From 876e0f30821ca99be1a10d618a85671077929858 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A1s=20Schmelczer?= Date: Sat, 2 Apr 2022 21:55:48 +0200 Subject: [PATCH] Move packages MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: András Schmelczer --- example/main.py | 5 +- example/predict_domain.py | 2 +- example/preprocess.py | 4 +- example/train.ipynb | 117 ++++++++++++++++-- good_ai/src/__init__.py | 1 - good_ai/src/good_ai/__init__.py | 5 +- good_ai/src/good_ai/good_ai/__init__.py | 2 + .../good_ai/{ => good_ai}/core/__init__.py | 0 .../{ => good_ai}/core/function_registry.py | 0 .../src/good_ai/{ => good_ai}/core/plugin.py | 0 .../good_ai/{ => good_ai}/deploy/__init__.py | 0 .../{ => good_ai}/deploy/process_batch.py | 2 +- .../src/good_ai/{ => good_ai}/deploy/serve.py | 0 .../good_ai/{ => good_ai}/models/__init__.py | 0 .../{ => good_ai}/models/load_model.py | 2 +- .../{ => good_ai}/models/save_model.py | 2 +- .../good_ai/{ => good_ai}/models/use_model.py | 0 .../{ => good_ai}/models/use_model_plugin.py | 0 good_ai/src/{ => good_ai}/open_s3/__init__.py | 0 good_ai/src/{ => good_ai}/open_s3/__main__.py | 0 .../{ => good_ai}/open_s3/helper/__init__.py | 0 .../open_s3/helper/human_readable_to_byte.py | 0 .../open_s3/helper/progress_bar.py | 0 .../src/{ => good_ai}/open_s3/large_file.py | 0 .../{ => good_ai}/open_s3/parse_arguments.py | 0 .../{sus => good_ai/utilities}/__init__.py | 0 .../src/{sus => good_ai/utilities}/clean.py | 0 .../utilities}/data/__init__.py | 0 .../utilities}/data/american_spellings.py | 0 .../utilities}/data/punctuations.py | 0 .../utilities}/evaluate_ranking/__init__.py | 0 .../evaluate_ranking/draw_f1_iso_lines.py | 0 .../evaluate_ranking/evaluate_ranking.py | 0 .../utilities}/external/__init__.py | 0 .../utilities}/external/negspacy/README.md | 0 .../utilities}/external/negspacy/__init__.py | 0 .../utilities}/external/negspacy/negation.py | 0 .../utilities}/external/negspacy/termsets.py | 4 +- .../utilities}/external/pylatexenc/README.md | 0 .../external/pylatexenc/__init__.py | 0 .../utilities}/external/pylatexenc/_util.py | 0 .../pylatexenc/latex2text/__init__.py | 0 .../pylatexenc/latex2text/__main__.py | 0 .../pylatexenc/latex2text/_defaultspecs.py | 0 .../pylatexenc/latexencode/__init__.py | 0 .../pylatexenc/latexencode/__main__.py | 0 .../latexencode/_partial_latex_encoder.py | 0 .../pylatexenc/latexencode/_uni2latexmap.py | 0 .../latexencode/_uni2latexmap_xml.py | 0 .../latexencode/_unicode_to_latex_encoder.py | 2 +- .../pylatexenc/latexwalker/__init__.py | 0 .../pylatexenc/latexwalker/__main__.py | 0 .../pylatexenc/latexwalker/_defaultspecs.py | 0 .../external/pylatexenc/macrospec/__init__.py | 0 .../pylatexenc/macrospec/_argparsers.py | 0 .../utilities}/external/pylatexenc/version.py | 0 .../utilities}/get_sentences.py | 0 .../utilities}/language/__init__.py | 0 .../language/english_name_of_language.py | 0 .../utilities}/language/is_english.py | 0 .../utilities}/language/predict_language.py | 0 .../utilities}/lemmatize_text.py | 0 .../utilities}/lemmatize_token.py | 0 .../utilities}/match_names/__init__.py | 0 .../utilities}/match_names/config.py | 0 .../utilities}/match_names/match_names.py | 0 .../utilities}/match_names/name_parts.py | 0 good_ai/src/{sus => good_ai/utilities}/nlp.py | 0 .../utilities}/parallel_map.py | 0 .../utilities}/publication_tei/__init__.py | 0 .../publication_tei/models/__init__.py | 0 .../publication_tei/models/affiliation.py | 0 .../publication_tei/models/author.py | 0 .../publication_tei/models/element.py | 0 .../models/publication_metadata.py | 0 .../utilities}/publication_tei/models/text.py | 0 .../publication_tei/publication_tei.py | 2 +- .../src/{sus => good_ai/utilities}/unique.py | 0 78 files changed, 123 insertions(+), 27 deletions(-) delete mode 100644 good_ai/src/__init__.py create mode 100644 good_ai/src/good_ai/good_ai/__init__.py rename good_ai/src/good_ai/{ => good_ai}/core/__init__.py (100%) rename good_ai/src/good_ai/{ => good_ai}/core/function_registry.py (100%) rename good_ai/src/good_ai/{ => good_ai}/core/plugin.py (100%) rename good_ai/src/good_ai/{ => good_ai}/deploy/__init__.py (100%) rename good_ai/src/good_ai/{ => good_ai}/deploy/process_batch.py (89%) rename good_ai/src/good_ai/{ => good_ai}/deploy/serve.py (100%) rename good_ai/src/good_ai/{ => good_ai}/models/__init__.py (100%) rename good_ai/src/good_ai/{ => good_ai}/models/load_model.py (90%) rename good_ai/src/good_ai/{ => good_ai}/models/save_model.py (93%) rename good_ai/src/good_ai/{ => good_ai}/models/use_model.py (100%) rename good_ai/src/good_ai/{ => good_ai}/models/use_model_plugin.py (100%) rename good_ai/src/{ => good_ai}/open_s3/__init__.py (100%) rename good_ai/src/{ => good_ai}/open_s3/__main__.py (100%) rename good_ai/src/{ => good_ai}/open_s3/helper/__init__.py (100%) rename good_ai/src/{ => good_ai}/open_s3/helper/human_readable_to_byte.py (100%) rename good_ai/src/{ => good_ai}/open_s3/helper/progress_bar.py (100%) rename good_ai/src/{ => good_ai}/open_s3/large_file.py (100%) rename good_ai/src/{ => good_ai}/open_s3/parse_arguments.py (100%) rename good_ai/src/{sus => good_ai/utilities}/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/clean.py (100%) rename good_ai/src/{sus => good_ai/utilities}/data/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/data/american_spellings.py (100%) rename good_ai/src/{sus => good_ai/utilities}/data/punctuations.py (100%) rename good_ai/src/{sus => good_ai/utilities}/evaluate_ranking/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/evaluate_ranking/draw_f1_iso_lines.py (100%) rename good_ai/src/{sus => good_ai/utilities}/evaluate_ranking/evaluate_ranking.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/negspacy/README.md (100%) rename good_ai/src/{sus => good_ai/utilities}/external/negspacy/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/negspacy/negation.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/negspacy/termsets.py (98%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/README.md (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/_util.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latex2text/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latex2text/__main__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latex2text/_defaultspecs.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latexencode/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latexencode/__main__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latexencode/_partial_latex_encoder.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latexencode/_uni2latexmap.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latexencode/_uni2latexmap_xml.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latexencode/_unicode_to_latex_encoder.py (99%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latexwalker/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latexwalker/__main__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/latexwalker/_defaultspecs.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/macrospec/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/macrospec/_argparsers.py (100%) rename good_ai/src/{sus => good_ai/utilities}/external/pylatexenc/version.py (100%) rename good_ai/src/{sus => good_ai/utilities}/get_sentences.py (100%) rename good_ai/src/{sus => good_ai/utilities}/language/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/language/english_name_of_language.py (100%) rename good_ai/src/{sus => good_ai/utilities}/language/is_english.py (100%) rename good_ai/src/{sus => good_ai/utilities}/language/predict_language.py (100%) rename good_ai/src/{sus => good_ai/utilities}/lemmatize_text.py (100%) rename good_ai/src/{sus => good_ai/utilities}/lemmatize_token.py (100%) rename good_ai/src/{sus => good_ai/utilities}/match_names/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/match_names/config.py (100%) rename good_ai/src/{sus => good_ai/utilities}/match_names/match_names.py (100%) rename good_ai/src/{sus => good_ai/utilities}/match_names/name_parts.py (100%) rename good_ai/src/{sus => good_ai/utilities}/nlp.py (100%) rename good_ai/src/{sus => good_ai/utilities}/parallel_map.py (100%) rename good_ai/src/{sus => good_ai/utilities}/publication_tei/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/publication_tei/models/__init__.py (100%) rename good_ai/src/{sus => good_ai/utilities}/publication_tei/models/affiliation.py (100%) rename good_ai/src/{sus => good_ai/utilities}/publication_tei/models/author.py (100%) rename good_ai/src/{sus => good_ai/utilities}/publication_tei/models/element.py (100%) rename good_ai/src/{sus => good_ai/utilities}/publication_tei/models/publication_metadata.py (100%) rename good_ai/src/{sus => good_ai/utilities}/publication_tei/models/text.py (100%) rename good_ai/src/{sus => good_ai/utilities}/publication_tei/publication_tei.py (98%) rename good_ai/src/{sus => good_ai/utilities}/unique.py (100%) diff --git a/example/main.py b/example/main.py index 3c45b24..5364246 100644 --- a/example/main.py +++ b/example/main.py @@ -1,9 +1,8 @@ import json -from open_s3 import LargeFile -from predict import predict_domain +from good_ai import LargeFile, process_batch +from predict_domain import predict_domain -from good_ai import process_batch if __name__ == "__main__": with open("data/s2-corpus-1583.json") as f: diff --git a/example/predict_domain.py b/example/predict_domain.py index c7bc775..da86e9a 100644 --- a/example/predict_domain.py +++ b/example/predict_domain.py @@ -7,7 +7,7 @@ from models import DomainPrediction from sklearn.pipeline import Pipeline from good_ai import use_model -from sus.clean import clean +from good_ai.utilities.clean import clean @use_model(model_key, version="latest") def predict_domain( diff --git a/example/preprocess.py b/example/preprocess.py index 83aba61..ad8944b 100644 --- a/example/preprocess.py +++ b/example/preprocess.py @@ -1,7 +1,7 @@ import re -from sus.clean import clean -from sus.lemmatize_text import lemmatize_text +from good_ai.utilities.clean import clean +from good_ai.utilities.lemmatize_text import lemmatize_text def preprocess(text: str) -> str: diff --git a/example/train.ipynb b/example/train.ipynb index 6b1865b..2948c0a 100644 --- a/example/train.ipynb +++ b/example/train.ipynb @@ -18,7 +18,23 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "ename": "ModuleNotFoundError", + "evalue": "No module named 'open_s3'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m/Users/andras/Projects/good-ai/example/train.ipynb Cell 2'\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mre\u001b[39;00m\n\u001b[1;32m 17\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mconfig\u001b[39;00m \u001b[39mimport\u001b[39;00m model_key\n\u001b[0;32m---> 18\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mgood_ai\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mutilities\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mclean\u001b[39;00m \u001b[39mimport\u001b[39;00m clean\n\u001b[1;32m 19\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mgood_ai\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mutilities\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mparallel_map\u001b[39;00m \u001b[39mimport\u001b[39;00m parallel_map\n\u001b[1;32m 20\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mgood_ai\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mutilities\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mlanguage\u001b[39;00m \u001b[39mimport\u001b[39;00m is_english, predict_language\n", + "File \u001b[0;32m~/Projects/good-ai/good_ai/src/good_ai/__init__.py:1\u001b[0m, in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39m.\u001b[39;00m\u001b[39mgood_ai\u001b[39;00m \u001b[39mimport\u001b[39;00m \u001b[39m*\u001b[39m\n\u001b[1;32m 2\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39m.\u001b[39;00m\u001b[39mutilities\u001b[39;00m \u001b[39mimport\u001b[39;00m \u001b[39m*\u001b[39m\n\u001b[1;32m 3\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39m.\u001b[39;00m\u001b[39mopen_s3\u001b[39;00m \u001b[39mimport\u001b[39;00m \u001b[39m*\u001b[39m\n", + "File \u001b[0;32m~/Projects/good-ai/good_ai/src/good_ai/good_ai/__init__.py:2\u001b[0m, in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39m.\u001b[39;00m\u001b[39mdeploy\u001b[39;00m \u001b[39mimport\u001b[39;00m process_batch\n\u001b[0;32m----> 2\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39m.\u001b[39;00m\u001b[39mmodels\u001b[39;00m \u001b[39mimport\u001b[39;00m save_model, use_model\n", + "File \u001b[0;32m~/Projects/good-ai/good_ai/src/good_ai/good_ai/models/__init__.py:1\u001b[0m, in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39m.\u001b[39;00m\u001b[39msave_model\u001b[39;00m \u001b[39mimport\u001b[39;00m save_model\n\u001b[1;32m 2\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39m.\u001b[39;00m\u001b[39muse_model\u001b[39;00m \u001b[39mimport\u001b[39;00m use_model\n", + "File \u001b[0;32m~/Projects/good-ai/good_ai/src/good_ai/good_ai/models/save_model.py:6\u001b[0m, in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mtyping\u001b[39;00m \u001b[39mimport\u001b[39;00m Optional, Union\n\u001b[1;32m 5\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mjoblib\u001b[39;00m \u001b[39mimport\u001b[39;00m dump\n\u001b[0;32m----> 6\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mopen_s3\u001b[39;00m \u001b[39mimport\u001b[39;00m LargeFile\n\u001b[1;32m 8\u001b[0m logger \u001b[39m=\u001b[39m logging\u001b[39m.