Merge pull request #123 from fmi-basel/add_task_metadata

Add task metadata
fmi-basel · Dec 10, 2024 · fbd30da · fbd30da
2 parents ee77d20 + 96de487
commit fbd30da
Show file tree

Hide file tree

Showing 5 changed files with 137 additions and 2 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -47,3 +47,41 @@ jobs:
 
       - name: Coverage
         uses: codecov/codecov-action@v3
+
+  deploy:
+    name: Deploy
+    needs: test
+    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/*'
diff --git a/README.md b/README.md
@@ -18,6 +18,14 @@ The workflow consists of the following tasks:
 
 See scMultipleX GitHub [Wiki](https://github.com/fmi-basel/gliberal-scMultipleX/wiki).
 
+# Making releases
+
+To make new releases, tag a specific commit in main (e.g. with v0.7.10) and push that tag to Github. The CI will take care of making a Github release and pushing it to PyPI.
+```
+git tag v0.7.10
+git push origin v0.7.10
+```
+
 # Contributors and License
 
 Unless otherwise stated in each individual module, all scMultipleX components are released according to a BSD 3-Clause License, and Copyright is with Friedrich Miescher Institute for Biomedical Research.

diff --git a/src/scmultiplex/__FRACTAL_MANIFEST__.json b/src/scmultiplex/__FRACTAL_MANIFEST__.json
@@ -3,6 +3,12 @@
   "task_list": [
     {
       "name": "scMultiplex Calculate Object Linking",
+      "category": "Registration",
+      "modality": "HCS",
+      "tags": [
+        "multiplexing",
+        "2D"
+      ],
       "executable_non_parallel": "fractal/_image_based_registration_hcs_init.py",
       "executable_parallel": "fractal/calculate_object_linking.py",
       "meta_non_parallel": {
@@ -108,6 +114,13 @@
     },
     {
       "name": "scMultiplex Calculate Linking Consensus",
+      "category": "Registration",
+      "modality": "HCS",
+      "tags": [
+        "multiplexing",
+        "2D",
+        "3D"
+      ],
       "executable_non_parallel": "fractal/_init_group_by_well_for_multiplexing.py",
       "executable_parallel": "fractal/calculate_linking_consensus.py",
       "meta_non_parallel": {
@@ -198,6 +211,13 @@
     },
     {
       "name": "scMultiplex Relabel by Linking Consensus",
+      "category": "Registration",
+      "modality": "HCS",
+      "tags": [
+        "multiplexing",
+        "2D",
+        "3D"
+      ],
       "executable_non_parallel": "fractal/_image_based_registration_hcs_allrounds_init.py",
       "executable_parallel": "fractal/relabel_by_linking_consensus.py",
       "meta_non_parallel": {
@@ -297,6 +317,12 @@
     },
     {
       "name": "scMultiplex Calculate Platymatch Registration",
+      "category": "Registration",
+      "modality": "HCS",
+      "tags": [
+        "multiplexing",
+        "3D"
+      ],
       "executable_non_parallel": "fractal/_image_based_registration_hcs_init.py",
       "executable_parallel": "fractal/calculate_platymatch_registration.py",
       "meta_non_parallel": {
@@ -455,6 +481,12 @@
     },
     {
       "name": "scMultiplex Surface Mesh Multiscale",
+      "category": "Image Processing",
+      "modality": "HCS",
+      "tags": [
+        "3D",
+        "mesh"
+      ],
       "executable_non_parallel": "fractal/_init_group_by_well_for_multiplexing.py",
       "executable_parallel": "fractal/surface_mesh_multiscale.py",
       "meta_non_parallel": {
@@ -634,6 +666,12 @@
     },
     {
       "name": "scMultiplex Segment by Intensity Threshold",
+      "category": "Segmentation",
+      "modality": "HCS",
+      "tags": [
+        "Classical segmentation",
+        "3D"
+      ],
       "executable_non_parallel": "fractal/init_select_multiplexing_round.py",
       "executable_parallel": "fractal/segment_by_intensity_threshold.py",
       "meta_non_parallel": {
@@ -867,6 +905,11 @@
     },
     {
       "name": "scMultiplex Spherical Harmonics from Label Image",
+      "category": "Measurement",
+      "modality": "HCS",
+      "tags": [
+        "3D"
+      ],
       "executable_non_parallel": "fractal/_init_group_by_well_for_multiplexing.py",
       "executable_parallel": "fractal/spherical_harmonics_from_labelimage.py",
       "meta_non_parallel": {
@@ -981,6 +1024,13 @@
     },
     {
       "name": "scMultiplex Mesh Measurements",
+      "category": "Measurement",
+      "modality": "HCS",
+      "tags": [
+        "3D",
+        "mesh",
+        "morphology"
+      ],
       "executable_non_parallel": "fractal/_init_group_by_well_for_multiplexing.py",
       "executable_parallel": "fractal/scmultiplex_mesh_measurements.py",
       "meta_non_parallel": {
@@ -1119,6 +1169,12 @@
     },
     {
       "name": "scMultiplex Feature Measurements",
+      "category": "Measurement",
+      "tags": [
+        "regionprops",
+        "morphology",
+        "intensity"
+      ],
       "executable_parallel": "fractal/scmultiplex_feature_measurements.py",
       "meta_parallel": {
         "cpus_per_task": 4,
@@ -1218,6 +1274,10 @@
     },
     {
       "name": "scMultiplex Expand Labels",
+      "tags": [
+        "2D",
+        "3D"
+      ],
       "executable_parallel": "fractal/expand_labels.py",
       "meta_parallel": {
         "cpus_per_task": 4,
@@ -1281,5 +1341,6 @@
     }
   ],
   "has_args_schemas": true,
-  "args_schema_version": "pydantic_v2"
+  "args_schema_version": "pydantic_v2",
+  "authors": "Nicole Repina, Enrico Tagliavini, Tim-Oliver Buchholz, Joel Luethi"
 }
diff --git a/src/scmultiplex/dev/create_manifest.py b/src/scmultiplex/dev/create_manifest.py
@@ -4,4 +4,5 @@
 
