Refactor code for python package by babsey · Pull Request #18 · INM-6/human-multi-area-model

babsey · 2025-03-17T13:29:58Z

Refactoring Summary

This pull request implements a major reorganization of the repository to improve code structure, modularity, and maintainability. The main changes are:

Python Package Structure:
All core simulation and analysis code is now structured as a Python package under src/humam/. This includes classes for network setup, simulation, and analysis, as well as parameter definitions and auxiliary scripts. Submodules are introduced for parameters, data loading, preprocessing, helpers, figures, theory, and workflow automation.
Separation of Publication Scripts:
Scripts specifically used to generate figures for the publication have been moved to misc/publication_figures/, clearly separating them from the core simulation code.
Jupyter Notebook Updates:
The main tutorial notebook (humam_tutorial.ipynb) has been updated to import from the new humam package, using consistent and clear import paths.
Workflow and File Organization:
Snakemake workflow scripts are now located under src/humam/snakemake/. The Snakefile and other workflow definitions have been updated accordingly.
.gitignore and documentation files (README.md, misc/README.md) are updated to reflect the new structure.
General Cleanup:
Redundant scripts and files are either moved to appropriate subdirectories or removed. The overall repository layout is clarified, with directory structures and file responsibilities now better documented.

These changes enable easier installation and usage as a Python package, and clarify the distinction between reusable simulation tools and manuscript-specific scripts.

…into pyproject

…toE parameter

Correct bug on the parameter definition in the jupyter notebook tutorial

…into pyproject

humam_tutorial.ipynb

terhorstd

LGTM

terhorstd

Appologies, clicked the wrong accept button...

approval was only for the visible subset of the last change

README.md

terhorstd · 2025-05-19T08:20:43Z

This is getting quite a big PR. Could you add a description at the top to summarize in a few bullet-points what needed to change? Not the technical details, but structurally where things can be found after the merge, or which dev-features were added.

shimoura · 2025-06-10T12:42:18Z

This is getting quite a big PR. Could you add a description at the top to summarize in a few bullet-points what needed to change? Not the technical details, but structurally where things can be found after the merge, or which dev-features were added.

I added a description to this PR. Check if you agree @babsey

shimoura

I believe it is all fine for me, only check the last changes I included, please. @babsey

README.md

babsey · 2025-06-25T06:58:41Z

The PR description looks fine to me. Thanks @shimoura !

babsey · 2025-09-08T08:40:27Z

@terhorstd friendly reminder!

babsey · 2025-10-31T10:20:58Z

@terhorstd Friendly reminder for the review.

I would like to test the offical HUMAM package for NEST Desktop before Hackathon in December.

terhorstd

Mostly code-quality comments. Consider using tools like isort, black, flake8, mypy, etc.

terhorstd · 2025-08-19T08:42:30Z

README.md

-6. Congratulations! Now you can run the model. Enjoy!<br> To run the model, click the `Run` on the title bar and choose `Run All Cells`. It takes several minutes until you get all results.<br>
-**Please note**: every time you click the `Try it on EBRAINS` button, the repository is loaded into your home directory on EBRAINS Lab and it overrides your old repository with the same name. Therefore, make sure you follow the [Fork the repository and save your changes](#fork-the-repository-and-save-your-changes) if you make changes and want to save them.
+3. If you’re using EBRAINS for the first time, click `Sign in with GenericOAuth2` to sign in on EBRAINS. To do this, you
+need an EBRAINS account.


Suggested change

need an EBRAINS account.

need an [EBRAINS account](https://ebrains.eu/register).

terhorstd · 2025-08-19T08:48:18Z

README.md


 #### Try it on EBRAINS
-1. Click [Try it on EBRAINS](https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FINM-6%2Fhuman-multi-area-model.git&urlpath=lab%2Ftree%2Fhuman-multi-area-model.git%2Fhumam_tutorial.ipynb&branch=main). If any error or unexpected happens during the following process, please close the browser tab and restart the [User instruction](https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fshimoura%2Fhuman-multi-area-model.git&urlpath=lab%2Ftree%2Fhuman-multi-area-model.git%2Fhumam_tutorial.ipynb&branch=add-downscaling-factor) process again.
+1. Click [Try it on EBRAINS](https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FINM-6%2Fhuman-multi-area-model.git&urlpath=lab%2Ftree%2Fhuman-multi-area-model.git%2Fhumam_tutorial.ipynb&branch=main). If any error or unexpected happens during the following process, please close the browser tab and restart the 


This is fine for main, but remember to put a note in your release process to change the branch=main to the release tag once you split of a release candidate branch.

