docs: New documentation #858

filimarc · 2024-06-26T13:33:42Z

Describe the work done

Update documentation to BSB versions 4.x
Fix BSB CLI

Issues related

Close #904 #897

Tasks

Updated documentation
Add tests for projects

📚 Documentation preview 📚: https://bsb--858.org.readthedocs.build/en/858/

Helveg

All of the proposed changes contain somewhat broken English ❤️ Can you run it through chatgpt to correct your modifications?

docs/connectivity/defining.rst

Helveg · 2024-07-15T17:48:33Z

Oh, also please either fill out the PR description, or remove the template. You linked issues 1, 2 and 3 ;)

Helveg

@filimarc run all these sentences through ChatGPT asking it to correct spelling, grammar, and to align the writing style with technical writing for technical documentation.

docs/getting-started/getting-started.rst

docs/getting-started/include_morphos.rst

docs/morphologies/intro.rst

docs/placement/intro.rst

docs/placement/placement-strategies.rst

docs/topology/partitions.rst

docs/topology/regions.rst

docs/placement/intro.rst

codecov · 2024-09-16T10:09:58Z

Codecov Report

Attention: Patch coverage is 55.88235% with 15 lines in your changes missing coverage. Please review.

Project coverage is 89.06%. Comparing base (ab77c6f) to head (047f1f5).
Report is 8 commits behind head on main.

Files with missing lines	Patch %	Lines
bsb/cli/commands/_commands.py	40.00%	6 Missing ⚠️
bsb/config/_distributions.py	50.00%	5 Missing ⚠️
bsb/topology/partition.py	33.33%	2 Missing ⚠️
bsb/cli/commands/_projects.py	0.00%	1 Missing ⚠️
bsb/placement/indicator.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #858      +/-   ##
==========================================
- Coverage   89.09%   89.06%   -0.03%     
==========================================
  Files         110      110              
  Lines       15164    15231      +67     
==========================================
+ Hits        13510    13566      +56     
- Misses       1654     1665      +11

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

merge python projects in getting started and move the rest to dev.

drodarie · 2024-11-14T15:22:09Z

We should start a new batch of review right away since there are a lot to check and we would like to merge it as soon as possible as new users will probably use the tool soon (Erice school).

move images in the images folder. The morphology and python stellate model should be removed from the repo when they will be available on the dbbs models public repo.

fix and comment distrib_placement.py

Make analysis more uniform

…d placement

May be sufficient for dbbs-lab/bsb-nest#13

split copy_configuration_template into two functions.

Helveg

I still had this pending :)

Helveg · 2024-12-29T14:56:43Z

bsb/cli/commands/_commands.py

@@ -222,7 +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")
+        parser.add_argument("-o", "--output_folder")


Suggested change

parser.add_argument("-o", "--output_folder")

parser.add_argument("-o", "--output-folder")

I think the CLI is kebab cased

Helveg · 2024-12-29T14:57:19Z

bsb/config/_distributions.py

    parameters: dict[str, typing.Any] = config.catch_all(type=types.any_())
+    """parameters to pass to the distribution"""


Suggested change

"""parameters to pass to the distribution"""

"""Parameters to pass to the distribution"""

Helveg · 2024-12-29T15:04:53Z

bsb/core.py

@@ -778,7 +796,7 @@ 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 an xterm is emulated.
+            # (e.g. MPI sets it to 0x0 unless a xterm is emulated.


It is "an xterm," because the choice between "a" and "an" depends on the sound that follows, not the written letter. Since "xterm" is pronounced with an initial vowel sound ("exterm"), "an" is correct.

Helveg · 2024-12-29T15:07:13Z

bsb/mixins.py

+    Parameters
+    ----------


That's not part of the docstring syntax we use

Helveg · 2024-12-29T15:47:34Z

bsb/morphologies/selector.py

@@ -82,7 +82,7 @@ def pick(self, morphology):

 @config.node
 class NeuroMorphoSelector(NameSelector, classmap_entry="from_neuromorpho"):
-    _url = "https://neuromorpho.org/"
+    _url = "http://cng.gmu.edu:8080/neuroMorpho/"  # "https://neuromorpho.org/"


Why did you change this? neuromorpho.org still seems to be working?

Helveg · 2024-12-29T16:28:19Z

docs/components/components.rst


-.. rubric:: Parametrization
+For each component, BSB provides interfaces, each with a set of functions that you must


Suggested change

For each component, BSB provides interfaces, each with a set of functions that you must

For each component, the BSB provides interfaces, each with a set of functions that you must

Helveg · 2024-12-29T16:29:08Z

docs/components/components.rst


-.. rubric:: Parametrization
+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.


Suggested change

implement. If these functions are present, the framework knows how to use your class.

implement. By implementing these functions the framework can seamlessly integrate your custom components

into a BSB workflow. Neat!

Helveg · 2024-12-29T16:31:26Z

docs/components/components.rst


-Parameters defined as class attributes --> can be specified in config/init. Make things
-explicitly visible and settable.
+Hence, the framework allows you to plug in user code pretty much anywhere. Neat.


Suggested change

Hence, the framework allows you to plug in user code pretty much anywhere. Neat.

Helveg · 2024-12-29T16:32:41Z

docs/conf.py

@@ -79,6 +79,7 @@
    "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),


Why ref itself?

Helveg · 2024-12-29T16:35:51Z

docs/config/nodes.rst

-        print("We only store referrers coming from a .square configuration attribute")
-
-todo: Mention ``pop_unique``
-


Where did all this go?

filimarc and others added 8 commits February 28, 2024 12:09

Renew placement documentation

1a8b541

Renew Connectivity docs

c95f4b1

Renew region and partition doc

63f1e8c

Merge branch 'main' into New_docs

8c580b6

Merge remote-tracking branch 'origin/main' into New_docs

dd172c1

Fix deprecated setup-python@v1

8921ac5

Merge branch 'main' into New_docs

d70c538

Remove outdated strategies

4cec130

Helveg requested changes Jul 2, 2024

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docs/connectivity/defining.rst Show resolved Hide resolved

Merge branch 'main' into New_docs

f7a425c

filimarc marked this pull request as draft July 15, 2024 14:14

Merge branch 'main' into New_docs

846934e

Helveg requested changes Jul 31, 2024

View reviewed changes

filimarc added 2 commits August 6, 2024 16:00

docs: Update connectivity documentation

592c20b

docs: Improve english

adca741

Helveg reviewed Aug 8, 2024

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Helveg reviewed Aug 8, 2024

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Helveg reviewed Aug 8, 2024

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filimarc and others added 8 commits August 9, 2024 10:36

docs: fix doc refs and initialisms

fc662cf

docs: update placement documentation

95c80ec

docs: add note for packing error

01136c8

docs: update cell types documentation

f77e952

docs: small updates to partition

5cdc0d4

docs: Add getting started for Simulations

73896b9

docs: Update Simulation intro page

168d0c5

docs: update simulation

c9a7170

filimarc changed the title ~~New documentation~~ docs: New documentation Sep 16, 2024

drodarie and others added 7 commits November 7, 2024 10:33

docs: Fix some typos and config for nest simulation tutorial.

047f1f5

docs: separate neuron and nest tutorials.

3044916

merge python projects in getting started and move the rest to dev.

docs: simplify the placement class for the tutorial

2438b79

docs: add missing nest config

1920d9c

docs: add tutorial-template files for NEURON sim | update gs

157401e

docs: Update neuron simulation guide

f54ffa3

docs: Add section for analyze neuron results | update neuron parts of gs

3b547b2

drodarie requested a review from Helveg November 14, 2024 15:20

drodarie and others added 12 commits November 19, 2024 19:55

docs: WIP on guide for neuron simulation

4986e73

move images in the images folder. The morphology and python stellate model should be removed from the repo when they will be available on the dbbs models public repo.

docs: fix naming in neuron gs

0919db7

docs: fix ref number in neuron gs

b42a978

docs: add section for simulation results

edc7a43

docs: fix guide neurons json indent and lines

45752c6

docs: Add explanation on distribution placement.

78be5e7

fix and comment distrib_placement.py

docs: Rework guides for simulations

11da986

Make analysis more uniform

docs: simplify writing components tutorial by splitting connection an…

8e4001d

…d placement

docs: Add FAQ for BSB-MUSIC related issue

1961dc4

May be sufficient for dbbs-lab/bsb-nest#13

docs: fix strategy in yaml gs

5d8ec80

docs: Add figures and rewrite scaffold page.

90fbd3f

docs: Improve documentation on parallelization + minor fixes

43991f2

filimarc marked this pull request as ready for review December 10, 2024 13:34

drodarie mentioned this pull request Dec 28, 2024

Error: Undefined Function 'copy_template()' in CLI Command 'bsb new' Causes Project Creation Failure #904

Closed

drodarie added 3 commits December 28, 2024 16:19

test: add tests for bsb new

17e27eb

split copy_configuration_template into two functions.

fix: add bsb-json dependencies for bsb project tests

d51b0ac

Merge branch 'main' into New_docs

07e30cc

drodarie merged commit 462fe9a into main Jan 7, 2025
10 checks passed

drodarie deleted the New_docs branch January 7, 2025 08:06

Helveg reviewed Jan 7, 2025

View reviewed changes

drodarie mentioned this pull request Jan 7, 2025

fix: Implement feedback on new docs #905

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docs: New documentation #858

docs: New documentation #858

filimarc commented Jun 26, 2024 •

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	parser.add_argument("-o", "--output_folder")
	parser.add_argument("-o", "--output-folder")

		parameters: dict[str, typing.Any] = config.catch_all(type=types.any_())
		"""parameters to pass to the distribution"""


		.. rubric:: Parametrization
		For each component, BSB provides interfaces, each with a set of functions that you must

	For each component, BSB provides interfaces, each with a set of functions that you must
	For each component, the 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.
	implement. By implementing these functions the framework can seamlessly integrate your custom components
	into a BSB workflow. Neat!

		print("We only store referrers coming from a .square configuration attribute")

		todo: Mention ``pop_unique``

docs: New documentation #858

docs: New documentation #858

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filimarc commented Jun 26, 2024 • edited by github-actions bot Loading

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filimarc commented Jun 26, 2024 •

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codecov bot commented Sep 16, 2024 •

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