diff --git a/README.md b/README.md index 5369f0a2..ab38c910 100644 --- a/README.md +++ b/README.md @@ -71,10 +71,10 @@ You can use your project to create reconstructions of your model, generating cel and connections: ``` -bsb compile -p +bsb compile ``` -This creates a [network file](bsb.readthedocs.io/getting-started/networks.html) and plots the network. +This creates a network file. ### Simulating a network diff --git a/bsb/cli/commands/_commands.py b/bsb/cli/commands/_commands.py index d60ea956..97d911c2 100644 --- a/bsb/cli/commands/_commands.py +++ b/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.", @@ -231,7 +231,7 @@ def get_options(self): def add_parser_arguments(self, parser): parser.add_argument("network") parser.add_argument("simulation") - parser.add_argument("-o", "--output_folder") + parser.add_argument("-o", "--output-folder") class CacheCommand(BaseCommand, name="cache"): # pragma: nocover diff --git a/bsb/config/_distributions.py b/bsb/config/_distributions.py index dffe1aa1..63e35274 100644 --- a/bsb/config/_distributions.py +++ b/bsb/config/_distributions.py @@ -29,7 +29,7 @@ class Distribution: ) """Name of the scipy.stats distribution function""" parameters: dict[str, typing.Any] = config.catch_all(type=types.any_()) - """parameters to pass to the distribution""" + """Parameters to pass to the distribution""" def __init__(self, **kwargs): if self.distribution == "constant": diff --git a/bsb/core.py b/bsb/core.py index 1dcf9e79..7b9e0c6c 100644 --- a/bsb/core.py +++ b/bsb/core.py @@ -795,7 +795,7 @@ def create_job_pool(self, fail_fast=None, quiet=False): ) try: # Check whether stdout is a TTY, and that it is larger than 0x0 - # (e.g. MPI sets it to 0x0 unless a xterm is emulated. + # (e.g. MPI sets it to 0x0 unless an xterm is emulated). tty = os.isatty(sys.stdout.fileno()) and sum(os.get_terminal_size()) except Exception: tty = False diff --git a/bsb/mixins.py b/bsb/mixins.py index e6c65baa..6f5275bc 100644 --- a/bsb/mixins.py +++ b/bsb/mixins.py @@ -27,11 +27,10 @@ def _all_chunks(iter_): def _queue_connectivity(self, pool: "JobPool"): - """Get the queued jobs of all the strategies we depend on. + """ + Get the queued jobs of all the strategies we depend on. - Parameters - ---------- - param pool : pool where the jobs will be queued + param pool: pool where the jobs will be queued type pool: bsb.services.pool.JobPool """ deps = set(_gutil.ichain(pool.get_submissions_of(strat) for strat in self.get_deps())) diff --git a/docs/cells/intro.rst b/docs/cells/intro.rst index 3f0e6d04..ed83a834 100644 --- a/docs/cells/intro.rst +++ b/docs/cells/intro.rst @@ -48,7 +48,7 @@ The :guilabel:`plotting` block allows you to specify formatting details. .. rubric:: Specifying spatial density You can set the spatial distribution for each cell type present in a -:ref:`NrrdVoxels ` partition. +:ref:`NrrdVoxels ` partition. To do so, you should first attach your nrrd volumetric density file(s) to the partition with either the :guilabel:`source` or :guilabel:`sources` blocks. diff --git a/docs/components/components.rst b/docs/components/components.rst index 8e5d8031..31279ec3 100644 --- a/docs/components/components.rst +++ b/docs/components/components.rst @@ -10,10 +10,9 @@ out of the box components for basic operations, but often you'll need to write y If you want to read a step by step tutorial on how to make your own component, check this :doc:`page ` -For each component, BSB provides interfaces, each with a set of functions that you must -implement. If these functions are present, the framework knows how to use your class. - -Hence, the framework allows you to plug in user code pretty much anywhere. Neat. +For each component, the BSB provides interfaces, each with a set of functions that you must +implement. By implementing these functions are present, the framework can seamlessly integrate +your custom components. Here is how you do it (theoretically): diff --git a/docs/conf.py b/docs/conf.py index 1aff02d8..880b55b9 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -79,7 +79,6 @@ "mpi4py": ("https://mpi4py.readthedocs.io/en/stable/", None), "arbor": ("https://docs.arbor-sim.org/en/latest/", None), "neo": ("https://neo.readthedocs.io/en/latest/", None), - "bsb": ("https://bsb.readthedocs.io/en/latest", None), } # Add any paths that contain templates here, relative to this directory.