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Merged
MBARIMike merged 3 commits into from
Jun 2, 2025
Merged

Run CI on only pushes to the main branch. #26

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4bb218d
Run CI on only pushes to the main branch.
MBARIMike Jun 2, 2025
f6f1424
Alter EXPECTED_SIZE_GITHUB to get test to pass now.
MBARIMike Jun 2, 2025
3ebeab3
Remove future deprecation warnings, namely using .iloc[] and .ffill().
MBARIMike Jun 2, 2025
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2 changes: 0 additions & 2 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,6 @@ on:
branches:
- main
pull_request:
branches:
- main

jobs:
lint:
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14 changes: 7 additions & 7 deletions notebooks/5.2-mpm-bg_biolume-PiO-paper.ipynb
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Expand Up @@ -151,9 +151,9 @@
"\n",
" # Find the high and low peaks\n",
" peaks, _ = signal.find_peaks(df[\"biolume_raw\"], height=max_bg)\n",
" s_peaks = pd.Series(df[\"biolume_raw\"][peaks], index=df.index[peaks])\n",
" nbflash_high = s_peaks[s_peaks > (pd.Series(s_med_bg[peaks], index=df.index[peaks]) + flash_threshold)]\n",
" nbflash_low = s_peaks[s_peaks <= (pd.Series(s_med_bg[peaks], index=df.index[peaks]) + flash_threshold)]\n",
" s_peaks = pd.Series(df[\"biolume_raw\"].iloc[peaks], index=df.index[peaks])\n",
" nbflash_high = s_peaks[s_peaks > (pd.Series(s_med_bg.iloc[peaks], index=df.index[peaks]) + flash_threshold)]\n",
" nbflash_low = s_peaks[s_peaks <= (pd.Series(s_med_bg.iloc[peaks], index=df.index[peaks]) + flash_threshold)]\n",
" nbflash_high_plot = nbflash_high.rename(\"nbflash_high\").hvplot(kind=\"scatter\", color=\"red\", marker=\"star\", s=50)\n",
" nbflash_low_plot = nbflash_low.rename(\"nbflash_low\").hvplot(kind=\"scatter\", color=\"goldenrod\", marker=\"star\", s=50)\n",
"\n",
Expand Down Expand Up @@ -206,7 +206,7 @@
"outputs": [],
"source": [
"# Compute flashes per liter - Units: flashes per liter = (flashes per second / mL/s) * 1000 mL/L\n",
"flow = ds_align[[\"biolume_flow\"]].sel(biolume_time=slice(\"2021-04-13 10:00:00\", \"2021-04-13 10:10:00\"))[\"biolume_flow\"].to_pandas().resample(\"1S\").mean().fillna(method=\"ffill\")\n",
"flow = ds_align[[\"biolume_flow\"]].sel(biolume_time=slice(\"2021-04-13 10:00:00\", \"2021-04-13 10:10:00\"))[\"biolume_flow\"].to_pandas().resample(\"1S\").mean().ffill()\n",
"nbflash_high_per_liter = nbflash_high_counts.divide(flow) * 1000\n",
"nbflash_low_per_liter = nbflash_low_counts.divide(flow) * 1000\n",
"\n",
Expand Down Expand Up @@ -402,7 +402,7 @@
" if tv > s_peaks.index[k+1]:\n",
" # Encountered a new simple_depth point\n",
" k += 1\n",
" if abs(s_peaks[k+1] - s_peaks[k]) > depth_threshold:\n",
" if abs(s_peaks.iloc[k+1] - s_peaks.iloc[k]) > depth_threshold:\n",
" # Completed downcast or upcast\n",
" count += 1\n",
" peaks_profiles.append(count)\n",
Expand Down Expand Up @@ -443,7 +443,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.11"
"version": "3.10.14"
},
"vscode": {
"interpreter": {
Expand All @@ -452,5 +452,5 @@
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
2 changes: 1 addition & 1 deletion src/data/test_process_i2map.py
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Expand Up @@ -30,7 +30,7 @@ def test_process_i2map(complete_i2map_processing):
# but it will alert us if a code change unexpectedly changes the file size.
# If code changes are expected to change the file size then we should
# update the expected size here.
EXPECTED_SIZE_GITHUB = 58843
EXPECTED_SIZE_GITHUB = 58836
EXPECTED_SIZE_ACT = 58816
EXPECTED_SIZE_LOCAL = 58896
if str(proc.args.base_path).startswith("/home/runner"):
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