Merge branch 'main' into neuron_v4

.github/devops/install-nest.sh

@@ -0,0 +1,10 @@
+git clone https://github.com/nest/nest-simulator $GITHUB_WORKSPACE/nest
+cd $GITHUB_WORKSPACE/nest
+git checkout tags/v$1
+mkdir build
+cd build
+pip install cython cmake
+cmake .. \
+  -DCMAKE_INSTALL_PREFIX=$2 \
+  -Dwith-mpi=ON
+make install

.github/workflows/build.yml

@@ -8,46 +8,33 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
     - uses: actions/[email protected]
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/[email protected]
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install apt dependencies
       run: |
-        sudo apt-get update
-        sudo apt-get install openmpi-bin libopenmpi-dev
-    - name: Cache pip
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
-          ${{ runner.os }}-
+        sudo apt update
+        # Install `libopenmpi` for MPI
+        sudo apt install openmpi-bin libopenmpi-dev
+        # Install `libhdf5` for `morphio`
+        sudo apt install libhdf5-dev
+
     - name: Install dependencies & self
       run: |
-        python -m pip install --upgrade pip
-        pip install wheel
-        # Install the regular requirements
-        pip install -r requirements.txt --prefer-binary
-        # 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
-        pip install "dbbs-models>=4.0.0a0"
+        # Install latest pip
+        pip install --upgrade pip
+        # Install bsb-core
+        pip install .[test,mpi]
+
     - name: Run tests & coverage
       run: |
         coverage run -p -m unittest discover -v -s ./tests
         mpiexec -n 2 coverage run -p -m unittest discover -v -s ./tests
         BSB_PROFILING=TRUE coverage run -p -m unittest tests.test_env_options
-        bash <(curl -s https://codecov.io/bash)
-    - name: Test default plugins
-      run: |
-        git clone https://github.com/dbbs-lab/bsb-hdf5
-        pip install -e bsb-hdf5/
-        coverage run -p -m unittest discover bsb-hdf5/test
-        bash <(curl -s https://codecov.io/bash)
+        bash <(curl -s https://codecov.io/bash)

.github/workflows/docs.yml

@@ -15,11 +15,11 @@ jobs:
         python-version: 3.9
     - name: Install MPI
       run: |
-        sudo apt-get update
-        sudo apt-get install -y openmpi-bin libopenmpi-dev
+        sudo apt update
+        sudo apt install -y openmpi-bin libopenmpi-dev
     - name: Install dependencies
       run: |
-        python -m pip install pip
+        python -m pip install --upgrade pip
         pip install -r docs/requirements.txt
     - name: Install self
       run: |

.gitignore

@@ -11,16 +11,17 @@ bsb-*/
 *.egg-info/
 pip-wheel-metadata/
 .python-version
+venv/
 dev_env/
 test_env/
 nrnmech.dll
 .coverage
 htmlcov/
-.idea/
 !morphologies.hdf5
 # Ignore report files
 *.io
 .vscode/
+.idea/
 bsb-*/
 
 

bsb/__init__.py

@@ -1,4 +1,13 @@
-__version__ = "4.0.0a56"
+"""
+`bsb-core` is the backbone package contain the essential code of the BSB: A component
+framework for multiscale bottom-up neural modelling.
+
+`bsb-core` needs to be installed alongside a bundle of desired bsb plugins, some of
+which are essential for `bsb-core` to function. First time users are recommended to
+install the `bsb` package instead.
+"""
+
+__version__ = "4.0.0b0"
 
 import functools
 
@@ -16,7 +25,10 @@ def _register(self, cls, method=None):  # pragma: nocover
 
     functools.singledispatchmethod.register = _register
 
-from .options import profiling as _pr
+try:
+    from .options import profiling as _pr
+except Exception:
+    _pr = False
 
 if _pr:
     from .profiling import activate_session

bsb/cell_types.py

@@ -1,15 +1,21 @@
 """
     Module for the CellType configuration node and its dependencies.
 """
+import typing
 
 from . import config
 from .config import types
 from .placement.indicator import PlacementIndications
 from ._util import obj_str_insert
 
+if typing.TYPE_CHECKING:
+    from .core import Scaffold
+
 
 @config.node
 class Plotting:
+    scaffold: "Scaffold"
+
     display_name = config.attr()
     """
     Label used to display this cell type in plots.
@@ -34,6 +40,8 @@ class CellType:
     Information on a population of cells.
     """
 
+    scaffold: "Scaffold"
+
     name = config.attr(key=True)
     """
     Name of the cell type, equivalent to the key it occurs under in the configuration.
@@ -123,7 +131,7 @@ def clear_connections(self):
         set that this cell type is a part of will be entirely removed.
         """
         for conn_set in self.scaffold.get_connectivity_sets():
-            if self is conn_set.presynaptic or self is conn_set.postsynaptic:
+            if self is conn_set.pre_type or self is conn_set.post_type:
                 conn_set.clear()
 
