From e52424ed8f398b8b888e08d4d75171238fbd1aa4 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Tue, 24 Jun 2025 15:36:52 +0100 Subject: [PATCH 1/9] build: medcat-v2 github actions --- .../main.yml => .github/workflows/medcat-v2-main.yml | 6 ++++-- .../release.yml => .github/workflows/medcat-v2-release.yml | 6 +++++- 2 files changed, 9 insertions(+), 3 deletions(-) rename medcat-v2/.github/workflows/main.yml => .github/workflows/medcat-v2-main.yml (93%) rename medcat-v2/.github/workflows/release.yml => .github/workflows/medcat-v2-release.yml (95%) diff --git a/medcat-v2/.github/workflows/main.yml b/.github/workflows/medcat-v2-main.yml similarity index 93% rename from medcat-v2/.github/workflows/main.yml rename to .github/workflows/medcat-v2-main.yml index fdc81319d..5e808eb1f 100644 --- a/medcat-v2/.github/workflows/main.yml +++ b/.github/workflows/medcat-v2-main.yml @@ -1,11 +1,13 @@ -name: build +name: medcat-v2-build on: push: branches: [ main ] pull_request: branches: [ main ] - +defaults: + run: + working-directory: ./medcat-v2 jobs: build: diff --git a/medcat-v2/.github/workflows/release.yml b/.github/workflows/medcat-v2-release.yml similarity index 95% rename from medcat-v2/.github/workflows/release.yml rename to .github/workflows/medcat-v2-release.yml index f76c73215..b6a47415d 100644 --- a/medcat-v2/.github/workflows/release.yml +++ b/.github/workflows/medcat-v2-release.yml @@ -1,4 +1,4 @@ -name: Release +name: medcat-v2-release on: push: @@ -8,6 +8,10 @@ on: permissions: contents: write +defaults: + run: + working-directory: ./medcat-v2 + jobs: build: name: Build and release From a753d09bd783767b08aaae7c9633f9534a195f5b Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Tue, 24 Jun 2025 15:42:00 +0100 Subject: [PATCH 2/9] build: Medcat-service actions --- {medcat-service/.github => .github}/dependabot.yml | 0 .../docker.yml => .github/workflows/medcat-service-docker.yml | 4 +++- .../workflows/medcat-service-run_tests.yml | 4 ++++ 3 files changed, 7 insertions(+), 1 deletion(-) rename {medcat-service/.github => .github}/dependabot.yml (100%) rename medcat-service/.github/workflows/docker.yml => .github/workflows/medcat-service-docker.yml (98%) rename medcat-service/.github/workflows/run_tests.yml => .github/workflows/medcat-service-run_tests.yml (96%) diff --git a/medcat-service/.github/dependabot.yml b/.github/dependabot.yml similarity index 100% rename from medcat-service/.github/dependabot.yml rename to .github/dependabot.yml diff --git a/medcat-service/.github/workflows/docker.yml b/.github/workflows/medcat-service-docker.yml similarity index 98% rename from medcat-service/.github/workflows/docker.yml rename to .github/workflows/medcat-service-docker.yml index 476d36a99..28a5bc6e2 100755 --- a/medcat-service/.github/workflows/docker.yml +++ b/.github/workflows/medcat-service-docker.yml @@ -11,7 +11,9 @@ on: # Allows you to run this workflow manually from the Actions tab workflow_dispatch: - +defaults: + run: + working-directory: ./medcat-service jobs: build: runs-on: ubuntu-latest diff --git a/medcat-service/.github/workflows/run_tests.yml b/.github/workflows/medcat-service-run_tests.yml similarity index 96% rename from medcat-service/.github/workflows/run_tests.yml rename to .github/workflows/medcat-service-run_tests.yml index 3c82261b9..0a86a49f6 100755 --- a/medcat-service/.github/workflows/run_tests.yml +++ b/.github/workflows/medcat-service-run_tests.yml @@ -13,6 +13,10 @@ on: # Allows you to run this workflow manually from the Actions tab workflow_dispatch: +defaults: + run: + working-directory: ./medcat-service + jobs: build: From ab8416ad263e5c8a46a0abc6db4e75b8497cf6f0 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Tue, 24 Jun 2025 15:53:46 +0100 Subject: [PATCH 3/9] Add License and initial Readme. build: Add v2 tutotials actions --- .../workflows/medcat-v2-tutorials-main.yml | 4 + LICENSE | 93 +++++++++++++++++++ README.md | 12 +++ 3 files changed, 109 insertions(+) rename medcat-v2-tutorials/.github/workflows/main.yml => .github/workflows/medcat-v2-tutorials-main.yml (97%) create mode 100644 LICENSE create mode 100644 README.md diff --git a/medcat-v2-tutorials/.github/workflows/main.yml b/.github/workflows/medcat-v2-tutorials-main.yml similarity index 97% rename from medcat-v2-tutorials/.github/workflows/main.yml rename to .github/workflows/medcat-v2-tutorials-main.yml index 851581f5e..3f8503b05 100644 --- a/medcat-v2-tutorials/.github/workflows/main.yml +++ b/.github/workflows/medcat-v2-tutorials-main.yml @@ -6,6 +6,10 @@ on: pull_request: branches: [ main ] +defaults: + run: + working-directory: ./medcat-v2-tutorials + jobs: basic-and-meta: runs-on: ubuntu-latest diff --git a/LICENSE b/LICENSE new file mode 100644 index 000000000..809108b85 --- /dev/null +++ b/LICENSE @@ -0,0 +1,93 @@ +Elastic License 2.0 + +URL: https://www.elastic.co/licensing/elastic-license + +## Acceptance + +By using the software, you agree to all of the terms and conditions below. + +## Copyright License + +The licensor grants you a non-exclusive, royalty-free, worldwide, +non-sublicensable, non-transferable license to use, copy, distribute, make +available, and prepare derivative works of the software, in each case subject to +the limitations and conditions below. + +## Limitations + +You may not provide the software to third parties as a hosted or managed +service, where the service provides users with access to any substantial set of +the features or functionality of the software. + +You may not move, change, disable, or circumvent the license key functionality +in the software, and you may not remove or obscure any functionality in the +software that is protected by the license key. + +You may not alter, remove, or obscure any licensing, copyright, or other notices +of the licensor in the software. Any use of the licensor’s trademarks is subject +to applicable law. + +## Patents + +The licensor grants you a license, under any patent claims the licensor can +license, or becomes able to license, to make, have made, use, sell, offer for +sale, import and have imported the software, in each case subject to the +limitations and conditions in this license. This license does not cover any +patent claims that you cause to be infringed by modifications or additions to +the software. If you or your company make any written claim that the software +infringes or contributes to infringement of any patent, your patent license for +the software granted under these terms ends immediately. If your company makes +such a claim, your patent license ends immediately for work on behalf of your +company. + +## Notices + +You must ensure that anyone who gets a copy of any part of the software from you +also gets a copy of these terms. + +If you modify the software, you must include in any modified copies of the +software prominent notices stating that you have modified the software. + +## No Other Rights + +These terms do not imply any licenses other than those expressly granted in +these terms. + +## Termination + +If you use the software in violation of these terms, such use is not licensed, +and your licenses will automatically terminate. If the licensor provides you +with a notice of your violation, and you cease all violation of this license no +later than 30 days after you receive that notice, your licenses will be +reinstated retroactively. However, if you violate these terms after such +reinstatement, any additional violation of these terms will cause your licenses +to terminate automatically and permanently. + +## No Liability + +*As far as the law allows, the software comes as is, without any warranty or +condition, and the licensor will not be liable to you for any damages arising +out of these terms or the use or nature of the software, under any kind of +legal claim.* + +## Definitions + +The **licensor** is the entity offering these terms, and the **software** is the +software the licensor makes available under these terms, including any portion +of it. + +**you** refers to the individual or entity agreeing to these terms. + +**your company** is any legal entity, sole proprietorship, or other kind of +organization that you work for, plus all organizations that have control over, +are under the control of, or are under common control with that +organization. **control** means ownership of substantially all the assets of an +entity, or the power to direct its management and policies by vote, contract, or +otherwise. Control can be direct or indirect. + +**your licenses** are all the licenses granted to you for the software under +these terms. + +**use** means anything you do with the software requiring one of your licenses. + +**trademark** means trademarks, service marks, and similar rights. diff --git a/README.md b/README.md new file mode 100644 index 000000000..ec07a0d33 --- /dev/null +++ b/README.md @@ -0,0 +1,12 @@ +# Cogstack NLP + +[![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2-main.yml/badge.svg?branch=main)](https://github.com/CogStack/MedCAT2/actions/workflows/main.yml?query=branch%3main) +[![Documentation Status](https://readthedocs.org/projects/medcat2/badge/?version=latest)](https://medcat2.readthedocs.io/en/latest/?badge=latest) +[![Latest release](https://img.shields.io/github/v/release/CogStack/MedCAT2)](https://github.com/CogStack/MedCAT2/releases/latest) + +Cogstack Natural Language Processing is for analysing clinical data using AI to draw insights from text in or documents in an Electronic Health Records. + + +**Official Docs [here](https://medcat2.readthedocs.io/en/latest/)** +**Discussion Forum [discourse](https://discourse.cogstack.org/)** + From 51b70c3dfa75c1386a45c332e2c5f31c158dbcdc Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Tue, 24 Jun 2025 15:59:34 +0100 Subject: [PATCH 4/9] Rename github actions --- .github/workflows/medcat-service-docker.yml | 2 +- .github/workflows/medcat-service-run_tests.yml | 2 +- .github/workflows/medcat-v2-main.yml | 2 +- .github/workflows/medcat-v2-release.yml | 2 +- .github/workflows/medcat-v2-tutorials-main.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/medcat-service-docker.yml b/.github/workflows/medcat-service-docker.yml index 28a5bc6e2..4aab28b07 100755 --- a/.github/workflows/medcat-service-docker.yml +++ b/.github/workflows/medcat-service-docker.yml @@ -1,4 +1,4 @@ -name: Docker +name: medcat-service - Build Images on: push: diff --git a/.github/workflows/medcat-service-run_tests.yml b/.github/workflows/medcat-service-run_tests.yml index 0a86a49f6..9cdda0e4d 100755 --- a/.github/workflows/medcat-service-run_tests.yml +++ b/.github/workflows/medcat-service-run_tests.yml @@ -1,4 +1,4 @@ -name: Run tests +name: medcat-service - Test on: diff --git a/.github/workflows/medcat-v2-main.yml b/.github/workflows/medcat-v2-main.yml index 5e808eb1f..08d633948 100644 --- a/.github/workflows/medcat-v2-main.yml +++ b/.github/workflows/medcat-v2-main.yml @@ -1,4 +1,4 @@ -name: medcat-v2-build +name: medcat-v2 - Test on: push: diff --git a/.github/workflows/medcat-v2-release.yml b/.github/workflows/medcat-v2-release.yml index b6a47415d..35c54b418 100644 --- a/.github/workflows/medcat-v2-release.yml +++ b/.github/workflows/medcat-v2-release.yml @@ -1,4 +1,4 @@ -name: medcat-v2-release +name: medcat-v2 - Build Python Package on: push: diff --git a/.github/workflows/medcat-v2-tutorials-main.yml b/.github/workflows/medcat-v2-tutorials-main.yml index 3f8503b05..de8b0b806 100644 --- a/.github/workflows/medcat-v2-tutorials-main.yml +++ b/.github/workflows/medcat-v2-tutorials-main.yml @@ -1,4 +1,4 @@ -name: build +name: medcat-v2-tutorials - Test on: push: From 8aac197be41d63bd7d22f187a76411de162f89d2 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Tue, 24 Jun 2025 16:10:16 +0100 Subject: [PATCH 5/9] Disable failing service build --- .github/workflows/medcat-service-docker.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/medcat-service-docker.yml b/.github/workflows/medcat-service-docker.yml index 4aab28b07..dfe1be570 100755 --- a/.github/workflows/medcat-service-docker.yml +++ b/.github/workflows/medcat-service-docker.yml @@ -15,7 +15,10 @@ defaults: run: working-directory: ./medcat-service jobs: + build: + # DIsable the build temporarily + if: false runs-on: ubuntu-latest outputs: image_version: ${{ steps.meta.outputs.version }} From 048ae2a096566f378e669dc724db2d752e3e745a Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Tue, 24 Jun 2025 16:12:05 +0100 Subject: [PATCH 6/9] Reame files --- .../{medcat-service-docker.yml => medcat-service_docker.yml} | 0 ...{medcat-service-run_tests.yml => medcat-service_run-tests.yml} | 0 ...{medcat-v2-tutorials-main.yml => medcat-v2-tutorials_main.yml} | 0 .github/workflows/{medcat-v2-main.yml => medcat-v2_main.yml} | 0 .../workflows/{medcat-v2-release.yml => medcat-v2_release.yml} | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{medcat-service-docker.yml => medcat-service_docker.yml} (100%) rename .github/workflows/{medcat-service-run_tests.yml => medcat-service_run-tests.yml} (100%) rename .github/workflows/{medcat-v2-tutorials-main.yml => medcat-v2-tutorials_main.yml} (100%) rename .github/workflows/{medcat-v2-main.yml => medcat-v2_main.yml} (100%) rename .github/workflows/{medcat-v2-release.yml => medcat-v2_release.yml} (100%) diff --git a/.github/workflows/medcat-service-docker.yml b/.github/workflows/medcat-service_docker.yml similarity index 100% rename from .github/workflows/medcat-service-docker.yml rename to .github/workflows/medcat-service_docker.yml diff --git a/.github/workflows/medcat-service-run_tests.yml b/.github/workflows/medcat-service_run-tests.yml similarity index 100% rename from .github/workflows/medcat-service-run_tests.yml rename to .github/workflows/medcat-service_run-tests.yml diff --git a/.github/workflows/medcat-v2-tutorials-main.yml b/.github/workflows/medcat-v2-tutorials_main.yml similarity index 100% rename from .github/workflows/medcat-v2-tutorials-main.yml rename to .github/workflows/medcat-v2-tutorials_main.yml diff --git a/.github/workflows/medcat-v2-main.yml b/.github/workflows/medcat-v2_main.yml similarity index 100% rename from .github/workflows/medcat-v2-main.yml rename to .github/workflows/medcat-v2_main.yml diff --git a/.github/workflows/medcat-v2-release.yml b/.github/workflows/medcat-v2_release.yml similarity index 100% rename from .github/workflows/medcat-v2-release.yml rename to .github/workflows/medcat-v2_release.yml From 029c52ab6aa7dbe61f73f60427c58ccbbe42ea79 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Tue, 24 Jun 2025 16:16:07 +0100 Subject: [PATCH 7/9] build: Move dev container --- {medcat-service/.devcontainer => .devcontainer}/devcontainer.json | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {medcat-service/.devcontainer => .devcontainer}/devcontainer.json (100%) diff --git a/medcat-service/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json similarity index 100% rename from medcat-service/.devcontainer/devcontainer.json rename to .devcontainer/devcontainer.json From 470d8ec6827e761200a5c7b1103cd64cf0237d2f Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Tue, 24 Jun 2025 17:31:06 +0100 Subject: [PATCH 8/9] Test parallel action --- .github/workflows/medcat-v2_main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/medcat-v2_main.yml b/.github/workflows/medcat-v2_main.yml index 08d633948..3c36cdba5 100644 --- a/.github/workflows/medcat-v2_main.yml +++ b/.github/workflows/medcat-v2_main.yml @@ -14,8 +14,8 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [ '3.9', '3.10', '3.11', '3.12' ] - max-parallel: 4 + python-version: [ '3.9', '3.10', '3.11', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12' ] + max-parallel: 20 steps: - uses: actions/checkout@v4 From 32da0732171206b1ff947b1203ee811d53a84356 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Tue, 24 Jun 2025 17:35:34 +0100 Subject: [PATCH 9/9] Test parallel action --- .github/workflows/medcat-v2_main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/medcat-v2_main.yml b/.github/workflows/medcat-v2_main.yml index 3c36cdba5..08d633948 100644 --- a/.github/workflows/medcat-v2_main.yml +++ b/.github/workflows/medcat-v2_main.yml @@ -14,8 +14,8 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [ '3.9', '3.10', '3.11', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12', '3.12' ] - max-parallel: 20 + python-version: [ '3.9', '3.10', '3.11', '3.12' ] + max-parallel: 4 steps: - uses: actions/checkout@v4