🎊

.github/workflows/ci.yml

@@ -123,7 +123,7 @@ jobs:
             docker.io/${{ steps.determine.outputs.dock_image }}
             ghcr.io/${{ steps.determine.outputs.dock_image }}
           # if non-x86_84 architectures are supported, add them here
-          platforms: linux/amd64  #,linux/arm64,linux/ppc64le
+          platforms: linux/amd64,linux/arm64,linux/ppc64le
           push: true
           cache-from: type=local,src=/tmp/.buildx-cache
           cache-to: type=local,dest=/tmp/.buildx-cache

Dockerfile

@@ -1,7 +1,4 @@
-# Python version can be changed, e.g.
-# FROM python:3.8
-# FROM docker.io/fnndsc/conda:python3.10.2-cuda11.6.0
-FROM docker.io/python:3.10.6-slim-bullseye
+FROM docker.io/fnndsc/mni-conda-base:civet2.1.1-python3.10.6
 
 LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
       org.opencontainers.image.title="create_tetra" \

README.md

@@ -1,16 +1,11 @@
-# create_tetra
+# pl-create_tetra
 
 [![Version](https://img.shields.io/docker/v/fnndsc/pl-create_tetra?sort=semver)](https://hub.docker.com/r/fnndsc/pl-create_tetra)
 [![MIT License](https://img.shields.io/github/license/fnndsc/pl-create_tetra)](https://github.com/FNNDSC/pl-create_tetra/blob/main/LICENSE)
 [![ci](https://github.com/FNNDSC/pl-create_tetra/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-create_tetra/actions/workflows/ci.yml)
 
 `pl-create_tetra` is a [_ChRIS_](https://chrisproject.org/)
-_ds_ plugin which takes in ...  as input files and
-creates ... as output files.
-
-## Abstract
-
-...
+*fs*-type plugin wrapper around `create_tetra`.
 
 ## Installation
 
@@ -25,85 +20,7 @@ To get started with local command-line usage, use [Apptainer](https://apptainer.
 (a.k.a. Singularity) to run `pl-create_tetra` as a container:
 
 ```shell
-singularity exec docker://fnndsc/pl-create_tetra create_tetra_wrapper [--args values...] input/ output/
-```
-
-To print its available options, run:
-
-```shell
-singularity exec docker://fnndsc/pl-create_tetra create_tetra_wrapper --help
-```
-
-## Examples
-
-`create_tetra_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-create_tetra:latest create_tetra_wrapper [--args] incoming/ outgoing/
-```
-
-## Development
-
-Instructions for developers.
-
-### Building
-
-Build a local container image:
-
-```shell
-docker build -t localhost/fnndsc/pl-create_tetra .
-```
-
-### Running
-
-Mount the source code `create_tetra_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/create_tetra_wrapper.py:/usr/local/lib/python3.10/site-packages/create_tetra_wrapper.py:ro \
-    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
-    localhost/fnndsc/pl-create_tetra create_tetra_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-create_tetra:dev --build-arg extras_require=dev .
-docker run --rm -it localhost/fnndsc/pl-create_tetra: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-create_tetra:1.2.3 .
-docker push docker.io/fnndsc/pl-create_tetra:1.2.3
-```
-
-### 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_.
-
-```shell
-docker run --rm localhost/fnndsc/pl-create_tetra:dev chris_plugin_info > chris_plugin_info.json
+apptainer exec docker://fnndsc/pl-create_tetra create_tetra_wrapper out/
 ```
 
+Its default behavior is to create a unit sphere `sphere_81920.obj` in the specified directory.

create_tetra_wrapper.py

@@ -1,8 +1,11 @@
 #!/usr/bin/env python
-
+import sys
 from pathlib import Path
 from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
 from importlib.metadata import Distribution
+import subprocess as sp
+import shlex
+import functools
 
 from chris_plugin import chris_plugin
 
@@ -24,26 +27,44 @@
 
 parser = ArgumentParser(description='A ChRIS fs plugin wrapper for create_tetra',
                         formatter_class=ArgumentDefaultsHelpFormatter)
-parser.add_argument('-n', '--name', default='foo',
-                    help='argument which sets example output file name')
+parser.add_argument('-c', '--center', default='0,0,0', type=str,
+                    help='center of sphere')
+parser.add_argument('-r', '--radius', default='1,1,1', type=str,
+                    help='radius of sphere')
+parser.add_argument('-t', '--triangles', default=81920, type=int,
+                    help='number of triangles')
+parser.add_argument('-o', '--output', default='sphere_81920.obj',
+                    help='output file name')
 parser.add_argument('-V', '--version', action='version',
                     version=f'%(prog)s {__version__}')
 
 
-# documentation: https://fnndsc.github.io/chris_plugin/chris_plugin.html#chris_plugin
 @chris_plugin(
     parser=parser,
     title='create_tetra',
-    category='',                 # ref. https://chrisstore.co/plugins
-    min_memory_limit='100Mi',    # supported units: Mi, Gi
-    min_cpu_limit='1000m',       # millicores, e.g. "1000m" = 1 CPU core
-    min_gpu_limit=0              # set min_gpu_limit=1 to enable GPU
+    category='Modeling',
+    min_memory_limit='100Mi',
+    min_cpu_limit='1000m',
+    min_gpu_limit=0
 )
-def main(options: Namespace, inputdir: Path, outputdir: Path):
-    print(DISPLAY_TITLE)
+def main(options: Namespace, outputdir: Path):
+    print(DISPLAY_TITLE, file=sys.stderr)
+
+    create_tetra = ('create_tetra',)
+    filename = (outputdir / options.output,)
+    center = parse_triplet(options.center)
+    radius = parse_triplet(options.radius)
+    n_triangles = (str(options.triangles),)
+
+    cmd = functools.reduce(lambda l, r: l + r, (create_tetra, filename, center, radius, n_triangles))
+    print('$> ' + shlex.join(map(str, cmd)), file=sys.stderr)
+
+    sp.run(cmd, check=True)
+
 
-    output_file = outputdir / f'{options.name}.txt'
-    output_file.write_text('did nothing successfully!')
+def parse_triplet(s: str) -> tuple[str, str, str]:
+    x, y, z = s.split(',')
+    return x, y, z
 
 
 if __name__ == '__main__':

setup.py

@@ -1,4 +1,8 @@
 from setuptools import setup
+import shutil
+
+if not shutil.which('create_tetra'):
+    raise Exception('create_tetra command not found')
 
 setup(
     name='create_tetra',

tests/test_main.py

@@ -0,0 +1,19 @@
+from pytest_mock import MockerFixture
+from pathlib import Path
+import subprocess
+from create_tetra_wrapper import parser, main
+
+
+def test_main(mocker: MockerFixture, tmp_path: Path):
+    """
+    Running main w/o options should create a unit sphere.
+    """
+    outputdir = tmp_path / 'outgoing'
+    output_file = outputdir / 'sphere_81920.obj'
+
+    options = parser.parse_args([])
+    spy = mocker.spy(subprocess, 'run')
+    main(options, outputdir)
+    assert output_file.exists()
+    spy.assert_called_once()
+    assert spy.call_args[0][0][0] == 'create_tetra'