Merge pull request #63 from pwalczysko/s3

livingobjects

Author: jburel

.github/workflows/build.yml

@@ -13,15 +13,15 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-24.04, windows-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.12'
       - name: Install Conda environment with Micromamba
-        uses: mamba-org/provision-with-micromamba@v15
+        uses: mamba-org/setup-micromamba@v3
         with:
           environment-file: binder/environment.yml
           environment-name: binder

binder/environment.yml

@@ -2,20 +2,20 @@ name: omero-guide-python
 channels:
   - conda-forge
 dependencies:
-  - python==3.9.*
+  - python==3.12.*
   - conda-forge::zeroc-ice==3.6.5
-  - distributed==2022.2.0
+  - distributed==2026.3.0
   - pip
   - pip:
     - matplotlib==3.8.4
     - pooch==1.8.1
-    - omero-py==5.19.2
+    - omero-py==5.22.1
     - scikit-image==0.22.0
-    - pandas==2.2.2
+    - pandas==3.0.2
     - jupyter==1.0.0
-    - ome-zarr==0.8.3
+    - ome-zarr==0.14.0
     - dask-image==2023.8.1
     - cellpose==3.0.7
-    - geojson==3.1.0
+    - geojson==3.2.0
     # dependency used to convert the OMERO masks into numpy array
-    - omero-cli-zarr==0.5.5
+    - omero-cli-zarr==0.8.0

notebooks/idr0044_zarr_segmentation_parallel.ipynb

@@ -90,8 +90,8 @@
    "outputs": [],
    "source": [
     "def load_binary_from_s3(id, resolution='4'):\n",
-    "    endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/'\n",
-    "    root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution)\n",
+    "    endpoint_url = 'https://livingobjects.ebi.ac.uk/'\n",
+    "    root = 'idr/zarr/v0.4/idr0044/%s.zarr/%s/' % (id, resolution)\n",
     "    return da.from_zarr(endpoint_url + root)"
    ]
   },

notebooks/idr0062_prediction_zarr_public_s3.ipynb

@@ -76,7 +76,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ENPOINT_URL = 'https://uk1s3.embassy.ebi.ac.uk/'"
+    "ENPOINT_URL = 'https://livingobjects.ebi.ac.uk/'"
    ]
   },
   {

notebooks/zarr-public-s3-multiscale.ipynb

@@ -62,7 +62,7 @@
     "# imageid = 9822151\n",
     "imageid = 9822152\n",
     "\n",
-    "endpoint = 'https://uk1s3.embassy.ebi.ac.uk'\n",
+    "endpoint = 'https://livingobjects.ebi.ac.uk'\n",
     "imagepath = f'idr/zarr/v0.1/{imageid}.zarr'"
    ]
   },

scripts/idr0044_zarr_segmentation_cluster.py

@@ -46,8 +46,8 @@
 
 # Load-binary
 def load_binary_from_s3(id, resolution='4'):
-    endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/'
-    root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution)
+    endpoint_url = 'https://livingobjects.ebi.ac.uk/'
+    root = 'idr/zarr/v0.4/iddr0044/%s.zarr/%s/' % (id, resolution)
     return da.from_zarr(endpoint_url + root)
 
 

scripts/idr0044_zarr_segmentation_parallel.py

@@ -45,8 +45,8 @@
 
 # Load-binary
 def load_binary_from_s3(id, resolution='4'):
-    endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/'
-    root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution)
+    endpoint_url = 'https://livingobjects.ebi.ac.uk/'
+    root = 'idr/zarr/v0.4/iddr0044/%s.zarr/%s/' % (id, resolution)
     return da.from_zarr(endpoint_url + root)