-from chirp.taxonomy import namespace
+from hoplite.taxonomy import namespace
+from hoplite.zoo import zoo_interface
 import numpy as np
 
 from absl.testing import absltest

chirp/inference/tests/embed_test.py

@@ -32,15 +32,13 @@
 from chirp.inference.search import display
 from chirp.inference.search import search
 from chirp.models import metrics
-from chirp.projects.zoo import models
-from chirp.projects.zoo import taxonomy_model_tf
-from chirp.projects.zoo import zoo_interface
-from chirp.taxonomy import namespace
 from etils import epath
-from ml_collections import config_dict
+from hoplite.taxonomy import namespace
+from hoplite.zoo import handcrafted_features_model
+from hoplite.zoo import placeholder_model
+from hoplite.zoo import zoo_interface
 import numpy as np
 import tensorflow as tf
-import tf_keras
 
 from absl.testing import absltest
 from absl.testing import parameterized
@@ -332,7 +330,7 @@ def test_keyed_write_logits(self):
     self.assertEqual(got_example['label'].shape, (0,))
 
   def test_logits_output_head(self):
-    base_model = models.PlaceholderModel(
+    base_model = placeholder_model.PlaceholderModel(
         sample_rate=22050,
         make_embeddings=True,
         make_logits=False,
@@ -566,11 +564,11 @@ def test_load_configs(self, config_name):
     self.assertIsNotNone(config)
 
   def test_handcrafted_features(self):
-    model = models.HandcraftedFeaturesModel.beans_baseline()
+    model = handcrafted_features_model.HandcraftedFeaturesModel.beans_baseline()
 
     audio = np.zeros([5 * 32000], dtype=np.float32)
     outputs = model.embed(audio)
-    # Five frames because we have 5s of audio with window 1.0 and hope 1.0.
+    # Five frames because we have 5s of audio with window 1.0 and hop 1.0.
     # Beans aggrregation with mfccs creates 20 MFCC channels, and then computes
     # four summary statistics for each, giving a total of 80 output channels.
     self.assertSequenceEqual([5, 1, 80], outputs.embeddings.shape)
@@ -603,15 +601,15 @@ def test_beam_pipeline(self):
         file_id_depth=0,
     )
 
-    metrics = embed_lib.build_run_pipeline(
+    run_metrics = embed_lib.build_run_pipeline(
         base_pipeline, output_dir, source_infos, embed_fn
     )
-    counter = metrics.query(
+    counter = run_metrics.query(
         beam.metrics.MetricsFilter().with_name('examples_processed')
     )['counters']
     self.assertEqual(counter[0].result, 1)
 
-    print(metrics)
+    print(run_metrics)
 
 
 if __name__ == '__main__':

chirp/inference/tf_examples.py

@@ -20,8 +20,8 @@
 import os
 from typing import Sequence
 
-from chirp.projects.zoo import zoo_interface
 from etils import epath
+from hoplite.zoo import zoo_interface
 import numpy as np
 import tensorflow as tf
 

chirp/preprocessing/pipeline.py

@@ -21,8 +21,8 @@
 from absl import logging
 from chirp import audio_utils
 from chirp.models import frontend
-from chirp.taxonomy import namespace
-from chirp.taxonomy import namespace_db
+from hoplite.taxonomy import namespace
+from hoplite.taxonomy import namespace_db
 import jax
 from jax import numpy as jnp
 import pandas as pd