Add task metadata & update template

.copier-answers.yml

@@ -1,10 +1,10 @@
 # Do not edit - changes here will be overwritten by Copier
-_commit: v0.3.0
+_commit: v0.4.2
 _src_path: gh:fractal-analytics-platform/fractal-tasks-template
 author_email: [email protected]
 author_name: Lorenzo Cerrone
 package_name: plantseg_tasks
 project_name: fractal-plantseg-tasks
-project_short_description: Package description.
-project_url: ''
+project_short_description: A collection of fractal tasks to run plantseg workflows.
+project_url: https://github.com/fractal-analytics-platform/fractal-plantseg-tasks
 

.github/workflows/build_and_test.yml

@@ -0,0 +1,92 @@
+# name: CI (build and test)
+
+# on:
+#   push:
+#     branches: ["main"]
+#     tags:
+#       - "*"
+#   pull_request:
+#     branches: ["main"]
+
+
+# jobs:
+#   tests:
+#     strategy:
+#       matrix:
+#         os: [ubuntu-22.04, macos-latest]
+#         python-version: ["3.9", "3.10", "3.11"]
+#         exclude:
+#           - os: macos-latest
+#             python-version: '3.9'
+#           - os: macos-latest
+#             python-version: '3.10'
+#     name: "Core, Python ${{ matrix.python-version }}, ${{ matrix.os }}"
+#     runs-on: ${{ matrix.os }}
+#     timeout-minutes: 10
+
+#     steps:
+#       - uses: actions/checkout@v4
+#         with:
+#           fetch-depth: 1
+
+#       - name: Set up Python ${{ matrix.python-version }}
+#         uses: actions/setup-python@v5
+#         with:
+#           python-version: ${{ matrix.python-version }}
+#           cache: "pip"
+
+#       - name: Install package
+#         run: python -m pip install -e .[dev]
+
+#       - name: Regenerate the manifest
+#         run: python src/plantseg_tasks/dev/create_manifest.py
+
+#       - name: Check if manifest has changed
+#         run: |
+#           if [ -n "$(git diff --exit-code ./src/plantseg_tasks/__FRACTAL_MANIFEST__.json)" ]; then
+#           echo "__FRACTAL_MANIFEST__.json has changed. Please run 'python src/plantseg_tasks/dev/create_manifest.py' and commit the changes."
+#             exit 1
+#           else
+#             echo "__FRACTAL_MANIFEST__.json has not changed."
+#           fi
+
+#       - name: Test core library with pytest
+#         run: 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/*'

.gitignore

@@ -1,3 +1,4 @@
+# Git ignored is sourced from https://github.com/pydev-guide/pyrepo-copier/blob/main/LICENSE
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -8,6 +9,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -20,11 +22,11 @@ parts/
 sdist/
 var/
 wheels/
-share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
+
+.DS_Store
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -39,17 +41,14 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
-.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
 *.cover
-*.py,cover
 .hypothesis/
 .pytest_cache/
-cover/
 
 # Translations
 *.mo
@@ -58,8 +57,6 @@ cover/
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
-db.sqlite3-journal
 
 # Flask stuff:
 instance/
@@ -72,63 +69,27 @@ instance/
 docs/_build/
 
 # PyBuilder
-.pybuilder/
 target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
 
-# IPython
-profile_default/
-ipython_config.py
-
 # pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
+.python-version
+
+# celery beat schedule file
 celerybeat-schedule
-celerybeat.pid
 
 # SageMath parsed files
 *.sage.py
 
-# Environments
+# dotenv
 .env
+
+# virtualenv
 .venv
-env/
 venv/
 ENV/
-env.bak/
-venv.bak/
 
 # Spyder project settings
 .spyderproject
@@ -142,26 +103,10 @@ venv.bak/
 
 # mypy
 .mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
 
-# Cython debug symbols
-cython_debug/
+# ruff
+.ruff_cache/
 
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
-.vscode
-*.ipynb
-
-# MacOS files
-.DS_Store
+# IDE settings
+.vscode/
+.idea/

create_env_script.sh

@@ -34,4 +34,4 @@ $COMMMAND run --name $ENVNAME pip install git+https://github.com/fractal-analyti
 
 
 echo "Downloading the __FRACTAL_MANIFEST__.json file file"
-curl -O https://raw.githubusercontent.com/fractal-analytics-platform/fractal-plantseg-tasks/$VERSION/__FRACTAL_MANIFEST__.json
+curl -O https://raw.githubusercontent.com/fractal-analytics-platform/fractal-plantseg-tasks/$VERSION/src/plantseg_tasks/__FRACTAL_MANIFEST__.json

pyproject.toml

@@ -5,25 +5,19 @@ build-backend = "hatchling.build"
 