\u001b[39mgetLogger(\u001b[39m\"\u001b[39m\u001b[39mmodels\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[1;32m 11\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39msave_model\u001b[39m(\n\u001b[1;32m 12\u001b[0m model: Union[Path, \u001b[39mstr\u001b[39m, \u001b[39mobject\u001b[39m], key: \u001b[39mstr\u001b[39m, keep_last_n: Optional[\u001b[39mint\u001b[39m] \u001b[39m=\u001b[39m \u001b[39mNone\u001b[39;00m\n\u001b[1;32m 13\u001b[0m ) \u001b[39m-\u001b[39m\u001b[39m>\u001b[39m \u001b[39mint\u001b[39m:\n", + "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'open_s3'" + ] + } + ], "source": [ "import json\n", "import matplotlib.pyplot as plt\n", @@ -30,19 +46,16 @@ "import pandas as pd\n", "from joblib import dump\n", "from sklearn.pipeline import Pipeline\n", - "from sklearn.feature_extraction.text import TfidfVectorizer, CountVectorizer\n", + "from sklearn.feature_extraction.text import TfidfVectorizer\n", "from sklearn import metrics\n", "from random import shuffle, seed\n", "from sklearn.model_selection import GridSearchCV\n", "from pprint import pprint\n", - "import re\n", "from config import model_key\n", - "from sus.clean import clean\n", - "from sus.parallel_map import parallel_map\n", - "from sus.language import is_english, predict_language\n", - "from sus.lemmatize_text import lemmatize_text\n", - "from open_s3 import LargeFile\n", - "from good_ai import save_model\n", + "from good_ai.utilities.clean import clean\n", + "from good_ai.utilities.parallel_map import parallel_map\n", + "from good_ai.utilities.language import is_english, predict_language\n", + "from good_ai import LargeFile, save_model\n", "from preprocess import preprocess\n", "from predict_domain import predict_domain" ] @@ -90,7 +103,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "100%|██████████| 5/5 [00:00<00:00, 43062.67it/s]\n" + "100%|██████████| 5/5 [00:00<00:00, 50412.31it/s]\n" ] } ], @@ -306,7 +319,89 @@ "cell_type": "code", "execution_count": 8, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "INFO:open_s3:Fetching online versions of domain-prediction-v2\n", + "INFO:open_s3:Found versions: [1, 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8b13789..0000000 --- a/good_ai/src/__init__.py +++ /dev/null @@ -1 +0,0 @@ - diff --git a/good_ai/src/good_ai/__init__.py b/good_ai/src/good_ai/__init__.py index 1a83f45..9cb0a76 100644 --- a/good_ai/src/good_ai/__init__.py +++ b/good_ai/src/good_ai/__init__.py @@ -1,2 +1,3 @@ -from .deploy import process_batch -from .models import save_model, use_model +from .good_ai import * +from .utilities import * +from .open_s3 import * diff --git a/good_ai/src/good_ai/good_ai/__init__.py b/good_ai/src/good_ai/good_ai/__init__.py new file mode 100644 index 0000000..1a83f45 --- /dev/null +++ b/good_ai/src/good_ai/good_ai/__init__.py @@ -0,0 +1,2 @@ +from .deploy import process_batch +from .models import save_model, use_model diff --git a/good_ai/src/good_ai/core/__init__.py b/good_ai/src/good_ai/good_ai/core/__init__.py similarity index 100% rename from good_ai/src/good_ai/core/__init__.py rename to good_ai/src/good_ai/good_ai/core/__init__.py diff --git a/good_ai/src/good_ai/core/function_registry.py b/good_ai/src/good_ai/good_ai/core/function_registry.py similarity index 100% rename from good_ai/src/good_ai/core/function_registry.py rename to good_ai/src/good_ai/good_ai/core/function_registry.py diff --git a/good_ai/src/good_ai/core/plugin.py b/good_ai/src/good_ai/good_ai/core/plugin.py similarity index 100% rename from good_ai/src/good_ai/core/plugin.py rename to good_ai/src/good_ai/good_ai/core/plugin.py diff --git a/good_ai/src/good_ai/deploy/__init__.py b/good_ai/src/good_ai/good_ai/deploy/__init__.py similarity index 100% rename from good_ai/src/good_ai/deploy/__init__.py rename to good_ai/src/good_ai/good_ai/deploy/__init__.py diff --git a/good_ai/src/good_ai/deploy/process_batch.py b/good_ai/src/good_ai/good_ai/deploy/process_batch.py similarity index 89% rename from good_ai/src/good_ai/deploy/process_batch.py rename to good_ai/src/good_ai/good_ai/deploy/process_batch.py index 500aca0..a910f5f 100644 --- a/good_ai/src/good_ai/deploy/process_batch.py +++ b/good_ai/src/good_ai/good_ai/deploy/process_batch.py @@ -1,7 +1,7 @@ from functools import partial, reduce from typing import Any, Callable, Iterable, Optional, Sequence -from sus.parallel_map import parallel_map +from good_ai.utilities.parallel_map import parallel_map from ..core import function_registry diff --git a/good_ai/src/good_ai/deploy/serve.py b/good_ai/src/good_ai/good_ai/deploy/serve.py similarity index 100% rename from good_ai/src/good_ai/deploy/serve.py rename to good_ai/src/good_ai/good_ai/deploy/serve.py diff --git a/good_ai/src/good_ai/models/__init__.py b/good_ai/src/good_ai/good_ai/models/__init__.py similarity index 100% rename from good_ai/src/good_ai/models/__init__.py rename to good_ai/src/good_ai/good_ai/models/__init__.py diff --git a/good_ai/src/good_ai/models/load_model.py b/good_ai/src/good_ai/good_ai/models/load_model.py similarity index 90% rename from good_ai/src/good_ai/models/load_model.py rename to good_ai/src/good_ai/good_ai/models/load_model.py index afd4b99..a3cdabf 100644 --- a/good_ai/src/good_ai/models/load_model.py +++ b/good_ai/src/good_ai/good_ai/models/load_model.py @@ -2,7 +2,7 @@ import logging from typing import Any, Optional from joblib import load -from open_s3 import LargeFile +from good_ai.open_s3 import LargeFile logger = logging.getLogger("models") diff --git a/good_ai/src/good_ai/models/save_model.py b/good_ai/src/good_ai/good_ai/models/save_model.py similarity index 93% rename from good_ai/src/good_ai/models/save_model.py rename to good_ai/src/good_ai/good_ai/models/save_model.py index 420a43b..17f8a26 100644 --- a/good_ai/src/good_ai/models/save_model.py +++ b/good_ai/src/good_ai/good_ai/models/save_model.py @@ -3,7 +3,7 @@ from pathlib import Path from typing import Optional, Union from joblib import dump -from open_s3 import LargeFile +from good_ai.open_s3 import LargeFile logger = logging.getLogger("models") diff --git a/good_ai/src/good_ai/models/use_model.py b/good_ai/src/good_ai/good_ai/models/use_model.py similarity index 100% rename from good_ai/src/good_ai/models/use_model.py rename to good_ai/src/good_ai/good_ai/models/use_model.py diff --git a/good_ai/src/good_ai/models/use_model_plugin.py b/good_ai/src/good_ai/good_ai/models/use_model_plugin.py similarity index 100% rename from good_ai/src/good_ai/models/use_model_plugin.py rename to good_ai/src/good_ai/good_ai/models/use_model_plugin.py diff --git a/good_ai/src/open_s3/__init__.py b/good_ai/src/good_ai/open_s3/__init__.py similarity index 100% rename from good_ai/src/open_s3/__init__.py rename to good_ai/src/good_ai/open_s3/__init__.py diff --git a/good_ai/src/open_s3/__main__.py b/good_ai/src/good_ai/open_s3/__main__.py similarity index 100% rename from good_ai/src/open_s3/__main__.py rename to good_ai/src/good_ai/open_s3/__main__.py diff --git a/good_ai/src/open_s3/helper/__init__.py b/good_ai/src/good_ai/open_s3/helper/__init__.py similarity index 100% rename from good_ai/src/open_s3/helper/__init__.py rename to good_ai/src/good_ai/open_s3/helper/__init__.py diff --git a/good_ai/src/open_s3/helper/human_readable_to_byte.py b/good_ai/src/good_ai/open_s3/helper/human_readable_to_byte.py similarity index 100% rename from good_ai/src/open_s3/helper/human_readable_to_byte.py rename to good_ai/src/good_ai/open_s3/helper/human_readable_to_byte.py diff --git a/good_ai/src/open_s3/helper/progress_bar.py b/good_ai/src/good_ai/open_s3/helper/progress_bar.py similarity index 100% rename from good_ai/src/open_s3/helper/progress_bar.py rename to good_ai/src/good_ai/open_s3/helper/progress_bar.py diff --git a/good_ai/src/open_s3/large_file.py b/good_ai/src/good_ai/open_s3/large_file.py similarity index 100% rename from good_ai/src/open_s3/large_file.py rename to good_ai/src/good_ai/open_s3/large_file.py diff --git a/good_ai/src/open_s3/parse_arguments.py b/good_ai/src/good_ai/open_s3/parse_arguments.py similarity index 100% rename from good_ai/src/open_s3/parse_arguments.py rename to good_ai/src/good_ai/open_s3/parse_arguments.py diff --git a/good_ai/src/sus/__init__.py b/good_ai/src/good_ai/utilities/__init__.py similarity index 100% rename from good_ai/src/sus/__init__.py rename to good_ai/src/good_ai/utilities/__init__.py diff --git a/good_ai/src/sus/clean.py b/good_ai/src/good_ai/utilities/clean.py similarity index 100% rename from good_ai/src/sus/clean.py rename to good_ai/src/good_ai/utilities/clean.py diff --git a/good_ai/src/sus/data/__init__.py b/good_ai/src/good_ai/utilities/data/__init__.py similarity index 100% rename from good_ai/src/sus/data/__init__.py rename to good_ai/src/good_ai/utilities/data/__init__.py diff --git a/good_ai/src/sus/data/american_spellings.py b/good_ai/src/good_ai/utilities/data/american_spellings.py similarity index 100% rename from good_ai/src/sus/data/american_spellings.py rename to good_ai/src/good_ai/utilities/data/american_spellings.py diff --git a/good_ai/src/sus/data/punctuations.py b/good_ai/src/good_ai/utilities/data/punctuations.py similarity index 100% rename from good_ai/src/sus/data/punctuations.py rename to good_ai/src/good_ai/utilities/data/punctuations.py diff --git a/good_ai/src/sus/evaluate_ranking/__init__.py b/good_ai/src/good_ai/utilities/evaluate_ranking/__init__.py similarity index 100% rename from good_ai/src/sus/evaluate_ranking/__init__.py rename to good_ai/src/good_ai/utilities/evaluate_ranking/__init__.py diff --git a/good_ai/src/sus/evaluate_ranking/draw_f1_iso_lines.py b/good_ai/src/good_ai/utilities/evaluate_ranking/draw_f1_iso_lines.py similarity index 100% rename from good_ai/src/sus/evaluate_ranking/draw_f1_iso_lines.py rename to good_ai/src/good_ai/utilities/evaluate_ranking/draw_f1_iso_lines.py diff --git a/good_ai/src/sus/evaluate_ranking/evaluate_ranking.py