Release v0.3.0rc2 (#67)

* Bump to 0.3.0rc2

Adding another RC as additionals PRs were merged

* Apply pre-commit to all files

* Apply pre-commit

* Add docker container

* Fix synthetic dataset

* run full test suite

Author: stes

.dockerignore

@@ -0,0 +1,7 @@
+conda/
+docs/
+__pycache__/
+tests/
+third_party/
+tools/
+PKGBUILD

.github/workflows/doc-coverage.yml

@@ -10,12 +10,12 @@ name: PR Status
 on:
   pull_request:
     branches:
-      - main 
+      - main
       - public
       - dev
 
-permissions: 
-  pull-requests: write 
+permissions:
+  pull-requests: write
 
 jobs:
   documentation-status:
@@ -26,7 +26,7 @@ jobs:
 
     steps:
     # NOTE(stes) currently not used, we check
-    # the entire codebase now by default. 
+    # the entire codebase now by default.
     #- uses: actions/checkout@v3
     #  with:
     #    ref: main
@@ -41,7 +41,7 @@ jobs:
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install package 
+    - name: Install package
       run: |
         python -m pip install --upgrade pip setuptools wheel
         pip install interrogate==1.5.0

Dockerfile

@@ -0,0 +1,70 @@
+## EXPERIMENT BASE CONTAINER
+FROM nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu20.04 AS cebra-base
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update -y \
+	&& apt-get install --no-install-recommends -yy git python3 python3-pip python-is-python3 \
+	&& rm -rf /var/lib/apt/lists/*
+
+RUN pip install --no-cache-dir torch==2.0.0+cu117 \
+	--index-url https://download.pytorch.org/whl/cu117
+RUN pip install --no-cache-dir --pre 'cebra[dev,datasets,integrations]' \
+	&& pip uninstall -y cebra
+
+
+## GIT repository
+FROM ubuntu AS repo
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update -y \
+	&& apt-get install --no-install-recommends -yy git python3 python3-pip python-is-python3 \
+	&& rm -rf /var/lib/apt/lists/*
+
+WORKDIR /repo
+COPY . /repo
+RUN git status --porcelain
+
+WORKDIR /target
+RUN git clone --filter=tree:0 --depth=1 file:///repo/.git /target
+RUN git log
+
+## CEBRA WHEEL
+FROM python:3.9 AS wheel
+
+RUN pip install --upgrade --no-cache-dir pip
+RUN pip install --upgrade --no-cache-dir build virtualenv
+
+WORKDIR /build
+COPY --from=repo /target .
+RUN make dist
+
+## CEBRA CONTAINER
+FROM cebra-base
+
+# install the cebra wheel
+ENV WHEEL=cebra-0.3.0rc2-py2.py3-none-any.whl
+WORKDIR /build
+COPY --from=wheel /build/dist/${WHEEL} .
+RUN pip install --no-cache-dir ${WHEEL}'[dev,integrations,datasets]'
+RUN rm -rf /build
+
+# add the repository
+WORKDIR /app
+COPY --from=repo /target .
+
+ENV PYTHONPATH=/app
+
+ARG UID
+ARG GID
+RUN groupadd -g $GID appgroup
+RUN useradd -u $UID -g $GID -ms "/bin/bash" appuser
+RUN chown -R appuser:appgroup /app
+USER appuser
+
+ARG GIT_HASH
+RUN if [ "$(git rev-parse HEAD)" != "${GIT_HASH}" ]; then \
+	git rev-parse HEAD; \
+	echo ${GIT_HASH}; \
+	exit 1; \
+    fi
+RUN git status --porcelain || exit 1

Makefile

@@ -10,7 +10,7 @@ build: dist
 archlinux:
 	mkdir -p dist/arch
 	cp PKGBUILD dist/arch
-	cp dist/cebra-0.3.0rc1.tar.gz dist/arch
+	cp dist/cebra-0.3.0rc2.tar.gz dist/arch
 	(cd dist/arch; makepkg --skipchecksums -f)
 
 # NOTE(stes): Ensure that no old tempfiles are present. Ideally, move this into

PKGBUILD

@@ -1,7 +1,7 @@
 # Maintainer: Steffen Schneider <[email protected]>
 pkgname=python-cebra
 _pkgname=cebra
-pkgver=0.3.0rc1
+pkgver=0.3.0rc2
 pkgrel=1
 pkgdesc="Consistent Embeddings of high-dimensional Recordings using Auxiliary variables"
 url="https://cebra.ai"

cebra/__init__.py

@@ -47,7 +47,7 @@
 
 import cebra.integrations.sklearn as sklearn
 
-__version__ = "0.3.0rc1"
+__version__ = "0.3.0rc2"
 __all__ = ["CEBRA"]
 __allow_lazy_imports = False
 __lazy_imports = {}

cebra/data/assets.py

@@ -28,7 +28,7 @@ def download_file_with_progress_bar(url: str,
                                     file_name: str,
                                     retry_count: int = 0) -> Optional[str]:
     """Download a file from the given URL.
-    
+
     During download, progress is reported using a progress bar. The downloaded
     file's checksum is compared to the provided ``expected_checksum``.
 

cebra/datasets/synthetic_data.py

@@ -97,9 +97,9 @@ def __init__(self, name, root=_DEFAULT_DATADIR, download=True):
         data = joblib.load(file_path)
         self.data = data  #NOTE: making it backwards compatible with synth notebook.
         self.name = name
-        self.neural = self.data['z']
-        self.latents = self.data['x']
-        self.u = self.data['u']
+        self.neural = self.data['x']
+        self.latents = self.data['z']
+        self.index = self.data['u']
         self.lam = self.data['lam']
 
     @property

cebra/integrations/sklearn/cebra.py

@@ -1417,8 +1417,9 @@ def load(cls,
                 f"Cannot use 'torch' backend with a dictionary-based checkpoint. "
                 f"Please try a different backend.")
         if not isinstance(checkpoint, dict) and backend == "sklearn":
-            raise RuntimeError(f"Cannot use 'sklearn' backend a non dictionary-based checkpoint. "
-                               f"Please try a different backend.")
+            raise RuntimeError(
+                f"Cannot use 'sklearn' backend a non dictionary-based checkpoint. "
+                f"Please try a different backend.")
 
         if backend == "sklearn":
             cebra_ = _load_cebra_with_sklearn_backend(checkpoint)

docs/source/api/sklearn/helpers.rst

@@ -4,4 +4,3 @@ Helper functions
 .. automodule:: cebra.integrations.sklearn.helpers
    :show-inheritance:
    :members:
-