From 8caf750e55c2d89082de5c57eef1300407bac1e0 Mon Sep 17 00:00:00 2001
From: drodarie <d.rodarie@gmail.com>
Date: Wed, 14 Jan 2026 16:51:35 +0100
Subject: [PATCH 1/7] fix: Replace MPI barrier with broadcast of boot status so
 that each process raises an error.

---
 packages/bsb-core/bsb/config/_attrs.py        | 12 +++++++++---
 .../bsb-core/bsb/morphologies/selector.py     | 15 +++++++++------
 packages/bsb-core/tests/test_issues.py        | 19 ++++++++++++++++++-
 3 files changed, 36 insertions(+), 10 deletions(-)

diff --git a/packages/bsb-core/bsb/config/_attrs.py b/packages/bsb-core/bsb/config/_attrs.py
index 107b9c48..6abecc5b 100644
--- a/packages/bsb-core/bsb/config/_attrs.py
+++ b/packages/bsb-core/bsb/config/_attrs.py
@@ -462,6 +462,7 @@ def _root_is_booted(obj):
 
 
 def _boot_nodes(top_node, scaffold):
+    fail_boot = False
     for node in walk_nodes(top_node):
         node.scaffold = scaffold
         # Boot attributes
@@ -476,9 +477,14 @@ def _boot_nodes(top_node, scaffold):
         try:
             run_hook(node, "boot")
         except Exception as e:
-            errr.wrap(BootError, e, prepend=f"Failed to boot {node}:")
-    # fixme: why is this here? Will deadlock in case of BootError on specific node only.
-    scaffold._comm.barrier()
+            fail_boot = [e, f"Failed to boot {node}:"]
+    fail_boot = scaffold._comm.allgather(fail_boot)
+    if any(fail_boot):
+        if fail_boot[scaffold._comm.get_rank()]:
+            e, prepend = fail_boot[scaffold._comm.get_rank()]
+            errr.wrap(BootError, e, prepend=prepend)
+        else:
+            raise BootError("Boot failed on other process.")
 
 
 def _unset_nodes(top_node):
diff --git a/packages/bsb-core/bsb/morphologies/selector.py b/packages/bsb-core/bsb/morphologies/selector.py
index a00d4343..d62c4254 100644
--- a/packages/bsb-core/bsb/morphologies/selector.py
+++ b/packages/bsb-core/bsb/morphologies/selector.py
@@ -87,15 +87,18 @@ class NeuroMorphoSelector(NameSelector, classmap_entry="from_neuromorpho"):
     _files = "dableFiles/"
 
     def __boot__(self):
+        fail_to_boot = False
         if self.scaffold.is_main_process():
             try:
                 morphos = self._scrape_nm(self.names)
-            except:
-                self.scaffold._comm.barrier()
-                raise
-            for name, morpho in morphos.items():
-                self.scaffold.morphologies.save(name, morpho, overwrite=True)
-        self.scaffold._comm.barrier()
+            except Exception:
+                fail_to_boot = True
+            else:
+                for name, morpho in morphos.items():
+                    self.scaffold.morphologies.save(name, morpho, overwrite=True)
+        self.scaffold._comm.bcast(fail_to_boot)
+        if fail_to_boot:
+            raise
 
     @classmethod
     def _swc_url(cls, archive, name):
diff --git a/packages/bsb-core/tests/test_issues.py b/packages/bsb-core/tests/test_issues.py
index 97830ccc..95f01a1c 100644
--- a/packages/bsb-core/tests/test_issues.py
+++ b/packages/bsb-core/tests/test_issues.py
@@ -2,13 +2,18 @@
 import unittest
 from types import NoneType
 
+from bsb_test import RandomStorageFixture, timeout
+
 from bsb import (
+    BootError,
     CellType,
     CfgReferenceError,
     Chunk,
+    Configuration,
     FixedPositions,
     PlacementIndications,
     Reference,
+    Scaffold,
     config,
 )
 
