From 744c4523c911d0ac2db6edd120f978acb2311290 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Tue, 29 Sep 2026 15:29:27 +0000 Subject: [PATCH 1/4] build(jupyterhub): Move github workflows to top level --- .github/dependabot.yml | 28 +++++ .../workflows/docker-build.yml | 0 .../workflows/docker-smoke-test.yml | 0 .../.github/dependabot.yml | 28 ----- .../.github/workflows/codeql.yml | 100 ------------------ 5 files changed, 28 insertions(+), 128 deletions(-) rename {apps/cogstack-jupyter-hub/.github => .github}/workflows/docker-build.yml (100%) rename {apps/cogstack-jupyter-hub/.github => .github}/workflows/docker-smoke-test.yml (100%) delete mode 100644 apps/cogstack-jupyter-hub/.github/dependabot.yml delete mode 100644 apps/cogstack-jupyter-hub/.github/workflows/codeql.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml index f33a02cd..ed5d2014 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -10,3 +10,31 @@ updates: directory: "/" schedule: interval: weekly + + # Keep GitHub Actions (in .github/workflows) up to date + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "monthly" + + + # Keep Dockerfile base images (in repo root) up to date + - package-ecosystem: "docker" + directory: "/apps/cogstack-jupyter-hub" + schedule: + interval: "weekly" + registries: + - dockerhub + + # Keep uv.lock Python dependencies up to date + - package-ecosystem: "uv" + directory: "/apps/cogstack-jupyter-hub" + schedule: + interval: "weekly" + +registries: + dockerhub: + type: "docker-registry" + url: "https://index.docker.io" + username: "${{secrets.DOCKER_HUB_USERNAME}}" + password: "${{secrets.DOCKER_HUB_ACCESS_TOKEN}}" diff --git a/apps/cogstack-jupyter-hub/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml similarity index 100% rename from apps/cogstack-jupyter-hub/.github/workflows/docker-build.yml rename to .github/workflows/docker-build.yml diff --git a/apps/cogstack-jupyter-hub/.github/workflows/docker-smoke-test.yml b/.github/workflows/docker-smoke-test.yml similarity index 100% rename from apps/cogstack-jupyter-hub/.github/workflows/docker-smoke-test.yml rename to .github/workflows/docker-smoke-test.yml diff --git a/apps/cogstack-jupyter-hub/.github/dependabot.yml b/apps/cogstack-jupyter-hub/.github/dependabot.yml deleted file mode 100644 index d4c4e51a..00000000 --- a/apps/cogstack-jupyter-hub/.github/dependabot.yml +++ /dev/null @@ -1,28 +0,0 @@ -version: 2 -updates: - # Keep GitHub Actions (in .github/workflows) up to date - - package-ecosystem: "github-actions" - directory: "/" - schedule: - interval: "monthly" - - # Keep Dockerfile base images (in repo root) up to date - - package-ecosystem: "docker" - directory: "/" - schedule: - interval: "weekly" - registries: - - dockerhub - - # Keep uv.lock Python dependencies up to date - - package-ecosystem: "uv" - directory: "/" - schedule: - interval: "weekly" - -registries: - dockerhub: - type: "docker-registry" - url: "https://index.docker.io" - username: "${{secrets.DOCKER_HUB_USERNAME}}" - password: "${{secrets.DOCKER_HUB_ACCESS_TOKEN}}" diff --git a/apps/cogstack-jupyter-hub/.github/workflows/codeql.yml b/apps/cogstack-jupyter-hub/.github/workflows/codeql.yml deleted file mode 100644 index 7dab8c41..00000000 --- a/apps/cogstack-jupyter-hub/.github/workflows/codeql.yml +++ /dev/null @@ -1,100 +0,0 @@ -# For most projects, this workflow file will not need changing; you simply need -# to commit it to your repository. -# -# You may wish to alter this file to override the set of languages analyzed, -# or to provide custom queries or build logic. -# -# ******** NOTE ******** -# We have attempted to detect the languages in your repository. Please check -# the `language` matrix defined below to confirm you have the correct set of -# supported CodeQL languages. -# -name: codeql-analysis-jupyter-hub - -on: - push: - branches: [ "main" ] - pull_request: - branches: [ "main" ] - schedule: - - cron: '20 1 * * 3' - -jobs: - analyze: - name: Analyze (${{ matrix.language }}) - # Runner size impacts CodeQL analysis time. To learn more, please see: - # - https://gh.io/recommended-hardware-resources-for-running-codeql - # - https://gh.io/supported-runners-and-hardware-resources - # - 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' }} - permissions: - # required for all workflows - security-events: write - - # required to fetch internal or private CodeQL packs - packages: read - - # only required for workflows in private repositories - actions: read - contents: read - - strategy: - fail-fast: false - matrix: - include: - - language: actions - build-mode: none - - language: python - build-mode: none - # 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 - # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis, - # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning. - # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how - # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages - steps: - - name: Checkout repository - uses: actions/checkout@v7 - - # 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@v4.38.0 - with: - languages: ${{ matrix.language }} - build-mode: ${{ matrix.build-mode }} - # If you wish to specify custom queries, you can do so here or in a config file. - # By default, queries listed here will override any specified in a config file. - # Prefix the list here with "+" to use these queries and those in the config file. - - # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs - # queries: security-extended,security-and-quality - - # If the analyze step fails for one of the languages you are analyzing with - # "We were unable to automatically build your code", modify the matrix above - # to set the build mode to "manual" for that language. Then modify this step - # to build your code. - # ℹī¸ Command-line programs to run using the OS shell. - # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun - - if: matrix.build-mode == 'manual' - shell: bash - run: | - echo 'If you are using a "manual" build mode for one or more of the' \ - 'languages you are analyzing, replace this with the commands to build' \ - 'your code, for example:' - echo ' make bootstrap' - echo ' make release' - exit 1 - - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v4.38.0 - with: - category: "/language:${{matrix.language}}" From 2d13d9b3658e68573d554e991f7b84f22caa9703 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Tue, 29 Sep 2026 15:40:22 +0000 Subject: [PATCH 2/4] build(jupyterhub): Update workflows to new path. Make docker consistent with other flows --- .github/dependabot.yml | 4 +- .github/workflows/docker-build.yml | 184 ++++++++++++------------ .github/workflows/docker-smoke-test.yml | 28 ++-- 3 files changed, 102 insertions(+), 114 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index ed5d2014..57d71b15 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -36,5 +36,5 @@ registries: dockerhub: type: "docker-registry" url: "https://index.docker.io" - username: "${{secrets.DOCKER_HUB_USERNAME}}" - password: "${{secrets.DOCKER_HUB_ACCESS_TOKEN}}" + username: "${{secrets.DOCKERHUB_USERNAME}}" + password: "${{secrets.DOCKERHUB_TOKEN}}" diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml index e0c2d819..d5213867 100644 --- a/.github/workflows/docker-build.yml +++ b/.github/workflows/docker-build.yml @@ -5,12 +5,15 @@ permissions: on: push: - branches: ['**'] - tags: ['v*.*.*'] + branches: [main] + tags: ['cogstack-jupyter-hub-v*.*.