build: Migrate MedCAT v1 Github Actions (#23)

* build: Migrate  MedCAT v1 tutorial action

* build: Migrate codeql.yml

* build: Regenerate default codeql.yml

* build(medcat-v1): Add MedCAT v1 github action

* build(medcat-v1): Add MedCAT v1 github action - fix setuptools_scm

* build(medcat-v1): Move the production action, disable for now

Author: alhendrickson

medcat-v1/.github/workflows/codeql.yml renamed to .github/workflows/codeql.yml

@@ -9,15 +9,15 @@
 # the `language` matrix defined below to confirm you have the correct set of
 # supported CodeQL languages.
 #
-name: "CodeQL"
+name: "CodeQL Advanced"
 
 on:
   push:
     branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
   schedule:
-    - cron: '36 14 * * 0'
+    - cron: '19 7 * * 0'
 
 jobs:
   analyze:
@@ -28,7 +28,6 @@ jobs:
     #   - https://gh.io/using-larger-runners (GitHub.com only)
     # Consider using larger runners or machines with greater resources for possible analysis time improvements.
     runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
-    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
     permissions:
       # required for all workflows
       security-events: write
@@ -44,11 +43,13 @@ jobs:
       fail-fast: false
       matrix:
         include:
+        - language: actions
+          build-mode: none
         - language: javascript-typescript
           build-mode: none
         - language: python
           build-mode: none
-        # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
         # Use `c-cpp` to analyze code written in C, C++ or both
         # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
         # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
@@ -60,6 +61,12 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v4
 
+    # Add any setup steps before running the `github/codeql-action/init` action.
+    # This includes steps like installing compilers or runtimes (`actions/setup-node`
+    # or others). This is typically only required for manual builds.
+    # - name: Setup runtime (example)
+    #   uses: actions/setup-example@v1
+
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v3

medcat-v1-tutorials/.github/workflows/main.yml renamed to .github/workflows/medcat-v1-tutorials_main.yml

@@ -1,10 +1,17 @@
-name: build
+name: medcat-v1-tutorials - Test
 
 on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
+    paths:
+      - 'medcat-v1/**'
+      - 'medcat-v1-tutorials/**'
+      - '.github/workflows/medcat-v1**'
+      - '.github/workflows/medcat-v1-tutorials**'
+defaults:
+  run:
+    working-directory: ./medcat-v1-tutorials
 
 jobs:
   main:

medcat-v1/.github/workflows/main.yml renamed to .github/workflows/medcat-v1_main.yml

@@ -1,11 +1,15 @@
-name: build
+name: medcat-v1 - build
 
 on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
-
+    paths:
+      - 'medcat-v1/**'
+      - '.github/workflows/medcat-v1**'
+defaults:
+  run:
+    working-directory: ./medcat-v1
 jobs:
   build:
 
@@ -70,12 +74,13 @@ jobs:
           python tests/check_deprecations.py "$VERSION" --next-version --remove-prefix
 
   publish-to-test-pypi:
-
+    # Disable pypy publish waiting for TEST_PYPI_API_TOKEN
     if: |
-      github.repository == 'CogStack/MedCAT' &&
+      github.repository == 'CogStack/cogstack-nlp' &&
       github.ref == 'refs/heads/main' &&
       github.event_name == 'push' &&
-      startsWith(github.ref, 'refs/tags') != true
+      startsWith(github.ref, 'refs/tags') != true &&
+      false 
     runs-on: ubuntu-24.04
     timeout-minutes: 45
     concurrency: publish-to-test-pypi

medcat-v1/.github/workflows/production.yml renamed to .github/workflows/medcat-v1_production.yml

@@ -1,16 +1,25 @@
-name: production
+# TODO: Fix Medcat V1 Release Actions
+# Disabled waiting for designed release process
+# Disabled waiting for PYPI_API_TOKEN
+name: medcat-v1 - production
 
 on:
   push:
-    branches: [ production, "v[0-9]+.[0-9]+.post" ]
-  release:
-    types: [ published , edited ]
-
+    branches: [ "medcat-v1/production", "medcat-v1/v[0-9]+.[0-9]+.post" ]
+  
+  # release:
+  #   types: [ published , edited ]
+defaults:
+  run:
+    working-directory: ./medcat-v1
 jobs:
   build-n-publish-to-pypi:
+
     runs-on: ubuntu-24.04
     concurrency: build-n-publish-to-pypi
-    if: github.repository == 'CogStack/MedCAT'
+    if: | 
+     github.repository == 'CogStack/cogstack-nlp' &&
+     false   
 
     steps:
       - name: Checkout production

medcat-v1-tutorials/.github/.DS_Store

@@ -3,3 +3,4 @@ requires = ["setuptools>=42", "setuptools_scm[toml]>=6.2", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
+root = "../"  # adjust this relative to your package