From 12c322d597395e463904060dce68938c8e5a5889 Mon Sep 17 00:00:00 2001 From: Tom Denton Date: Wed, 8 Jan 2025 13:51:19 -0800 Subject: [PATCH] Test PR. PiperOrigin-RevId: 713405276 --- .github/workflows/ci_pip.yml | 12 +- .github/workflows/ci_poetry.yml | 10 +- .github/workflows/ci_poetry_with_jax.yml | 12 +- README.md | 7 +- .../agile/1_embed_audio_v2.ipynb | 14 +- .../agile/2_agile_modeling_v2.ipynb | 20 +- .../agile/audio_loader.py | 4 +- .../agile/classifier.py | 6 +- .../agile/classifier_data.py | 2 +- .../agile/colab_utils.py | 10 +- .../agile/convert_legacy.py | 12 +- {hoplite => perch_hoplite}/agile/embed.py | 10 +- .../agile/embedding_display.py | 6 +- .../agile/ingest_annotations.py | 10 +- {hoplite => perch_hoplite}/agile/metrics.py | 0 .../agile/source_info.py | 2 +- .../agile/tests/classifier_data_test.py | 6 +- .../agile/tests/classifier_test.py | 6 +- .../agile/tests/convert_legacy_test.py | 10 +- .../agile/tests/embed_test.py | 8 +- .../agile/tests/embedding_display_test.py | 10 +- .../agile/tests/ingest_annotations_test.py | 16 +- .../agile/tests/metrics_test.py | 2 +- .../agile/tests/source_info_test.py | 4 +- .../agile/tests/test_utils.py | 0 .../agile/tests/testdata/config.json | 0 .../embeddings-1730850444-00000-of-00001 | Bin .../agile/tests/testdata/hawaii.csv | 0 {hoplite => perch_hoplite}/audio_io.py | 2 +- {hoplite => perch_hoplite}/db/README.md | 0 {hoplite => perch_hoplite}/db/brutalism.py | 4 +- {hoplite => perch_hoplite}/db/db_loader.py | 6 +- {hoplite => perch_hoplite}/db/in_mem_impl.py | 2 +- {hoplite => perch_hoplite}/db/interface.py | 0 .../db/score_functions.py | 0 .../db/search_results.py | 0 .../db/sqlite_usearch_impl.py | 11 +- .../db/tests/brutalism_test.py | 4 +- .../db/tests/hoplite_test.py | 6 +- .../db/tests/test_utils.py | 6 +- {hoplite => perch_hoplite}/path_utils.py | 0 {hoplite => perch_hoplite}/taxonomy/README.md | 0 .../taxonomy/annotations.py | 0 .../taxonomy/annotations_fns.py | 4 +- .../taxonomy/class_utils.py | 2 +- {hoplite => perch_hoplite}/taxonomy/ebird.py | 4 +- .../taxonomy/namespace.py | 0 .../taxonomy/namespace_db.py | 4 +- .../taxonomy/namespace_db_test.py | 4 +- .../taxonomy/taxonomy_database.json | 0 {hoplite => perch_hoplite}/zoo/README.md | 0 {hoplite => perch_hoplite}/zoo/aves_model.py | 2 +- .../zoo/handcrafted_features_model.py | 2 +- .../zoo/model_configs.py | 24 +- {hoplite => perch_hoplite}/zoo/models_tf.py | 10 +- .../zoo/placeholder_model.py | 4 +- .../zoo/taxonomy_model_tf.py | 4 +- .../zoo/tests_tf/tf_test.py | 8 +- .../zoo/zoo_interface.py | 2 +- {hoplite => perch_hoplite}/zoo/zoo_test.py | 4 +- poetry.lock | 1775 ++++++++++------- pyproject.toml | 2 +- 62 files changed, 1234 insertions(+), 861 deletions(-) rename {hoplite => perch_hoplite}/agile/1_embed_audio_v2.ipynb (95%) rename {hoplite => perch_hoplite}/agile/2_agile_modeling_v2.ipynb (95%) rename {hoplite => perch_hoplite}/agile/audio_loader.py (96%) rename {hoplite => perch_hoplite}/agile/classifier.py (98%) rename {hoplite => perch_hoplite}/agile/classifier_data.py (99%) rename {hoplite => perch_hoplite}/agile/colab_utils.py (93%) rename {hoplite => perch_hoplite}/agile/convert_legacy.py (97%) rename {hoplite => perch_hoplite}/agile/embed.py (97%) rename {hoplite => perch_hoplite}/agile/embedding_display.py (99%) rename {hoplite => perch_hoplite}/agile/ingest_annotations.py (97%) rename {hoplite => perch_hoplite}/agile/metrics.py (100%) rename {hoplite => perch_hoplite}/agile/source_info.py (99%) rename {hoplite => perch_hoplite}/agile/tests/classifier_data_test.py (98%) rename {hoplite => perch_hoplite}/agile/tests/classifier_test.py (97%) rename {hoplite => perch_hoplite}/agile/tests/convert_legacy_test.py (96%) rename {hoplite => perch_hoplite}/agile/tests/embed_test.py (94%) rename {hoplite => perch_hoplite}/agile/tests/embedding_display_test.py (96%) rename {hoplite => perch_hoplite}/agile/tests/ingest_annotations_test.py (93%) rename {hoplite => perch_hoplite}/agile/tests/metrics_test.py (96%) rename {hoplite => perch_hoplite}/agile/tests/source_info_test.py (98%) rename {hoplite => perch_hoplite}/agile/tests/test_utils.py (100%) rename {hoplite => perch_hoplite}/agile/tests/testdata/config.json (100%) rename {hoplite => perch_hoplite}/agile/tests/testdata/embeddings-1730850444-00000-of-00001 (100%) rename {hoplite => perch_hoplite}/agile/tests/testdata/hawaii.csv (100%) rename {hoplite => perch_hoplite}/audio_io.py (99%) rename {hoplite => perch_hoplite}/db/README.md (100%) rename {hoplite => perch_hoplite}/db/brutalism.py (98%) rename {hoplite => perch_hoplite}/db/db_loader.py (96%) rename {hoplite => perch_hoplite}/db/in_mem_impl.py (99%) rename {hoplite => perch_hoplite}/db/interface.py (100%) rename {hoplite => perch_hoplite}/db/score_functions.py (100%) rename {hoplite => perch_hoplite}/db/search_results.py (100%) rename {hoplite => perch_hoplite}/db/sqlite_usearch_impl.py (99%) rename {hoplite => perch_hoplite}/db/tests/brutalism_test.py (96%) rename {hoplite => perch_hoplite}/db/tests/hoplite_test.py (98%) rename {hoplite => perch_hoplite}/db/tests/test_utils.py (96%) rename {hoplite => perch_hoplite}/path_utils.py (100%) rename {hoplite => perch_hoplite}/taxonomy/README.md (100%) rename {hoplite => perch_hoplite}/taxonomy/annotations.py (100%) rename {hoplite => perch_hoplite}/taxonomy/annotations_fns.py (98%) rename {hoplite => perch_hoplite}/taxonomy/class_utils.py (96%) rename {hoplite => perch_hoplite}/taxonomy/ebird.py (98%) rename {hoplite => perch_hoplite}/taxonomy/namespace.py (100%) rename {hoplite => perch_hoplite}/taxonomy/namespace_db.py (98%) rename {hoplite => perch_hoplite}/taxonomy/namespace_db_test.py (99%) rename {hoplite => perch_hoplite}/taxonomy/taxonomy_database.json (100%) rename {hoplite => perch_hoplite}/zoo/README.md (100%) rename {hoplite => perch_hoplite}/zoo/aves_model.py (98%) rename {hoplite => perch_hoplite}/zoo/handcrafted_features_model.py (99%) rename {hoplite => perch_hoplite}/zoo/model_configs.py (90%) rename {hoplite => perch_hoplite}/zoo/models_tf.py (98%) rename {hoplite => perch_hoplite}/zoo/placeholder_model.py (96%) rename {hoplite => perch_hoplite}/zoo/taxonomy_model_tf.py (99%) rename {hoplite => perch_hoplite}/zoo/tests_tf/tf_test.py (98%) rename {hoplite => perch_hoplite}/zoo/zoo_interface.py (99%) rename {hoplite => perch_hoplite}/zoo/zoo_test.py (97%) diff --git a/.github/workflows/ci_pip.yml b/.github/workflows/ci_pip.yml index 67b6e44..d420cdf 100644 --- a/.github/workflows/ci_pip.yml +++ b/.github/workflows/ci_pip.yml @@ -30,14 +30,14 @@ jobs: pip install requests pip install tensorflow-cpu pip install tensorflow-hub - pip install