Merge pull request #1 from fractal-analytics-platform/add_task_metadata

Add task metadata

Author: lorenzocerrone

.copier-answers.yml

@@ -1,10 +1,10 @@
 # Do not edit - changes here will be overwritten by Copier
-_commit: 0.4.0
+_commit: v0.4.2
 _src_path: gh:fractal-analytics-platform/fractal-tasks-template
 author_email: [email protected]
 author_name: Lorenzo Cerrone
 package_name: ilastik_tasks
 project_name: ilastik-tasks
-project_short_description: Package description.
-project_url: ''
+project_short_description: Collection of Fractal task to run Headless ilastik workflows
+project_url: https://github.com/fractal-analytics-platform/fractal-ilastik-tasks
 

.github/workflows/build_and_test.yml

@@ -3,6 +3,8 @@ name: CI (build and test)
 on:
   push:
     branches: ["main"]
+    tags:
+      - "*"
   pull_request:
     branches: ["main"]
 
@@ -52,4 +54,42 @@ jobs:
           fi
 
       - name: Test core library with pytest
-        run: micromamba run -n ilastik-tasks python -m pytest tests
+        run: micromamba run -n ilastik-tasks python -m pytest tests
+  
+  deploy:
+    name: Deploy
+    needs: tests
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing on PyPi
+      # see https://docs.pypi.org/trusted-publishers/
+      id-token: write
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: 👷 Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: 🚢 Publish to PyPI
+        # TODO remove the "if: false" line when the package is ready for pypi release
+        if: false
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: './dist/*'

create_env_script.sh

@@ -14,15 +14,15 @@ else
     LOCATION="--prefix $ENVPREFIX/$ENVNAME"
 fi
 
-echo "Creating environment $ENVNAME with $PYTORCH_PACKAGE"
+echo "Creating environment $ENVNAME"
 $COMMMAND run $COMMMAND create $LOCATION \
                                --override-channels \
                                -c pytorch \
                                -c ilastik-forge \
                                -c conda-forge $PYTHON ilastik \
                                --no-channel-priority --yes
 
-echo "Installing plantseg-tasks version $VERSION"
+echo "Installing ilastik-tasks version $VERSION"
 $COMMMAND run --name $ENVNAME pip install git+https://github.com/fractal-analytics-platform/fractal-ilastik-tasks@$VERSION
 
 echo "Downloading the __FRACTAL_MANIFEST__.json file file"

pyproject.toml

@@ -5,25 +5,19 @@ build-backend = "hatchling.build"
 
 # https://hatch.pypa.io/latest/config/metadata/
 [tool.hatch.version]
-#path = "src/ilastik_tasks/__init__.py"
 source = "vcs"
 
 # read more about configuring hatch at:
 # https://hatch.pypa.io/latest/config/build/
 [tool.hatch.build.targets.wheel]
-only-include = ["src"]
-sources = ["src"]
-
-# Always include the __FRACTAL_MANIFEST__.json file in the package
-[tool.hatch.build]
-include = ["__FRACTAL_MANIFEST__.json"]
+packages = ["src/ilastik_tasks"]
 
 
 # Project metadata (see https://peps.python.org/pep-0621)
 [project]
 name = "ilastik-tasks"
 dynamic = ["version"]
-description = "Package description."
+description = "Collection of Fractal task to run Headless ilastik workflows"
 readme = "README.md"
 license = { text = "BSD-3-Clause" }
 authors = [
@@ -32,7 +26,7 @@ authors = [
 
 # Required Python version and dependencies
 requires-python = ">=3.9"
-dependencies = ["fractal-tasks-core == 1.3.0", "scikit-image"]
+dependencies = ["fractal-tasks-core == 1.3.3", "scikit-image", "numpy < 2"]
 
 # Optional dependencies (e.g. for `pip install -e ".[dev]"`, see
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies)

src/ilastik_tasks/__FRACTAL_MANIFEST__.json

@@ -3,6 +3,10 @@
   "task_list": [
     {
       "name": "Ilastik Pixel Classification Segmentation",
+      "category": "Segmentation",
+      "tags": [
+        "Pixel Classifier"
+      ],
       "executable_parallel": "ilastik_pixel_classification_segmentation.py",
       "meta_parallel": {
         "cpus_per_task": 8,
@@ -104,5 +108,6 @@
     }
   ],
   "has_args_schemas": true,
-  "args_schema_version": "pydantic_v2"
+  "args_schema_version": "pydantic_v2",
+  "authors": "Lorenzo Cerrone"
 }

src/ilastik_tasks/__init__.py

@@ -1,5 +1,5 @@
 """
-Package description.
+Collection of Fractal task to run Headless ilastik workflows
 """
 from importlib.metadata import PackageNotFoundError, version
 

src/ilastik_tasks/dev/create_manifest.py

@@ -6,4 +6,5 @@
 
 if __name__ == "__main__":
     PACKAGE = "ilastik_tasks"
-    create_manifest(package=PACKAGE)
+    AUTHORS = "Lorenzo Cerrone"
+    create_manifest(package=PACKAGE, authors=AUTHORS)

src/ilastik_tasks/dev/task_list.py

@@ -7,5 +7,9 @@
         name="Ilastik Pixel Classification Segmentation",
         executable="ilastik_pixel_classification_segmentation.py",
         meta={"cpus_per_task": 8, "mem": 8000},
+        category="Segmentation",
+        tags=[
+            "Pixel Classifier",
+        ],
     ),
 ]