 # https://hatch.pypa.io/latest/config/metadata/
 [tool.hatch.version]
-#path = "src/plantseg_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/plantseg_tasks"]
 
 
 # Project metadata (see https://peps.python.org/pep-0621)
 [project]
 name = "fractal-plantseg-tasks"
 dynamic = ["version"]
-description = "Package description."
+description = "A collection of fractal tasks to run plantseg 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 == 1.2.1"]
+dependencies = ["fractal-tasks-core == 1.3.3"]
 
 # Optional dependencies (e.g. for `pip install -e ".[dev]"`, see
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies)

src/plantseg_tasks/__FRACTAL_MANIFEST__.json

@@ -2,7 +2,12 @@
   "manifest_version": "2",
   "task_list": [
     {
-      "name": "H5 Converter Task",
+      "name": "Convert H5 to OME-Zarr",
+      "category": "Conversion",
+      "tags": [
+        "H5",
+        "HDF5"
+      ],
       "executable_non_parallel": "convert_h5_to_ome_zarr.py",
       "meta_non_parallel": {
         "cpus_per_task": 1,
@@ -250,7 +255,8 @@
       "docs_info": "## convert_h5_to_ome_zarr\nH5 to OME-Zarr converter task.\n"
     },
     {
-      "name": "Tiff Converter Task",
+      "name": "Convert Tiff to OME-Zarr",
+      "category": "Conversion",
       "executable_non_parallel": "convert_tiff_to_ome_zarr.py",
       "meta_non_parallel": {
         "cpus_per_task": 1,
@@ -494,7 +500,13 @@
       "docs_info": "## convert_tiff_to_ome_zarr\nTIFF to OME-Zarr converter task.\n"
     },
     {
-      "name": "PlantSeg Workflow Task",
+      "name": "PlantSeg Segmentation",
+      "category": "Segmentation",
+      "tags": [
+        "Neural Network Segmentation",
+        "Deep Learning",
+        "Instance Segmentation"
+      ],
       "executable_parallel": "plantseg_workflow.py",
       "meta_parallel": {
         "cpus_per_task": 1,
@@ -712,5 +724,6 @@
     }
   ],
   "has_args_schemas": true,
-  "args_schema_version": "pydantic_v2"
+  "args_schema_version": "pydantic_v2",
+  "authors": "Lorenzo Cerrone"
 }

src/plantseg_tasks/__init__.py

@@ -1,4 +1,4 @@
-"""Package description."""
+"""A collection of fractal tasks to run plantseg workflows."""
 
 from importlib.metadata import PackageNotFoundError, version
 

src/plantseg_tasks/dev/create_manifest.py

@@ -33,4 +33,7 @@
 ]
 if __name__ == "__main__":
     PACKAGE = "plantseg_tasks"
-    create_manifest(package=PACKAGE, custom_pydantic_models=custom_pydantic_models)
+    AUTHORS = "Lorenzo Cerrone"
+    create_manifest(
+        package=PACKAGE, authors=AUTHORS, custom_pydantic_models=custom_pydantic_models
+    )

src/plantseg_tasks/dev/task_list.py

@@ -7,15 +7,24 @@
         name="Convert H5 to OME-Zarr",
         executable="convert_h5_to_ome_zarr.py",
         meta={"cpus_per_task": 1, "mem": 8000},
+        category="Conversion",
+        tags=["H5", "HDF5"],
     ),
     NonParallelTask(
         name="Convert Tiff to OME-Zarr",
         executable="convert_tiff_to_ome_zarr.py",
         meta={"cpus_per_task": 1, "mem": 8000},
+        category="Conversion",
     ),
     ParallelTask(
         name="PlantSeg Segmentation",
         executable="plantseg_workflow.py",
         meta={"cpus_per_task": 1, "mem": 32000, "needs_gpu": True},
+        category="Segmentation",
+        tags=[
+            "Neural Network Segmentation",
+            "Deep Learning",
+            "Instance Segmentation",
+        ],
     ),
 ]