CU-8699brxuh update to v0.5.0

notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb

@@ -26,17 +26,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "from typing import Any, overload, Iterator, Optional, cast\n",
     "\n",
     "import re\n",
     "\n",
-    "from medcat2.config.config import Config\n",
-    "from medcat2.tokenizing.tokens import BaseDocument, BaseEntity, BaseToken\n",
-    "from medcat2.tokenizing.tokens import MutableDocument, MutableEntity, MutableToken\n",
+    "from medcat.config.config import Config\n",
+    "from medcat.tokenizing.tokens import BaseDocument, BaseEntity, BaseToken\n",
+    "from medcat.tokenizing.tokens import MutableDocument, MutableEntity, MutableToken\n",
     "\n",
     "\n",
     "# define \"whitespace\"\n",
@@ -376,7 +376,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -388,7 +388,7 @@
     }
    ],
    "source": [
-    "from medcat2.tokenizing.tokenizers import register_tokenizer, list_available_tokenizers\n",
+    "from medcat.tokenizing.tokenizers import register_tokenizer, list_available_tokenizers\n",
     "register_tokenizer(\"whitespace-tokenizer\", WhitespaceTokenizer)\n",
     "print(\"Registered tokenizers:\", list_available_tokenizers())"
    ]
@@ -404,7 +404,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -416,7 +416,7 @@
     }
    ],
    "source": [
-    "from medcat2.tokenizing.tokenizers import create_tokenizer\n",
+    "from medcat.tokenizing.tokenizers import create_tokenizer\n",
     "tokenizer = create_tokenizer(\"whitespace-tokenizer\")\n",
     "print(\"We've got one:\", tokenizer)"
    ]

notebooks/advanced/2._Create_and_use_component.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# How to create and use a (core) component with medcat2\n",
+    "# How to create and use a (core) component with medcat v2\n",
     "\n",
     "The overall process is quite simple:\n",
     "- Implement and extend `CoreComponent`\n",
@@ -26,20 +26,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "# for init args\n",
     "from typing import Optional, Any\n",
     "\n",
-    "from medcat2.tokenizing.tokenizers import BaseTokenizer\n",
-    "from medcat2.vocab import Vocab\n",
-    "from medcat2.cdb.cdb import CDB\n",
+    "from medcat.tokenizing.tokenizers import BaseTokenizer\n",
+    "from medcat.vocab import Vocab\n",
+    "from medcat.cdb.cdb import CDB\n",
     "# for the component itself\n",
-    "from medcat2.components.types import AbstractCoreComponent, CoreComponentType\n",
-    "from medcat2.tokenizing.tokens import MutableDocument, MutableEntity\n",
-    "from medcat2.components.ner.vocab_based_annotator import maybe_annotate_name\n",
+    "from medcat.components.types import AbstractCoreComponent, CoreComponentType\n",
+    "from medcat.tokenizing.tokens import MutableDocument, MutableEntity\n",
+    "from medcat.components.ner.vocab_based_annotator import maybe_annotate_name\n",
     "\n",
     "# for the randomness\n",
     "import random\n",
@@ -143,11 +143,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from medcat2.components.types import register_core_component\n",
+    "from medcat.components.types import register_core_component\n",
     "register_core_component(CoreComponentType.ner, RandomNER.name, RandomNER)"
    ]
   },
@@ -160,7 +160,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -241,9 +241,9 @@
     }
    ],
    "source": [
-    "from medcat2.config.config import Config\n",
-    "from medcat2.preprocessors.cleaners import NameDescriptor\n",
-    "from medcat2.cat import CAT\n",
+    "from medcat.config.config import Config\n",
+    "from medcat.preprocessors.cleaners import NameDescriptor\n",
+    "from medcat.cat import CAT\n",
     "import numpy as np\n",
     "\n",
     "from pprint import pprint\n",

notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb

@@ -34,7 +34,7 @@
    "source": [
     "import os\n",
     "import numpy as np\n",
-    "from medcat2.vocab import Vocab\n",
+    "from medcat.vocab import Vocab\n",
     "\n",
     "vocab = Vocab()"
    ]
@@ -124,9 +124,9 @@
    ],
    "source": [
     "import pandas as pd\n",
-    "from medcat2.model_creation.cdb_maker import CDBMaker\n",
-    "from medcat2.cdb import CDB\n",
-    "from medcat2.config import Config\n",
+    "from medcat.model_creation.cdb_maker import CDBMaker\n",
+    "from medcat.cdb import CDB\n",
+    "from medcat.config import Config\n",
     "\n",
     "# first we need a config\n",
     "# we can use the default for now\n",
@@ -299,7 +299,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from medcat2.cat import CAT\n",
+    "from medcat.cat import CAT\n",
     "\n",
     "cat = CAT(cdb, vocab, cnf)"
    ]
@@ -379,20 +379,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved at models/base_model\n"
+      "Saved at models/base_model_15ba4a6c78264c90\n"
      ]
     }
    ],
    "source": [
     "save_path = \"models\"\n",
-    "mpp = cat.save_model_pack(save_path, pack_name=\"base_model\")\n",
+    "mpp = cat.save_model_pack(save_path, pack_name=\"base_model\", add_hash_to_pack_name=False)\n",
     "print(\"Saved at\", mpp)"
    ]
   }

notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb

@@ -15,12 +15,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
-    "from medcat2.cat import CAT\n",
+    "from medcat.cat import CAT\n",
     "\n",
     "\n",
     "# NOTE: can refer to the .zip or the folder - both will work just fine\n",
@@ -143,7 +143,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -156,7 +156,7 @@
    ],
    "source": [
     "save_path = \"models\"\n",
-    "mpp = cat.save_model_pack(save_path, pack_name=\"unsup_trained_model\")\n",
+    "mpp = cat.save_model_pack(save_path, pack_name=\"unsup_trained_model\", add_hash_to_pack_name=False)\n",
     "print(\"Saved at\", mpp)"
    ]
   }

notebooks/introductory/basic/3._Supervised_training_on_model.ipynb

@@ -22,13 +22,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
     "\n",
-    "from medcat2.cat import CAT\n",
+    "from medcat.cat import CAT\n",
     "\n",
     "model_path = os.path.join(\"models\", \"unsup_trained_model.zip\")\n",
     "\n",
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -63,7 +63,7 @@
    ],
    "source": [
     "import pandas as pd\n",
-    "from medcat2.model_creation.cdb_maker import CDBMaker\n",
+    "from medcat.model_creation.cdb_maker import CDBMaker\n",
     "\n",
     "cdb_maker = CDBMaker(cat.config, cat.cdb)\n",
     "\n",
@@ -208,7 +208,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -224,7 +224,7 @@
    ],
    "source": [
     "new_model_folder, new_model_name = \"models\", \"sup_trained_model\"\n",
-    "cat.save_model_pack(new_model_folder, pack_name=new_model_name)\n"
+    "cat.save_model_pack(new_model_folder, pack_name=new_model_name, add_hash_to_pack_name=False)\n"
    ]
   }
  ],

notebooks/introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb

@@ -76,7 +76,7 @@
     }
    ],
    "source": [
-    "! pip install \"medcat2[meta-cat] @ git+https://github.com/CogStack/MedCAT2@v0.3.3\" # NOTE: VERSION-STRING"
+    "! pip install \"medcat[meta-cat] @ git+https://github.com/CogStack/MedCAT2@v0.5.0\" # NOTE: VERSION-STRING"
    ]
   },
   {
@@ -91,7 +91,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "feefc4ff",
    "metadata": {},
    "outputs": [
@@ -106,9 +106,9 @@
    ],
    "source": [
     "import os\n",
-    "from medcat2.cat import CAT\n",
-    "from medcat2.components.addons.meta_cat.meta_cat import MetaCATAddon\n",
-    "from medcat2.config.config_meta_cat import ConfigMetaCAT\n",
+    "from medcat.cat import CAT\n",
+    "from medcat.components.addons.meta_cat.meta_cat import MetaCATAddon\n",
+    "from medcat.config.config_meta_cat import ConfigMetaCAT\n",
     "\n",
     "BASIC_MODELS_FOLDER = os.path.join(\"..\", \"basic\", \"models\")\n",
     "MODEL_NAME = \"sup_trained_model.zip\"\n",

notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb

@@ -131,7 +131,7 @@
     }
    ],
    "source": [
-    "! pip install \"medcat2[meta-cat,spacy,deid] @ git+https://github.com/CogStack/MedCAT2@v0.3.3\""
+    "! pip install \"medcat[meta-cat,spacy,deid] @ git+https://github.com/CogStack/MedCAT2@v0.5.0\""
    ]
   },
   {
@@ -147,7 +147,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "486327da",
    "metadata": {},
    "outputs": [
@@ -163,7 +163,7 @@
    "source": [
     "model_path = \"models/medcat1_model_pack.zip\"\n",
     "new_model_folder = \"models\"  # file in this folder\n",
-    "! python -m  medcat2.utils.legacy.legacy_converter $model_path $new_model_folder --verbose"
+    "! python -m  medcat.utils.legacy.legacy_converter $model_path $new_model_folder --verbose"
    ]
   }
  ],

requirements.txt

@@ -1,4 +1,4 @@
-medcat2 @ git+https://github.com/CogStack/MedCAT2@v0.3.3
+medcat @ git+https://github.com/CogStack/MedCAT2@v0.5.0
 ipykernel
 pytest-xdist~=3.6.0
 nbmake<1.6