replace figshare with scverse S3 (#177)

* replace figshare with scverse S3

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* uv

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

---------

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

Author: Zethson

.github/workflows/build.yaml

@@ -24,7 +24,7 @@ jobs:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           cache-dependency-glob: pyproject.toml
 

.github/workflows/release.yaml

@@ -25,7 +25,7 @@ jobs:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           cache-dependency-glob: pyproject.toml
       - name: Build package

.github/workflows/test.yaml

@@ -33,7 +33,7 @@ jobs:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
       - name: Get test environments
         id: get-envs
         run: |
@@ -67,7 +67,7 @@ jobs:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.env.python }}
           cache-dependency-glob: pyproject.toml

pyproject.toml

@@ -29,7 +29,6 @@ dependencies = [
   # for debug logging (referenced from the issue template)
   "requests",
   "rich",
-  "session-info2",
   "xarray",
   "zarr<3",
 ]
@@ -59,7 +58,6 @@ optional-dependencies.ehrapy = [
 optional-dependencies.lamin = [
   "lamindb",
   #"omop", # Not needed and causing an issue in the readthedocs build https://github.com/laminlabs/lamindb/issues/3081
-  "rich",
 ]
 optional-dependencies.test = [
   "coverage",

src/ehrdata/dt/datasets.py

@@ -565,7 +565,7 @@ def mimic_2_preprocessed() -> EHRData:
         >>> edata = ed.dt.mimic_2_preprocessed()
     """
     _download(
-        url="https://figshare.com/ndownloader/files/39727936",
+        url="https://scverse-exampledata.s3.eu-west-1.amazonaws.com/ehrapy/mimic_2_preprocessed.h5ad",
         output_path=DEFAULT_DATA_PATH,
         output_filename="mimic_2_preprocessed.h5ad",
         raw_format="h5ad",
@@ -590,7 +590,6 @@ def diabetes_130_raw(
     Examples:
         >>> import ehrdata as ed
         >>> edata = ed.dt.diabetes_130_raw()
-
     """
     import os
 
@@ -607,7 +606,7 @@ def diabetes_130_raw(
         )
 
     _download(
-        url="https://figshare.com/ndownloader/files/45110029",
+        url="https://scverse-exampledata.s3.eu-west-1.amazonaws.com/ehrapy/diabetes_130_raw.csv",
         output_path=DEFAULT_DATA_PATH,
         output_filename="diabetes_130_raw.csv",
         raw_format="csv",
@@ -636,7 +635,6 @@ def diabetes_130_fairlearn(
     Examples:
         >>> import ehrdata as ed
         >>> edata = ed.dt.diabetes_130_fairlearn()
-
     """
     import os
 
@@ -653,7 +651,7 @@ def diabetes_130_fairlearn(
         )
 
     _download(
-        url="https://figshare.com/ndownloader/files/45110371",
+        url="https://scverse-exampledata.s3.eu-west-1.amazonaws.com/ehrapy/diabetes_130_fairlearn.csv",
         output_path=DEFAULT_DATA_PATH,
         output_filename="diabetes_130_fairlearn.csv",
         raw_format="csv",