Add docs, examples, tests

Author: Jennings Zhang

.github/workflows/ci.yml

@@ -15,9 +15,38 @@ on:
       - "v?[0-9]+.[0-9]+.[0-9]+*"
 
 jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: docker/setup-buildx-action@v2
+      - name: Cache Docker layers
+        uses: actions/cache@v3
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+      - name: Build
+        uses: docker/build-push-action@v3
+        with:
+          build-args: extras_require=dev
+          context: .
+          load: true
+          push: false
+          tags: "localhost/fnndsc/pl-adapt_object_mesh:dev"
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache
+      - name: Run pytest
+        run: |
+          docker run -v "$GITHUB_WORKSPACE:/app:ro" -w /app localhost/fnndsc/pl-adapt_object_mesh:dev \
+            pytest -o cache_dir=/tmp/pytest
+
   build:
     name: Build
     runs-on: ubuntu-22.04
+    needs: [ test ]
 
     # A local registry helps us reuse the built image between steps
     services:

README.md

@@ -4,106 +4,36 @@
 [![MIT License](https://img.shields.io/github/license/fnndsc/pl-adapt_object_mesh)](https://github.com/FNNDSC/pl-adapt_object_mesh/blob/main/LICENSE)
 [![ci](https://github.com/FNNDSC/pl-adapt_object_mesh/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-adapt_object_mesh/actions/workflows/ci.yml)
 
-`pl-adapt_object_mesh` is a [_ChRIS_](https://chrisproject.org/)
-_ds_ plugin which takes in ...  as input files and
-creates ... as output files.
-
-## Abstract
+![before and after](examples/before_and_after.png)
 
-...
+`pl-adapt_object_mesh` is a [_ChRIS_](https://chrisproject.org/)
+_ds_ plugin wrapper for
+[`adapt_object_mesh`](https://github.com/aces/surface-extraction/blob/clasp_3-0-3/src/adapt_object_mesh.c),
+a polygonal mesh smoothing program from [CIVET](http://mcin.ca/technology/civet/).
+It implements 
+It runs `adapt_object_mesh` on every `.obj` file in its input directory,
+writing outputs to an output directory, and printing logs to log files
+which are created next to the output surfaces.
 
 ## Installation
 
 `pl-adapt_object_mesh` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
 run from either within _ChRIS_ or the command-line.
 
-[![Get it from chrisstore.co](https://ipfs.babymri.org/ipfs/QmaQM9dUAYFjLVn3PpNTrpbKVavvSTxNLE5BocRCW1UoXG/light.png)](https://chrisstore.co/plugin/pl-adapt_object_mesh)
+[![Get it from chrisstore.co](https://raw.githubusercontent.com/FNNDSC/ChRIS_store_ui/963938c241636e4c3dc4753ee1327f56cb82d8b5/src/assets/public/badges/light.svg)](https://chrisstore.co/plugin/pl-adapt_object_mesh)
 
 ## Local Usage
 
 To get started with local command-line usage, use [Apptainer](https://apptainer.org/)
-(a.k.a. Singularity) to run `pl-adapt_object_mesh` as a container:
-
-```shell
-singularity exec docker://fnndsc/pl-adapt_object_mesh adapt_object_mesh_wrapper [--args values...] input/ output/
-```
-
+(a.k.a. Singularity) to run `pl-adapt_object_mesh` as a container.
 To print its available options, run:
 
 ```shell
-singularity exec docker://fnndsc/pl-adapt_object_mesh adapt_object_mesh_wrapper --help
-```
-
-## Examples
-
-`adapt_object_mesh_wrapper` requires two positional arguments: a directory containing
-input data, and a directory where to create output data.
-First, create the input directory and move input data into it.
-
-```shell
-mkdir incoming/ outgoing/
-mv some.dat other.dat incoming/
-singularity exec docker://fnndsc/pl-adapt_object_mesh:latest adapt_object_mesh_wrapper [--args] incoming/ outgoing/
-```
-
-## Development
-
-Instructions for developers.
-
-### Building
-
-Build a local container image:
-
-```shell
-docker build -t localhost/fnndsc/pl-adapt_object_mesh .
-```
-
-### Running
-
-Mount the source code `adapt_object_mesh_wrapper.py` into a container to try out changes without rebuild.
-
-```shell
-docker run --rm -it --userns=host -u $(id -u):$(id -g) \
-    -v $PWD/adapt_object_mesh_wrapper.py:/usr/local/lib/python3.10/site-packages/adapt_object_mesh_wrapper.py:ro \
-    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
-    localhost/fnndsc/pl-adapt_object_mesh adapt_object_mesh_wrapper /incoming /outgoing
-```
-
-### Testing
-
-Run unit tests using `pytest`.
-It's recommended to rebuild the image to ensure that sources are up-to-date.
-Use the option `--build-arg extras_require=dev` to install extra dependencies for testing.
-
-```shell
-docker build -t localhost/fnndsc/pl-adapt_object_mesh:dev --build-arg extras_require=dev .
-docker run --rm -it localhost/fnndsc/pl-adapt_object_mesh:dev pytest
-```
-
-## Release
-
-Steps for release can be automated by [Github Actions](.github/workflows/ci.yml).
-This section is about how to do those steps manually.
-
-### Increase Version Number
-
-Increase the version number in `setup.py` and commit this file.
-
-### Push Container Image
-
-Build and push an image tagged by the version. For example, for version `1.2.3`:
-
-```
-docker build -t docker.io/fnndsc/pl-adapt_object_mesh:1.2.3 .
-docker push docker.io/fnndsc/pl-adapt_object_mesh:1.2.3
+apptainer exec docker://fnndsc/pl-adapt_object_mesh adapt_object_mesh_wrapper --help
 ```
 
-### Get JSON Representation
-
-Run [`chris_plugin_info`](https://github.com/FNNDSC/chris_plugin#usage)
-to produce a JSON description of this plugin, which can be uploaded to a _ChRIS Store_.
+## Example
 
 ```shell
-docker run --rm localhost/fnndsc/pl-adapt_object_mesh:dev chris_plugin_info > chris_plugin_info.json
+singularity exec docker://fnndsc/pl-adapt_object_mesh:latest adapt_object_mesh_wrapper --iterations 50 incoming/ outgoing/
 ```
-