git+https://github.com/google-research/hoplite.git + pip install git+https://github.com/google-research/perch-hoplite.git - name: Test db with unittest - run: python -m unittest discover -s hoplite/db/tests -p "*test.py" + run: python -m unittest discover -s perch_hoplite/db/tests -p "*test.py" - name: Test taxonomy with unittest - run: python -m unittest discover -s hoplite/taxonomy -p "*test.py" + run: python -m unittest discover -s perch_hoplite/taxonomy -p "*test.py" - name: Test zoo with unittest - run: python -m unittest discover -s hoplite/zoo -p "*test.py" + run: python -m unittest discover -s perch_hoplite/zoo -p "*test.py" - name: Test zoo tensorflow models with unittest - run: python -m unittest discover -s hoplite/zoo/tests_tf -p "*test.py" + run: python -m unittest discover -s perch_hoplite/zoo/tests_tf -p "*test.py" - name: Test agile with unittest - run: python -m unittest discover -s hoplite/agile/tests -p "*test.py" + run: python -m unittest discover -s perch_hoplite/agile/tests -p "*test.py" diff --git a/.github/workflows/ci_poetry.yml b/.github/workflows/ci_poetry.yml index cfdad04..7c5f8a4 100644 --- a/.github/workflows/ci_poetry.yml +++ b/.github/workflows/ci_poetry.yml @@ -31,12 +31,12 @@ jobs: sudo apt-get install libsndfile1 ffmpeg poetry install - name: Test db with unittest - run: poetry run python -m unittest discover -s hoplite/db/tests -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/db/tests -p "*test.py" - name: Test taxonomy with unittest - run: poetry run python -m unittest discover -s hoplite/taxonomy -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/taxonomy -p "*test.py" - name: Test zoo with unittest - run: poetry run python -m unittest discover -s hoplite/zoo -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/zoo -p "*test.py" - name: Test zoo tensorflow models with unittest - run: poetry run python -m unittest discover -s hoplite/zoo/tests_tf -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/zoo/tests_tf -p "*test.py" - name: Test agile with unittest - run: poetry run python -m unittest discover -s hoplite/agile/tests -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/agile/tests -p "*test.py" diff --git a/.github/workflows/ci_poetry_with_jax.yml b/.github/workflows/ci_poetry_with_jax.yml index 4b05caf..7d0abe6 100644 --- a/.github/workflows/ci_poetry_with_jax.yml +++ b/.github/workflows/ci_poetry_with_jax.yml @@ -1,4 +1,4 @@ -name: ci_poetry +name: ci_poetry_with_jax on: push: @@ -31,12 +31,12 @@ jobs: sudo apt-get install libsndfile1 ffmpeg poetry install --with jax - name: Test db with unittest - run: poetry run python -m unittest discover -s hoplite/db/tests -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/db/tests -p "*test.py" - name: Test taxonomy with unittest - run: poetry run python -m unittest discover -s hoplite/taxonomy -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/taxonomy -p "*test.py" - name: Test zoo with unittest - run: poetry run python -m unittest discover -s hoplite/zoo -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/zoo -p "*test.py" - name: Test zoo tensorflow models with unittest - run: poetry run python -m unittest discover -s hoplite/zoo/tests_tf -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/zoo/tests_tf -p "*test.py" - name: Test agile with unittest - run: poetry run python -m unittest discover -s hoplite/agile/tests -p "*test.py" + run: poetry run python -m unittest discover -s perch_hoplite/agile/tests -p "*test.py" diff --git a/README.md b/README.md index 8fda5c3..6e53019 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,14 @@ # Perch Hoplite -![CI](https://github.com/google-research/hoplite/actions/workflows/ci_pip.yml/badge.svg) +![CI](https://github.com/google-research/perch-hoplite/actions/workflows/ci_pip.yml/badge.svg) Hoplite is a system for storing large volumes of embeddings from machine perception models. We focus on combining vector search with active learning workflows, aka [agile modeling](https://arxiv.org/abs/2302.12948). While we get this documentation ready, we recommend checking out the main -[Perch repository](https://github.com/google-research/perch). +[Perch repository](https://github.com/google-research/perch), which includes +embedding model training code. This repository consists of four sub-libraries: @@ -47,7 +48,7 @@ pip install tensorflow-hub Then to install with pip: ```bash -pip install git+https://github.com/google-research/hoplite.git +pip install git+https://github.com/google-research/perch-hoplite.git ``` Then run the tests and check that they pass: diff --git a/hoplite/agile/1_embed_audio_v2.ipynb b/perch_hoplite/agile/1_embed_audio_v2.ipynb similarity index 95% rename from hoplite/agile/1_embed_audio_v2.ipynb rename to perch_hoplite/agile/1_embed_audio_v2.ipynb index e0addf3..e7f7025 100644 --- a/hoplite/agile/1_embed_audio_v2.ipynb +++ b/perch_hoplite/agile/1_embed_audio_v2.ipynb @@ -14,13 +14,13 @@ "import numpy as np\n", "from etils import epath\n", "\n", - "from hoplite.agile import colab_utils\n", - "from hoplite.agile import embed\n", - "from hoplite.agile import source_info\n", - "from hoplite.db import interface\n", - "from hoplite.db import brutalism\n", - "from hoplite.db import db_loader\n", - "from hoplite.db import sqlite_usearch_impl\n" + "from perch_hoplite.agile import colab_utils\n", + "from perch_hoplite.agile import embed\n", + "from perch_hoplite.agile import source_info\n", + "from perch_hoplite.db import interface\n", + "from perch_hoplite.db import brutalism\n", + "from perch_hoplite.db import db_loader\n", + "from perch_hoplite.db import sqlite_usearch_impl\n" ] }, { diff --git a/hoplite/agile/2_agile_modeling_v2.ipynb b/perch_hoplite/agile/2_agile_modeling_v2.ipynb similarity index 95% rename from hoplite/agile/2_agile_modeling_v2.ipynb rename to perch_hoplite/agile/2_agile_modeling_v2.ipynb index ad6960d..8d4feaf 100644 --- a/hoplite/agile/2_agile_modeling_v2.ipynb +++ b/perch_hoplite/agile/2_agile_modeling_v2.ipynb @@ -15,16 +15,16 @@ "from matplotlib import pyplot as plt\n", "import numpy as np\n", "\n", - "from hoplite.agile import audio_loader\n", - "from hoplite.agile import classifier\n", - "from hoplite.agile import classifier_data\n", - "from hoplite.agile import embedding_display\n", - "from hoplite.agile import source_info\n", - "from hoplite.db import brutalism\n", - "from hoplite.db import score_functions\n", - "from hoplite.db import search_results\n", - "from hoplite.db import sqlite_usearch_impl\n", - "from hoplite.zoo import model_configs\n" + "from perch_hoplite.agile import audio_loader\n", + "from perch_hoplite.agile import