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add base images to core #5

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Aug 9, 2024
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6 changes: 6 additions & 0 deletions .github/dependabot.yml
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version: 2
updates:
- package-ecosystem: "github-actions"
directory: "/"
schedule:
interval: "daily"
2 changes: 2 additions & 0 deletions .github/workflows/daily-build.yaml
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Expand Up @@ -4,6 +4,8 @@ on:
push:
branches:
- main
paths:
- 'base_images/**'
pull_request:
schedule:
# build daily
Expand Down
1 change: 1 addition & 0 deletions base_images/.gitignore
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.idea
7 changes: 7 additions & 0 deletions base_images/CHANGELOG.md
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# OpenProblems Base Images v1.0.0

Relocated the base images from base_images repo to core repo.

## MAJOR CHANGES

* Change container registry from `ghcr.io/openproblems-bio/base_images` to docker hub `openproblems/base_*` (PR #5).
13 changes: 13 additions & 0 deletions base_images/README.md
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# Base images


<!-- This file is rendered by running 'quarto render README.qmd' -->

Repository for base Docker images for openproblems-bio on Docker-hub.

This repository currently contains the following images:

- [`openproblems/base_python:1.0.0`](src/python)
- [`openproblems/base_pytorch_nvidia:1.0.0`](src/pytorch_nvidia)
- [`openproblems/base_r:1.0.0`](src/r)
- [`openproblems/base_tensorflow_nvidia:1.0.0`](src/tensorflow_nvidia)
29 changes: 29 additions & 0 deletions base_images/README.qmd
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---
title: Base images
format: gfm
---

<!-- This file is rendered by running 'quarto render README.qmd' -->

```{r include=FALSE}
# run 'viash ns list' and read as yaml

ns_list_yaml <- system("viash ns list --format yaml", intern = TRUE)
ns_list <- yaml::yaml.load(ns_list_yaml)
```

Repository for base Docker images for openproblems-bio on Docker-hub.

This repository currently contains the following images:

```{r echo=FALSE, output="asis"}
for (comp in ns_list) {
image_name <- paste0(
comp$package_config$organization, "/",
comp$name, ":",
comp$version
)
cat(paste0("* [`", image_name, "`](", dirname(comp$build_info$config), ")"))
cat("\n")
}
```
5 changes: 5 additions & 0 deletions base_images/_viash.yaml
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organization: openproblems
version: 1.0.0
viash_version: 0.9.0-RC6
links:
repository: https://github.com/openproblems-bio/base_images
16 changes: 16 additions & 0 deletions base_images/src/python/config.vsh.yaml
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name: base_python
description: A Python 3.11 image with anndata preinstalled.
engines:
- type: docker
image: python:3.11
setup:
- type: apt
packages:
- procps
- type: python
packages:
- anndata~=0.10.0
- scanpy~=1.10.0
- pyyaml
- requests
- jsonschema
16 changes: 16 additions & 0 deletions base_images/src/pytorch_nvidia/config.vsh.yaml
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name: base_pytorch_nvidia
description: An nvcr.io pytorch 24.06-py3 with anndata preinstalled.
engines:
- type: docker
image: nvcr.io/nvidia/pytorch:24.06-py3
setup:
- type: apt
packages:
- procps
- type: python
packages:
- anndata~=0.10.0
- scanpy~=1.10.0
- pyyaml
- requests
- jsonschema
29 changes: 29 additions & 0 deletions base_images/src/r/config.vsh.yaml
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name: base_r
description: An R2U 22.04 image with anndata preinstalled.
engines:
- type: docker
image: rocker/r2u:22.04
setup:
- type: apt
packages:
- procps
- libhdf5-dev
- libgeos-dev
- python3
- python3-pip
- python3-dev
- python-is-python3
- type: python
packages:
- rpy2
- anndata~=0.10.0
- scanpy~=1.10.0
- pyyaml
- requests
- jsonschema
- type: r
packages:
- anndata
- BiocManager
- reticulate
- bit64
16 changes: 16 additions & 0 deletions base_images/src/tensorflow_nvidia/config.vsh.yaml
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name: base_tensorflow_nvidia
description: An nvcr.io tensorflow 24.06-tf2-py3 with anndata preinstalled.
engines:
- type: docker
image: nvcr.io/nvidia/tensorflow:24.06-tf2-py3
setup:
- type: apt
packages:
- procps
- type: python
packages:
- anndata~=0.10.0
- scanpy~=1.10.0
- pyyaml
- requests
- jsonschema