Update morphology metadata only once after saving the entire MS (#733)

* update meta only once during generated MS saving

* bump deps

* bump v to match with bsb-hdf5

* skip deps

* moved plugins to their own section to avoid circular conflicts during CI

* add missing dependency

* add missing requirements

* bump to bsb-hdf5 0.8.1

.github/workflows/build.yml

@@ -31,8 +31,13 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install wheel
+        # Install the regular requirements
         pip install -r requirements.txt --prefer-binary
-        pip install -e .
+        # Install the default plugins, without dependencies, to avoid circular dependency
+        # conflicts with the BSB itself
+        pip install -r plugins.txt --prefer-binary --no-deps
+        # Install the BSB from the repo without dependencies, already installed above.
+        pip install -e . --no-deps
     - name: Run tests & coverage
       run: |
         coverage run -p -m unittest discover -v -s ./tests

bsb/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "4.0.0a54"
+__version__ = "4.0.0a55"
 
 import functools
 

bsb/placement/distributor.py

@@ -321,10 +321,13 @@ def _specials(self, partitions, indicator, positions):
             mr = self.scaffold.morphologies
             uid = uuid.uuid4()
             loaders = []
+            all_meta = mr.get_all_meta()
             for gen_morpho, i in generated.items():
                 name = f"{prefix}-{uid}-{i}"
-                saved = mr.save(name, gen_morpho)
+                saved = mr.save(name, gen_morpho, update_meta=False)
+                all_meta[name] = saved.get_meta()
                 loaders.append(saved)
+            mr.set_all_meta(all_meta)
             morphologies = MorphologySet(loaders, indices)
         if not isinstance(morphologies, MorphologySet) and morphologies is not None:
             morphologies = MorphologySet(loaders, morphologies)

docs/requirements.txt

@@ -10,4 +10,4 @@ toml==0.10.2
 furo==2023.3.27
 appdirs==1.4.4
 sphinx-copybutton==0.5.0
-sphinxext-bsb==0.2.0
+sphinxext-bsb==0.2.1

plugins.txt

@@ -0,0 +1,5 @@
+# Plugins
+bsb-hdf5==0.8.1
+
+# Plugin dependencies
+shortuuid

requirements.txt

@@ -11,6 +11,8 @@ errr==1.2.0
 psutil==5.9.4
 coverage==7.0.4
 appdirs==1.4.4
+tqdm==4.65.0
+quantities==0.14.1
 
 # IO
 h5py==3.7.0
@@ -29,9 +31,6 @@ nrn-patch==4.0.0a4
 NEURON==8.2.2
 nrn-subprocess==1.3.4
 
-# Plugins
-bsb-hdf5==0.7.4
-
 # HTTP
 requests==2.30.0
 urllib3==2.0.2

setup.py

@@ -17,7 +17,7 @@
     long_description = fh.read()
 
 requires = [
-    "bsb-hdf5~=0.7.4",
+    "bsb-hdf5~=0.8.1",
     "h5py~=3.0",
     "numpy~=1.19",
     "scipy~=1.5",
@@ -111,7 +111,7 @@
             "sphinxemoji",
             "sphinx_design~=0.2",
             "sphinx-copybutton~=0.5",
-            "sphinxext-bsb~=0.2.0",
+            "sphinxext-bsb~=0.2.1",
             "snakeviz",
         ],
         "arbor": ["arbor~=0.6", "arborize[arbor]==4.0.0a4"],