Merge master

.github/workflows/ci.yml

@@ -13,13 +13,13 @@ jobs:
     name: Build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Node.js
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
-          node-version: 18
-      - uses: pnpm/action-setup@v2
+          node-version: 20.9.0
+      - uses: pnpm/action-setup@v3
         name: Install pnpm
         with:
           version: 8
@@ -28,7 +28,7 @@ jobs:
         id: pnpm
         shell: bash
         run: echo "STORE_PATH=$(pnpm store path --silent)" >> "$GITHUB_OUTPUT"
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         name: Setup pnpm cache
         with:
           path: ${{ steps.pnpm.outputs.STORE_PATH }}
@@ -40,7 +40,7 @@ jobs:
       - name: Build website
         run: pnpm build
       - name: Upload pages artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
           path: ./build
 
@@ -64,4 +64,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

docs/internal/deployments/data.tsx

@@ -140,7 +140,7 @@ const deployments: DeploymentInfo[] = [
     ),
   },
   {
-    url: "https://fetalmri-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/",
+    url: "https://fetalmri-cube.apps.shift.nerc.mghpcc.org/api/v1/",
     description: "Fetal MRI dataset CUBE",
     host: "NERC (OpenShift)",
     src: {
@@ -160,7 +160,7 @@ const deployments: DeploymentInfo[] = [
     ),
   },
   {
-    url: "https://publictesting-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/api/v1/",
+    url: "https://cube-for-testing-chrisui.apps.shift.nerc.mghpcc.org/api/v1/",
     description:
       "Public CUBE for testing against the CUBE API in CI environments.",
     host: "NERC (OpenShift)",

docs/run/chrisui_openshift.md

@@ -33,9 +33,10 @@ oc new-app --name chrisui \
   being able to generate the version string. See https://github.com/FNNDSC/ChRIS_ui/pull/508
 - Increase memory limit for build to 4GB
 - (optional) Set RunPolicy=SerialLatestOnly
+- (optional) Set `successfulBuildsHistoryLimit` and `failedBuildsHistoryLimit`
 
 ```shell
-oc patch bc/chrisui --patch '{"spec":{"resources":{"limits":{"memory":"3814Mi"}},"runPolicy":"SerialLatestOnly","source":{"git":{"ref":"refs/heads/master"}}}}'
+oc patch bc/chrisui --patch '{"spec":{"resources":{"limits":{"memory":"3814Mi"}},"runPolicy":"SerialLatestOnly","source":{"git":{"ref":"refs/heads/master"}}",successfulBuildsHistoryLimit":2,"failedBuildsHistoryLimit":2}}'
 ```
 
 ### 4. Create a Route

docs/tutorials/convert_python_app.md

@@ -0,0 +1,109 @@
+---
+title: "HOW TO: Convert an existing Python app"
+toc_min_heading_level: 2
+toc_max_heading_level: 3
+---
+
+This guide will show you how to convert (almost) any existing Python program into a
+[_ChRIS_ _ds_ plugin](../chris_plugins#ds-type-plugins)!
+It's easier done than said.
+
+:::tip
+
+This guide assumes working knowledge of Python, Python packaging, and Docker.
+
+:::
+
+## 1. Install `chris_plugin`
+
+```shell
+pip install -U chris_plugin
+```
+
+## 2. Use `argparse`
+
+Changes are, your Python program is already using
+[argparse](https://docs.python.org/3/library/argparse.html).
+If not, you'll need to add it:
+
+```python
+from argparse import ArgumentParser
+parser = ArgumentParser()
+```
+
+## 3. Add a `main` function
+
+You probably have this too, though here we need to do something special:
+
+A ChRIS plugin processes data from an input directory and writes its results to an output directory.
+Hence, these data directories should be parameters to your `main` function.
+
+The `main` function should be **decorated** with the **`@chris_plugin`** decorator, which takes the
+parser you created.
+
+```python
+from chris_plugin import chris_plugin
+
+@chris_plugin(parser=parser)
+def main(options, inputdir, outputdir):
+    ...
+```
+
+
+## 4. Customize `setup.py`
+
+Once again, your app should already have a `setup.py`!
+
+As a command-line app, `setup.py` must specify
+[entrypoints](https://setuptools.pypa.io/en/latest/userguide/entry_point.html).
+
+It should look like this:
+
+```python
+from setuptools import setup
+
+setup(
+    name             = 'chris-plugin-example',
+    version          = '1.0.0',
+    description      = 'A ChRIS DS plugin that I made',
+    author           = 'FNNDSC',
+    author_email     = '[email protected]',
+    url              = 'https://github.com/FNNDSC/chris-plugin-example',
+    # if your app is a single script file, use py_modules
+    # if your app is a folder containing Python packages, set packages=...
+    py_modules       = ['app'],
+    install_requires = ['chris_plugin'],
+    license          = 'MIT',
+    python_requires  = '>=3.10',
+    entry_points     = {
+        'console_scripts': [
+            # here you need to declare the name of your executable program
+            # and your main function
+            'my_command = app:main'
+            ]
+        }
+)
+```
+
+## 5. Create `Dockerfile`
+
+`Dockerfile` are instructions for how to build a container image from your source code.
+
+```Dockerfile
+FROM python:3.10
+WORKDIR /usr/local/src
+COPY . .
+RUN pip install .
+CMD ["my_command", "--help"]
+```
+
+## 6. Done!
+
+A JSON description of your ChRIS plugin can be created using the `chris_plugin_info` command:
+
+```shell
+chris_plugin_info --dock-image docker.io/fnndsc/pl-app:v1.0.0 > description.json
+```
+
+The file `description.json` is a representation of your plugin which can be uploaded to a _ChRIS backend_.
+The instructions to do so are [here](./upload_plugin).

docs/tutorials/upload_plugin/index.md

@@ -91,3 +91,17 @@ Use [chrisomatic](https://github.com/FNNDSC/chrisomatic) to upload a list of plu
 
 _ChRIS_ plugin GitHub repositories can be configured to be automatically uploaded
 using [GitHub Actions](../../chris_plugins/github_actions.md).
+
+## Non-canonical methods
+
+While not _officially_ supported, a python helper script, [plugin2cube](https://github.com/FNNDSC/plugin2cube), is available that can effect registration by directly speaking to the `CUBE` API.
+
+In some cases this can be a quicker/simpler way to register a plugin. It does however require the `CUBE` *admin* username and password and knowledge of the compute environments on a `CUBE`, and assumes that the host executing the script has `docker` installed.
+
+For example:
+
+```shell
+plugin2cube --CUBEurl http://rc-live.tch.harvard.edu:32222/api/v1/ \
+            --CUBEuser XXXXXX --CUBEpasswd  XXXXXX                 \
+            --computenames galena-avx --dock_image ghcr.io/fnndsc/pl-dicom_repack:1.1.4
+```