terhorstd · 2025-12-03T15:26:15Z

src/humam/data_preprocessing/__init__.py

@@ -0,0 +1 @@
+from . import connectivity, cytoarchitecture


Check if this could better be

Suggested change

from . import connectivity, cytoarchitecture

__all__ = ["connectivity", "cytoarchitecture"]

src/humam/data_preprocessing/connectivity.py

terhorstd · 2025-12-03T15:28:26Z

src/humam/data_preprocessing/connectivity.py

        N_syn_ext : DataFrame
            Population resolved internal syapse numbers.
        """
+        from itertools import product


Import not at top of file.

terhorstd · 2025-12-03T15:44:24Z

src/humam/network.py

+    import os
+    import yaml
+    import pandas as pd
+


Import not at top of file.

terhorstd · 2025-12-03T15:44:46Z

src/humam/simulation.py

+        from datetime import datetime
+


Import not at top of file.

terhorstd · 2025-12-03T15:45:11Z

src/humam/simulation.py

+        from dicthash import dicthash
+


Import not at top of file.

terhorstd · 2025-12-03T15:45:30Z

src/humam/simulation.py

+        import yaml
+


Import not at top of file.

terhorstd · 2025-12-03T15:45:46Z

src/humam/simulation.py

+    import os
+    import yaml
+


Import not at top of file.

Add pre-commit validation

Co-authored-by: Dennis Terhorst <terhorstd@users.noreply.github.com>

babsey added 20 commits March 7, 2025 11:50

Add pyproject.toml and update src

7619537

Add .egg-info to .gitignore

6829604

Refactor code for pyproject

bfdc6d3

Update pyproject and requirements

ad44300

Update tutorial

4921250

Update gitignore

6fa7593

Update Snakefile

9ceab48

Deepcopy of default params

b8e2d10

Update tutorial

0b6da52

Add pyproject.toml and update src

b5d6738

Add .egg-info to .gitignore

cc7606e

Refactor code for pyproject

7804d66

Update pyproject and requirements

09e7382

Update tutorial

e929a3c

Update gitignore

e87b9dc

Update Snakefile

47a998e

Deepcopy of default params

b6ae0ca

Update tutorial

98c223d

Merge branch 'pyproject' of github.com:babsey/human-multi-area-model …

86c48da

…into pyproject

Update tutorial

4cf15da

babsey requested a review from shimoura March 17, 2025 13:29

babsey and others added 7 commits March 17, 2025 15:21

Bump version

a840bfd

Update classifiers in pyproject

ba454cd

Fix imports in init files

c1ff534

solve bug on notebook tutorial, correct the definition of cc_scalingE…

7ac2722

…toE parameter

Merge pull request INM-6#19 from shimoura/enhance-notebook-tutorial

f9956c0

Correct bug on the parameter definition in the jupyter notebook tutorial

Pack it for pypi

35b0eb6

Merge branch 'pyproject' of github.com:babsey/human-multi-area-model …

8b5bd0d

…into pyproject

terhorstd reviewed Mar 24, 2025

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terhorstd reviewed Mar 24, 2025

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babsey added 3 commits May 6, 2025 11:46

Fix reqs

3ef5d5b

Merge gitignore

5d900a4

Clean authors

e745aa4

terhorstd previously approved these changes May 6, 2025

View reviewed changes

terhorstd reviewed May 6, 2025

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terhorstd self-requested a review May 6, 2025 16:31

Update directory paths in main README file

00324d7

shimoura reviewed May 7, 2025

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README.md Outdated Show resolved Hide resolved

babsey added 4 commits May 9, 2025 17:43

Add build-system in pyproject

6e4d863

Try to get version

cca2782

Add EOF

4fa9751

Fix __init__

3671665

shimoura added 2 commits June 10, 2025 17:32

Update installation instructions in main README and in related files

0425da9

Remove unnecessary dependencies from humam.yml

cce9e63

shimoura approved these changes Jun 10, 2025

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README.md Show resolved Hide resolved

terhorstd requested changes Dec 3, 2025

View reviewed changes

babsey and others added 8 commits December 4, 2025 16:04

Add pre-commit configs

1607052

Run pre-commit

dbfd253

Fix invalid escape sequence

dc223cc

Fix flake8 failed validations.

9297338

Fix README

8bd8dc6

Merge pull request #1 from babsey/pre-commit

f024831

Add pre-commit validation

Apply suggestions from code review

13de6ae

Co-authored-by: Dennis Terhorst <terhorstd@users.noreply.github.com>

Apply code-suggestion and use pre-commit

ba86966

	need an EBRAINS account.
	need an [EBRAINS account](https://ebrains.eu/register).

	from . import connectivity, cytoarchitecture
	__all__ = ["connectivity", "cytoarchitecture"]

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babsey commented Mar 17, 2025 • edited by shimoura Loading Uh oh! There was an error while loading. Please reload this page.

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terhorstd commented May 19, 2025

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babsey commented Mar 17, 2025 •

edited by shimoura

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