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Unpin fsspec version constraint (close #508) #536

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Unpin fsspec version constraint (close #508) #536

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93c6ccb
Unpin fsspec version constraint, and make it `!=2023.9.0` (close #508)
tcompa Sep 25, 2023
3d72418
Update CHANGELOG
tcompa Sep 25, 2023
3f40284
Merge branch 'main' into 508-unpin-fsspec
tcompa Sep 27, 2023
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -9,7 +9,6 @@ This release includes work on Pydantic models for NGFF specs and on ROI tables.
* Extract `num_levels` and `coarsening_xy` parameters from NGFF objects, rather than from `metadata` task input (\#528).
* Transform several `lib_zattrs_utils.py` functions (`get_axes_names`, `extract_zyx_pixel_sizes` and `get_acquisition_paths`) into `lib_ngff.py` methods (\#528).
* Load Zarr attributes from groups, rather than from `.zattrs` files (\#528).

* Regions of interest:
* Set `FOV_ROI_table` and `well_ROI_table` ZYX origin to zero (\#524).
* Remove heuristics to determine whether to reset origin, in `cellpose_segmentation` task (\#524).
Expand All @@ -20,6 +19,8 @@ This release includes work on Pydantic models for NGFF specs and on ROI tables.
* Fix bug in creation of bounding-box ROIs when `cellpose_segmentation` loops of FOVs (\#524).
* Update type of `metadata` parameter of `prepare_FOV_ROI_table` and `prepare_well_ROI_table` functions (\#524).
* Fix `reset_origin` so that it returns an updated copy of its input (\#524).
* Dependency:
* Relax `fsspec<=2023.6` constraint into `fsspec!=2023.9.0` (\#536).

# 0.11.0

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16 changes: 8 additions & 8 deletions fractal_tasks_core/__FRACTAL_MANIFEST__.json
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Expand Up @@ -25,7 +25,7 @@
"metadata": {
"title": "Metadata",
"type": "object",
"description": "This parameter is not used by this task (standard argument for Fractal tasks, managed by Fractal server)."
"description": "This parameter is not used by this task. (standard argument for Fractal tasks, managed by Fractal server)."
},
"allowed_channels": {
"title": "Allowed Channels",
Expand Down Expand Up @@ -331,7 +331,7 @@
"metadata": {
"title": "Metadata",
"type": "object",
"description": "Dictionary containing metadata about the OME-Zarr. This task requires the following elements to be present in the metadata. `num_levels (int)`: number of pyramid levels in the image (this determines how many pyramid levels are built for the segmentation); `coarsening_xy (int)`: coarsening factor in XY of the downsampling when building the pyramid `plate`: List of plates (e.g. `[\"MyPlate.zarr\"]`); `well`: List of wells in the OME-Zarr plate (e.g. `[\"MyPlate.zarr/B/03\", \"MyPlate.zarr/B/05\"]`); `image: List of images in the OME-Zarr plate (e.g. `[\"MyPlate.zarr/B/03/0\", \"MyPlate.zarr/B/05/0\"]`). (standard argument for Fractal tasks, managed by Fractal server)."
"description": "Dictionary containing metadata about the OME-Zarr. This task requires the key `copy_ome_zarr` to be present in the metadata (as defined in `copy_ome_zarr` task). (standard argument for Fractal tasks, managed by Fractal server)."
},
"overwrite": {
"title": "Overwrite",
Expand Down Expand Up @@ -386,7 +386,7 @@
"metadata": {
"title": "Metadata",
"type": "object",
"description": "dictionary containing metadata about the OME-Zarr. This task requires the following elements to be present in the metadata. `num_levels (int)`: number of pyramid levels in the image; this determines how many pyramid levels are built for the segmentation. `coarsening_xy (int)`: coarsening factor in XY of the downsampling when building the pyramid. (standard argument for Fractal tasks, managed by Fractal server)."
"description": "This parameter is not used by this task. (standard argument for Fractal tasks, managed by Fractal server)."
},
"level": {
"title": "Level",
Expand Down Expand Up @@ -564,7 +564,7 @@
"metadata": {
"title": "Metadata",
"type": "object",
"description": "Dictionary containing metadata about the OME-Zarr. This task requires the following elements to be present in the metadata. `num_levels (int)`: number of pyramid levels in the image (this determines how many pyramid levels are built for the segmentation), `coarsening_xy (int)`: coarsening factor in XY of the downsampling when building the pyramid. (standard argument for Fractal tasks, managed by Fractal server)."
"description": "This parameter is not used by this task. (standard argument for Fractal tasks, managed by Fractal server)."
},
"illumination_profiles_folder": {
"title": "Illumination Profiles Folder",
Expand Down Expand Up @@ -645,7 +645,7 @@
"metadata": {
"title": "Metadata",
"type": "object",
"description": "Dictionary containing metadata about the OME-Zarr. This task requires the following elements to be present in the metadata. `num_levels (int)`: number of pyramid levels in the image (this determines how many pyramid levels are built for the segmentation); `coarsening_xy (int)`: coarsening factor in XY of the downsampling when building the pyramid. (standard argument for Fractal tasks, managed by Fractal server)."
"description": "This parameter is not used by this task. (standard argument for Fractal tasks, managed by Fractal server)."
},
"workflow_file": {
"title": "Workflow File",
Expand Down Expand Up @@ -1014,7 +1014,7 @@
"metadata": {
"title": "Metadata",
"type": "object",
"description": "Dictionary containing metadata about the OME-Zarr. This task requires the following elements to be present in the metadata. `coarsening_xy (int)`: coarsening factor in XY of the downsampling when building the pyramid. (standard argument for Fractal tasks, managed by Fractal server)."
"description": "This parameter is not used by this task. (standard argument for Fractal tasks, managed by Fractal server)."
},
"wavelength_id": {
"title": "Wavelength Id",
Expand Down Expand Up @@ -1087,7 +1087,7 @@
"metadata": {
"title": "Metadata",
"type": "object",
"description": "Dictionary containing metadata about the OME-Zarr. This task does not use the metadata."
"description": "This parameter is not used by this task. (standard argument for Fractal tasks, managed by Fractal server)."
},
"roi_table": {
"title": "Roi Table",
Expand Down Expand Up @@ -1153,7 +1153,7 @@
"metadata": {
"title": "Metadata",
"type": "object",
"description": "Dictionary containing metadata about the OME-Zarr. This task requires the following elements to be present in the metadata. `coarsening_xy (int)`: coarsening factor in XY of the downsampling when building the pyramid. (standard argument for Fractal tasks, managed by Fractal server). `num_levels (int)`: number of pyramid levels in the image; this determines how many pyramid levels are built for the segmentation."
"description": "This parameter is not used by this task. (standard argument for Fractal tasks, managed by Fractal server)."
},
"registered_roi_table": {
"title": "Registered Roi Table",
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