@@ -45,7 +50,7 @@ class Root430:
     extensions = config.dict(type=Extension, required=True)
 
 
-class TestIssues(unittest.TestCase):
+class TestIssues(RandomStorageFixture, unittest.TestCase, engine_name="hdf5"):
     def test_430(self):
         with self.assertRaises(CfgReferenceError, msg="Regression of issue #430"):
             _config = Root430(
@@ -62,3 +67,15 @@ def test_802(self):
                 Chunk((0, 0, 0), (100, 100, 100)),
                 {CellType(spatial=dict(radius=1, count=1)): PlacementIndications()},
             )
+
+    @timeout(3)
+    def test_211(self):
+        """
+        Test if the absence of a file does not make the reconstruction
+        get stuck in parallel.
+        """
+        cfg = Configuration.default(
+            files=dict(annotations={"file": "path/to/missing/file.nrrd", "type": "nrrd"}),
+        )
+        with self.assertRaises(BootError):
+            Scaffold(cfg, self.storage)

From 7ffbefba8fa49c268ba70ab28571227c8eed0ca1 Mon Sep 17 00:00:00 2001
From: drodarie <d.rodarie@gmail.com>
Date: Wed, 14 Jan 2026 17:01:54 +0100
Subject: [PATCH 2/7] fix: cleanup morphologies obtained from
 NeuromorphoSelector upon unsetting the node.

---
 packages/bsb-core/bsb/config/_attrs.py         |  2 +-
 packages/bsb-core/bsb/morphologies/selector.py | 11 ++++++++++-
 packages/bsb-core/tests/test_selectors.py      |  3 +--
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/packages/bsb-core/bsb/config/_attrs.py b/packages/bsb-core/bsb/config/_attrs.py
index 6abecc5b..c1a7db67 100644
--- a/packages/bsb-core/bsb/config/_attrs.py
+++ b/packages/bsb-core/bsb/config/_attrs.py
@@ -489,13 +489,13 @@ def _boot_nodes(top_node, scaffold):
 
 def _unset_nodes(top_node):
     for node in walk_nodes(top_node):
+        run_hook(node, "unboot")
         with contextlib.suppress(Exception):
             del node.scaffold
         node._config_parent = None
         node._config_key = None
         if hasattr(node, "_config_index"):
             node._config_index = None
-        run_hook(node, "unboot")
 
 
 class ConfigurationAttribute:
diff --git a/packages/bsb-core/bsb/morphologies/selector.py b/packages/bsb-core/bsb/morphologies/selector.py
index d62c4254..2c4c8fc6 100644
--- a/packages/bsb-core/bsb/morphologies/selector.py
+++ b/packages/bsb-core/bsb/morphologies/selector.py
@@ -1,5 +1,6 @@
 import abc
 import concurrent
+import contextlib
 import re
 import tempfile
 import typing
@@ -12,7 +13,7 @@
 from .. import config
 from ..config import types
 from ..config._attrs import cfglist
-from ..exceptions import MissingMorphologyError, SelectorError
+from ..exceptions import MissingMorphologyError, MorphologyRepositoryError, SelectorError
 from .parsers import parse_morphology_file
 
 if typing.TYPE_CHECKING:  # pragma: nocover
@@ -100,6 +101,14 @@ def __boot__(self):
         if fail_to_boot:
             raise
 
+    def __unboot__(self):
+        if self.scaffold.is_main_process():
+            for name in self.names:
+                with contextlib.suppress(MorphologyRepositoryError):
+                    # remove morphology if it was saved in the scaffold.
+                    self.scaffold.morphologies.remove(name)
+        self.scaffold._comm.barrier()
+
     @classmethod
     def _swc_url(cls, archive, name):
         return (
diff --git a/packages/bsb-core/tests/test_selectors.py b/packages/bsb-core/tests/test_selectors.py
index b4612eb3..1d7c73a9 100644
--- a/packages/bsb-core/tests/test_selectors.py
+++ b/packages/bsb-core/tests/test_selectors.py
@@ -1,6 +1,6 @@
 import unittest
 
