CHANGELOG.md

OpenProblems Base Images v1.1.0

BREAKING CHANGES

• Moved location of the base images:

  • ghcr.io/openproblems-bio/base_python -> ghcr.io/openproblems-bio/base_images/python
  • ghcr.io/openproblems-bio/base_pytorch_nvidia -> ghcr.io/openproblems-bio/base_images/pytorch_nvidia
  • ghcr.io/openproblems-bio/base_r -> ghcr.io/openproblems-bio/base_images/r

• python: Upgraded AnnData to 0.10 and Scanpy to 1.10.

• pytorch_nvidia: Upgraded AnnData to 0.10 and Scanpy to 1.10.

• r: Upgraded AnnData to 0.10 and Scanpy to 1.10.

NEW FUNCTIONALITY

• tensorflow_nvidia: Added a new image based on nvcr.io/nvidia/tensorflow:24.06-tf2-py3.

MINOR CHANGES

• pytorch_nvidia: Upgraded base image from nvcr.io/nvidia/pytorch:24.03-py3 to nvcr.io/nvidia/pytorch:24.06-py3.

• Bumped Viash version to 0.9.0-RC6.

• Updated CI to use viash-actions@v6. Build but not push images on PRs.

OpenProblems Base Images v1.0.5

MINOR CHANGES

• Switch back to CRAN reticulate

OpenProblems Base Images v1.0.4

MINOR CHANGES

• Switch to rstudio/reticulate to circumvent a bug in the reticulate package.

OpenProblems Base Images v1.0.3

NEW FUNCTIONALITY

• Added base_pytorch_nvidia image based on nvcr.io/pytorch.

MINOR CHANGES

• base_python: Upgraded to Python 3.11.

• base_r: Upgraded to Python 3.11.

OpenProblems Base Images v1.0.2

MINOR CHANGES

• base_r: added bit64 as a dependency.

OpenProblems Base Images v1.0.1

MINOR CHANGES

• base_python: Added scanpy as a dependency.

• base_r: Added scanpy as a dependency.

OpenProblems Base Images v1.0.0

Initial release containing the following base images:

• ghcr.io/openproblems-bio/base/python_3_10:1.0.0, a Python 3.10 image with the following extra packages preinstalled:

  • Apt: procps
  • Python: anndata~=0.8.0, mudata~=0.2.0, scanpy~=1.9.2

• ghcr.io/openproblems-bio/base/r2u_22_04:1.0.0, an R2U 22.04 image with the following extra packages preinstalled:

  • Apt: python3 and procps
  • Python: anndata~=0.8.0, mudata~=0.2.0, scanpy~=1.9.2
  • R: anndata