b/good_ai/src/good_ai/utilities/evaluate_ranking/evaluate_ranking.py similarity index 100% rename from good_ai/src/sus/evaluate_ranking/evaluate_ranking.py rename to good_ai/src/good_ai/utilities/evaluate_ranking/evaluate_ranking.py diff --git a/good_ai/src/sus/external/__init__.py b/good_ai/src/good_ai/utilities/external/__init__.py similarity index 100% rename from good_ai/src/sus/external/__init__.py rename to good_ai/src/good_ai/utilities/external/__init__.py diff --git a/good_ai/src/sus/external/negspacy/README.md b/good_ai/src/good_ai/utilities/external/negspacy/README.md similarity index 100% rename from good_ai/src/sus/external/negspacy/README.md rename to good_ai/src/good_ai/utilities/external/negspacy/README.md diff --git a/good_ai/src/sus/external/negspacy/__init__.py b/good_ai/src/good_ai/utilities/external/negspacy/__init__.py similarity index 100% rename from good_ai/src/sus/external/negspacy/__init__.py rename to good_ai/src/good_ai/utilities/external/negspacy/__init__.py diff --git a/good_ai/src/sus/external/negspacy/negation.py b/good_ai/src/good_ai/utilities/external/negspacy/negation.py similarity index 100% rename from good_ai/src/sus/external/negspacy/negation.py rename to good_ai/src/good_ai/utilities/external/negspacy/negation.py diff --git a/good_ai/src/sus/external/negspacy/termsets.py b/good_ai/src/good_ai/utilities/external/negspacy/termsets.py similarity index 98% rename from good_ai/src/sus/external/negspacy/termsets.py rename to good_ai/src/good_ai/utilities/external/negspacy/termsets.py index a226aba..14660da 100644 --- a/good_ai/src/sus/external/negspacy/termsets.py +++ b/good_ai/src/good_ai/utilities/external/negspacy/termsets.py @@ -40,7 +40,7 @@ preceding = [ "doubt", "negative for", "no", - "versus", + "vergood_ai.utilities", "without", "doesn't", "doesnt", @@ -104,7 +104,7 @@ pseudo_clinical = pseudo + [ "not ruled out", "not been ruled out", "not drain", - "no suspicious change", + "no good_ai.utilitiespicious change", "no interval change", "no significant interval change", ] diff --git a/good_ai/src/sus/external/pylatexenc/README.md b/good_ai/src/good_ai/utilities/external/pylatexenc/README.md similarity index 100% rename from good_ai/src/sus/external/pylatexenc/README.md rename to good_ai/src/good_ai/utilities/external/pylatexenc/README.md diff --git a/good_ai/src/sus/external/pylatexenc/__init__.py b/good_ai/src/good_ai/utilities/external/pylatexenc/__init__.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/__init__.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/__init__.py diff --git a/good_ai/src/sus/external/pylatexenc/_util.py b/good_ai/src/good_ai/utilities/external/pylatexenc/_util.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/_util.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/_util.py diff --git a/good_ai/src/sus/external/pylatexenc/latex2text/__init__.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latex2text/__init__.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latex2text/__init__.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latex2text/__init__.py diff --git a/good_ai/src/sus/external/pylatexenc/latex2text/__main__.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latex2text/__main__.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latex2text/__main__.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latex2text/__main__.py diff --git a/good_ai/src/sus/external/pylatexenc/latex2text/_defaultspecs.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latex2text/_defaultspecs.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latex2text/_defaultspecs.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latex2text/_defaultspecs.py diff --git a/good_ai/src/sus/external/pylatexenc/latexencode/__init__.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/__init__.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latexencode/__init__.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/__init__.py diff --git a/good_ai/src/sus/external/pylatexenc/latexencode/__main__.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/__main__.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latexencode/__main__.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/__main__.py diff --git a/good_ai/src/sus/external/pylatexenc/latexencode/_partial_latex_encoder.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/_partial_latex_encoder.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latexencode/_partial_latex_encoder.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/_partial_latex_encoder.py diff --git a/good_ai/src/sus/external/pylatexenc/latexencode/_uni2latexmap.