Fix slm requirement in Python API (#15)

* fix slm requirement in Python API

* swap to quantity

* Update requirements-min.txt

* Update pyproject.toml

.gitignore

@@ -168,3 +168,6 @@ cython_debug/
 
 # Mac finder
 .DS_Store
+
+# PyCharm
+.idea/

pyproject.toml

@@ -34,6 +34,7 @@ keywords = [
 dependencies = [
     "pynwb>=2.5.0",
     "hdmf>=3.10.0",
+    "numpy<2.0",  # TODO: remove when HDMF supports
 ]
 
 # TODO: add URLs before release

requirements-min.txt

@@ -3,3 +3,4 @@
 # NOTE: it may be possible to relax these minimum requirements
 pynwb==2.5.0
 hdmf==3.10.0
+numpy<2.0  # TODO: remove when HDMF supports it

spec/ndx-patterned-ogen.extensions.yaml

@@ -1,4 +1,5 @@
 groups:
+
   - neurodata_type_def: OptogeneticStimulus2DPattern
     neurodata_type_inc: LabMetaData
     doc: Container to store the information about a generic 2D stimulus pattern (spatial information).
@@ -34,6 +35,8 @@ groups:
         shape:
           -
           -
+
+
   - neurodata_type_def: OptogeneticStimulus3DPattern
     neurodata_type_inc: LabMetaData
     doc: Container to store the information about a generic 3D stimulus pattern (spatial information).
@@ -71,6 +74,8 @@ groups:
           -
           -
           -
+
+
   - neurodata_type_def: SpiralScanning
     neurodata_type_inc: LabMetaData
     doc: Container to store the parameters defining a spiral scanning pattern.
@@ -89,6 +94,8 @@ groups:
         dtype: text
         doc: Describe any additional details about the pattern.
         required: false
+
+
   - neurodata_type_def: TemporalFocusing
     neurodata_type_inc: LabMetaData
     doc: Container to store the parameters defining a temporal focusing beam-shaping.
@@ -107,6 +114,8 @@ groups:
         dtype: text
         doc: Describe any additional details about the pattern.
         required: false
+
+
   - neurodata_type_def: PatternedOptogeneticStimulusSite
     neurodata_type_inc: OptogeneticStimulusSite
     doc: Patterned optogenetic stimulus site.
@@ -121,7 +130,9 @@ groups:
       - name: spatial_light_modulator
         target_type: Device
         doc: Spatial light modulator used to generate photostimulation pattern.
-        required: false
+        quantity: "?"
+
+
   - neurodata_type_def: SpatialLightModulator2D
     neurodata_type_inc: Device
     doc: 2D spatial light modulator used in the experiment.
@@ -138,6 +149,8 @@ groups:
           - width, height
         shape:
           - 2
+
+
   - neurodata_type_def: SpatialLightModulator3D
     neurodata_type_inc: Device
     doc: 3D spatial light modulator used in the experiment.
@@ -154,6 +167,8 @@ groups:
           - width, height, depth
         shape:
           - 3
+
+
   - neurodata_type_def: LightSource
     neurodata_type_inc: Device
     doc: Light source used in the experiment.
@@ -189,6 +204,8 @@ groups:
         dtype: text
         doc: Model of light source device.
         required: false
+
+
   - neurodata_type_def: OptogeneticStimulusTarget
     neurodata_type_inc: LabMetaData
     doc: Container to store the targated rois in a photostimulation experiment.
@@ -200,6 +217,8 @@ groups:
         neurodata_type_inc: DynamicTableRegion
         doc: A table region referencing a PlaneSegmentation object storing segmented ROIs that receive photostimulation.
         quantity: "?"
+
+
   - neurodata_type_def: PatternedOptogeneticStimulusTable
     neurodata_type_inc: TimeIntervals
     doc: Table to hold all patterned optogenetic stimulus onsets.

src/pynwb/ndx_patterned_ogen/patterned_ogen.py

@@ -30,6 +30,7 @@ class PatternedOptogeneticStimulusSite(OptogeneticStimulusSite):
             "name": "spatial_light_modulator",
             "type": Device,
             "doc": "Spatial light modulator used to generate photostimulation pattern.",
+            "default": None,
         },
         {"name": "light_source", "type": Device, "doc": "Light source used to apply photostimulation."},
     )