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[MAINT] Fixing Unit Tests for Python 3.11 and 3.12 support #800

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merged 9 commits into from
Jun 27, 2024
Merged

[MAINT] Fixing Unit Tests for Python 3.11 and 3.12 support #800

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3b13c41
MAINT: Fixing regex matching in tests files
kmilo9999 Jun 21, 2024
cc2ef7d
MAINT: Added python 3.11 to workflow
kmilo9999 Jun 22, 2024
1e5efee
MAINT: temporarely adding the new AttributeError message
kmilo9999 Jun 24, 2024
d73eb27
TST: Fixing reg expressions for python 3.11+
kmilo9999 Jun 25, 2024
e4c406d
STY: Fixing flake8 errors in hnn_core/tests/test_extracellular.py
kmilo9999 Jun 25, 2024
c9f0ca5
MAINT: Added python 3.12 to unit tests
kmilo9999 Jun 25, 2024
d975341
STY: Fixed flake8 errors for python 3.12
kmilo9999 Jun 25, 2024
171d827
TST: Removing python 3.9 and 3.10 form workflow matrix
kmilo9999 Jun 25, 2024
fff005d
STY: fixed flake8 erross
kmilo9999 Jun 25, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/unix_unit_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
strategy:
matrix:
os: [ubuntu-latest,macos-latest]
python-version: [3.8, 3.9, '3.10']
python-version: [3.8, 3.9, '3.10', 3.11, 3.12]
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Suggested change
python-version: [3.8, 3.9, '3.10', 3.11, 3.12]
python-version: [3.8, 3.11, 3.12]

Really great work getting this working @kmilo9999!

As per our discussion, I think these will be the versions we stick with for now. Definitely will be keeping in mind the idea of having a separate branch for testing the full matrix in the future

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@gtdang gtdang Jun 25, 2024 •
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Ah nice catch. I was discussing with a colleague that one possibility is to have a separate full-matrix workflow that tests the main branch as a cron job. You can set up a workflow to run on a monthly or 2-week basis or something.

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Should I remove 3.9 and 3.10 from the windows workflow too?

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Yes

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Done


steps:
- uses: actions/checkout@v4
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2 changes: 1 addition & 1 deletion .github/workflows/windows_unit_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ jobs:
strategy:
matrix:
os: [windows-latest]
python-version: [3.8, 3.9, '3.10']
python-version: [3.8, 3.9, '3.10', 3.11, 3.12]

steps:
- uses: actions/checkout@v4
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16 changes: 8 additions & 8 deletions hnn_core/gui/gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -156,18 +156,18 @@ def __init__(self, theme_color="#8A2BE2",
"btn_full_w": Layout(height=f"{button_height}px", width='100%'),
"del_fig_btn": Layout(height=f"{button_height}px", width='auto'),
"log_out": Layout(border='1px solid gray',
height=f"{log_window_height-10}px",
height=f"{log_window_height - 10}px",
overflow='auto'),
"viz_config": Layout(width='99%'),
"simulations_list": Layout(width=f'{left_sidebar_width-50}px'),
"simulations_list": Layout(width=f'{left_sidebar_width - 50}px'),
"visualization_window": Layout(
width=f"{viz_win_width-10}px",
height=f"{main_content_height-10}px",
width=f"{viz_win_width - 10}px",
height=f"{main_content_height - 10}px",
border='1px solid gray',
overflow='scroll'),
"visualization_output": Layout(
width=f"{viz_win_width-50}px",
height=f"{main_content_height-100}px",
width=f"{viz_win_width - 50}px",
height=f"{main_content_height - 100}px",
border='1px solid gray',
overflow='scroll'),
"left_sidebar": Layout(width=f"{left_sidebar_width}px",
Expand All @@ -179,7 +179,7 @@ def __init__(self, theme_color="#8A2BE2",
flex_wrap="wrap",
),
"config_box": Layout(width=f"{left_sidebar_width}px",
height=f"{config_box_height-100}px"),
height=f"{config_box_height - 100}px"),
"drive_widget": Layout(width="auto"),
"drive_textbox": Layout(width='270px', height='auto'),
# simulation status related
Expand Down Expand Up @@ -1566,7 +1566,7 @@ def _create_zip(csv_data_list, simulation_name):
with io.BytesIO() as zip_buffer:
with zipfile.ZipFile(zip_buffer, 'w', zipfile.ZIP_DEFLATED) as zf:
for index, csv_data in enumerate(csv_data_list):
zf.writestr(f'{simulation_name}_{index+1}.csv', csv_data)
zf.writestr(f'{simulation_name}_{index + 1}.csv', csv_data)
zip_buffer.seek(0)
return zip_buffer.read()

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4 changes: 2 additions & 2 deletions hnn_core/tests/test_drives.py
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Expand Up @@ -76,7 +76,7 @@ def test_external_drive_times():
events_per_cycle = 5
cycle_events_isi = 20
with pytest.raises(ValueError,
match=r'Burst duration (?s).* cannot be greater than'):
match=r'(?s)Burst duration .* cannot be greater than'):
_create_bursty_input(t0=t0, t0_stdev=t0_stdev,
tstop=tstop, f_input=f_input,
events_jitter_std=events_jitter_std,
Expand Down Expand Up @@ -339,7 +339,7 @@ def test_add_drives():
net.add_bursty_drive('bursty_drive', tstart=10, tstop=1,
location='distal', burst_rate=10)

msg = (r'Burst duration (?s).* cannot be greater than '
msg = (r'(?s)Burst duration .* cannot be greater than '
'burst period')
with pytest.raises(ValueError, match=msg):
net.add_bursty_drive('bursty_drive', location='distal',
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6 changes: 4 additions & 2 deletions hnn_core/tests/test_extracellular.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,9 +41,11 @@ def test_extracellular_api():
# all remaining input arguments checked by ExtracellularArray

rec_arr = ExtracellularArray(electrode_pos)
with pytest.raises(AttributeError, match="can't set attribute"):
with pytest.raises(AttributeError,
match="has no setter|can't set attribute"):
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rec_arr.times = [1, 2, 3]
with pytest.raises(AttributeError, match="can't set attribute"):
with pytest.raises(AttributeError,
match="has no setter|can't set attribute"):
rec_arr.voltages = [1, 2, 3]
with pytest.raises(TypeError, match="trial index must be int"):
_ = rec_arr['0']
Expand Down
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