diff --git a/cogstack-es/ReadMe.md b/cogstack-es/ReadMe.md index 14a4da42..1f8c7bf0 100644 --- a/cogstack-es/ReadMe.md +++ b/cogstack-es/ReadMe.md @@ -6,9 +6,9 @@ This project is responsible for logging in and performing a search for Elasticse This package is distributed through PyPI and can be installed using one of: ``` -pip install cogstack-es[ES9] # For Elasticsearch 9 -pip install cogstack-es[ES8] # For Elasticsearch 8 -pip install cogstack-es[OS] # For Opensearch +pip install "cogstack-es[ES9]" # For Elasticsearch 9 +pip install "cogstack-es[ES8]" # For Elasticsearch 8 +pip install "cogstack-es[OS]" # For Opensearch ``` PS: diff --git a/medcat-v2/docs/migration_guide_v2.md b/medcat-v2/docs/migration_guide_v2.md index 203a6713..02e3e2c9 100644 --- a/medcat-v2/docs/migration_guide_v2.md +++ b/medcat-v2/docs/migration_guide_v2.md @@ -70,6 +70,7 @@ Here's a list of the additional features you can opt for with what they're used | Transformer NER | `deid` | Enables transformer-based NER, primarily used for de-identification models | | Relation Extraction | `rel-cat` | Adds support for extracting relations between entities | | Dictionary NER | `dict-ner` | Example dictionary NER module (experimental and rarely needed) | +| Embedding linker | `embed-linker` | Linker that uses more sophisiticated context embeddings for linking | ## Summary of Changes @@ -122,15 +123,12 @@ The v2 tutorials are available [here](https://github.com/CogStack/cogstack-nlp/t ## Updated `working_with_cogstack` scripts The `working_with_cogstack` scripts have also been upgraded to support v2. -The changes are currently in [this PR](https://github.com/CogStack/working_with_cogstack/pull/20). -They have not yet been merged in to the `main` branch but will be in the near future. -At that point, there will probably be a separate branch to keep track of v1-specific scripts. +However, they have been split into `cogstack-es` which lives [here](https://github.com/CogStack/cogstack-nlp/tree/main/cogstack-es), but notably also available on PyPI (i.e `pip install "cogstack-es[ES9]"`); and `medcat-scripts` available [here](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-scripts) which can be fetched using `python -m medcat download-scripts` (in v2.3.0 onwards). ## MedCATtrainer -MedCATtrainer has been modified to work with v2 in [this PR](https://github.com/CogStack/MedCATtrainer/pull/253). -However, as of writing, this change has not yet been merged in or been released. -The v2-supporting release will most likely be released as **v3** on the trainer side. +MedCATtrainer has been modified to work with v2 in [here](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer). +The v2-supporting releases are those from **v3** on the trainer side. ## Feedback welcome! @@ -181,12 +179,12 @@ A: Training now uses a dedicated `medcat.trainer.Trainer` class. See tutorials a **Q: Are v1 `working_with_cogstack` scripts still supported?** -A: No. Many will break due to internal changes. Please refer to the new scripts in the [relevant branch](https://github.com/CogStack/working_with_cogstack/pull/20). +A: No. You should use [medcat scripts](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-scripts) and [cogstack-es](https://github.com/CogStack/cogstack-nlp/tree/main/cogstack-es) by doing `python -m medcat download-scripts` (in v2.3.0 onwards) and `pip install "cogstack-es[ES9]"`. **Q: Does MedCATtrainer work out of the box for v2?** -A: No. While the [changes have been ported](https://github.com/CogStack/MedCATtrainer/pull/253), there is currently no release for these changes and it is unlikely to already be spun up yet. But it will be soon. +A: Yes. Trainer versions from v3 onwards will work natively with v2. **Q: Does `medcat-service` work for serving a model?**