Bump setuptools from 69.5.1 to 78.1.1

.github/workflows/linters.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.9'
+          python-version: '3.11'
       - run: python -m pip install flake8
       - uses: liskin/gh-problem-matcher-wrap@a89a18291dcde8d4e6158adf736b5432987bbf95
         with:
@@ -26,7 +26,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.9'
+          python-version: '3.11'
       - run: python -m pip install isort==5.*
       - uses: liskin/gh-problem-matcher-wrap@a89a18291dcde8d4e6158adf736b5432987bbf95
         with:

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 default_language_version:
-    python: python3.9
+    python: python3.11
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0

frontend/src/components/Workspace/FlowChart/FlowChartNode/FlowChartUtils.ts

@@ -15,6 +15,8 @@ export function isValidConnection(connection: Connection) {
     // NOTE: SpikingActivityData is the same as FluoData. Just renamed for suite2p_spike_deconv.
     if (source === "SpikingActivityData") {
       return target === "FluoData" || target === "SpikingActivityData"
+    } else if (target === "BaseData" || source === "BaseData") {
+      return true
     } else {
       return source === target
     }

pyproject.toml

@@ -16,6 +16,7 @@ classifiers = [
   "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
   "Operating System :: POSIX :: Linux",
   "Operating System :: Microsoft :: Windows",
   "Operating System :: MacOS :: MacOS X",
@@ -49,7 +50,7 @@ exclude = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = "^3.11"
 fastapi = "0.104.*"
 uvicorn = "0.24.*"
 numpy = "1.24.3"
@@ -85,6 +86,7 @@ matplotlib = "3.7.*"
 concurrent-log-handler = "^0.9.25"
 numpydoc = "*"
 yapf = "*"
+setuptools = "<79"
 
 [tool.poetry.group.dev]
 optional = true

studio/app/common/dataclass/image.py

@@ -43,7 +43,7 @@ def __init__(
             create_directory(_dir)
 
             _path = join_filepath([_dir, f"{file_name}.tif"])
-            tifffile.imsave(_path, data)
+            tifffile.imwrite(_path, data)
             self.path = [_path]
 
             del data

studio/app/optinist/dataclass/roi.py

@@ -35,7 +35,7 @@ def __init__(
         _dir = join_filepath([output_dir, "tiff", file_name])
         create_directory(_dir)
         self.path = join_filepath([_dir, f"{file_name}.tif"])
-        tifffile.imsave(self.path, images)
+        tifffile.imwrite(self.path, images)
 
         del images, data
         gc.collect()

studio/app/optinist/wrappers/__init__.py

@@ -1,5 +1,6 @@
 from studio.app.optinist.wrappers.caiman import caiman_wrapper_dict
 from studio.app.optinist.wrappers.custom import custom_wrapper_dict
+from studio.app.optinist.wrappers.data_utils import utils_wrapper_dict
 from studio.app.optinist.wrappers.lccd import lccd_wrapper_dict
 from studio.app.optinist.wrappers.maintenance import maintenance_wrapper_dict
 from studio.app.optinist.wrappers.optinist import optinist_wrapper_dict
@@ -10,5 +11,6 @@
 wrapper_dict.update(**suite2p_wrapper_dict)
 wrapper_dict.update(**lccd_wrapper_dict)
 wrapper_dict.update(**optinist_wrapper_dict)
+wrapper_dict.update(**utils_wrapper_dict)
 wrapper_dict.update(**maintenance_wrapper_dict)
 wrapper_dict.update(**custom_wrapper_dict)

studio/app/optinist/wrappers/custom/conda/custom.yaml

@@ -1,3 +1,7 @@
 dependencies:
-  - python=3.9
-  - numpy<2 # Exclude numpy 2.x versions
+  - python=3.11
+  - numpy<2
+  - pip
+  - h5py
+  - pip:
+      # - scikit-learn

studio/app/optinist/wrappers/data_utils/__init__.py

@@ -0,0 +1,47 @@
+from studio.app.optinist.wrappers.data_utils.data_concat import data_concat
+from studio.app.optinist.wrappers.data_utils.data_slice import data_slice
+from studio.app.optinist.wrappers.data_utils.data_transpose import data_transpose
+from studio.app.optinist.wrappers.data_utils.fluo_from_hdf5 import fluo_from_hdf5
+from studio.app.optinist.wrappers.data_utils.microscope_to_img import microscope_to_img
+from studio.app.optinist.wrappers.data_utils.roi_fluo_from_hdf5 import (
+    roi_fluo_from_hdf5,
+)
+from studio.app.optinist.wrappers.data_utils.roi_from_hdf5 import roi_from_hdf5
+from studio.app.optinist.wrappers.data_utils.vacant_roi import vacant_roi
+
+utils_wrapper_dict = {
+    "utils": {
+        "data_concat": {
+            "function": data_concat,
+            "conda_name": "optinist",
+        },
+        "data_slice": {
+            "function": data_slice,
+            "conda_name": "optinist",
+        },
+        "data_transpose": {
+            "function": data_transpose,
+            "conda_name": "optinist",
+        },
+        "fluo_from_hdf5": {
+            "function": fluo_from_hdf5,
+            "conda_name": "optinist",
+        },
+        "roi_from_hdf5": {
+            "function": roi_from_hdf5,
+            "conda_name": "optinist",
+        },
+        "roi_fluo_from_hdf5": {
+            "function": roi_fluo_from_hdf5,
+            "conda_name": "optinist",
+        },
+        "microscope_to_img": {
+            "function": microscope_to_img,
+            "conda_name": "microscope",
+        },
+        "vacant_roi": {
+            "function": vacant_roi,
+            "conda_name": "optinist",
+        },
+    },
+}