fix: CLI bsb simulate command (#909)

* fix: BSB simulate output flag. Update acknowledgements

* docs: update bsb simulate command docs

* fix: readthedocs config

Author: drodarie

.readthedocs.yml

@@ -1,5 +1,9 @@
 version: 2
 
+sphinx:
+  # Path to your Sphinx configuration file.
+  configuration: docs/conf.py
+
 build:
   os: ubuntu-22.04
   tools:

README.md

@@ -98,7 +98,16 @@ Take a look at the [contribution guide](CONTRIBUTING.md)
 This research has received funding from the European Union’s Horizon 2020 Framework
 Program for Research and Innovation under the Specific Grant Agreement No. 945539
 (Human Brain Project SGA3) and Specific Grant Agreement No. 785907 (Human Brain
-Project SGA2) and from Centro Fermi project “Local Neuronal Microcircuits” to ED. We
-acknowledge the use of EBRAINS platform and Fenix Infrastructure resources, which are
+Project SGA2) and from Centro Fermi project “Local Neuronal Microcircuits” to ED. 
+The project is also receiving funding from the Virtual Brain Twin Project under the 
+European Union's Research and Innovation Program Horizon Europe under grant agreement 
+No 101137289. 
+
+We acknowledge the use of EBRAINS platform and Fenix Infrastructure resources, which are
 partially funded from the European Union’s Horizon 2020 research and innovation
-programme through the ICEI project under the grant agreement No. 800858
+programme under the Specific Grant Agreement No. 101147319 (EBRAINS 2.0 Project) and 
+through the ICEI project under the grant agreement No. 800858 respectively.
+
+## Supported by
+
+[![JetBrains logo](https://resources.jetbrains.com/storage/products/company/brand/logos/jetbrains.svg)](https://jb.gg/OpenSourceSupport)

bsb/cli/commands/_commands.py

@@ -207,7 +207,7 @@ def handler(self, context):
             for name, sim in extra_simulations.items():
                 if name not in network.simulations and name == sim_name:
                     network.simulations[sim_name] = sim
-        root = pathlib.Path(getattr(context.arguments, "output-folder", "./"))
+        root = pathlib.Path(getattr(context.arguments, "output_folder", "./"))
         if not root.is_dir() or not os.access(root, os.W_OK):
             return report(
                 f"Output provided '{root.absolute()}' is not an existing directory with write access.",

docs/cli/commands.rst

@@ -114,6 +114,12 @@ Run a simulation from a compiled network architecture.
 * ``path/to/netw.hdf5``: Path to the network file.
 * ``sim-name``: Name of the simulation.
 
+.. rubric:: Flags
+
+* ``-o``, ``--output-folder``: Output the simulation results to an existing folder.
+  If omitted, the current folder is used.
+
+
 .. _bsb_cache:
 
 Check the global cache