 if __name__ == "__main__":
     PACKAGE = "scmultiplex"
-    create_manifest(package=PACKAGE)
+    AUTHORS = "Nicole Repina, Enrico Tagliavini, Tim-Oliver Buchholz, Joel Luethi"
+    create_manifest(package=PACKAGE, authors=AUTHORS)
diff --git a/src/scmultiplex/dev/task_list.py b/src/scmultiplex/dev/task_list.py
@@ -23,64 +23,91 @@
         executable="fractal/calculate_object_linking.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
+        category="Registration",
+        modality="HCS",
+        tags=["multiplexing", "2D"],
     ),
     CompoundTask(
         name="scMultiplex Calculate Linking Consensus",
         executable_init="fractal/_init_group_by_well_for_multiplexing.py",
         executable="fractal/calculate_linking_consensus.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
+        category="Registration",
+        modality="HCS",
+        tags=["multiplexing", "2D", "3D"],
     ),
     CompoundTask(
         name="scMultiplex Relabel by Linking Consensus",
         executable_init="fractal/_image_based_registration_hcs_allrounds_init.py",
         executable="fractal/relabel_by_linking_consensus.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 64000},
+        category="Registration",
+        modality="HCS",
+        tags=["multiplexing", "2D", "3D"],
     ),
     CompoundTask(
         name="scMultiplex Calculate Platymatch Registration",
         executable_init="fractal/_image_based_registration_hcs_init.py",
         executable="fractal/calculate_platymatch_registration.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
+        category="Registration",
+        modality="HCS",
+        tags=["multiplexing", "3D"],
     ),
     CompoundTask(
         name="scMultiplex Surface Mesh Multiscale",
         executable_init="fractal/_init_group_by_well_for_multiplexing.py",
         executable="fractal/surface_mesh_multiscale.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
+        category="Image Processing",
+        modality="HCS",
+        tags=["3D", "mesh"],
     ),
     CompoundTask(
         name="scMultiplex Segment by Intensity Threshold",
         executable_init="fractal/init_select_multiplexing_round.py",
         executable="fractal/segment_by_intensity_threshold.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
+        category="Segmentation",
+        modality="HCS",
+        tags=["Classical segmentation", "3D"],
     ),
     CompoundTask(
         name="scMultiplex Spherical Harmonics from Label Image",
         executable_init="fractal/_init_group_by_well_for_multiplexing.py",
         executable="fractal/spherical_harmonics_from_labelimage.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
+        category="Measurement",
+        modality="HCS",
+        tags=["3D"],
     ),
     CompoundTask(
         name="scMultiplex Mesh Measurements",
         executable_init="fractal/_init_group_by_well_for_multiplexing.py",
         executable="fractal/scmultiplex_mesh_measurements.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
+        category="Measurement",
+        modality="HCS",
+        tags=["3D", "mesh", "morphology"],
     ),
     ParallelTask(
         name="scMultiplex Feature Measurements",
         executable="fractal/scmultiplex_feature_measurements.py",
         meta={"cpus_per_task": 4, "mem": 16000},
+        category="Measurement",
+        tags=["regionprops", "morphology", "intensity"],
     ),
     ParallelTask(
         name="scMultiplex Expand Labels",
         executable="fractal/expand_labels.py",
         meta={"cpus_per_task": 4, "mem": 16000},
+        tags=["2D", "3D"],
     ),
 ]