*'] + paths: + - "apps/cogstack-jupyter-hub/**" + - ".github/workflows/docker-build.yml" pull_request: - branches: ['**'] - release: - types: [published] + paths: + - "apps/cogstack-jupyter-hub/**" + - ".github/workflows/docker-build.yml" workflow_dispatch: concurrency: @@ -21,7 +24,7 @@ jobs: # ---------- AMD64 ---------- build-amd64: runs-on: ubuntu-22.04 - if: ${{ github.event_name != 'pull_request' }} + if: github.event_name == 'push' outputs: hub_digest: ${{ steps.hub.outputs.digest }} su_digest: ${{ steps.su.outputs.digest }} @@ -36,15 +39,14 @@ jobs: with: images: cogstacksystems/jupyter-hub tags: | - # vX.Y.Z -> X.Y.Z and X.Y (strip leading "v") - type=semver,pattern={{version}},prefix=v - type=semver,pattern={{major}}.{{minor}},prefix=v - # latest on main and on v-tags - type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') }} - # branch tag for non-PR branches - type=ref,event=branch,enable=${{ github.event_name != 'pull_request' }} - # short sha - type=sha,format=short + type=raw,value=latest,enable={{is_default_branch}} + type=schedule + type=ref,event=branch + type=ref,event=tag + type=ref,event=pr + type=sha,enable={{is_default_branch}} + type=match,pattern=cogstack-jupyter-hub-v(\d+\.\d+\.\d+),group=1 + flavor: latest=false - name: Docker meta (singleuser) id: meta_su @@ -52,27 +54,26 @@ jobs: with: images: cogstacksystems/jupyter-singleuser tags: | - # vX.Y.Z -> X.Y.Z and X.Y (strip "v") - type=semver,pattern={{version}},prefix=v - type=semver,pattern={{major}}.{{minor}},prefix=v - # latest on main AND on v-tags - type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') }} - # branches (non-PR) - type=ref,event=branch,enable=${{ github.event_name != 'pull_request' }} - # short sha - type=sha,format=short - + type=raw,value=latest,enable={{is_default_branch}} + type=schedule + type=ref,event=branch + type=ref,event=tag + type=ref,event=pr + type=sha,enable={{is_default_branch}} + type=match,pattern=cogstack-jupyter-hub-v(\d+\.\d+\.\d+),group=1 + flavor: latest=false + - uses: docker/login-action@v4.6.0 with: - username: ${{ secrets.DOCKER_HUB_USERNAME }} - password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_TOKEN }} - name: Build & push hub (amd64) id: hub uses: docker/build-push-action@v7 with: - context: . - file: Dockerfile_hub + context: apps/cogstack-jupyter-hub + file: apps/cogstack-jupyter-hub/Dockerfile_hub platforms: linux/amd64 build-args: | CPU_ARCHITECTURE=amd64 @@ -89,8 +90,8 @@ jobs: id: su uses: docker/build-push-action@v7 with: - context: . - file: Dockerfile_singleuser + context: apps/cogstack-jupyter-hub + file: apps/cogstack-jupyter-hub/Dockerfile_singleuser platforms: linux/amd64 build-args: | CPU_ARCHITECTURE=amd64 @@ -106,7 +107,7 @@ jobs: # ---------- ARM64 ---------- build-arm64: runs-on: ubuntu-22.04-arm - if: ${{ github.event_name != 'pull_request' }} + if: github.event_name == 'push' outputs: hub_digest: ${{ steps.hub.outputs.digest }} su_digest: ${{ steps.su.outputs.digest }} @@ -121,44 +122,42 @@ jobs: with: images: cogstacksystems/jupyter-hub tags: | - # vX.Y.Z -> X.Y.Z and X.Y (strip "v") - type=semver,pattern={{version}},prefix=v - type=semver,pattern={{major}}.{{minor}},prefix=v - # latest on main AND on v-tags - type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') }} - # branches (non-PR) - type=ref,event=branch,enable=${{ github.event_name != 'pull_request' }} - # short sha - type=sha,format=short - + type=raw,value=latest,enable={{is_default_branch}} + type=schedule + type=ref,event=branch + type=ref,event=tag + type=ref,event=pr + type=sha,enable={{is_default_branch}} + type=match,pattern=cogstack-jupyter-hub-v(\d+\.\d+\.\d+),group=1 + flavor: latest=false + - name: Docker meta (singleuser) id: meta_su uses: docker/metadata-action@v6 with: images: cogstacksystems/jupyter-singleuser tags: | - # vX.Y.Z -> X.Y.Z and X.Y (strip "v") - type=semver,pattern={{version}},prefix=v - type=semver,pattern={{major}}.