Merge pull request #1 from FNNDSC/tag-index

Tag-based overhaul

.github/workflows/ci.yml

@@ -19,7 +19,6 @@ on:
 jobs:
   build:
     name: Build
-    if: github.event_name == 'push' || github.event_name == 'release'
     runs-on: ubuntu-22.04
 
     steps:
@@ -81,6 +80,14 @@ jobs:
           tags: ${{ steps.info.outputs.local_tag }}
           load: true
           cache-from: type=gha
+          build-args: extras_require=dev
+
+      - name: Unit tests
+        run: |
+          docker run --rm \
+            -v '${{ github.workspace }}:/src' -w /src \
+            ${{ steps.info.outputs.local_tag }} \
+            pytest -v --color=yes -o cache_dir=/tmp/pytest
 
       - name: Login to DockerHub
         if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, 'docker.io')

Dockerfile

@@ -1,22 +1,26 @@
-# Python version can be changed, e.g.
-# FROM python:3.8
-# FROM ghcr.io/mamba-org/micromamba:1.5.1-focal-cuda-11.3.1
-FROM docker.io/python:3.12.1-slim-bookworm
+FROM docker.io/mambaorg/micromamba:1.5.5-bookworm-slim AS micromamba
+FROM micromamba AS builder
 
-LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
-      org.opencontainers.image.title="Publish ChRIS Public Dataset" \
-      org.opencontainers.image.description="Mark the outputs of a feed as compatible with the public dataset viewer feature of ChRIS_ui."
+RUN \
+    --mount=type=cache,sharing=private,target=/home/mambauser/.mamba/pkgs,uid=57439,gid=57439 \
+    --mount=type=cache,sharing=private,target=/opt/conda/pkgs,uid=57439,gid=57439 \
+    micromamba -y -n base install -c conda-forge python=3.12.1 nibabel=5.2.0 numpy=1.26.3 tqdm=4.66.1 pydantic=2.6.0
 
-ARG SRCDIR=/usr/local/src/pl-visual-dataset
+ARG SRCDIR=/home/mambauser/pl-visual-dataset
+RUN mkdir "${SRCDIR}"
 WORKDIR ${SRCDIR}
 
 COPY requirements.txt .
-RUN --mount=type=cache,sharing=private,target=/root/.cache/pip pip install -r requirements.txt
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+RUN pip install -r requirements.txt
 
-COPY . .
+COPY --chown=mambauser:mambauser . .
 ARG extras_require=none
-RUN pip install ".[${extras_require}]" \
-    && cd / && rm -rf ${SRCDIR}
+RUN pip install ".[${extras_require}]" && cd / && rm -rf ${SRCDIR}
 WORKDIR /
 
-CMD ["pub"]
+CMD ["visualdataset"]
+
+LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
+      org.opencontainers.image.title="Create ChRIS Visual Dataset" \
+      org.opencontainers.image.description="Prepare a dataset for visualization with ChRIS_ui"

requirements.txt

@@ -1,2 +1,5 @@
 chris_plugin==0.4.0
+nibabel~=5.2.0
+numpy~=1.26.3
+tqdm~=4.66.1
 pydantic~=2.6.0

setup.py

@@ -19,18 +19,18 @@ def get_version(rel_path: str) -> str:
 
 
 setup(
-    name='publish-chris-dataset',
-    version=get_version('pubchrisvisual/__init__.py'),
-    description='Mark the outputs of a feed as compatible with the public dataset viewer feature of ChRIS_ui.',
+    name='chrisvisualdataset',
+    version=get_version('visualdataset/__init__.py'),
+    description='Prepare the outputs of a feed for the "visual datasets" feature of ChRIS_ui.',
     author='FNNDSC',
     author_email='[email protected]',
     url='https://github.com/FNNDSC/pl-visual-dataset',
-    packages=['pubchrisvisual'],
+    packages=['visualdataset'],
     install_requires=['chris_plugin'],
     license='MIT',
     entry_points={
         'console_scripts': [
-            'pubone = pubchrisvisual.one:main'
+            'visualdataset = visualdataset.__main__:main'
         ]
     },
     classifiers=[
@@ -42,7 +42,8 @@ def get_version(rel_path: str) -> str:
     extras_require={
         'none': [],
         'dev': [
-            'pytest~=7.1'
+            'pytest~=8.0',
+            'pytest-unordered~=0.5.2'
         ]
     }
 )

tests/example_matchers.py

@@ -0,0 +1,25 @@
+from typing import Sequence
+
+from pydantic import TypeAdapter
+
+from visualdataset.args_types import Matcher
+
+FETAL_ATLAS_MATCHERS: Sequence[Matcher] = [
+    *(Matcher(key='age', value=str(age), regex=f'Age {age}/') for age in range(10, 40, 1)),
+
+    Matcher(key='author', value='Ahmed Serag et al.', regex=r'/serag\.nii\.gz$'),
+    Matcher(key='author', value='Ali Gholipour et al., CRL', regex=r'/ali.*\.nii\.gz$'),
+    Matcher(key='author', value='Kiho Im et al., FNNDSC', regex=r'/kiho\.nii\.gz$'),
+
+    Matcher(key='institution', value="Boston Children's Hospital", regex=r'/(kiho|ali).*\.nii\.gz$'),
+    Matcher(key='institution', value="Imperial College London", regex=r'/serag\.nii\.gz$'),
+
+    Matcher(key='type', value='T2 MRI', regex=r'/(ali|aliexp|kiho|serag)\.nii\.gz$'),
+    Matcher(key='type', value='labels', regex=r'/(ali|aliexp)_.+\.nii\.gz$'),
+    Matcher(key='labels', value='tissue', regex=r'/(ali|aliexp)_tissue\.nii\.gz$'),
+    Matcher(key='labels', value='parcellation', regex=r'/(ali|aliexp)_regional\.nii\.gz$'),
+]
+
+if __name__ == '__main__':
+    adapter = TypeAdapter(Sequence[Matcher])
+    print(adapter.dump_json(FETAL_ATLAS_MATCHERS).decode('utf-8'))