Merge pull request #7 from CogStack/revert-6-CU-869az43jq-distribut-cogstack-es

Revert "CU-869az43jq: MedCAT v2: Distribute cogstack-es and medcat-scripts"

Author: vladd-bit

.github/workflows/submodule_sync.yml

@@ -0,0 +1,54 @@
+name: submodules-sync
+
+on:
+  push:
+    branches: ['**']
+    tags: ['v*.*.*']
+  pull_request:
+    branches: ['**']
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  sync:
+    name: 'Submodules Sync'
+    runs-on: ubuntu-22.04
+    if: github.actor != 'github-actions[bot]'
+
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v5
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          submodules: recursive
+          persist-credentials: false
+
+      - name: Sync submodule URLs
+        run: |
+          git submodule sync --recursive
+
+      - name: Update submodules
+        run: |
+          git -c protocol.version=2 submodule update --init --remote --recursive --jobs 8
+
+      - name: Commit and push submodule updates
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          set -euo pipefail
+          git config user.name 'github-actions[bot]'
+          git config user.email '41898282+github-actions[bot]@users.noreply.github.com'
+          git remote set-url origin https://x-access-token:${GH_TOKEN}@github.com/${{ github.repository }}
+          # Stage only submodule pointer updates and .gitmodules
+          git add .gitmodules $(git config -f .gitmodules --get-regexp path | awk '{print $2}') || true
+          if git diff --cached --quiet; then
+            echo "No submodule pointer changes to commit"
+            exit 0
+          fi
+          git commit -m "chore(submodules): auto-update pointers [skip ci]"
+          git push

.gitmodules

@@ -0,0 +1,6 @@
+
+[submodule "notebooks/demo_working_with_cogstack"]
+	path = notebooks/demo_working_with_cogstack
+	url = https://github.com/CogStack/working_with_cogstack.git
+	branch = main
+	ignore = all

Dockerfile_singleuser

@@ -7,9 +7,6 @@ ARG http_proxy
 ARG https_proxy
 ARG no_proxy
 
-# NOTE: set to ES8 or Elasticsearch 8 or OS for Opensearch
-ARG COGSTACK_BACKEND=ES9
-
 # set to "true" for the GPU build
 ARG GPU_BUILD=false
 
@@ -215,20 +212,16 @@ RUN uv pip install --upgrade --system pip setuptools wheel
 
 # install the rest of the packages including medcat
 COPY ./requirements.txt /srv/jupyterhub/
+# install requirements for working with cogstack scripts
+COPY notebooks/demo_working_with_cogstack/requirements.txt /srv/jupyterhub/working_with_cogstack_requirements.txt
 
 RUN if [ "$GPU_BUILD" = "true" ] && [ "$CPU_ARCHITECTURE" = "amd64" ]; then \
       uv pip install --system --no-cache-dir -r /srv/jupyterhub/requirements.txt && \
-      # NOTE: it'll create the medcat-scripts folder within
-      uv run python -m medcat download-scripts /srv/jupyterhub/ && \
-      uv pip install --system --no-cache-dir -r /srv/jupyterhub/medcat-scripts/requirements.txt ; \
+      uv pip install --system --no-cache-dir -r /srv/jupyterhub/working_with_cogstack_requirements.txt ; \
     else \
       uv pip install --system --no-cache-dir -r /srv/jupyterhub/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/ && \
-      uv run python -m medcat download-scripts /srv/jupyterhub/ && \
-      uv pip install --system --no-cache-dir -r /srv/jupyterhub/medcat-scripts/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/ ; \
-    fi && \
-    # install cogstack-es (Cogstack class)
-    uv pip install "cogstack-es[$COGSTACK_BACKEND]" && \
-    mv /srv/jupyterhub/medcat-scripts/notebooks/* /home/jovyan/work/. # move notebooks
+      uv pip install --system --no-cache-dir -r /srv/jupyterhub/working_with_cogstack_requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/ ; \
+    fi
 
 #######################################################################################################
 

requirements.txt

@@ -1,6 +1,4 @@
 wheel==0.45.1
-medcat==2.2.0
-# TODO: cogstack-es
 virtualenv==20.31.2
 ipywidgets==8.1.7
 requests>=2.32.2