Merge branch 'main' of github.com:ETH-PEACH-Lab/datascience-visualisa…

…tion

.copier-answers.yml

@@ -6,12 +6,12 @@ author_name: My Name
 has_binder: true
 has_settings: false
 kind: frontend
-labextension_name: jupyterlab_apod
+labextension_name: cluster_viz
 project_short_description: ' Show a random NASA Astronomy Picture of the Day in a
     JupyterLab panel
 
     '
-python_name: jupyterlab_apod
+python_name: cluster_viz
 repository: ''
 test: true
 

.github/workflows/build.yml

@@ -41,7 +41,7 @@ jobs:
         python -m pip install .[test]
 
         jupyter labextension list
-        jupyter labextension list 2>&1 | grep -ie "jupyterlab_apod.*OK"
+        jupyter labextension list 2>&1 | grep -ie "cluster_viz.*OK"
         python -m jupyterlab.browser_check
 
     - name: Package the extension
@@ -50,13 +50,13 @@ jobs:
 
         pip install build
         python -m build
-        pip uninstall -y "jupyterlab_apod" jupyterlab
+        pip uninstall -y "cluster_viz" jupyterlab
 
     - name: Upload extension packages
       uses: actions/upload-artifact@v4
       with:
         name: extension-artifacts
-        path: dist/jupyterlab_apod*
+        path: dist/cluster_viz*
         if-no-files-found: error
 
   test_isolated:
@@ -79,11 +79,11 @@ jobs:
         sudo rm -rf $(which node)
         sudo rm -rf $(which node)
 
-        pip install "jupyterlab>=4.0.0,<5" jupyterlab_apod*.whl
+        pip install "jupyterlab>=4.0.0,<5" cluster_viz*.whl
 
 
         jupyter labextension list
-        jupyter labextension list 2>&1 | grep -ie "jupyterlab_apod.*OK"
+        jupyter labextension list 2>&1 | grep -ie "cluster_viz.*OK"
         python -m jupyterlab.browser_check --no-browser-test
 
   integration-tests:
@@ -109,7 +109,7 @@ jobs:
     - name: Install the extension
       run: |
         set -eux
-        python -m pip install "jupyterlab>=4.0.0,<5" jupyterlab_apod*.whl
+        python -m pip install "jupyterlab>=4.0.0,<5" cluster_viz*.whl
 
     - name: Install dependencies
       working-directory: ui-tests
@@ -138,7 +138,7 @@ jobs:
       if: always()
       uses: actions/upload-artifact@v4
       with:
-        name: jupyterlab_apod-playwright-tests
+        name: cluster_viz-playwright-tests
         path: |
           ui-tests/test-results
           ui-tests/playwright-report

.github/workflows/check-release.yml

@@ -26,5 +26,5 @@ jobs:
       - name: Upload Distributions
         uses: actions/upload-artifact@v4
         with:
-          name: jupyterlab_apod-releaser-dist-${{ github.run_number }}
+          name: cluster_viz-releaser-dist-${{ github.run_number }}
           path: .jupyter_releaser_checkout/dist

.gitignore

@@ -10,9 +10,9 @@ backend/api_key.txt
 *.egg-info/
 .ipynb_checkpoints
 *.tsbuildinfo
-jupyterlab_apod/labextension
+cluster_viz/labextension
 # Version file is handled by hatchling
-jupyterlab_apod/_version.py
+cluster_viz/_version.py
 /secrets
 # Integration tests
 ui-tests/test-results/

.prettierignore

@@ -3,5 +3,5 @@ node_modules
 **/lib
 **/package.json
 !/package.json
-jupyterlab_apod
+cluster_viz
 backend

DEPLOYMENT.md

@@ -0,0 +1,18 @@
+# Using the GitHub Container Registry for Deployment
+
+1. Create a personal token: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens
+
+```
+docker login ghcr.io --username github-account
+[Paste your GitHub token on this prompt]
+```
+2. Build the image for the server
+```
+docker image build --platform linux/amd64 -t cluster-jupyter . 
+```
+
+2. Tag and push your Docker images
+```
+docker tag cluster-jupyter ghcr.io/eth-peach-lab/datascience-visualisation/cluster-jupyter:latest
+docker push ghcr.io/eth-peach-lab/datascience-visualisation/cluster-jupyter:latest
+```

Dockerfile

@@ -0,0 +1,7 @@
+FROM quay.io/jupyter/minimal-notebook:hub-5.1.0
+USER root
+RUN pip install --no-cache -U cluster_viz 
+EXPOSE 8000
+EXPOSE 8888
+USER ${NB_USER}
+CMD ["/bin/bash","-c", "jupyterhub-singleuser"]

README.md

@@ -1,4 +1,4 @@
-# jupyterlab_apod
+# cluster_Viz
 
 [![Github Actions Status](/workflows/Build/badge.svg)](/actions/workflows/build.yml)
 
@@ -16,15 +16,15 @@
 To install the extension, execute:
 
 ```bash
-pip install jupyterlab_apod
+pip install cluster_viz
 ```
 
 ## Uninstall
 
 To remove the extension, execute:
 
 ```bash
-pip uninstall jupyterlab_apod
+pip uninstall cluster_viz
 ```
 
 ## Contributing
@@ -39,7 +39,7 @@ The `jlpm` command is JupyterLab's pinned version of
 
 ```bash
 # Clone the repo to your local environment
-# Change directory to the jupyterlab_apod directory
+# Change directory to the cluster_viz directory
 # Install package in development mode
 pip install -e "."
 # Link your development version of the extension with JupyterLab
@@ -68,12 +68,12 @@ jupyter lab build --minimize=False
 ### Development uninstall
 
 ```bash
-pip uninstall jupyterlab_apod
+pip uninstall cluster_viz
 ```
 
 In development mode, you will also need to remove the symlink created by `jupyter labextension develop`
 command. To find its location, you can run `jupyter labextension list` to figure out where the `labextensions`
-folder is located. Then you can remove the symlink named `jupyterlab_apod` within that folder.
+folder is located. Then you can remove the symlink named `cluster_viz` within that folder.
 
 ### Testing the extension
 

RELEASE.md

@@ -1,4 +1,4 @@
-# Making a new release of jupyterlab_apod
+# Making a new release of cluster_viz
 
 The extension can be published to `PyPI` and `npm` manually or using the [Jupyter Releaser](https://github.com/jupyter-server/jupyter_releaser).
 

binder/environment.yml

@@ -1,4 +1,4 @@
-# a mybinder.org-ready environment for demoing jupyterlab_apod
+# a mybinder.org-ready environment for demoing cluster_viz
 # this environment may also be used locally on Linux/MacOS/Windows, e.g.
 #
 #   conda env update --file binder/environment.yml

binder/postBuild

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-""" perform a development install of jupyterlab_apod
+""" perform a development install of cluster_viz
 
     On Binder, this will run _after_ the environment has been fully created from
     the environment.yml in this directory.
@@ -43,5 +43,5 @@ _("jupyter", "server", "extension", "list")
 _("jupyter", "labextension", "list")
 
 
-print("JupyterLab with jupyterlab_apod is ready to run with:\n")
+print("JupyterLab with cluster_viz is ready to run with:\n")
 print("\tjupyter lab\n")

jupyterlab_apod/__init__.py → cluster_viz/__init__.py

@@ -5,12 +5,12 @@
     # in editable mode with pip. It is highly recommended to install
     # the package from a stable release or in editable mode: https://pip.pypa.io/en/stable/topics/local-project-installs/#editable-installs
     import warnings
-    warnings.warn("Importing 'jupyterlab_apod' outside a proper installation.")
+    warnings.warn("Importing 'cluster_viz' outside a proper installation.")
     __version__ = "dev"
 
 
 def _jupyter_labextension_paths():
     return [{
         "src": "labextension",
-        "dest": "jupyterlab_apod"
+        "dest": "cluster_viz"
     }]

install.json

@@ -1,5 +1,5 @@
 {
   "packageManager": "python",
-  "packageName": "jupyterlab_apod",
-  "uninstallInstructions": "Use your Python package manager (pip, conda, etc.) to uninstall the package jupyterlab_apod"
+  "packageName": "cluster_viz",
+  "uninstallInstructions": "Use your Python package manager (pip, conda, etc.) to uninstall the package cluster_viz"
 }

package.json

@@ -1,15 +1,15 @@
 {
-    "name": "jupyterlab_apod",
-    "version": "0.1.0",
+    "name": "cluster_viz",
+    "version": "0.2.1",
     "description": "Show a random NASA Astronomy Picture of the Day in a JupyterLab panel",
     "keywords": [
         "jupyter",
         "jupyterlab",
         "jupyterlab-extension"
     ],
-    "homepage": "",
+    "homepage": "https://github.com/ETH-PEACH-Lab/datascience-visualisation",
     "bugs": {
-        "url": "/issues"
+        "url": "https://github.com/ETH-PEACH-Lab/datascience-visualisation/issues"
     },
     "license": "BSD-3-Clause",
     "author": "My Name",