classifier\n", + "from perch_hoplite.agile import classifier_data\n", + "from perch_hoplite.agile import embedding_display\n", + "from perch_hoplite.agile import source_info\n", + "from perch_hoplite.db import brutalism\n", + "from perch_hoplite.db import score_functions\n", + "from perch_hoplite.db import search_results\n", + "from perch_hoplite.db import sqlite_usearch_impl\n", + "from perch_hoplite.zoo import model_configs\n" ] }, { diff --git a/hoplite/agile/audio_loader.py b/perch_hoplite/agile/audio_loader.py similarity index 96% rename from hoplite/agile/audio_loader.py rename to perch_hoplite/agile/audio_loader.py index 365fd92..d4dcf4a 100644 --- a/hoplite/agile/audio_loader.py +++ b/perch_hoplite/agile/audio_loader.py @@ -19,9 +19,9 @@ from typing import Callable from etils import epath -from hoplite import audio_io -from hoplite.agile import source_info import numpy as np +from perch_hoplite import audio_io +from perch_hoplite.agile import source_info def make_filepath_loader( diff --git a/hoplite/agile/classifier.py b/perch_hoplite/agile/classifier.py similarity index 98% rename from hoplite/agile/classifier.py rename to perch_hoplite/agile/classifier.py index 1db9302..c9c0d30 100644 --- a/hoplite/agile/classifier.py +++ b/perch_hoplite/agile/classifier.py @@ -22,11 +22,11 @@ from typing import Any, Iterator, Sequence from etils import epath -from hoplite.agile import classifier_data -from hoplite.agile import metrics -from hoplite.db import interface as db_interface from ml_collections import config_dict import numpy as np +from perch_hoplite.agile import classifier_data +from perch_hoplite.agile import metrics +from perch_hoplite.db import interface as db_interface import tensorflow as tf import tqdm diff --git a/hoplite/agile/classifier_data.py b/perch_hoplite/agile/classifier_data.py similarity index 99% rename from hoplite/agile/classifier_data.py rename to perch_hoplite/agile/classifier_data.py index 061e8e8..a08eaf3 100644 --- a/hoplite/agile/classifier_data.py +++ b/perch_hoplite/agile/classifier_data.py @@ -19,8 +19,8 @@ import itertools from typing import Any, Iterator, Sequence -from hoplite.db import interface import numpy as np +from perch_hoplite.db import interface @dataclasses.dataclass diff --git a/hoplite/agile/colab_utils.py b/perch_hoplite/agile/colab_utils.py similarity index 93% rename from hoplite/agile/colab_utils.py rename to perch_hoplite/agile/colab_utils.py index 5acff51..873cb6d 100644 --- a/hoplite/agile/colab_utils.py +++ b/perch_hoplite/agile/colab_utils.py @@ -18,12 +18,12 @@ import dataclasses from etils import epath -from hoplite.agile import embed -from hoplite.agile import source_info -from hoplite.db import db_loader -from hoplite.db import sqlite_usearch_impl -from hoplite.zoo import model_configs from ml_collections import config_dict +from perch_hoplite.agile import embed +from perch_hoplite.agile import source_info +from perch_hoplite.db import db_loader +from perch_hoplite.db import sqlite_usearch_impl +from perch_hoplite.zoo import model_configs @dataclasses.dataclass diff --git a/hoplite/agile/convert_legacy.py b/perch_hoplite/agile/convert_legacy.py similarity index 97% rename from hoplite/agile/convert_legacy.py rename to perch_hoplite/agile/convert_legacy.py index a7d9b31..711cb4b 100644 --- a/hoplite/agile/convert_legacy.py +++ b/perch_hoplite/agile/convert_legacy.py @@ -19,14 +19,14 @@ from typing import Sequence from etils import epath -from hoplite.agile import embed -from hoplite.agile import source_info -from hoplite.db import db_loader -from hoplite.db import in_mem_impl -from hoplite.db import interface -from hoplite.db import sqlite_usearch_impl from ml_collections import config_dict import numpy as np +from perch_hoplite.agile import embed +from perch_hoplite.agile import source_info +from perch_hoplite.db import db_loader +from perch_hoplite.db import in_mem_impl +from perch_hoplite.db import interface +from perch_hoplite.db import sqlite_usearch_impl import tensorflow as tf import tqdm diff --git a/hoplite/agile/embed.py b/perch_hoplite/agile/embed.py similarity index 97% rename from hoplite/agile/embed.py rename to perch_hoplite/agile/embed.py index 4d7726c..42c4592 100644 --- a/hoplite/agile/embed.py +++ b/perch_hoplite/agile/embed.py @@ -20,13 +20,13 @@ from absl import logging import audioread -from hoplite import audio_io -from hoplite.agile import source_info -from hoplite.db import interface as hoplite_interface -from hoplite.zoo import model_configs -from hoplite.zoo import zoo_interface from ml_collections import config_dict import numpy as np +from perch_hoplite import audio_io +from perch_hoplite.agile import source_info +from perch_hoplite.db import interface as hoplite_interface +from perch_hoplite.zoo import model_configs +from perch_hoplite.zoo import zoo_interface import soundfile diff --git a/hoplite/agile/embedding_display.py b/perch_hoplite/agile/embedding_display.py similarity index 99% rename from hoplite/agile/embedding_display.py rename to perch_hoplite/agile/embedding_display.py index 3d5459d..19162d4 100644 --- a/hoplite/agile/embedding_display.py +++ b/perch_hoplite/agile/embedding_display.py @@ -19,9 +19,6 @@ import functools from typing import Callable, Iterator, Sequence -from hoplite import audio_io -from hoplite.db import interface -from hoplite.db import search_results import IPython from IPython.display import clear_output from IPython.display import display as ipy_display @@ -30,6 +27,9 @@ from librosa import display as librosa_display from matplotlib import pyplot as plt import numpy as np +from perch_hoplite import audio_io +from perch_hoplite.db import interface +from perch_hoplite.db import search_results @dataclasses.dataclass diff --git a/hoplite/agile/ingest_annotations.py b/perch_hoplite/agile/ingest_annotations.py similarity index 97% rename from hoplite/agile/ingest_annotations.py rename to perch_hoplite/agile/ingest_annotations.py index 7cf40f3..356a7c3 100644 --- a/hoplite/agile/ingest_annotations.py +++ b/perch_hoplite/agile/ingest_annotations.py @@ -20,13 +20,13 @@ from typing import Callable from etils import epath -from hoplite.agile import embed -from hoplite.agile import source_info -from hoplite.db import db_loader -from hoplite.db import interface -from hoplite.taxonomy import annotations_fns from ml_collections import config_dict import pandas as pd +from perch_hoplite.agile import embed +from perch_hoplite.agile import source_info +from perch_hoplite.db import db_loader +from perch_hoplite.db import interface +from perch_hoplite.taxonomy import annotations_fns import tqdm BASE_PATH = epath.Path('gs://chirp-public-bucket/soundscapes/') diff --git a/hoplite/agile/metrics.py b/perch_hoplite/agile/metrics.py similarity index 100% rename from hoplite/agile/metrics.py rename to perch_hoplite/agile/metrics.py diff --git a/hoplite/agile/source_info.py b/perch_hoplite/agile/source_info.py similarity index 99% rename from hoplite/agile/source_info.py rename to perch_hoplite/agile/source_info.py index 333723c..7234f52 100644 --- a/hoplite/agile/source_info.py +++ b/perch_hoplite/agile/source_info.py @@ -20,8 +20,8 @@ from absl import logging from etils import epath -from hoplite.db import interface as hoplite_interface from ml_collections import config_dict +from perch_hoplite.db import interface as hoplite_interface import soundfile import tqdm diff --git a/hoplite/agile/tests/classifier_data_test.py b/perch_hoplite/agile/tests/classifier_data_test.py similarity index 98% rename from hoplite/agile/tests/classifier_data_test.py rename to perch_hoplite/agile/tests/classifier_data_test.py index 2c074c0..f0f9990 100644 --- a/hoplite/agile/tests/classifier_data_test.py +++ b/perch_hoplite/agile/tests/classifier_data_test.py @@ -18,10 +18,10 @@ import shutil import tempfile -from hoplite.agile import classifier_data -from hoplite.db import interface -from hoplite.db.tests import test_utils as db_test_utils import numpy as np +from perch_hoplite.agile import classifier_data +from perch_hoplite.db import interface +from perch_hoplite.db.tests import test_utils as db_test_utils from absl.testing import absltest diff --git a/hoplite/agile/tests/classifier_test.py b/perch_hoplite/agile/tests/classifier_test.py similarity index 97% rename from hoplite/agile/tests/classifier_test.py rename to perch_hoplite/agile/tests/classifier_test.py index 931f2e2..46ad787 100644 --- a/hoplite/agile/tests/classifier_test.py +++ b/perch_hoplite/agile/tests/classifier_test.py @@ -18,12 +18,12 @@ import os import tempfile -from hoplite.agile import classifier -from hoplite.agile import classifier_data -from hoplite.db.tests import test_utils as db_test_utils from ml_collections import config_dict import numpy as np import pandas as pd +from perch_hoplite.agile import classifier +from perch_hoplite.agile import classifier_data +from perch_hoplite.db.tests import test_utils as db_test_utils from absl.testing import absltest diff --git a/hoplite/agile/tests/convert_legacy_test.py b/perch_hoplite/agile/tests/convert_legacy_test.py similarity index 96% rename from hoplite/agile/tests/convert_legacy_test.py rename to perch_hoplite/agile/tests/convert_legacy_test.py index 926bd75..3750f91 100644 --- a/hoplite/agile/tests/convert_legacy_test.py +++ b/perch_hoplite/agile/tests/convert_legacy_test.py @@ -26,11 +26,11 @@ import tempfile from etils import epath -from hoplite import audio_io -from hoplite import path_utils -from hoplite.agile import convert_legacy -from hoplite.agile.tests import test_utils from ml_collections import config_dict +from perch_hoplite import audio_io +from perch_hoplite import path_utils +from perch_hoplite.agile import convert_legacy +from perch_hoplite.agile.tests import test_utils from absl.testing import absltest from absl.testing import parameterized @@ -96,7 +96,7 @@ def write_placeholder_embeddings( ) audio_iterator = audio_io.multi_load_audio_window( filepaths=[s.filepath for s in source_infos], - offsets=[0 for s in source_infos], + offsets=[0 for _ in source_infos], audio_loader=audio_loader, ) with tf_examples.EmbeddingsTFRecordMultiWriter( diff --git a/hoplite/agile/tests/embed_test.py b/perch_hoplite/agile/tests/embed_test.py similarity index 94% rename from hoplite/agile/tests/embed_test.py rename to perch_hoplite/agile/tests/embed_test.py index c5cd18e..4b36c46 100644 --- a/hoplite/agile/tests/embed_test.py +++ b/perch_hoplite/agile/tests/embed_test.py @@ -18,11 +18,11 @@ import shutil import tempfile -from hoplite.agile import embed -from hoplite.agile import source_info -from hoplite.agile.tests import test_utils -from hoplite.db import db_loader from ml_collections import config_dict +from perch_hoplite.agile import embed +from perch_hoplite.agile import source_info +from perch_hoplite.agile.tests import test_utils +from perch_hoplite.db import db_loader from absl.testing import absltest diff --git a/hoplite/agile/tests/embedding_display_test.py b/perch_hoplite/agile/tests/embedding_display_test.py similarity index 96% rename from hoplite/agile/tests/embedding_display_test.py rename to perch_hoplite/agile/tests/embedding_display_test.py index 67692db..b060c27 100644 --- a/hoplite/agile/tests/embedding_display_test.py +++ b/perch_hoplite/agile/tests/embedding_display_test.py @@ -20,14 +20,14 @@ import tempfile from unittest import mock -from hoplite.agile import audio_loader -from hoplite.agile import embedding_display -from hoplite.agile import source_info -from hoplite.agile.tests import test_utils -from hoplite.db import interface import IPython import ipywidgets import numpy as np +from perch_hoplite.agile import audio_loader +from perch_hoplite.agile import embedding_display +from perch_hoplite.agile import source_info +from perch_hoplite.agile.tests import test_utils +from perch_hoplite.db import interface from absl.testing import absltest diff --git a/hoplite/agile/tests/ingest_annotations_test.py b/perch_hoplite/agile/tests/ingest_annotations_test.py similarity index 93% rename from hoplite/agile/tests/ingest_annotations_test.py rename to perch_hoplite/agile/tests/ingest_annotations_test.py index a9bf15d..550c688 100644 --- a/hoplite/agile/tests/ingest_annotations_test.py +++ b/perch_hoplite/agile/tests/ingest_annotations_test.py @@ -20,16 +20,16 @@ import tempfile from etils import epath -from hoplite import path_utils -from hoplite.agile import embed -from hoplite.agile import ingest_annotations -from hoplite.agile.tests import test_utils -from hoplite.db import interface -from hoplite.db.tests import test_utils as db_test_utils -from hoplite.taxonomy import annotations -from hoplite.taxonomy import annotations_fns from ml_collections import config_dict import numpy as np +from perch_hoplite import path_utils +from perch_hoplite.agile import embed +from perch_hoplite.agile import ingest_annotations +from perch_hoplite.agile.tests import test_utils +from perch_hoplite.db import interface +from perch_hoplite.db.tests import test_utils as db_test_utils +from perch_hoplite.taxonomy import annotations +from perch_hoplite.taxonomy import annotations_fns from absl.testing import absltest diff --git a/hoplite/agile/tests/metrics_test.py b/perch_hoplite/agile/tests/metrics_test.py similarity index 96% rename from