-from bsb_test import RandomStorageFixture, skip_parallel, skipIfOffline
+from bsb_test import RandomStorageFixture, skipIfOffline
 
 from bsb import (
     MPI,
@@ -105,7 +105,6 @@ def test_nm_selector(self):
         m = s.morphologies.select(*ct.spatial.morphologies)[0]
         self.assertEqual(name, m.get_meta()["neuron_name"], "meta not stored")
 
-    @skip_parallel  # https://github.com/dbbs-lab/bsb/issues/187
     @skipIfOffline(scheme=NeuroMorphoScheme())
     def test_nm_selector_wrong_name(self):
         ct = CellType(

From f8041ac3f186c3380d5cedd28e4bbb115b19f0c4 Mon Sep 17 00:00:00 2001
From: drodarie <d.rodarie@gmail.com>
Date: Wed, 14 Jan 2026 17:11:35 +0100
Subject: [PATCH 3/7] fix: allow again test_nm_scheme in parallel

---
 packages/bsb-core/tests/test_util.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/packages/bsb-core/tests/test_util.py b/packages/bsb-core/tests/test_util.py
index fbf0ee7d..e4c538d1 100644
--- a/packages/bsb-core/tests/test_util.py
+++ b/packages/bsb-core/tests/test_util.py
@@ -5,7 +5,6 @@
     FixedPosConfigFixture,
     NumpyTestCase,
     RandomStorageFixture,
-    skip_parallel,
     skipIfOffline,
 )
 from scipy.spatial.transform import Rotation
@@ -70,7 +69,6 @@ def test_rotation_matrix_from_vectors(self):
 
 
 class TestUriSchemes(RandomStorageFixture, unittest.TestCase, engine_name="fs"):
-    @skip_parallel  # see https://github.com/dbbs-lab/bsb/issues/197
     @skipIfOffline(scheme=NeuroMorphoScheme())
     def test_nm_scheme(self):
         file = FileDependency(

From d7bbb6d2ef77c56e924122d94b4630d0f9b07aca Mon Sep 17 00:00:00 2001
From: drodarie <d.rodarie@gmail.com>
Date: Wed, 14 Jan 2026 17:45:12 +0100
Subject: [PATCH 4/7] fix: remove old codecov badge in bsb-core README.md

---
 packages/bsb-core/README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/packages/bsb-core/README.md b/packages/bsb-core/README.md
index 1f1725e7..7cb0e521 100644
--- a/packages/bsb-core/README.md
+++ b/packages/bsb-core/README.md
@@ -1,7 +1,6 @@
 [![Build Status](https://github.com/dbbs-lab/bsb/actions/workflows/main.yml/badge.svg)](https://github.com/dbbs-lab/bsb/actions/workflows/main.yml)
 [![Documentation](https://readthedocs.org/projects/bsb-core/badge/?version=latest)](https://bsb-core.readthedocs.io/en/latest/?badge=latest)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
-[![codecov](https://codecov.io/gh/dbbs-lab/bsb-core/branch/main/graph/badge.svg)](https://codecov.io/gh/dbbs-lab/bsb-core)
 
 # bsb-core
 

From 97fb9f798f63baafaa787a7aa0a3b2d459bba97a Mon Sep 17 00:00:00 2001
From: drodarie <d.rodarie@gmail.com>
Date: Wed, 14 Jan 2026 19:23:06 +0100
Subject: [PATCH 5/7] fix: Use ContextManager to deal with error broadcast. Add
 to MPIService functions

---
 packages/bsb-core/bsb/config/_attrs.py        | 17 ++-----
 .../bsb-core/bsb/morphologies/selector.py     | 21 ++++-----
 packages/bsb-core/bsb/services/mpi.py         | 47 +++++++++++++++++++
 3 files changed, 61 insertions(+), 24 deletions(-)

diff --git a/packages/bsb-core/bsb/config/_attrs.py b/packages/bsb-core/bsb/config/_attrs.py
index c1a7db67..2cf31321 100644
--- a/packages/bsb-core/bsb/config/_attrs.py
+++ b/packages/bsb-core/bsb/config/_attrs.py
@@ -462,7 +462,6 @@ def _root_is_booted(obj):
 
 
 def _boot_nodes(top_node, scaffold):
-    fail_boot = False
     for node in walk_nodes(top_node):
         node.scaffold = scaffold
         # Boot attributes
@@ -474,17 +473,11 @@ def _boot_nodes(top_node, scaffold):
                     boot(node, scaffold)
                     booted.add(boot)
         # Boot node hook
-        try:
-            run_hook(node, "boot")
-        except Exception as e:
-            fail_boot = [e, f"Failed to boot {node}:"]
-    fail_boot = scaffold._comm.allgather(fail_boot)
-    if any(fail_boot):
-        if fail_boot[scaffold._comm.get_rank()]:
-            e, prepend = fail_boot[scaffold._comm.get_rank()]
-            errr.wrap(BootError, e, prepend=prepend)
-        else:
-            raise BootError("Boot failed on other process.")
+        with scaffold._comm.try_all(BootError("Boot failed on other process.")):
+            try:
+                run_hook(node, "boot")
+            except Exception as e:
+                errr.wrap(BootError, e, prepend=f"Failed to boot {node}:")
 
 
 def _unset_nodes(top_node):
diff --git a/packages/bsb-core/bsb/morphologies/selector.py b/packages/bsb-core/bsb/morphologies/selector.py
index 2c4c8fc6..87404b72 100644
--- a/packages/bsb-core/bsb/morphologies/selector.py
+++ b/packages/bsb-core/bsb/morphologies/selector.py
@@ -88,18 +88,15 @@ class NeuroMorphoSelector(NameSelector, classmap_entry="from_neuromorpho"):
     _files = "dableFiles/"
 
     def __boot__(self):
-        fail_to_boot = False
-        if self.scaffold.is_main_process():
-            try:
-                morphos = self._scrape_nm(self.names)
-            except Exception:
-                fail_to_boot = True
-            else:
-                for name, morpho in morphos.items():
-                    self.scaffold.morphologies.save(name, morpho, overwrite=True)
-        self.scaffold._comm.bcast(fail_to_boot)
-        if fail_to_boot:
-            raise
+        with self.scaffold._comm.try_main():
+            if self.scaffold.is_main_process():
+                try:
+                    morphos = self._scrape_nm(self.names)
+                except Exception:
+                    raise
+                else:
+                    for name, morpho in morphos.items():
+                        self.scaffold.morphologies.save(name, morpho, overwrite=True)
 
     def __unboot__(self):
         if self.scaffold.is_main_process():
diff --git a/packages/bsb-core/bsb/services/mpi.py b/packages/bsb-core/bsb/services/mpi.py
index 09c88940..bcda38f5 100644
--- a/packages/bsb-core/bsb/services/mpi.py
+++ b/packages/bsb-core/bsb/services/mpi.py
@@ -1,5 +1,6 @@
 import functools
 import os
+from contextlib import AbstractContextManager
 
 from ..exceptions import DependencyError
 from ._util import MockModule
@@ -74,6 +75,52 @@ def Unlock(self, rank):
 
             return WindowMock()
 
+    def try_all(self, default_exception):
+        """
+        Create a context manager that checks if any exception is raised by any processes
+        within the context, and make all other processes raise an exception in that case
+
+        :param Exception default_exception: Exception instance to raise for all processes
+          that did not raise during the context.
+        :return: context manager
+        """
+        comm = self
+
+        class bcast_all(AbstractContextManager):
+            def __enter__(self):
+                pass
+
+            def __exit__(self, exctype, excinst, exctb):
+                exceptions = comm.allgather(excinst)
+                if any(exceptions):
+                    if exceptions[comm.get_rank()]:
+                        raise exceptions[comm.get_rank()]
+                    else:
+                        raise default_exception
+
+        return bcast_all()
+
+    def try_main(self):
+        """
+        Create a context manager that checks if any exception is raised by the main
+        process within the context, and make all other processes raise this exception in
+        that case
+
+        :return: context manager
+        """
+        comm = self
+
+        class bcast(AbstractContextManager):
+            def __enter__(self):
+                pass
+
+            def __exit__(self, exctype, excinst, exctb):
+                exception = comm.bcast(excinst)
+                if exception is not None:
+                    raise exception
+
+        return bcast()
+
 