     # This property was mostly added so that accidental assignment to `ct.morphologies`

bsb/cli/commands/_commands.py

@@ -209,7 +209,7 @@ def handler(self, context):
             append += ", ".join(f"'{name}'" for name in extra_simulations.keys())
             errr.wrap(type(e), e, append=append)
         else:
-            result.write(f"{uuid4()}.nio", "ow")
+            result.write(getattr(context.arguments, "output", f"{uuid4()}.nio"), "ow")
 
     def get_options(self):
         return {
@@ -220,6 +220,7 @@ def get_options(self):
     def add_parser_arguments(self, parser):
         parser.add_argument("network")
         parser.add_argument("simulation")
+        parser.add_argument("-o", "--output")
 
 
 class CacheCommand(BaseCommand, name="cache"):  # pragma: nocover

bsb/config/__init__.py

@@ -10,6 +10,8 @@
 import sys
 import glob
 import itertools
+import typing
+from importlib.machinery import ModuleSpec
 from shutil import copy2 as copy_file
 import builtins
 import traceback
@@ -35,6 +37,7 @@
 from .._util import ichain
 from ._make import walk_node_attributes, walk_nodes, compose_nodes, get_config_attributes
 from ._hooks import on, before, after, run_hook, has_hook
+from ._distributions import Distribution
 from .. import plugins
 from ..exceptions import ConfigTemplateNotFoundError, ParserError, PluginError
 from . import parsers
@@ -43,6 +46,12 @@
 _path = __path__
 ConfigurationAttribute.__module__ = __name__
 
+if typing.TYPE_CHECKING:
+    from ._config import Configuration
+
+# Add some static type hinting, to help tools figure out this dynamic module
+Configuration: "Configuration"
+
 
 # ConfigurationModule should not inherit from `ModuleType`, otherwise Sphinx doesn't
 # document all the properties.
@@ -80,11 +89,14 @@ def __init__(self, name):
     run_hook = staticmethod(run_hook)
     has_hook = staticmethod(has_hook)
 
+    Distribution = Distribution
+
     _parser_classes = {}
 
     # The __path__ attribute needs to be retained to mark this module as a package with
     # submodules (config.refs, config.parsers.json, ...)
     __path__ = _path
+    __spec__ = ModuleSpec(__name__, __loader__, origin=__file__)
 
     # Load the Configuration class on demand, not on import, to avoid circular
     # dependencies.
@@ -208,14 +220,16 @@ def _try_parsers(content, classes, ext=None, path=None):  # pragma: nocover
     if ext is not None:
 
         def file_has_parser_ext(kv):
-            return ext in getattr(kv[1], "data_extensions", ())
+            return ext not in getattr(kv[1], "data_extensions", ())
 
         classes = builtins.dict(sorted(classes.items(), key=file_has_parser_ext))
     exc = {}
     for name, cls in classes.items():
         try:
             tree, meta = cls().parse(content, path=path)
         except Exception as e:
+            if getattr(e, "_bsbparser_show_user", False):
+                raise e from None
             exc[name] = e
         else:
             return (name, tree, meta)
@@ -257,7 +271,7 @@ def parser_method(self, file=None, data=None, path=None):
         return _from_parsed(self, name, tree, meta, file)
 
     parser_method.__name__ = "from_" + name
-    parser_method.__doc__ = _parser_method_docs(parser)
+    # parser_method.__doc__ = _parser_method_docs(parser)
     return parser_method
 
 

bsb/config/_attrs.py

@@ -111,7 +111,7 @@ class Example:
     :param kwargs: All keyword arguments are passed to the constructor of the
       :func:`attribute <.config.attr>`.
     """
-    if "required" not in kwargs:
+    if "required" not in kwargs and "default" not in kwargs:
         kwargs["required"] = True
     if "type" not in kwargs:
         kwargs["type"] = str
@@ -508,15 +508,18 @@ def is_node_type(self):
 
     def tree(self, instance):
         val = _getattr(instance, self.attr_name)
+        return self.tree_of(val)
+
+    def tree_of(self, value):
         # Allow subnodes and other class values to convert themselves to their tree
         # representation
-        if hasattr(val, "__tree__"):
-            val = val.__tree__()
+        if hasattr(value, "__tree__"):
+            value = value.__tree__()
         # Check if the type handler specifies any inversion function to convert tree
         # values back to how they were found in the document.
-        if hasattr(self.type, "__inv__") and val is not None:
-            val = self.type.__inv__(val)
-        return val
+        if hasattr(self.type, "__inv__") and value is not None:
+            value = self.type.__inv__(value)
+        return value
 
     def flag_dirty(self, instance):
         instance._config_state[self.attr_name] = False
@@ -538,6 +541,10 @@ def should_call_default(self):
 
 
 class cfglist(builtins.list):
+    """
+    Extension of the builtin list to manipulate lists of configuration nodes.
+    """
+
     def get_node_name(self):
         return self._config_parent.get_node_name() + "." + self._config_attr_name
 
@@ -675,10 +682,14 @@ def _set_type(self, type, key=None):
 
     def tree(self, instance):
         val = _getattr(instance, self.attr_name)
-        return [e if not hasattr(e, "__tree__") else e.__tree__() for e in val]
+        return [self.tree_of(e) for e in val]
 
 
 class cfgdict(builtins.dict):
+    """
+    Extension of the builtin dictionary to manipulate dicts of configuration nodes.
+    """
+
     def __getattr__(self, name):
         try:
             return self[name]
@@ -815,7 +826,7 @@ def _set_type(self, type, key=None):
 
     def tree(self, instance):
         val = _getattr(instance, self.attr_name).items()
-        return {k: v if not hasattr(v, "__tree__") else v.__tree__() for k, v in val}
+        return {k: self.tree_of(v) for k, v in val}
 
 
 class ConfigurationReferenceAttribute(ConfigurationAttribute):