hoplite/agile/tests/metrics_test.py rename to perch_hoplite/agile/tests/metrics_test.py index 4d3cc23..e28e5e5 100644 --- a/hoplite/agile/tests/metrics_test.py +++ b/perch_hoplite/agile/tests/metrics_test.py @@ -15,8 +15,8 @@ """Tests for metrics.""" -from hoplite.agile import metrics import numpy as np +from perch_hoplite.agile import metrics from absl.testing import absltest diff --git a/hoplite/agile/tests/source_info_test.py b/perch_hoplite/agile/tests/source_info_test.py similarity index 98% rename from hoplite/agile/tests/source_info_test.py rename to perch_hoplite/agile/tests/source_info_test.py index 1e5cd5b..88b2a4d 100644 --- a/hoplite/agile/tests/source_info_test.py +++ b/perch_hoplite/agile/tests/source_info_test.py @@ -18,8 +18,8 @@ import shutil import tempfile -from hoplite.agile import source_info -from hoplite.agile.tests import test_utils +from perch_hoplite.agile import source_info +from perch_hoplite.agile.tests import test_utils from absl.testing import absltest diff --git a/hoplite/agile/tests/test_utils.py b/perch_hoplite/agile/tests/test_utils.py similarity index 100% rename from hoplite/agile/tests/test_utils.py rename to perch_hoplite/agile/tests/test_utils.py diff --git a/hoplite/agile/tests/testdata/config.json b/perch_hoplite/agile/tests/testdata/config.json similarity index 100% rename from hoplite/agile/tests/testdata/config.json rename to perch_hoplite/agile/tests/testdata/config.json diff --git a/hoplite/agile/tests/testdata/embeddings-1730850444-00000-of-00001 b/perch_hoplite/agile/tests/testdata/embeddings-1730850444-00000-of-00001 similarity index 100% rename from hoplite/agile/tests/testdata/embeddings-1730850444-00000-of-00001 rename to perch_hoplite/agile/tests/testdata/embeddings-1730850444-00000-of-00001 diff --git a/hoplite/agile/tests/testdata/hawaii.csv b/perch_hoplite/agile/tests/testdata/hawaii.csv similarity index 100% rename from hoplite/agile/tests/testdata/hawaii.csv rename to perch_hoplite/agile/tests/testdata/hawaii.csv diff --git a/hoplite/audio_io.py b/perch_hoplite/audio_io.py similarity index 99% rename from hoplite/audio_io.py rename to perch_hoplite/audio_io.py index 88591d9..c2e4971 100644 --- a/hoplite/audio_io.py +++ b/perch_hoplite/audio_io.py @@ -24,9 +24,9 @@ import warnings from etils import epath -from hoplite import path_utils import librosa import numpy as np +from perch_hoplite import path_utils import requests import soundfile diff --git a/hoplite/db/README.md b/perch_hoplite/db/README.md similarity index 100% rename from hoplite/db/README.md rename to perch_hoplite/db/README.md diff --git a/hoplite/db/brutalism.py b/perch_hoplite/db/brutalism.py similarity index 98% rename from hoplite/db/brutalism.py rename to perch_hoplite/db/brutalism.py index 4b3fc1d..1554e16 100644 --- a/hoplite/db/brutalism.py +++ b/perch_hoplite/db/brutalism.py @@ -19,9 +19,9 @@ import threading from typing import Any, Callable, Sequence -from hoplite.db import interface -from hoplite.db import search_results import numpy as np +from perch_hoplite.db import interface +from perch_hoplite.db import search_results def worker_initializer(state): diff --git a/hoplite/db/db_loader.py b/perch_hoplite/db/db_loader.py similarity index 96% rename from hoplite/db/db_loader.py rename to perch_hoplite/db/db_loader.py index 53a1fa9..befbc10 100644 --- a/hoplite/db/db_loader.py +++ b/perch_hoplite/db/db_loader.py @@ -18,10 +18,10 @@ import dataclasses from etils import epath -from hoplite.db import in_mem_impl -from hoplite.db import interface -from hoplite.db import sqlite_usearch_impl from ml_collections import config_dict +from perch_hoplite.db import in_mem_impl +from perch_hoplite.db import interface +from perch_hoplite.db import sqlite_usearch_impl import tqdm diff --git a/hoplite/db/in_mem_impl.py b/perch_hoplite/db/in_mem_impl.py similarity index 99% rename from hoplite/db/in_mem_impl.py rename to perch_hoplite/db/in_mem_impl.py index 92b1913..2ae2e9d 100644 --- a/hoplite/db/in_mem_impl.py +++ b/perch_hoplite/db/in_mem_impl.py @@ -19,9 +19,9 @@ import dataclasses from typing import Any, Sequence -from hoplite.db import interface from ml_collections import config_dict import numpy as np +from perch_hoplite.db import interface @dataclasses.dataclass diff --git a/hoplite/db/interface.py b/perch_hoplite/db/interface.py similarity index 100% rename from hoplite/db/interface.py rename to perch_hoplite/db/interface.py diff --git a/hoplite/db/score_functions.py b/perch_hoplite/db/score_functions.py similarity index 100% rename from hoplite/db/score_functions.py rename to perch_hoplite/db/score_functions.py diff --git a/hoplite/db/search_results.py b/perch_hoplite/db/search_results.py similarity index 100% rename from hoplite/db/search_results.py rename to perch_hoplite/db/search_results.py diff --git a/hoplite/db/sqlite_usearch_impl.py b/perch_hoplite/db/sqlite_usearch_impl.py similarity index 99% rename from hoplite/db/sqlite_usearch_impl.py rename to perch_hoplite/db/sqlite_usearch_impl.py index 9cc6b51..a24432a 100644 --- a/hoplite/db/sqlite_usearch_impl.py +++ b/perch_hoplite/db/sqlite_usearch_impl.py @@ -23,9 +23,9 @@ from typing import Any from etils import epath -from hoplite.db import interface from ml_collections import config_dict import numpy as np +from perch_hoplite.db import interface from usearch import index as uindex @@ -114,11 +114,14 @@ def create( # TODO(tomdenton): Check that config is consistent with the DB. metadata = _get_metadata(cursor, None) - if (USEARCH_CONFIG_KEY in metadata + if ( + USEARCH_CONFIG_KEY in metadata and usearch_cfg is not None - and metadata[USEARCH_CONFIG_KEY] != usearch_cfg): + and metadata[USEARCH_CONFIG_KEY] != usearch_cfg + ): raise ValueError( - 'A usearch_cfg was provided, but one already exists in the DB.') + 'A usearch_cfg was provided, but one already exists in the DB.' + ) elif USEARCH_CONFIG_KEY in metadata: usearch_cfg = metadata[USEARCH_CONFIG_KEY] elif usearch_cfg is None: diff --git a/hoplite/db/tests/brutalism_test.py b/perch_hoplite/db/tests/brutalism_test.py similarity index 96% rename from hoplite/db/tests/brutalism_test.py rename to perch_hoplite/db/tests/brutalism_test.py index ec49d9e..df203b6 100644 --- a/hoplite/db/tests/brutalism_test.py +++ b/perch_hoplite/db/tests/brutalism_test.py @@ -18,9 +18,9 @@ import shutil import tempfile -from hoplite.db import brutalism -from hoplite.db.tests import test_utils import numpy as np +from perch_hoplite.db import brutalism +from perch_hoplite.db.tests import test_utils from absl.testing import absltest from absl.testing import parameterized diff --git a/hoplite/db/tests/hoplite_test.py b/perch_hoplite/db/tests/hoplite_test.py