update template

Author: lorenzocerrone

create_env_script.sh

@@ -6,7 +6,7 @@ ENVPREFIX="NULL"
 
 # Do NOT change the following lines
 ENVNAME=ilastik-tasks-$VERSION
-PYTHON="python=3.9"
+PYTHON="python=3.10"
 
 if [ "$ENVPREFIX" == "NULL" ]; then
     LOCATION="--name $ENVNAME"
@@ -19,7 +19,7 @@ $COMMMAND run $COMMMAND create $LOCATION \
                                --override-channels \
                                -c pytorch \
                                -c ilastik-forge \
-                               -c conda-forge $PYTHON ilastik vigra \
+                               -c conda-forge $PYTHON ilastik-core vigra \
                                --no-channel-priority --yes
 
 echo "Installing ilastik-tasks version $VERSION"

pyproject.toml

@@ -23,14 +23,15 @@ license = { text = "BSD-3-Clause" }
 authors = [{ name = "Lorenzo Cerrone", email = "[email protected]" }]
 
 # Required Python version and dependencies
-requires-python = ">=3.9"
-dependencies = ["fractal-tasks-core == 1.3.3", "scikit-image", "numpy < 2"]
+requires-python = ">=3.10"
+dependencies = ["fractal-tasks-core == 1.4.3"]
 
 # Optional dependencies (e.g. for `pip install -e ".[dev]"`, see
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies)
 [project.optional-dependencies]
 dev = [
     "devtools",
+    "pooch",
     "hatch",
     "pytest",
     "requests",
@@ -42,7 +43,7 @@ dev = [
 # https://docs.astral.sh/ruff
 [tool.ruff]
 line-length = 88
-target-version = "py39"
+target-version = "py311"
 src = ["src"]
 
 # https://docs.astral.sh/ruff/rules

src/ilastik_tasks/__FRACTAL_MANIFEST__.json

@@ -7,6 +7,7 @@
       "tags": [
         "Pixel Classifier"
       ],
+      "docs_info": "### Purpose\n\nThis task is used to apply a ilastik pixel classifier to an image.\n\n### Outputs\n\n- The `ilastik_pixel_classification_segmentation`: Generates a new label image named `output_label_name`.\n\n### Limitations\n\n- The task can only be used with single and dual channels pixel classifiers models.",
       "executable_parallel": "ilastik_pixel_classification_segmentation.py",
       "meta_parallel": {
         "cpus_per_task": 8,
@@ -119,7 +120,7 @@
         "type": "object",
         "title": "IlastikPixelClassificationSegmentation"
       },
-      "docs_info": "## ilastik_pixel_classification_segmentation\nRun Ilastik Pixel Classification on a Zarr image.\n"
+      "docs_link": "https://github.com/fractal-analytics-platform/fractal-ilastik-tasks"
     }
   ],
   "has_args_schemas": true,

src/ilastik_tasks/dev/create_manifest.py

@@ -6,7 +6,4 @@
     PACKAGE = "ilastik_tasks"
     AUTHORS = "Lorenzo Cerrone"
     docs_link = "https://github.com/fractal-analytics-platform/fractal-ilastik-tasks"
-    if docs_link:
-        create_manifest(package=PACKAGE, authors=AUTHORS, docs_link=docs_link)
-    else:
-        create_manifest(package=PACKAGE, authors=AUTHORS)
+    create_manifest(package=PACKAGE, authors=AUTHORS, docs_link=docs_link)

src/ilastik_tasks/dev/docs_info/ilastik_pixel_classifier.md

@@ -0,0 +1,11 @@
+### Purpose
+
+This task is used to apply a ilastik pixel classifier to an image.
+
+### Outputs
+
+- The `ilastik_pixel_classification_segmentation`: Generates a new label image named `output_label_name`.
+
+### Limitations
+
+- The task can only be used with single and dual channels pixel classifiers models.

src/ilastik_tasks/dev/docs_info/thresholding_task.md

@@ -11,6 +11,6 @@
         tags=[
             "Pixel Classifier",
         ],
-        docs_info="file:docs_info/thresholding_task.md"
+        docs_info="file:docs_info/ilastik_pixel_classifier.md"
     ),
 ]