{{minor}},prefix=v - # latest on main AND on v-tags - type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') }} - # branches (non-PR) - type=ref,event=branch,enable=${{ github.event_name != 'pull_request' }} - # short sha - type=sha,format=short - + type=raw,value=latest,enable={{is_default_branch}} + type=schedule + type=ref,event=branch + type=ref,event=tag + type=ref,event=pr + type=sha,enable={{is_default_branch}} + type=match,pattern=cogstack-jupyter-hub-v(\d+\.\d+\.\d+),group=1 + flavor: latest=false + - uses: docker/login-action@v4.6.0 with: - username: ${{ secrets.DOCKER_HUB_USERNAME }} - password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_TOKEN }} - name: Build & push hub (arm64) id: hub uses: docker/build-push-action@v7 with: - context: . - file: Dockerfile_hub + context: apps/cogstack-jupyter-hub + file: apps/cogstack-jupyter-hub/Dockerfile_hub platforms: linux/arm64 build-args: | CPU_ARCHITECTURE=arm64 @@ -174,8 +173,8 @@ jobs: id: su uses: docker/build-push-action@v7 with: - context: . - file: Dockerfile_singleuser + context: apps/cogstack-jupyter-hub + file: apps/cogstack-jupyter-hub/Dockerfile_singleuser platforms: linux/arm64 build-args: | CPU_ARCHITECTURE=arm64 @@ -191,7 +190,7 @@ jobs: # ---------- GPU (unchanged, amd64-only) ---------- build-gpu: runs-on: ubuntu-22.04 - if: ${{ github.event_name != 'pull_request' }} + if: github.event_name == 'push' steps: - uses: actions/checkout@v7 with: { submodules: recursive, fetch-depth: 0 } @@ -203,15 +202,14 @@ jobs: with: images: cogstacksystems/jupyter-singleuser-gpu tags: | - # vX.Y.Z -> X.Y.Z and X.Y (strip "v") - type=semver,pattern={{version}},prefix=v - type=semver,pattern={{major}}.{{minor}},prefix=v - # latest on main AND on v-tags - type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') }} - # branches (non-PR) - type=ref,event=branch,enable=${{ github.event_name != 'pull_request' }} - # short sha - type=sha,format=short + type=raw,value=latest,enable={{is_default_branch}} + type=schedule + type=ref,event=branch + type=ref,event=tag + type=ref,event=pr + type=sha,enable={{is_default_branch}} + type=match,pattern=cogstack-jupyter-hub-v(\d+\.\d+\.\d+),group=1 + flavor: latest=false - name: Free disk space run: | sudo rm -rf /usr/share/dotnet /opt/ghc /usr/local/lib/android @@ -220,14 +218,14 @@ jobs: - uses: docker/login-action@v4.6.0 with: - username: ${{ secrets.DOCKER_HUB_USERNAME }} - password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_TOKEN }} - name: Build & push singleuser GPU (amd64) uses: docker/build-push-action@v7 with: - context: . - file: Dockerfile_singleuser + context: apps/cogstack-jupyter-hub + file: apps/cogstack-jupyter-hub/Dockerfile_singleuser platforms: linux/amd64 build-args: | CPU_ARCHITECTURE=amd64 @@ -241,13 +239,13 @@ jobs: manifest: runs-on: ubuntu-22.04 - if: ${{ github.event_name != 'pull_request' }} + if: github.event_name == 'push' needs: [build-amd64, build-arm64] steps: - uses: docker/login-action@v4.6.0 with: - username: ${{ secrets.DOCKER_HUB_USERNAME }} - password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_TOKEN }} # Recompute tags (must match both builds) - name: Docker meta (hub) @@ -256,15 +254,14 @@ jobs: with: images: cogstacksystems/jupyter-hub tags: | - # vX.Y.Z -> X.Y.Z and X.Y (strip "v") - type=semver,pattern={{version}},prefix=v - type=semver,pattern={{major}}.{{minor}},prefix=v - # latest on main AND on v-tags - type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') }} - # branches (non-PR) - type=ref,event=branch,enable=${{ github.event_name != 'pull_request' }} - # short sha - type=sha,format=short + type=raw,value=latest,enable={{is_default_branch}} + type=schedule + type=ref,event=branch + type=ref,event=tag + type=ref,event=pr + type=sha,enable={{is_default_branch}} + type=match,pattern=cogstack-jupyter-hub-v(\d+\.\d+\.