similarity index 98% rename from hoplite/db/tests/hoplite_test.py rename to perch_hoplite/db/tests/hoplite_test.py index 60170d9..5aed302 100644 --- a/hoplite/db/tests/hoplite_test.py +++ b/perch_hoplite/db/tests/hoplite_test.py @@ -18,10 +18,10 @@ import shutil import tempfile -from hoplite.db import brutalism -from hoplite.db import interface -from hoplite.db.tests import test_utils import numpy as np +from perch_hoplite.db import brutalism +from perch_hoplite.db import interface +from perch_hoplite.db.tests import test_utils from absl.testing import absltest from absl.testing import parameterized diff --git a/hoplite/db/tests/test_utils.py b/perch_hoplite/db/tests/test_utils.py similarity index 96% rename from hoplite/db/tests/test_utils.py rename to perch_hoplite/db/tests/test_utils.py index 307890f..0439fad 100644 --- a/hoplite/db/tests/test_utils.py +++ b/perch_hoplite/db/tests/test_utils.py @@ -15,11 +15,11 @@ """Utility functions for testing.""" -from hoplite.db import in_mem_impl -from hoplite.db import interface -from hoplite.db import sqlite_usearch_impl from ml_collections import config_dict import numpy as np +from perch_hoplite.db import in_mem_impl +from perch_hoplite.db import interface +from perch_hoplite.db import sqlite_usearch_impl CLASS_LABELS = ('alpha', 'beta', 'gamma', 'delta', 'epsilon', 'zeta') diff --git a/hoplite/path_utils.py b/perch_hoplite/path_utils.py similarity index 100% rename from hoplite/path_utils.py rename to perch_hoplite/path_utils.py diff --git a/hoplite/taxonomy/README.md b/perch_hoplite/taxonomy/README.md similarity index 100% rename from hoplite/taxonomy/README.md rename to perch_hoplite/taxonomy/README.md diff --git a/hoplite/taxonomy/annotations.py b/perch_hoplite/taxonomy/annotations.py similarity index 100% rename from hoplite/taxonomy/annotations.py rename to perch_hoplite/taxonomy/annotations.py diff --git a/hoplite/taxonomy/annotations_fns.py b/perch_hoplite/taxonomy/annotations_fns.py similarity index 98% rename from hoplite/taxonomy/annotations_fns.py rename to perch_hoplite/taxonomy/annotations_fns.py index 6817c4f..b6a0bdc 100644 --- a/hoplite/taxonomy/annotations_fns.py +++ b/perch_hoplite/taxonomy/annotations_fns.py @@ -19,9 +19,9 @@ import os from etils import epath -from hoplite.taxonomy import annotations -from hoplite.taxonomy import namespace_db import pandas as pd +from perch_hoplite.taxonomy import annotations +from perch_hoplite.taxonomy import namespace_db _DEPRECATED2NEW = { 'mallar': 'mallar3', diff --git a/hoplite/taxonomy/class_utils.py b/perch_hoplite/taxonomy/class_utils.py similarity index 96% rename from hoplite/taxonomy/class_utils.py rename to perch_hoplite/taxonomy/class_utils.py index d28b341..56cca90 100644 --- a/hoplite/taxonomy/class_utils.py +++ b/perch_hoplite/taxonomy/class_utils.py @@ -15,7 +15,7 @@ """Convenience utilities for handling class lists.""" -from hoplite.taxonomy import namespace_db +from perch_hoplite.taxonomy import namespace_db def get_class_lists(species_class_list_name: str, add_taxonomic_labels: bool): diff --git a/hoplite/taxonomy/ebird.py b/perch_hoplite/taxonomy/ebird.py similarity index 98% rename from hoplite/taxonomy/ebird.py rename to perch_hoplite/taxonomy/ebird.py index cceafe7..02ea030 100644 --- a/hoplite/taxonomy/ebird.py +++ b/perch_hoplite/taxonomy/ebird.py @@ -18,10 +18,10 @@ from absl import app from absl import flags -from hoplite.taxonomy import namespace -from hoplite.taxonomy import namespace_db import numpy as np import pandas as pd +from perch_hoplite.taxonomy import namespace +from perch_hoplite.taxonomy import namespace_db _SOURCE_FILE = flags.DEFINE_string( 'source_file', 'source_data/ebird_taxonomy_v2022.csv', 'CSV file to load.' diff --git a/hoplite/taxonomy/namespace.py b/perch_hoplite/taxonomy/namespace.py similarity index 100% rename from hoplite/taxonomy/namespace.py rename to perch_hoplite/taxonomy/namespace.py diff --git a/hoplite/taxonomy/namespace_db.py b/perch_hoplite/taxonomy/namespace_db.py similarity index 98% rename from hoplite/taxonomy/namespace_db.py rename to perch_hoplite/taxonomy/namespace_db.py index 57e9781..45fe324 100644 --- a/hoplite/taxonomy/namespace_db.py +++ b/perch_hoplite/taxonomy/namespace_db.py @@ -20,8 +20,8 @@ import os import typing -from hoplite import path_utils -from hoplite.taxonomy import namespace +from perch_hoplite import path_utils +from perch_hoplite.taxonomy import namespace TAXONOMY_DATABASE_FILENAME = "taxonomy/taxonomy_database.json" diff --git a/hoplite/taxonomy/namespace_db_test.py b/perch_hoplite/taxonomy/namespace_db_test.py similarity index 99% rename from hoplite/taxonomy/namespace_db_test.py rename to perch_hoplite/taxonomy/namespace_db_test.py index ef97c24..14ce88e 100644 --- a/hoplite/taxonomy/namespace_db_test.py +++ b/perch_hoplite/taxonomy/namespace_db_test.py @@ -20,9 +20,9 @@ import tempfile from absl import logging -from hoplite.taxonomy import namespace -from hoplite.taxonomy import namespace_db import numpy as np +from perch_hoplite.taxonomy import namespace +from perch_hoplite.taxonomy import namespace_db import tensorflow as tf from absl.testing import absltest diff --git a/hoplite/taxonomy/taxonomy_database.json b/perch_hoplite/taxonomy/taxonomy_database.json similarity index 100% rename from hoplite/taxonomy/taxonomy_database.json rename to perch_hoplite/taxonomy/taxonomy_database.json diff --git a/hoplite/zoo/README.md b/perch_hoplite/zoo/README.md similarity index 100% rename from hoplite/zoo/README.md rename to perch_hoplite/zoo/README.md diff --git a/hoplite/zoo/aves_model.py b/perch_hoplite/zoo/aves_model.py similarity index 98% rename from hoplite/zoo/aves_model.py rename to perch_hoplite/zoo/aves_model.py index 428e4c9..ea70c68 100644 --- a/hoplite/zoo/aves_model.py +++ b/perch_hoplite/zoo/aves_model.py @@ -20,7 +20,6 @@ import functools from typing import Any -from hoplite.zoo import zoo_interface import jax from jax import numpy as jnp from jax import random @@ -30,6 +29,7 @@ from jaxonnxruntime.core import onnx_node from ml_collections.config_dict import config_dict import numpy as np +from perch_hoplite.zoo import zoo_interface import onnx diff --git a/hoplite/zoo/handcrafted_features_model.py b/perch_hoplite/zoo/handcrafted_features_model.py similarity index 99% rename from hoplite/zoo/handcrafted_features_model.py rename to perch_hoplite/zoo/handcrafted_features_model.py index e923e29..8736595 100644 --- a/hoplite/zoo/handcrafted_features_model.py +++ b/perch_hoplite/zoo/handcrafted_features_model.py @@ -17,10 +17,10 @@ import dataclasses -from hoplite.zoo import zoo_interface import librosa from