Merge pull request #5 from fractal-analytics-platform/template_update

Template update

Author: lorenzocerrone

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Do not edit - changes here will be overwritten by Copier
-_commit: v0.4.2
+_commit: v0.4.5
 _src_path: gh:fractal-analytics-platform/fractal-tasks-template
 author_email: [email protected]
 author_name: Lorenzo Cerrone

.github/workflows/build_and_test.yml

@@ -2,20 +2,22 @@ name: CI (build and test)
 
 on:
   push:
-    branches: ["main"]
+    branches:
+      - main
     tags:
       - "*"
   pull_request:
-    branches: ["main"]
+  workflow_dispatch:
+  release:
+    types: [published]
 
 
 jobs:
   tests:
     strategy:
       matrix:
-        #os: [ubuntu-22.04, macos-latest]
-        os: [macos-latest]
-        python-version: ["3.9"]
+        os: [ubuntu-22.04, macos-latest]
+        python-version: ["3.10"]
     name: "Core, Python ${{ matrix.python-version }}, ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
     timeout-minutes: 10
@@ -27,13 +29,15 @@ jobs:
 
       - uses: mamba-org/setup-micromamba@v1
         with:
+          # Using the newest version of micromamba
+          # causes a weird bug in the manifest generation
           micromamba-version: '1.5.6-0' # any version from https://github.com/mamba-org/micromamba-releases
           environment-name: 'ilastik-tasks'
           create-args: >-
             --override-channels
             -c pytorch
-            -c ilastik-forge 
-            -c conda-forge python=${{ matrix.python-version }} ilastik 
+            -c ilastik-forge
+            -c conda-forge python=${{ matrix.python-version }} ilastik-core 
             --no-channel-priority
 
           post-cleanup: 'all'

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

@@ -20,23 +20,30 @@ dynamic = ["version"]
 description = "Collection of Fractal task to run Headless ilastik workflows"
 readme = "README.md"
 license = { text = "BSD-3-Clause" }
-authors = [
-    { name = "Lorenzo Cerrone", email = "[email protected]" },
-]
+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", "hatch", "pytest", "requests", "jsonschema", "ruff", "pre-commit"]
+dev = [
+    "devtools",
+    "pooch",
+    "hatch",
+    "pytest",
+    "requests",
+    "jsonschema",
+    "ruff",
+    "pre-commit",
+]
 
 # https://docs.astral.sh/ruff
 [tool.ruff]
 line-length = 88
-target-version = "py39"
+target-version = "py311"
 src = ["src"]
 
 # https://docs.astral.sh/ruff/rules
@@ -69,4 +76,4 @@ ignore = [
 [tool.ruff.format]
 docstring-code-format = true
 docstring-code-line-length = 89
-skip-magic-trailing-comma = false  # default is false
+skip-magic-trailing-comma = false # default is false

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

@@ -5,4 +5,5 @@
 if __name__ == "__main__":
     PACKAGE = "ilastik_tasks"
     AUTHORS = "Lorenzo Cerrone"
-    create_manifest(package=PACKAGE, authors=AUTHORS)
+    docs_link = "https://github.com/fractal-analytics-platform/fractal-ilastik-tasks"
+    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/task_list.py

@@ -11,5 +11,6 @@
         tags=[
             "Pixel Classifier",
         ],
+        docs_info="file:docs_info/ilastik_pixel_classifier.md"
     ),
 ]