CU-8699g0f70 master to main (#547)

* CU-8699g0f70: Update new branch in README

* CU-8699g0f70: Update new branch in README (missing parts)

* CU-8699g0f70: Update branch in contributions file

* CU-8699g0f70: Update reference to branch in CDB maker

* CU-8699g0f70: Fix links in main docs page (branch name)

* CU-8699g0f70: Update branch in main workflow

* CU-8699g0f70: Update branch in CodeQL workflow

Author: mart-r

.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'
 

.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

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)

README.md

@@ -1,10 +1,10 @@
-# Medical  <img src="https://raw.githubusercontent.com/CogStack/MedCAT/master/media/cat-logo.png" width=45> oncept Annotation Tool
+# Medical  <img src="https://raw.githubusercontent.com/CogStack/MedCAT/main/media/cat-logo.png" width=45> 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:

docs/main.md

@@ -1,6 +1,6 @@
-# Medical  <img src="https://github.com/CogStack/MedCAT/blob/master/media/cat-logo.png?raw=true" width=45>oncept Annotation Tool
+# Medical  <img src="https://github.com/CogStack/MedCAT/blob/main/media/cat-logo.png?raw=true" width=45>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

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/<example> it creates a CDB or
+    """Given a CSV as shown in https://github.com/CogStack/MedCAT/tree/main/examples/<example> it creates a CDB or
     updates an existing one.
 
     Args: