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[BBPBGLIB-1125] GH forkflow for building a wheel #121

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merged 45 commits into from
Mar 11, 2024
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@atemerev atemerev commented Feb 6, 2024

Context

Build and upload a PyPI wheel

Scope

New Github actions workflow

Testing

Should see if it works with Github actions

Review

  • PR description is complete
  • Coding style (imports, function length, New functions, classes or files) are good
  • [N/A] Unit/Scientific test added
  • [N/A] Updated Readme, in-code, developer documentation

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WeinaJi and others added 6 commits February 13, 2024 16:29
## Context
After deprecating BlueConfig files, we no longer support legacy node
format, MVD3 or NCS. Therefore, this PR removes the corresponding node
loaders.

## Scope
In `cell_reader.py`: keeping only `load_sonata` and removing the other
readers.
In `metype.py`: removing `Cell_V5`.


## Testing
Adapt the current unit tests to use SONATA nodes.

## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or
files) are good
* [x] Unit/Scientific test added
* [x] Updated Readme, in-code, developer documentation
## Context
Addresses BBPBGLIB-1124.
Removes code related to hoc targets, as well as the need of using a hoc
TargetManager.

## Scope
Few functions were implemented in the python Targetmanager in order to
remove the hoc version:
getMETypes(), getPointList() and location_to_point()

## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or
files) are good
* [ ] Unit/Scientific test added
* [ ] Updated Readme, in-code, developer documentation
## Context
After removing BlueConfig, we only support SONATA edges files loaded via
`libsonata` API. This PR removes the synpase loaders that were used to
support non-SONATA files.

## Scope
Remove `SynapseReader.mod`. 
In `synapse_reader.py`, remove class `SynReaderNRN` which was used to
load non-SONATA .h5 files via `HDF5Reader`.

## Testing
Remove the test for `SynReaderNRN`

## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or
files) are good
* [ ] Unit/Scientific test added
* [x] Updated Readme, in-code, developer documentation
…th errors (#120)

## Context

In the simulation config, synapse_configure contains HOC code.
Neurodamus should fail fast when there is an error in configuration,
instead of passing it forward.

## Scope

Error check is added to connection.py

## Testing

TBD

## Review
* [X] PR description is complete
* [X] Coding style (imports, function length, New functions, classes or
files) are good
* [x] Unit/Scientific test added
* [N/A] Updated Readme, in-code, developer documentation
## Context
After the deprecation of BlueConfig files, out.dat is not generated
anymore.
Remove the SpikeWriter mod file and the code that was handling the old
out.dat spike file.

## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or
files) are good
* [ ] Unit/Scientific test added
* [ ] Updated Readme, in-code, developer documentation
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@atemerev atemerev closed this Feb 29, 2024
@atemerev atemerev reopened this Feb 29, 2024
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@WeinaJi WeinaJi linked an issue Mar 7, 2024 that may be closed by this pull request
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@WeinaJi WeinaJi requested a review from jorblancoa March 8, 2024 10:13
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WeinaJi commented Mar 8, 2024

looks good to me. @jorblancoa , can you also have a look ?

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looks good to me also!

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@atemerev atemerev merged commit 64b73fd into main Mar 11, 2024
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@atemerev atemerev deleted the atemerev/pypi-publish branch March 11, 2024 12:11
WeinaJi added a commit that referenced this pull request Oct 14, 2024
## Context

Build and upload a PyPI wheel

## Scope

New Github actions workflow

## Testing

Should see if it works with Github actions

## Review
* [X] PR description is complete
* [X] Coding style (imports, function length, New functions, classes or
files) are good
* [N/A] Unit/Scientific test added
* [N/A] Updated Readme, in-code, developer documentation

---------

Co-authored-by: WeinaJi <weina.ji@epfl.ch>
Co-authored-by: Jorge Blanco Alonso <41900536+jorblancoa@users.noreply.github.com>
Co-authored-by: Erik Heeren <erik.heeren@epfl.ch>
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Provide neurodamus package on PyPI
6 participants