\d+),group=1 + flavor: latest=false - name: Docker meta (singleuser) id: meta_su @@ -272,15 +269,14 @@ jobs: with: images: cogstacksystems/jupyter-singleuser tags: | - # vX.Y.Z -> X.Y.Z and X.Y (strip "v") - type=semver,pattern={{version}},prefix=v - type=semver,pattern={{major}}.{{minor}},prefix=v - # latest on main AND on v-tags - type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') }} - # branches (non-PR) - type=ref,event=branch,enable=${{ github.event_name != 'pull_request' }} - # short sha - type=sha,format=short + type=raw,value=latest,enable={{is_default_branch}} + type=schedule + type=ref,event=branch + type=ref,event=tag + type=ref,event=pr + type=sha,enable={{is_default_branch}} + type=match,pattern=cogstack-jupyter-hub-v(\d+\.\d+\.\d+),group=1 + flavor: latest=false - name: Create hub multi-arch manifests shell: bash @@ -345,4 +341,4 @@ jobs: --tag "${img}:${tag}" \ "${img}@${AMD64}" \ "${img}@${ARM64}" - done < <(printf "%s" "${{ steps.meta_su.outputs.tags }}") \ No newline at end of file + done < <(printf "%s" "${{ steps.meta_su.outputs.tags }}") diff --git a/.github/workflows/docker-smoke-test.yml b/.github/workflows/docker-smoke-test.yml index 47c6e398..b23eb047 100644 --- a/.github/workflows/docker-smoke-test.yml +++ b/.github/workflows/docker-smoke-test.yml @@ -4,27 +4,15 @@ permissions: contents: read on: - pull_request: + push: + branches: [main] + tags: ['cogstack-jupyter-hub-v*.*.*'] paths: - - "Dockerfile_hub" - - "Dockerfile_singleuser" - - "docker/**" - - "env/**" - - "config/**" - - "scripts/**" - - "export_env_vars.sh" + - "apps/cogstack-jupyter-hub/**" - ".github/workflows/docker-smoke-test.yml" - push: - branches: - - "main" + pull_request: paths: - - "Dockerfile_hub" - - "Dockerfile_singleuser" - - "docker/**" - - "env/**" - - "config/**" - - "scripts/**" - - "export_env_vars.sh" + - "apps/cogstack-jupyter-hub/**" - ".github/workflows/docker-smoke-test.yml" workflow_dispatch: @@ -32,6 +20,10 @@ concurrency: group: docker-smoke-${{ github.ref }} cancel-in-progress: true +defaults: + run: + working-directory: apps/cogstack-jupyter-hub + jobs: smoke: runs-on: ubuntu-22.04 From a89e5f2baf9984bc70c0b4eba570e62120529003 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Tue, 29 Sep 2026 15:48:21 +0000 Subject: [PATCH 3/4] build(jupyterhub): Update workflows to new path. Make docker consistent with other flows --- .github/workflows/{docker-build.yml => jupyter-docker-build.yml} | 0 .../{docker-smoke-test.yml => jupyter-docker-smoke-test.yml} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{docker-build.yml => jupyter-docker-build.yml} (100%) rename .github/workflows/{docker-smoke-test.yml => jupyter-docker-smoke-test.yml} (100%) diff --git a/.github/workflows/docker-build.yml b/.github/workflows/jupyter-docker-build.yml similarity index 100% rename from .github/workflows/docker-build.yml rename to .github/workflows/jupyter-docker-build.yml diff --git a/.github/workflows/docker-smoke-test.yml b/.github/workflows/jupyter-docker-smoke-test.yml similarity index 100% rename from .github/workflows/docker-smoke-test.yml rename to .github/workflows/jupyter-docker-smoke-test.yml From e127444c80569263d75c27b869aea123d49770e3 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Tue, 29 Sep 2026 16:09:37 +0000 Subject: [PATCH 4/4] chore: Update README.md for cogstack-platform --- README.md | 72 ++++++++++++++++++++++++++--- apps/cogstack-jupyter-hub/README.md | 11 +++-- 2 files changed, 72 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index b76ef1b0..22c4de98 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,76 @@ +

+ CogStack AI Logo + +

+

+ Unlock the power of healthcare data with CogStack AI. +

+ +--- + +

+ + Website + + + Documentation + + + Community Forum + +

+ # Cogstack Platform -This repository contains tools and services used to support CogStack deployments +This repository contains applications, tools and services used in cogstack deployments. See the latest documentation on [Readthedocs](https://docs.cogstack.org/en/latest/) ## Project contents + +### Apps + + + + + + + + + + +
+ + OCR Service +
OCR Service + +
+ Document and image text extraction built on Tesseract OCR + 		+ + CogStack Jupyter Hub +
CogStack Jupyter Hub + +
+ Custom JupyterHub images and notebooks for CogStack analysis +
+ + CogStack Cohorter +
CogStack Cohorter + +
+ Cohort definition tooling with NL2DSL and web UI + 		+ + CogStack Dashboards Demo +
CogStack Dashboards Demo + +
+ Demo scripts and visualisations for CogStack dashboards +
+ +### Tools - Source for the official cogstack documentation. This git repo stores the top level documetation that hosts on https://docs.cogstack.org - CogStack deployment instructions and examples - Helm Charts for deployments - CogStack platform tools eg Observability. - -### Apps -- OCR Service -- CogStack Cohorter -- Cogstack Dashboards Demo \ No newline at end of file diff --git a/apps/cogstack-jupyter-hub/README.md b/apps/cogstack-jupyter-hub/README.md index 2dcda5bd..f6b8d94d 100644 --- a/apps/cogstack-jupyter-hub/README.md +++ b/apps/cogstack-jupyter-hub/README.md @@ -1,17 +1,15 @@ # Cogstack-Jupyter-Hub -[![docker-jupyter-hub-all](https://github.com/CogStack/cogstack-jupyter-hub/actions/workflows/docker-build.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-jupyter-hub/actions/workflows/docker-build.yml) +[![docker-jupyter-hub-all](https://github.com/CogStack/cogstack-platform/actions/workflows/jupyter-docker-build.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-platform/actions/workflows/jupyter-docker-build.yml) ## Introduction -This repo has been reinstated. The custom jupyter-hub image is specified in the [CogStack-Nifi](https://github.com/CogStack/CogStack-NiFi/tree/main/services/jupyter-hub) project. - This repository contains a custom Jupyter Hub Docker image with example notebooks to play with. \ The notebooks provided are usually kept up to date with the example data that has been generated using Synthea and MTSamples in the [CogStack-NiFi](https://github.com/cogstack/cogstack-nifi) repository. Additionally, the [working with cogstack](https://github.com/CogStack/working_with_cogstack) scripts are included for production use. -All notebooks are available in the [notebooks](./notebooks/) folder. +The custom jupyter-hub image is specified in the [CogStack-Nifi](https://github.com/CogStack/CogStack-NiFi/tree/main/services/jupyter-hub) project. -The previous version of the jupyter notebook provided a simple but common environment for people to work on, the new version operates in a centralised manner, the hub docker container starts individual containers for each user, it also allows for easier sharing of data between users via groups (this feature needs testing). +All notebooks are available in the [notebooks](./notebooks/) folder. There are 3 images built in this repo: @@ -28,6 +26,9 @@ Images are available for both x86/ARM architectures (post version 1.2.7): Full and more in-depth knowledge on the configuration itself is available in the primary repository [official documentation](https://cogstack-nifi.readthedocs.io/en/latest/deploy/services.html#id12). +The previous version of the jupyter notebook provided a simple but common environment for people to work on, the new version operates in a centralised manner, the hub docker container starts individual containers for each user, it also allows for easier sharing of data between users via groups (this feature needs testing). + + ## Usage & configuration ENV variables are located in: [env/jupyter.env](./env/jupyter.env) and [env/general.env](./env/general.env).\