ml_collections import config_dict import numpy as np +from perch_hoplite.zoo import zoo_interface @dataclasses.dataclass diff --git a/hoplite/zoo/model_configs.py b/perch_hoplite/zoo/model_configs.py similarity index 90% rename from hoplite/zoo/model_configs.py rename to perch_hoplite/zoo/model_configs.py index afcaa05..3698ff9 100644 --- a/hoplite/zoo/model_configs.py +++ b/perch_hoplite/zoo/model_configs.py @@ -19,8 +19,8 @@ import enum import importlib -from hoplite.zoo import zoo_interface from ml_collections import config_dict +from perch_hoplite.zoo import zoo_interface class ModelConfigName(enum.Enum): @@ -68,25 +68,27 @@ def load_model(self) -> zoo_interface.EmbeddingModel: def get_model_class(model_key: str) -> type[zoo_interface.EmbeddingModel]: """Import and return the model class.""" if model_key == 'taxonomy_model_tf': - module = importlib.import_module('hoplite.zoo.taxonomy_model_tf') + module = importlib.import_module('perch_hoplite.zoo.taxonomy_model_tf') return module.TaxonomyModelTF elif model_key == 'google_whale': - module = importlib.import_module('hoplite.zoo.models_tf') + module = importlib.import_module('perch_hoplite.zoo.models_tf') return module.GoogleWhaleModel elif model_key == 'placeholder_model': - module = importlib.import_module('hoplite.zoo.placeholder_model') + module = importlib.import_module('perch_hoplite.zoo.placeholder_model') return module.PlaceholderModel elif model_key == 'birdnet': - module = importlib.import_module('hoplite.zoo.models_tf') + module = importlib.import_module('perch_hoplite.zoo.models_tf') return module.BirdNet elif model_key == 'tfhub_model': - module = importlib.import_module('hoplite.zoo.models_tf') + module = importlib.import_module('perch_hoplite.zoo.models_tf') return module.TFHubModel elif model_key == 'aves': - module = importlib.import_module('hoplite.zoo.aves_model') + module = importlib.import_module('perch_hoplite.zoo.aves_model') return module.AVES elif model_key == 'handcrafted_features_model': - module = importlib.import_module('hoplite.zoo.handcrafted_features_model') + module = importlib.import_module( + 'perch_hoplite.zoo.handcrafted_features_model' + ) return module.HandcraftedFeaturesModel else: raise ValueError(f'Unknown model key: {model_key}') @@ -135,7 +137,7 @@ def get_preset_model_config(preset_name: str | ModelConfigName) -> PresetInfo: model_config.hop_size_s = 5.0 model_config.sample_rate = 32000 taxonomy_model_tf = importlib.import_module( - 'hoplite.zoo.taxonomy_model_tf') + 'perch_hoplite.zoo.taxonomy_model_tf') model_config.tfhub_version = 1 model_config.tfhub_path = taxonomy_model_tf.SURFPERCH_TF_HUB_URL model_config.model_path = '' @@ -188,7 +190,9 @@ def get_preset_model_config(preset_name: str | ModelConfigName) -> PresetInfo: model_config.sample_rate = 16000 elif preset_name == ModelConfigName.BEANS_BASELINE: model_key = 'handcrafted_features_model' - module = importlib.import_module('hoplite.zoo.handcrafted_features_model') + module = importlib.import_module( + 'perch_hoplite.zoo.handcrafted_features_model' + ) model_config = module.HandcraftedFeaturesModel.beans_baseline_config() embedding_dim = 80 else: diff --git a/hoplite/zoo/models_tf.py b/perch_hoplite/zoo/models_tf.py similarity index 98% rename from hoplite/zoo/models_tf.py rename to perch_hoplite/zoo/models_tf.py index 5a1142c..c5e79c9 100644 --- a/hoplite/zoo/models_tf.py +++ b/perch_hoplite/zoo/models_tf.py @@ -21,12 +21,12 @@ from absl import logging from etils import epath -from hoplite.taxonomy import namespace -from hoplite.taxonomy import namespace_db -from hoplite.zoo import taxonomy_model_tf -from hoplite.zoo import zoo_interface from ml_collections import config_dict import numpy as np +from perch_hoplite.taxonomy import namespace +from perch_hoplite.taxonomy import namespace_db +from perch_hoplite.zoo import taxonomy_model_tf +from perch_hoplite.zoo import zoo_interface import tensorflow as tf import tensorflow.compat.v1 as tf1 import tensorflow_hub as hub @@ -138,7 +138,7 @@ class BirbSepModelTF1(zoo_interface.EmbeddingModel): Example usage: ``` - from hoplite.zoo import models + from perch_hoplite.zoo import models birbsep1_config = config_dict.ConfigDict({ 'model_path': $MODEL_PATH, 'window_size_s': 60.0, diff --git a/hoplite/zoo/placeholder_model.py b/perch_hoplite/zoo/placeholder_model.py similarity index 96% rename from hoplite/zoo/placeholder_model.py rename to perch_hoplite/zoo/placeholder_model.py index 60adaf9..7d6494f 100644 --- a/hoplite/zoo/placeholder_model.py +++ b/perch_hoplite/zoo/placeholder_model.py @@ -17,10 +17,10 @@ import dataclasses -from hoplite.taxonomy import namespace_db -from hoplite.zoo import zoo_interface from ml_collections import config_dict import numpy as np +from perch_hoplite.taxonomy import namespace_db +from perch_hoplite.zoo import zoo_interface @dataclasses.dataclass diff --git a/hoplite/zoo/taxonomy_model_tf.py b/perch_hoplite/zoo/taxonomy_model_tf.py similarity index 99% rename from hoplite/zoo/taxonomy_model_tf.py rename to perch_hoplite/zoo/taxonomy_model_tf.py index 99ae428..7026dd4 100644 --- a/hoplite/zoo/taxonomy_model_tf.py +++ b/perch_hoplite/zoo/taxonomy_model_tf.py @@ -20,10 +20,10 @@ from absl import logging from etils import epath -from hoplite.taxonomy import namespace -from hoplite.zoo import zoo_interface from ml_collections import config_dict import numpy as np +from perch_hoplite.taxonomy import namespace +from perch_hoplite.zoo import zoo_interface import tensorflow as tf import tensorflow_hub as hub diff --git a/hoplite/zoo/tests_tf/tf_test.py b/perch_hoplite/zoo/tests_tf/tf_test.py similarity index 98% rename from hoplite/zoo/tests_tf/tf_test.py rename to perch_hoplite/zoo/tests_tf/tf_test.py index 1d891be..5084076 100644 --- a/hoplite/zoo/tests_tf/tf_test.py +++ b/perch_hoplite/zoo/tests_tf/tf_test.py @@ -18,12 +18,12 @@ import os import tempfile -from hoplite.taxonomy import namespace -from hoplite.zoo import models_tf -from hoplite.zoo import placeholder_model -from hoplite.zoo import taxonomy_model_tf from ml_collections import config_dict import numpy as np +from perch_hoplite.taxonomy import namespace +from perch_hoplite.zoo import models_tf +from perch_hoplite.zoo import placeholder_model +from perch_hoplite.zoo import taxonomy_model_tf import tensorflow as tf import tf_keras diff --git a/hoplite/zoo/zoo_interface.py b/perch_hoplite/zoo/zoo_interface.py similarity index 99% rename from hoplite/zoo/zoo_interface.py rename to perch_hoplite/zoo/zoo_interface.py index d9b58d9..97c0ea6 100644 --- a/hoplite/zoo/zoo_interface.py +++ b/perch_hoplite/zoo/zoo_interface.py @@ -21,10 +21,10 @@ from absl import