 class MPIModule(MockModule):
     """

From 088262b026d8f21a2f2a21521e28b8ce57784ba8 Mon Sep 17 00:00:00 2001
From: drodarie <d.rodarie@gmail.com>
Date: Thu, 15 Jan 2026 12:41:20 +0100
Subject: [PATCH 6/7] fix: Use decorator instead of class for ContextManager
 functions

---
 packages/bsb-core/bsb/config/_attrs.py        |  2 +-
 .../bsb-core/bsb/morphologies/selector.py     | 22 +++----
 packages/bsb-core/bsb/services/mpi.py         | 64 ++++++++++---------
 3 files changed, 44 insertions(+), 44 deletions(-)

diff --git a/packages/bsb-core/bsb/config/_attrs.py b/packages/bsb-core/bsb/config/_attrs.py
index 2cf31321..6d977ae3 100644
--- a/packages/bsb-core/bsb/config/_attrs.py
+++ b/packages/bsb-core/bsb/config/_attrs.py
@@ -473,7 +473,7 @@ def _boot_nodes(top_node, scaffold):
                     boot(node, scaffold)
                     booted.add(boot)
         # Boot node hook
-        with scaffold._comm.try_all(BootError("Boot failed on other process.")):
+        with scaffold._comm.try_all(BootError("Boot failed on different rank.")):
             try:
                 run_hook(node, "boot")
             except Exception as e:
diff --git a/packages/bsb-core/bsb/morphologies/selector.py b/packages/bsb-core/bsb/morphologies/selector.py
index 87404b72..6c922593 100644
--- a/packages/bsb-core/bsb/morphologies/selector.py
+++ b/packages/bsb-core/bsb/morphologies/selector.py
@@ -90,21 +90,17 @@ class NeuroMorphoSelector(NameSelector, classmap_entry="from_neuromorpho"):
     def __boot__(self):
         with self.scaffold._comm.try_main():
             if self.scaffold.is_main_process():
-                try:
-                    morphos = self._scrape_nm(self.names)
-                except Exception:
-                    raise
-                else:
-                    for name, morpho in morphos.items():
-                        self.scaffold.morphologies.save(name, morpho, overwrite=True)
+                morphos = self._scrape_nm(self.names)
+                for name, morpho in morphos.items():
+                    self.scaffold.morphologies.save(name, morpho, overwrite=True)
 
     def __unboot__(self):
-        if self.scaffold.is_main_process():
-            for name in self.names:
-                with contextlib.suppress(MorphologyRepositoryError):
-                    # remove morphology if it was saved in the scaffold.
-                    self.scaffold.morphologies.remove(name)
-        self.scaffold._comm.barrier()
+        with self.scaffold._comm.try_main():
+            if self.scaffold.is_main_process():
+                for name in self.names:
+                    with contextlib.suppress(MorphologyRepositoryError):
+                        # remove morphology if it was saved in the scaffold.
+                        self.scaffold.morphologies.remove(name)
 
     @classmethod
     def _swc_url(cls, archive, name):
diff --git a/packages/bsb-core/bsb/services/mpi.py b/packages/bsb-core/bsb/services/mpi.py
index bcda38f5..635ba5cc 100644
--- a/packages/bsb-core/bsb/services/mpi.py
+++ b/packages/bsb-core/bsb/services/mpi.py
@@ -1,6 +1,6 @@
+import contextlib
 import functools
 import os
-from contextlib import AbstractContextManager
 
 from ..exceptions import DependencyError
 from ._util import MockModule
@@ -75,7 +75,8 @@ def Unlock(self, rank):
 
             return WindowMock()
 
-    def try_all(self, default_exception):
+    @contextlib.contextmanager
+    def try_all(self, default_exception=None):
         """
         Create a context manager that checks if any exception is raised by any processes
         within the context, and make all other processes raise an exception in that case
@@ -84,42 +85,45 @@ def try_all(self, default_exception):
           that did not raise during the context.
         :return: context manager
         """
-        comm = self
-
-        class bcast_all(AbstractContextManager):
-            def __enter__(self):
-                pass
-
-            def __exit__(self, exctype, excinst, exctb):
-                exceptions = comm.allgather(excinst)
-                if any(exceptions):
-                    if exceptions[comm.get_rank()]:
-                        raise exceptions[comm.get_rank()]
-                    else:
-                        raise default_exception
-
-        return bcast_all()
-
+        exc_instance = None
+        default_exception = default_exception or RuntimeError(
+            "An error occurred on a different rank"
+        )
+        try:
+            yield
+        except Exception as e:
+            exc_instance = e
+        finally:
+            exceptions = self.allgather(exc_instance)
+            if any(exceptions):
+                raise (
+                    exceptions[self.get_rank()]
+                    if exceptions[self.get_rank()]
+                    else default_exception
+                )
+
+    @contextlib.contextmanager
     def try_main(self):
         """
         Create a context manager that checks if any exception is raised by the main
         process within the context, and make all other processes raise this exception in
         that case
+        Warning: All processes will still enter the context, but only main exception will
+        be raised.
 
         :return: context manager
         """
-        comm = self
-
-        class bcast(AbstractContextManager):
-            def __enter__(self):
-                pass
-
-            def __exit__(self, exctype, excinst, exctb):
-                exception = comm.bcast(excinst)
-                if exception is not None:
-                    raise exception
-
-        return bcast()
+        exc_instance = None
+        try:
+            # All processes have to enter the context
+            # contextlib will throw an error if one does not yield
+            yield
+        except Exception as e:
+            exc_instance = e
+        finally:
+            exception = self.bcast(exc_instance)
+            if exception is not None:
+                raise exception
 
 
 class MPIModule(MockModule):

From 413a0b43d6ae84e48ef4451a9aa9b2ec170a2462 Mon Sep 17 00:00:00 2001
From: drodarie <d.rodarie@gmail.com>
Date: Mon, 19 Jan 2026 13:07:57 +0100
Subject: [PATCH 7/7] fix: implement review feedback

---
 packages/bsb-core/bsb/services/mpi.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/packages/bsb-core/bsb/services/mpi.py b/packages/bsb-core/bsb/services/mpi.py
index 635ba5cc..22e758cd 100644
--- a/packages/bsb-core/bsb/services/mpi.py
+++ b/packages/bsb-core/bsb/services/mpi.py
@@ -93,14 +93,14 @@ def try_all(self, default_exception=None):
             yield
         except Exception as e:
             exc_instance = e
-        finally:
-            exceptions = self.allgather(exc_instance)
-            if any(exceptions):
-                raise (
-                    exceptions[self.get_rank()]
-                    if exceptions[self.get_rank()]
-                    else default_exception
-                )
+
+        exceptions = self.allgather(exc_instance)
+        if any(exceptions):
+            raise (
+                exceptions[self.get_rank()]
+                if exceptions[self.get_rank()]
+                else default_exception
+            )
 
     @contextlib.contextmanager
     def try_main(self):
@@ -120,10 +120,10 @@ def try_main(self):
             yield
         except Exception as e:
             exc_instance = e
-        finally:
-            exception = self.bcast(exc_instance)
-            if exception is not None:
-                raise exception
+
+        exception = self.bcast(exc_instance)
+        if exception is not None:
+            raise exception
 
 
 class MPIModule(MockModule):