Adapt CEBRA-Lens so that compatible with unified CEBRA

.github/workflows/publish-book.yml

@@ -0,0 +1,33 @@
+name: publish-book
+
+on:
+  push:
+    branches:
+    - main
+
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install .[docs]
+        pip install jupyter-book sphinxcontrib-mermaid
+
+    - name: Build the book
+      run: |
+        jupyter-book build .
+
+    - name: GitHub Pages action
+      uses: peaceiris/actions-gh-pages@v3.9.3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./_build/html

.github/workflows/python-package.yml

@@ -0,0 +1,67 @@
+name: python-package
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-14, windows-latest]
+        python-version: ["3.10"]
+        include:
+          - os: ubuntu-latest
+            path: ~/.cache/pip
+          - os: macos-14
+            path: ~/Library/Caches/pip
+          - os: windows-latest
+            path: ~\AppData\Local\pip\Cache
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          channels: conda-forge,defaults
+          channel-priority: strict
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install PyTables through Conda
+        shell: bash -el {0}
+        run: |
+          conda install pytables==3.8.0 "numpy<2"
+
+      - name: Install dependencies
+        shell: bash -el {0}
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          pip install -r requirements.txt
+
+      - name: Run the formatter
+        shell: bash -el {0}
+        run: |
+          make format
+
+      - name: Run the spelling detector
+        shell: bash -el {0}
+        run: |
+          make codespell
+
+      - name: Check the documentation coverage
+        shell: bash -el {0}
+        run: |
+          make interrogate
+
+      - name: Run all pytest tests
+        shell: bash -el {0}
+        run: |
+          pip install pytest
+          pytest tests/

Makefile

@@ -0,0 +1,54 @@
+CEBRA_LENS_VERSION := 0.1.0.dev0
+
+dist:
+	python3 -m pip install virtualenv
+	python3 -m pip install --upgrade build twine
+	python3 -m build --wheel --sdist
+
+build: dist
+
+test:
+	python -m pytest --ff tests
+
+interrogate:
+	interrogate \
+		--ignore-property-decorators \
+		--ignore-init-method \
+		--verbose \
+		--ignore-semiprivate \
+		--ignore-private \
+		--ignore-magic \
+		--omit-covered-files \
+		-f 80 \
+		cebra_lens
+
+docs:
+	jupyter-book build docs
+
+docs-touch:
+	find docs/docs -iname '*.md' -exec touch {} \;
+	jupyter-book build docs/docs
+
+docs-strict:
+	jupyter-book build docs --keep-going --strict
+
+# Serve the docs
+serve_docs:
+	python -m http.server 8080 --bind 127.0.0.1 -d docs/_build/html
+
+# Serve the entire page
+serve_page:
+	python -m http.server 8080 --bind 127.0.0.1 -d docs/_build/html
+
+# Format code in the main package and docs
+format:
+	yapf -i -p -r cebra_lens
+	yapf -i -p -r tests
+	isort cebra_lens/
+	isort tests/
+
+codespell:
+	codespell cebra_lens/ tests/ docs/docs/*.md -L "nce, nd"
+
+
+.PHONY: docs docs-touch docs-strict serve_docs serve_page

cebra_lens/__init__.py

@@ -1,15 +1,15 @@
 # example of structure so that you can directly use the functions get_layer_activations instead of having to do CEBRA_Lens.activations.get_layer_activations
 from .activations import *
-from .quantification import *
-from .quantification.decoding import *
-from .quantification.distance import *
 from .quantification.cka_metric import *
+from .quantification.decoder import *
+from .quantification.distance import *
 from .quantification.rdm_metric import *
 from .quantification.tsne import *
-from .matplotlib import *
+from .utils import *
 from .utils_allen import *
 from .utils_hpc import *
-from .utils import *
+from .utils_plot import *
+from .utils_wrapper import *
 
 # selects what files can be imported when doing from CEBRA_Lens import * --> keep env clean
 # __all__ = ['get_layer_activations']