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Rt notebook fix 2 #1702

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Rt notebook fix 2 #1702

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93c85cd
Stopped rt notebook creating side-effect csvs
MichaelClerx Jan 6, 2025
7ccd8fb
Made notebook tests run with notebook path as working directory
MichaelClerx Jan 6, 2025
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4 changes: 2 additions & 2 deletions examples/miscellaneous/model-rt-estimation-renewal-equation.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -1028,7 +1028,7 @@
"metadata": {},
"outputs": [],
"source": [
"pois_intervals.to_csv('pois_rt.csv')"
"#pois_intervals.to_csv('pois_rt.csv')"
]
},
{
Expand Down Expand Up @@ -1844,7 +1844,7 @@
"metadata": {},
"outputs": [],
"source": [
"negbin_intervals.to_csv('negbin_rt.csv')"
"#negbin_intervals.to_csv('negbin_rt.csv')"
]
},
{
Expand Down
101 changes: 0 additions & 101 deletions examples/miscellaneous/negbin_rt.csv
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101 changes: 0 additions & 101 deletions examples/miscellaneous/pois_rt.csv
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7 changes: 4 additions & 3 deletions run-tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -432,7 +432,7 @@ def list_notebooks(root, recursive=True, ignore_list=None, notebooks=None):

def test_notebook(path):
"""
Tests a notebook in a subprocess, exists if it doesn't finish.
Tests a notebook in a subprocess, exits if it doesn't finish.
"""
import nbconvert
import pints
Expand All @@ -442,7 +442,7 @@ def test_notebook(path):

# Load notebook, convert to python
e = nbconvert.exporters.PythonExporter()
code, __ = e.from_filename(path)
code, _ = e.from_filename(path)

# Remove coding statement, if present
code = '\n'.join([x for x in code.splitlines() if x[:9] != '# coding'])
Expand All @@ -455,7 +455,8 @@ def test_notebook(path):
cmd = [sys.executable, '-c', code]
try:
p = subprocess.Popen(
cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env
cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env,
cwd=os.path.dirname(path)
)
stdout, stderr = p.communicate()
# TODO: Use p.communicate(timeout=3600)
Expand Down
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