diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 9984edc1..dce6b898 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -13,9 +13,9 @@ name: "CodeQL" on: push: - branches: [ "master" ] + branches: [ "main" ] pull_request: - branches: [ "master" ] + branches: [ "main" ] schedule: - cron: '36 14 * * 0' diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e4dc454b..5ecc1e25 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -2,9 +2,9 @@ name: build on: push: - branches: [ master ] + branches: [ main ] pull_request: - branches: [ master ] + branches: [ main ] jobs: build: @@ -62,7 +62,7 @@ jobs: }); core.setOutput('latest_version', latestRelease.data.tag_name); - name: Make sure there's no deprecated methods that should be removed. - # only run this for master -> production PR. I.e just before doing a release. + # only run this for main -> production PR. I.e just before doing a release. if: github.event.pull_request.base.ref == 'main' && github.event.pull_request.head.ref == 'production' env: VERSION: ${{ steps.get_latest_release.outputs.latest_version }} @@ -73,7 +73,7 @@ jobs: if: | github.repository == 'CogStack/MedCAT' && - github.ref == 'refs/heads/master' && + github.ref == 'refs/heads/main' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags') != true runs-on: ubuntu-24.04 @@ -82,10 +82,10 @@ jobs: needs: [build] steps: - - name: Checkout master + - name: Checkout main uses: actions/checkout@v4 with: - ref: 'master' + ref: 'main' fetch-depth: 0 - name: Set up Python 3.9 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3e430cda..397aa058 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -54,7 +54,7 @@ When making changes to MedCAT, make sure you have the dependencies defined in [r Please make sure the code additions are adequately tested and well documented. Before submitting a pull request, please ensure that the changes satisfy following: -- The changes are based on the `master` branch (i.e merge the master branch in before submitting a PR) +- The changes are based on the `main` branch (i.e merge the main branch in before submitting a PR) - There are no issues with types/mypy (run `python -m mypy --follow-imports=normal medcat` in the project root) - There are no issues with flake8 (run `flake8 medcat` in the project root) - All tests are successful (run `python -m unittest discover` in the project root) diff --git a/README.md b/README.md index 25808fc8..2da4c17c 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ -# Medical oncept Annotation Tool +# Medical oncept Annotation Tool **NB! [MedCAT v2](https://github.com/CogStack/MedCAT2) will soon be released.** **MedCAT v1.16.0 will be the latest MedCAT v1 minor release.** **However, we will likely continue to support v1.16.x with patch releases for some time.** -[![Build Status](https://github.com/CogStack/MedCAT/actions/workflows/main.yml/badge.svg?branch=master)](https://github.com/CogStack/MedCAT/actions/workflows/main.yml?query=branch%3Amaster) +[![Build Status](https://github.com/CogStack/MedCAT/actions/workflows/main.yml/badge.svg?branch=main)](https://github.com/CogStack/MedCAT/actions/workflows/main.yml?query=branch%3Amain) [![Documentation Status](https://readthedocs.org/projects/medcat/badge/?version=latest)](https://medcat.readthedocs.io/en/latest/?badge=latest) [![Latest release](https://img.shields.io/github/v/release/CogStack/MedCAT)](https://github.com/CogStack/MedCAT/releases/latest) [![pypi Version](https://img.shields.io/pypi/v/medcat.svg?style=flat-square&logo=pypi&logoColor=white)](https://pypi.org/project/medcat/) @@ -40,7 +40,7 @@ To download any of these models, please [follow this link](https://uts.nlm.nih.g branch and will still be supported until 1. July 2021 (with respect to potential bug fixes), after it will still be available but not updated anymore. - **Paper**: [What’s in a Summary? Laying the Groundwork for Advances in Hospital-Course Summarization](https://www.aclweb.org/anthology/2021.naacl-main.382.pdf) -- ([more...](https://github.com/CogStack/MedCAT/blob/master/media/news.md)) +- ([more...](https://github.com/CogStack/MedCAT/blob/main/media/news.md)) ## Installation To install the latest version of MedCAT run the following command: diff --git a/docs/main.md b/docs/main.md index f80b12b1..b8796487 100644 --- a/docs/main.md +++ b/docs/main.md @@ -1,6 +1,6 @@ -# Medical oncept Annotation Tool +# Medical oncept Annotation Tool -[![Build Status](https://github.com/CogStack/MedCAT/actions/workflows/main.yml/badge.svg?branch=master)](https://github.com/CogStack/MedCAT/actions/workflows/main.yml?query=branch%3Amaster) +[![Build Status](https://github.com/CogStack/MedCAT/actions/workflows/main.yml/badge.svg?branch=main)](https://github.com/CogStack/MedCAT/actions/workflows/main.yml?query=branch%3Amain) [![Documentation Status](https://readthedocs.org/projects/medcat/badge/?version=latest)](https://medcat.readthedocs.io/en/latest/?badge=latest) [![Latest release](https://img.shields.io/github/v/release/CogStack/MedCAT)](https://github.com/CogStack/MedCAT/releases/latest) [![pypi Version](https://img.shields.io/pypi/v/medcat.svg?style=flat-square&logo=pypi&logoColor=white)](https://pypi.org/project/medcat/) @@ -108,10 +108,10 @@ python medcat/utils/model_creator.py tests/model_creator/config_example.yml | Model creator parameter | Description | | -------- | ----------- | -| concept_csv_file | Path to file containing UMLS concepts, including primary names, synonyms, types and source ontology. See [examples](https://github.com/CogStack/MedCAT/tree/master/examples) and [tests/model_creator/umls_sample.csv](https://github.com/CogStack/MedCAT/tree/master/tests/model_creator/umls_sample.csv) for format description and examples. | +| concept_csv_file | Path to file containing UMLS concepts, including primary names, synonyms, types and source ontology. See [examples](https://github.com/CogStack/MedCAT/tree/main/examples) and [tests/model_creator/umls_sample.csv](https://github.com/CogStack/MedCAT/tree/main/tests/model_creator/umls_sample.csv) for format description and examples. | | unsupervised_training_data_file | Path to file containing text dataset used for spell checking and unsupervised training.| | output_dir | Path to output directory for writing the CDB and vocab models. | -| medcat_config_file | Path to optional config file for adjusting MedCAT properties, see [configs](https://github.com/CogStack/MedCAT/tree/master/configs), [medcat/config.py](https://github.com/CogStack/MedCAT/tree/master/medcat/config.py) and [tests/model_creator/medcat.txt](https://github.com/CogStack/MedCAT/tree/master/tests/model_creator/medcat.txt)| +| medcat_config_file | Path to optional config file for adjusting MedCAT properties, see [configs](https://github.com/CogStack/MedCAT/tree/main/configs), [medcat/config.py](https://github.com/CogStack/MedCAT/tree/main/medcat/config.py) and [tests/model_creator/medcat.txt](https://github.com/CogStack/MedCAT/tree/main/tests/model_creator/medcat.txt)| | unigram_table_size | Optional parameter for setting the initialization size of the unigram table in the vocab model. Default is 100000000, while for testing with a small unsupervised training data file a much smaller size could work. | ## Models diff --git a/medcat/cdb_maker.py b/medcat/cdb_maker.py index fbe3b97a..2856867d 100644 --- a/medcat/cdb_maker.py +++ b/medcat/cdb_maker.py @@ -19,7 +19,7 @@ class CDBMaker(object): - """Given a CSV as shown in https://github.com/CogStack/MedCAT/tree/master/examples/ it creates a CDB or + """Given a CSV as shown in https://github.com/CogStack/MedCAT/tree/main/examples/ it creates a CDB or updates an existing one. Args: