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Add test and delete lint errors #61

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7da37a7
clean: remove old notebooks
theodchrn Jan 15, 2026
e381a8e
fix: typos and minor errors in dealing w bayes matrices
theodchrn Jan 15, 2026
9d7d7a7
add: tests and possibility to save and load datasets to tfrec and
theodchrn Feb 4, 2026
840196b
improve: plotting modules
theodchrn Feb 4, 2026
b576664
improve: test units
theodchrn Feb 4, 2026
e5302f4
change global classes behaviour: no need for duplicate in Mouse_Results,
theodchrn Feb 4, 2026
bd17f14
add: possibility to randomize the spikes inside the dataset for control
theodchrn Feb 4, 2026
8c665ad
add: helper function for comparing bayes and ann
theodchrn Feb 4, 2026
84bd76e
add: data helper behaviour without windowsize ms
theodchrn Feb 4, 2026
701805e
fix: lots of typos and ruff linting issues
theodchrn Feb 4, 2026
475d9de
Initial plan
Copilot Feb 5, 2026
8d8a660
Fix review comments: remove debug code, add comments, fix variable na…
Copilot Feb 5, 2026
0f0bbc1
Remove unused variables and rename dir to directory to avoid shadowin…
Copilot Feb 5, 2026
8c9b092
Fix linting issues: remove unused assignment, fix imports, clean up u…
Copilot Feb 5, 2026
4bc80c7
Improve exception handling and variable naming clarity
Copilot Feb 5, 2026
f754b45
Merge pull request #62 from MobsLab/copilot/sub-pr-61
theodchrn Feb 5, 2026
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22 changes: 11 additions & 11 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
@@ -1,25 +1,25 @@
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
hooks:
- id: trailing-whitespace
files: .*.py$
- id: end-of-file-fixer
- id: trailing-whitespace
files: .*.py$
- id: check-yaml
- id: check-added-large-files
- id: check-toml
- id: end-of-file-fixer
files: .*.py$
- id: check-yaml
- id: check-added-large-files
- id: check-toml

- repo: https://github.com/astral-sh/ruff-pre-commit
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.11.8
hooks:
- id: ruff
args: [ --fix, --exit-zero ]
args: [--fix]
- id: ruff-format

- repo: local
- repo: local
hooks:
- id: pytest
- id: pytest
name: pytest
entry: uv run pytest tests/
language: system
Expand Down
127 changes: 58 additions & 69 deletions neuroEncoder
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Original file line number Diff line number Diff line change
Expand Up @@ -245,7 +245,7 @@ def main(args):

# Now that we have the linearization function, we can get the true target
helper.get_true_target(
l_function, in_place=True, show=show_figures, speedMask=True
windowSizeMS, l_function, in_place=True, show=show_figures, speedMask=True
)
Comment on lines 247 to 249
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Copilot AI Feb 4, 2026

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Incorrect function call: The method signature for get_true_target was changed to accept windowSizeMS as the first parameter (line 436-438), but this call doesn't provide it. This will cause a TypeError since windowSizeMS is now a required positional argument. The call should be: helper.get_true_target(windowSizeMS, l_function, in_place=True, show=show_figures, speedMask=True)

Copilot uses AI. Check for mistakes.

Parameters = Params(
Expand Down Expand Up @@ -551,7 +551,7 @@ def main(args):
):
print("Testing sleep set")
# Test sleep as NN
outputs_sleep = TrainerBayes.test_sleep_as_NN(
TrainerBayes.test_sleep_as_NN(
DataHelper.fullBehavior,
bayesMatrices,
windowSizeMS=windowSizeMS,
Expand Down Expand Up @@ -687,9 +687,10 @@ def main(args):
or args.redo
):
num_augmentations = args.num_augmentations
print("num_augmentations", num_augmentations)
if num_augmentations is None:
num_augmentations = 4 if args.window < 0.504 else 2
if Parameters.dataAugmentation:
print("num_augmentations", num_augmentations)
if num_augmentations is None:
num_augmentations = 4 if args.window < 0.504 else 2
NNTrainer.train(
DataHelper.fullBehavior,
windowSizeMS=windowSizeMS,
Expand Down Expand Up @@ -750,22 +751,19 @@ def main(args):
strideFactor=strideFactor,
extract_spikes_counts=True,
)
try:
print_results.print_results(
NNTrainer.folderResult,
windowSizeMS=windowSizeMS,
show=show_figures,
lossSelection=0.5,
euclidean=False,
target=args.target,
phase="training",
useSpeedMask=True,
training_data=NNTrainer.training_data,
force=args.redo,
l_function=l_function,
)
except:
pass
print_results.print_results(
NNTrainer.folderResult,
windowSizeMS=windowSizeMS,
show=show_figures,
lossSelection=0.5,
euclidean=False,
target=args.target,
phase="training",
useSpeedMask=True,
training_data=NNTrainer.training_data,
force=args.redo,
l_function=l_function,
)

if (
not os.path.exists(
Expand All @@ -792,22 +790,19 @@ def main(args):
strideFactor=strideFactor,
extract_spikes_counts=True,
)
try:
print_results.print_results(
NNTrainer.folderResult,
windowSizeMS=windowSizeMS,
show=show_figures,
lossSelection=0.5,
euclidean=False,
force=args.redo,
target=args.target,
phase=args.phase,
training_data=NNTrainer.training_data,
useSpeedMask=True,
l_function=l_function,
)
except:
pass
print_results.print_results(
NNTrainer.folderResult,
windowSizeMS=windowSizeMS,
show=show_figures,
lossSelection=0.5,
euclidean=False,
force=args.redo,
target=args.target,
phase=args.phase,
training_data=NNTrainer.training_data,
useSpeedMask=True,
l_function=l_function,
)

if (
not os.path.exists(
Expand All @@ -834,22 +829,19 @@ def main(args):
extract_spikes_counts=True,
)

try:
print_results.print_results(
NNTrainer.folderResult,
windowSizeMS=windowSizeMS,
show=show_figures,
lossSelection=0.5,
euclidean=False,
target=args.target,
phase="cond",
training_data=NNTrainer.training_data,
useSpeedMask=True,
l_function=l_function,
force=args.redo,
)
except:
pass
print_results.print_results(
NNTrainer.folderResult,
windowSizeMS=windowSizeMS,
show=show_figures,
lossSelection=0.5,
euclidean=False,
target=args.target,
phase="cond",
training_data=NNTrainer.training_data,
useSpeedMask=True,
l_function=l_function,
force=args.redo,
)

if (
not os.path.exists(
Expand All @@ -876,22 +868,19 @@ def main(args):
extract_spikes_counts=True,
)

try:
print_results.print_results(
NNTrainer.folderResult,
windowSizeMS=windowSizeMS,
show=show_figures,
lossSelection=0.5,
euclidean=False,
target=args.target,
phase="post",
training_data=NNTrainer.training_data,
useSpeedMask=True,
l_function=l_function,
force=args.redo,
)
except:
pass
print_results.print_results(
NNTrainer.folderResult,
windowSizeMS=windowSizeMS,
show=show_figures,
lossSelection=0.5,
euclidean=False,
target=args.target,
phase="post",
training_data=NNTrainer.training_data,
useSpeedMask=True,
l_function=l_function,
force=args.redo,
)

if args.test_sleep and (
not os.path.exists(
Expand Down
30 changes: 22 additions & 8 deletions neuroencoders/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,12 +22,26 @@
__version__ = "0.0.0" # fallback if not installed

from . import (
decoder,
fullEncoder,
importData,
openEphysExport,
resultAnalysis,
simpleBayes,
transformData,
utils,
decoder as decoder,
)
from . import (
fullEncoder as fullEncoder,
)
from . import (
importData as importData,
)
from . import (
openEphysExport as openEphysExport,
)
from . import (
resultAnalysis as resultAnalysis,
)
from . import (
simpleBayes as simpleBayes,
)
from . import (
transformData as transformData,
)
from . import (
utils as utils,
)
4 changes: 2 additions & 2 deletions neuroencoders/decoder/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,5 @@
- Decoder (from decode)
"""

from . import decode
from .decode import Decoder
from . import decode as decode
from .decode import Decoder as Decoder
4 changes: 2 additions & 2 deletions neuroencoders/fullEncoder/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,5 @@
- an_network (module containing neural network architectures)
"""

from . import an_network
from .an_network import LSTMandSpikeNetwork
from . import an_network as an_network
from .an_network import LSTMandSpikeNetwork as LSTMandSpikeNetwork
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