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/_uni2latexmap.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latexencode/_uni2latexmap.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/_uni2latexmap.py diff --git a/good_ai/src/sus/external/pylatexenc/latexencode/_uni2latexmap_xml.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/_uni2latexmap_xml.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latexencode/_uni2latexmap_xml.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/_uni2latexmap_xml.py diff --git a/good_ai/src/sus/external/pylatexenc/latexencode/_unicode_to_latex_encoder.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/_unicode_to_latex_encoder.py similarity index 99% rename from good_ai/src/sus/external/pylatexenc/latexencode/_unicode_to_latex_encoder.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/_unicode_to_latex_encoder.py index fbc5a47..dee6128 100644 --- a/good_ai/src/sus/external/pylatexenc/latexencode/_unicode_to_latex_encoder.py +++ b/good_ai/src/good_ai/utilities/external/pylatexenc/latexencode/_unicode_to_latex_encoder.py @@ -342,7 +342,7 @@ class UnicodeToLatexEncoder(object): Possible protection schemes are: - - 'braces' (the default): Any suspicious replacement text (that + - 'braces' (the default): Any good_ai.utilitiespicious replacement text (that might look fragile) is placed in curly braces ``{...}``. - 'braces-all': All replacement latex escapes are surrounded in diff --git a/good_ai/src/sus/external/pylatexenc/latexwalker/__init__.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latexwalker/__init__.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latexwalker/__init__.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latexwalker/__init__.py diff --git a/good_ai/src/sus/external/pylatexenc/latexwalker/__main__.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latexwalker/__main__.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latexwalker/__main__.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latexwalker/__main__.py diff --git a/good_ai/src/sus/external/pylatexenc/latexwalker/_defaultspecs.py b/good_ai/src/good_ai/utilities/external/pylatexenc/latexwalker/_defaultspecs.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/latexwalker/_defaultspecs.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/latexwalker/_defaultspecs.py diff --git a/good_ai/src/sus/external/pylatexenc/macrospec/__init__.py b/good_ai/src/good_ai/utilities/external/pylatexenc/macrospec/__init__.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/macrospec/__init__.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/macrospec/__init__.py diff --git a/good_ai/src/sus/external/pylatexenc/macrospec/_argparsers.py b/good_ai/src/good_ai/utilities/external/pylatexenc/macrospec/_argparsers.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/macrospec/_argparsers.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/macrospec/_argparsers.py diff --git a/good_ai/src/sus/external/pylatexenc/version.py b/good_ai/src/good_ai/utilities/external/pylatexenc/version.py similarity index 100% rename from good_ai/src/sus/external/pylatexenc/version.py rename to good_ai/src/good_ai/utilities/external/pylatexenc/version.py diff --git a/good_ai/src/sus/get_sentences.py b/good_ai/src/good_ai/utilities/get_sentences.py similarity index 100% rename from good_ai/src/sus/get_sentences.py rename to good_ai/src/good_ai/utilities/get_sentences.py diff --git a/good_ai/src/sus/language/__init__.py b/good_ai/src/good_ai/utilities/language/__init__.py similarity index 100% rename from good_ai/src/sus/language/__init__.py rename to good_ai/src/good_ai/utilities/language/__init__.py diff --git a/good_ai/src/sus/language/english_name_of_language.py b/good_ai/src/good_ai/utilities/language/english_name_of_language.py similarity index 100% rename from good_ai/src/sus/language/english_name_of_language.py rename to good_ai/src/good_ai/utilities/language/english_name_of_language.py diff --git a/good_ai/src/sus/language/is_english.py b/good_ai/src/good_ai/utilities/language/is_english.py similarity index 100% rename from good_ai/src/sus/language/is_english.py rename to good_ai/src/good_ai/utilities/language/is_english.py diff --git a/good_ai/src/sus/language/predict_language.py b/good_ai/src/good_ai/utilities/language/predict_language.py similarity index 100% rename from good_ai/src/sus/language/predict_language.py rename to good_ai/src/good_ai/utilities/language/predict_language.py diff --git a/good_ai/src/sus/lemmatize_text.py b/good_ai/src/good_ai/utilities/lemmatize_text.py similarity index 100% rename from good_ai/src/sus/lemmatize_text.py rename to good_ai/src/good_ai/utilities/lemmatize_text.py diff --git a/good_ai/src/sus/lemmatize_token.py b/good_ai/src/good_ai/utilities/lemmatize_token.py similarity index 100% rename from good_ai/src/sus/lemmatize_token.py rename to good_ai/src/good_ai/utilities/lemmatize_token.py diff --git a/good_ai/src/sus/match_names/__init__.py b/good_ai/src/good_ai/utilities/match_names/__init__.py similarity index 100% rename from good_ai/src/sus/match_names/__init__.py rename to good_ai/src/good_ai/utilities/match_names/__init__.py diff --git a/good_ai/src/sus/match_names/config.py b/good_ai/src/good_ai/utilities/match_names/config.py similarity index 100% rename from good_ai/src/sus/match_names/config.py rename to good_ai/src/good_ai/utilities/match_names/config.py diff --git a/good_ai/src/sus/match_names/match_names.py b/good_ai/src/good_ai/utilities/match_names/match_names.py similarity index 100% rename from good_ai/src/sus/match_names/match_names.py rename to good_ai/src/good_ai/utilities/match_names/match_names.py diff --git a/good_ai/src/sus/match_names/name_parts.py b/good_ai/src/good_ai/utilities/match_names/name_parts.py similarity index 100% rename from good_ai/src/sus/match_names/name_parts.py rename to good_ai/src/good_ai/utilities/match_names/name_parts.py diff --git a/good_ai/src/sus/nlp.py b/good_ai/src/good_ai/utilities/nlp.py similarity index 100% rename from good_ai/src/sus/nlp.py rename to good_ai/src/good_ai/utilities/nlp.py diff --git a/good_ai/src/sus/parallel_map.py b/good_ai/src/good_ai/utilities/parallel_map.py similarity index 100% rename from good_ai/src/sus/parallel_map.py rename to good_ai/src/good_ai/utilities/parallel_map.py diff --git a/good_ai/src/sus/publication_tei/__init__.py b/good_ai/src/good_ai/utilities/publication_tei/__init__.py similarity index 100% rename from good_ai/src/sus/publication_tei/__init__.py rename to good_ai/src/good_ai/utilities/publication_tei/__init__.py diff --git a/good_ai/src/sus/publication_tei/models/__init__.py b/good_ai/src/good_ai/utilities/publication_tei/models/__init__.py similarity index 100% rename from good_ai/src/sus/publication_tei/models/__init__.py rename to good_ai/src/good_ai/utilities/publication_tei/models/__init__.py diff --git a/good_ai/src/sus/publication_tei/models/affiliation.py b/good_ai/src/good_ai/utilities/publication_tei/models/affiliation.py similarity index 100% rename from good_ai/src/sus/publication_tei/models/affiliation.py rename to good_ai/src/good_ai/utilities/publication_tei/models/affiliation.py diff --git a/good_ai/src/sus/publication_tei/models/author.py b/good_ai/src/good_ai/utilities/publication_tei/models/author.py similarity index 100% rename from good_ai/src/sus/publication_tei/models/author.py rename to good_ai/src/good_ai/utilities/publication_tei/models/author.py diff --git a/good_ai/src/sus/publication_tei/models/element.py b/good_ai/src/good_ai/utilities/publication_tei/models/element.py similarity index 100% rename from good_ai/src/sus/publication_tei/models/element.py rename to good_ai/src/good_ai/utilities/publication_tei/models/element.py diff --git a/good_ai/src/sus/publication_tei/models/publication_metadata.py b/good_ai/src/good_ai/utilities/publication_tei/models/publication_metadata.py similarity index 100% rename from good_ai/src/sus/publication_tei/models/publication_metadata.py rename to good_ai/src/good_ai/utilities/publication_tei/models/publication_metadata.py diff --git a/good_ai/src/sus/publication_tei/models/text.py b/good_ai/src/good_ai/utilities/publication_tei/models/text.py similarity index 100% rename from good_ai/src/sus/publication_tei/models/text.py rename to good_ai/src/good_ai/utilities/publication_tei/models/text.py diff --git a/good_ai/src/sus/publication_tei/publication_tei.py b/good_ai/src/good_ai/utilities/publication_tei/publication_tei.py similarity index 98% rename from good_ai/src/sus/publication_tei/publication_tei.py rename to good_ai/src/good_ai/utilities/publication_tei/publication_tei.py index 44d79ab..7f7c714 100644 --- a/good_ai/src/sus/publication_tei/publication_tei.py +++ b/good_ai/src/good_ai/utilities/publication_tei/publication_tei.py @@ -3,7 +3,7 @@ from typing import Any, List, Optional, Union from bs4 import BeautifulSoup from bs4.element import NavigableString, Tag -from sus.publication_tei.models.element import Paragraph +from good_ai.utilities.publication_tei.models.element import Paragraph from ..clean import clean from .models import Affiliation, Author, Element, Meta, PublicationMetadata, Text, Title diff --git a/good_ai/src/sus/unique.py b/good_ai/src/good_ai/utilities/unique.py similarity index 100% rename from good_ai/src/sus/unique.py rename to good_ai/src/good_ai/utilities/unique.py