@@ -23,7 +23,7 @@
     "style": "style/index.css",
     "repository": {
         "type": "git",
-        "url": ".git"
+        "url": "https://github.com/ETH-PEACH-Lab/datascience-visualisation"
     },
     "scripts": {
         "build": "jlpm build:lib && jlpm build:labextension:dev",
@@ -35,7 +35,7 @@
         "clean": "jlpm clean:lib",
         "clean:lib": "rimraf lib tsconfig.tsbuildinfo",
         "clean:lintcache": "rimraf .eslintcache .stylelintcache",
-        "clean:labextension": "rimraf jupyterlab_apod/labextension jupyterlab_apod/_version.py",
+        "clean:labextension": "rimraf cluster_viz/labextension cluster_viz/_version.py",
         "clean:all": "jlpm clean:lib && jlpm clean:labextension && jlpm clean:lintcache",
         "eslint": "jlpm eslint:check --fix",
         "eslint:check": "eslint . --cache --ext .ts,.tsx",
@@ -119,7 +119,7 @@
     },
     "jupyterlab": {
         "extension": true,
-        "outputDir": "jupyterlab_apod/labextension",
+        "outputDir": "cluster_viz/labextension",
         "sharedPackages": {
             "@jupyter-widgets/base": {
                 "bundled": false,

pyproject.toml

@@ -3,8 +3,9 @@ requires = ["hatchling>=1.5.0", "jupyterlab>=4.0.0,<5", "hatch-nodejs-version>=0
 build-backend = "hatchling.build"
 
 [project]
-name = "jupyterlab_apod"
+name = "cluster_viz"
 readme = "README.md"
+homepage = "https://github.com/ETH-PEACH-Lab/datascience-visualisation"  # Add your repository or website URL here
 license = { file = "LICENSE" }
 requires-python = ">=3.8"
 classifiers = [
@@ -33,24 +34,24 @@ source = "nodejs"
 fields = ["description", "authors", "urls"]
 
 [tool.hatch.build.targets.sdist]
-artifacts = ["jupyterlab_apod/labextension"]
+artifacts = ["cluster_viz/labextension"]
 exclude = [".github", "binder"]
 
 [tool.hatch.build.targets.wheel.shared-data]
-"jupyterlab_apod/labextension" = "share/jupyter/labextensions/jupyterlab_apod"
-"install.json" = "share/jupyter/labextensions/jupyterlab_apod/install.json"
+"cluster_viz/labextension" = "share/jupyter/labextensions/cluster_viz"
+"install.json" = "share/jupyter/labextensions/cluster_viz/install.json"
 
 [tool.hatch.build.hooks.version]
-path = "jupyterlab_apod/_version.py"
+path = "cluster_viz/_version.py"
 
 [tool.hatch.build.hooks.jupyter-builder]
 dependencies = ["hatch-jupyter-builder>=0.5"]
 build-function = "hatch_jupyter_builder.npm_builder"
 ensured-targets = [
-    "jupyterlab_apod/labextension/static/style.js",
-    "jupyterlab_apod/labextension/package.json",
+    "cluster_viz/labextension/static/style.js",
+    "cluster_viz/labextension/package.json",
 ]
-skip-if-exists = ["jupyterlab_apod/labextension/static/style.js"]
+skip-if-exists = ["cluster_viz/labextension/static/style.js"]
 
 [tool.hatch.build.hooks.jupyter-builder.build-kwargs]
 build_cmd = "build:prod"
@@ -60,7 +61,7 @@ npm = ["jlpm"]
 build_cmd = "install:extension"
 npm = ["jlpm"]
 source_dir = "src"
-build_dir = "jupyterlab_apod/labextension"
+build_dir = "cluster_viz/labextension"
 
 [tool.jupyter-releaser.options]
 version_cmd = "hatch version"

src/__tests__/jupyterlab_apod.spec.ts

@@ -2,7 +2,7 @@
  * Example of [Jest](https://jestjs.io/docs/getting-started) unit tests
  */
 
-describe('jupyterlab_apod', () => {
+describe('cluster_viz', () => {
   it('should be tested', () => {
     expect(1 + 1).toEqual(2);
   });

src/backend/Clusterers/clusterer.py

@@ -43,9 +43,10 @@ def embed_cell(self, code_str: str, desc_str: str) -> list[float]:
             list[float]: A list representing the embedded vector of the code snippet and its description.
         """
 
-        code_embedding = self._process_code(code_str)
+        # code_embedding = self._process_code(code_str)
         desc_embedding = self._process_summary(desc_str)
-        return torch.mean(torch.stack([code_embedding, desc_embedding]), dim=0).detach().numpy().reshape(-1).tolist()
+        # return torch.mean(torch.stack([code_embedding, desc_embedding]), dim=0).detach().numpy().reshape(-1).tolist()
+        return desc_embedding.detach().numpy().reshape(-1).tolist()
 
 
     def cluster(self, data: dict, classes: list[str]) -> dict: