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Merged
tsmbland merged 4 commits into from
Aug 25, 2026
Merged

Update notebook, tests and linkchecker #95

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b488ead
Update notebook
tsmbland Aug 25, 2026
2cfa926
No longer copy input data
tsmbland Aug 25, 2026
6d08a0f
Update tests
tsmbland Aug 25, 2026
bbb30ae
Add lycheeignore
tsmbland Aug 25, 2026
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4 changes: 4 additions & 0 deletions .lycheeignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# Stack Exchange blocks Lychee's automated requests with HTTP 403.
https://stackoverflow\.com/.*
https://unix\.stackexchange\.com/.*
https://apple\.stackexchange\.com/.*
2 changes: 1 addition & 1 deletion data/README.txt
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@@ -1 +1 @@
This is a placeholder directory for input/output data for example analyses.
This is a placeholder directory for output data for example analyses.
20 changes: 2 additions & 18 deletions muse2_data_analysis/helpers.py
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Expand Up @@ -6,20 +6,7 @@

DATA_DIR = Path(__file__).parent.parent.absolute() / "data"
EXAMPLE_NAME = "muse1_default"
_INPUT_DIR = DATA_DIR / f"{EXAMPLE_NAME}_input"
_OUTPUT_DIR = DATA_DIR / f"{EXAMPLE_NAME}_output"


def get_example_input_dir() -> Path:
"""Get the directory for example input data.

If the folder does not exist, we create it by extracting an example from muse2.
"""
if _INPUT_DIR.exists():
return _INPUT_DIR

run_muse2("example", "extract", EXAMPLE_NAME, str(_INPUT_DIR))
return _INPUT_DIR
_OUTPUT_DIR = DATA_DIR / f"{EXAMPLE_NAME}"

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def get_example_output_dir() -> Path:
Expand All @@ -30,9 +17,6 @@ def get_example_output_dir() -> Path:
if _OUTPUT_DIR.exists():
return _OUTPUT_DIR

# Ensure INPUT_DIR exists
get_example_input_dir()

# Run the example model
run_muse2("run", str(_INPUT_DIR), "--output-dir", str(_OUTPUT_DIR))
run_muse2("example", "run", EXAMPLE_NAME, "--output-dir", str(_OUTPUT_DIR))
return _OUTPUT_DIR
2 changes: 1 addition & 1 deletion notebooks/capacity.ipynb
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Expand Up @@ -56,7 +56,7 @@
"assets = pd.read_csv(OUTPUT_DIR / \"assets.csv\")\n",
"asset_capacities = pd.read_csv(OUTPUT_DIR / \"asset_capacities.csv\")\n",
"\n",
"merged = asset_capacities.merge(assets, on=[\"asset_id\", \"group_id\"])\n",
"merged = asset_capacities.merge(assets, on=\"asset_id\")\n",
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"agg_capacities = merged.groupby([\"milestone_year\", \"agent_id\", \"process_id\"])[\n",
" \"capacity\"\n",
"].sum()\n",
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4 changes: 2 additions & 2 deletions notebooks/prices.ipynb
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Expand Up @@ -23,8 +23,8 @@
"\n",
"from muse2_data_analysis.helpers import get_example_output_dir\n",
"\n",
"INPUT_DIR = get_example_output_dir()\n",
"prices = pd.read_csv(INPUT_DIR / \"commodity_prices.csv\")\n",
"OUTPUT_DIR = get_example_output_dir()\n",
"prices = pd.read_csv(OUTPUT_DIR / \"commodity_prices.csv\")\n",
"prices.head()"
]
},
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44 changes: 5 additions & 39 deletions tests/test_helpers.py
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Expand Up @@ -6,35 +6,6 @@
from muse2_data_analysis import helpers


@patch("muse2_data_analysis.helpers.run_muse2")
def test_get_example_input_dir_returns_existing_directory(
run_muse2_mock: Mock, tmp_path: Path
) -> None:
"""Check that get_example_input_dir returns an existing input directory."""
input_dir = tmp_path / "input"
input_dir.mkdir()

with patch.object(helpers, "_INPUT_DIR", input_dir):
assert helpers.get_example_input_dir() == input_dir

run_muse2_mock.assert_not_called()


@patch("muse2_data_analysis.helpers.run_muse2")
def test_get_example_input_dir_extracts_example_when_missing(
run_muse2_mock: Mock, tmp_path: Path
) -> None:
"""Check that get_example_input_dir extracts the example when missing."""
input_dir = tmp_path / "input"

with patch.object(helpers, "_INPUT_DIR", input_dir):
assert helpers.get_example_input_dir() == input_dir

run_muse2_mock.assert_called_once_with(
"example", "extract", helpers.EXAMPLE_NAME, str(input_dir)
)


@patch("muse2_data_analysis.helpers.run_muse2")
def test_get_example_output_dir_returns_existing_directory(
run_muse2_mock: Mock, tmp_path: Path
Expand All @@ -50,20 +21,15 @@ def test_get_example_output_dir_returns_existing_directory(


@patch("muse2_data_analysis.helpers.run_muse2")
@patch("muse2_data_analysis.helpers.get_example_input_dir")
def test_get_example_output_dir_runs_example_when_missing(
get_example_input_dir_mock: Mock, run_muse2_mock: Mock, tmp_path: Path
run_muse2_mock: Mock, tmp_path: Path
) -> None:
"""Check that get_example_output_dir ensures input exists and runs the model."""
input_dir = tmp_path / "input"
"""Check that get_example_output_dir runs the example when output is missing."""
output_dir = tmp_path / "output"
get_example_input_dir_mock.return_value = input_dir

with patch.object(helpers, "_INPUT_DIR", input_dir):
with patch.object(helpers, "_OUTPUT_DIR", output_dir):
assert helpers.get_example_output_dir() == output_dir
with patch.object(helpers, "_OUTPUT_DIR", output_dir):
assert helpers.get_example_output_dir() == output_dir

get_example_input_dir_mock.assert_called_once_with()
run_muse2_mock.assert_called_once_with(
"run", str(input_dir), "--output-dir", str(output_dir)
"example", "run", helpers.EXAMPLE_NAME, "--output-dir", str(output_dir)
)
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