logging from etils import epath -from hoplite.taxonomy import namespace import librosa from ml_collections import config_dict import numpy as np +from perch_hoplite.taxonomy import namespace import tensorflow as tf LogitType = Dict[str, np.ndarray] diff --git a/hoplite/zoo/zoo_test.py b/perch_hoplite/zoo/zoo_test.py similarity index 97% rename from hoplite/zoo/zoo_test.py rename to perch_hoplite/zoo/zoo_test.py index 29c5273..983fdbc 100644 --- a/hoplite/zoo/zoo_test.py +++ b/perch_hoplite/zoo/zoo_test.py @@ -15,9 +15,9 @@ """Tests for mass-embedding functionality.""" -from hoplite.zoo import model_configs -from hoplite.zoo import zoo_interface import numpy as np +from perch_hoplite.zoo import model_configs +from perch_hoplite.zoo import zoo_interface from absl.testing import absltest from absl.testing import parameterized diff --git a/poetry.lock b/poetry.lock index af49451..bd77d20 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand. [[package]] name = "absl-py" @@ -6,6 +6,8 @@ version = "1.4.0" description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." optional = false python-versions = ">=3.6" +groups = ["main", "jax", "tf"] +markers = "python_version <= \"3.11\"" files = [ {file = "absl-py-1.4.0.tar.gz", hash = "sha256:d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d"}, {file = "absl_py-1.4.0-py3-none-any.whl", hash = "sha256:0d3fe606adfa4f7db64792dd4c7aee4ee0c38ab75dfd353b7a83ed3e957fcb47"}, @@ -17,6 +19,8 @@ version = "2.4.4" description = "Happy Eyeballs for asyncio" optional = false python-versions = ">=3.8" +groups = ["main"] +markers = "python_version <= \"3.11\"" files = [ {file = "aiohappyeyeballs-2.4.4-py3-none-any.whl", hash = "sha256:a980909d50efcd44795c4afeca523296716d50cd756ddca6af8c65b996e27de8"}, {file = "aiohappyeyeballs-2.4.4.tar.gz", hash = "sha256:5fdd7d87889c63183afc18ce9271f9b0a7d32c2303e394468dd45d514a757745"}, @@ -24,87 +28,89 @@ files = [ 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Formerly nbconvert's ExecutePreprocessor." optional = false -python-versions = ">=3.8.0" +python-versions = ">=3.9.0" +groups = ["main"] +markers = "python_version <= \"3.11\"" files = [ - {file = "nbclient-0.10.1-py3-none-any.whl", hash = "sha256:949019b9240d66897e442888cfb618f69ef23dc71c01cb5fced8499c2cfc084d"}, - {file = "nbclient-0.10.1.tar.gz", hash = "sha256:3e93e348ab27e712acd46fccd809139e356eb9a31aab641d1a7991a6eb4e6f68"}, + {file = "nbclient-0.10.2-py3-none-any.whl", hash = "sha256:4ffee11e788b4a27fabeb7955547e4318a5298f34342a4bfd01f2e1faaeadc3d"}, + {file = "nbclient-0.10.2.tar.gz", hash = "sha256:90b7fc6b810630db87a6d0c2250b1f0ab4cf4d3c27a299b0cde78a4ed3fd9193"}, ] [package.dependencies] @@ -2891,23 +3064,25 @@ traitlets = ">=5.4" [package.extras] dev = ["pre-commit"] -docs = ["autodoc-traits", "flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "mock", "moto", "myst-parser", "nbconvert (>=7.0.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling", "testpath", "xmltodict"] -test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"] +docs = ["autodoc-traits", "flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "mock", "moto", "myst-parser", "nbconvert (>=7.1.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling", "testpath", "xmltodict"] +test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.1.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"] [[package]] name = "nbconvert" -version = "7.16.4" +version = "7.16.5" description = "Converting Jupyter Notebooks (.ipynb files) to other formats. Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script. nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)." optional = false python-versions = ">=3.8" +groups = ["main"] +markers = "python_version <= \"3.11\"" files = [ - {file = "nbconvert-7.16.4-py3-none-any.whl", hash = "sha256:05873c620fe520b6322bf8a5ad562692343fe3452abda5765c7a34b7d1aa3eb3"}, - {file = "nbconvert-7.16.4.tar.gz", hash = "sha256:86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4"}, + {file = "nbconvert-7.16.5-py3-none-any.whl", hash = "sha256:e12eac052d6fd03040af4166c563d76e7aeead2e9aadf5356db552a1784bd547"}, + {file = "nbconvert-7.16.5.tar.gz", hash = "sha256:c83467bb5777fdfaac5ebbb8e864f300b277f68692ecc04d6dab72f2d8442344"}, ] [package.dependencies] beautifulsoup4 = "*" -bleach = "!=5.0.0" +bleach = {version = "!=5.0.0", extras = ["css"]} defusedxml = "*" jinja2 = ">=3.0" jupyter-core = ">=4.7" @@ 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jupyterlab-server = ">=2.27.1,<3" notebook-shim = ">=0.2,<0.3" tornado = ">=6.2.0" @@ -2992,6 +3172,8 @@ version = "0.2.4" description = "A shim layer for notebook traits and config" optional = false python-versions = ">=3.7" +groups = ["main"] +markers = "python_version <= \"3.11\"" files = [ {file = "notebook_shim-0.2.4-py3-none-any.whl", hash = "sha256:411a5be4e9dc882a074ccbcae671eda64cceb068767e9a3419096986560e1cef"}, {file = "notebook_shim-0.2.4.tar.gz", hash = "sha256:b4b2cfa1b65d98307ca24361f5b30fe785b53c3fd07b7a47e89acb5e6ac638cb"}, @@ -3009,6 +3191,8 @@ version = "0.60.0" description = "compiling Python code using LLVM" optional = false python-versions = ">=3.9" +groups = ["main"] +markers = "python_version <= \"3.11\"" files = [ {file = "numba-0.60.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5d761de835cd38fb400d2c26bb103a2726f548dc30368853121d66201672e651"}, {file = "numba-0.60.0-cp310-cp310-macosx_11_0_arm64.whl", hash = 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TOML parser" optional = false python-versions = ">=3.8" +groups = ["main"] +markers = "python_version < \"3.11\"" files = [ {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"}, {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"}, @@ -5199,6 +5524,8 @@ version = "1.0.0" description = "List processing tools and functional utilities" optional = false python-versions = ">=3.8" +groups = ["jax"] +markers = "python_version <= \"3.11\"" files = [ {file = "toolz-1.0.0-py3-none-any.whl", hash = "sha256:292c8f1c4e7516bf9086f8850935c799a874039c8bcf959d47b600e4c44a6236"}, {file = "toolz-1.0.0.tar.gz", hash = "sha256:2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02"}, @@ -5210,6 +5537,8 @@ version = "6.4.2" description = "Tornado is a Python web framework and asynchronous networking library, originally 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Available keys are documented at: # https://packaging.python.org/en/latest/specifications/declaring-project-metadata -name = "hoplite" +name = "perch-hoplite" description = "Tooling for agile modeling on large machine perception embedding databases." readme = "README.md" requires-python = ">=3.10"