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fix: three code-review issues in analysis/satp-circe-notebook #131

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MitchellAcoustics merged 2 commits into from
Mar 1, 2026
Merged

fix: three code-review issues in analysis/satp-circe-notebook #131

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Copilot Mar 1, 2026
8130501
fix: code review fixes — install_r_packages empty list, docstring for…
Copilot Mar 1, 2026
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99 changes: 53 additions & 46 deletions src/soundscapy/r_wrapper/_circe_wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,32 +20,34 @@ def extract_bfgs_fit(bfgs_model: ro.ListVector) -> dict[str, Any]:

Parameters
----------
bfgs_model (RS4): Fitted model object from the circe package.
bfgs_model : ro.ListVector
Fitted model object from the circe package.

Returns
-------
dict: Dictionary containing fit statistics.
dict
Dictionary containing fit statistics.

Examples
--------
>>> # doctest: +SKIP
>>> import soundscapy as sspy
>>> from soundscapy.satp import CircModelE
>>> data = sspy.isd.load()
>>> data_paqs = data[PAQ_IDS]
>>> data_paqs = data_paqs.dropna()
>>> data_cor = data_paqs.corr()
>>> n = len(data_paqs)
>>> circ_model = CircModelE.CIRCUMPLEX
>>> circe_res = sspyr.bfgs(
... data_cor=data_cor,
... n=n,
... scales=PAQ_IDS,
... m_val=3,
... equal_ang=circ_model.equal_ang,
... equal_com=circ_model.equal_com,
... )
>>> fit_stats = sspy.r_wrapper.extract_bfgs_fit(circe_res)
>>> # doctest: +SKIP
>>> import soundscapy as sspy
>>> from soundscapy.satp import CircModelE
>>> data = sspy.isd.load()
>>> data_paqs = data[PAQ_IDS]
>>> data_paqs = data_paqs.dropna()
>>> data_cor = data_paqs.corr()
>>> n = len(data_paqs)
>>> circ_model = CircModelE.CIRCUMPLEX
>>> circe_res = sspyr.bfgs(
... data_cor=data_cor,
... n=n,
... scales=PAQ_IDS,
... m_val=3,
... equal_ang=circ_model.equal_ang,
... equal_com=circ_model.equal_com,
... )
>>> fit_stats = sspy.r_wrapper.extract_bfgs_fit(circe_res)

"""
# Session must already be active (bfgs_model was produced by bfgs()), but
Expand Down Expand Up @@ -98,38 +100,43 @@ def bfgs(

Parameters
----------
data_cor (pd.DataFrame): Correlation matrix of the data.
n (int): Number of observations (participants) used to compute the correlation
matrix. Used by CircE_BFGS for chi-square and RMSEA calculations.
scales (list[str], optional): List of scale names. Defaults to PAQ_IDS.
m_val (int, optional): Number of dimensions. Defaults to 3.
equal_ang (bool, optional): Whether to enforce equal angles constraint.
Defaults to True.
equal_com (bool, optional): Whether to enforce equal communalities constraint.
Defaults to True.
data_cor : pd.DataFrame
Correlation matrix of the data.
n : int
Number of observations (participants) used to compute the correlation
matrix. Used by CircE_BFGS for chi-square and RMSEA calculations.
scales : list[str], optional
List of scale names. Defaults to PAQ_IDS.
m_val : int, optional
Number of dimensions. Defaults to 3.
equal_ang : bool, optional
Whether to enforce equal angles constraint. Defaults to True.
equal_com : bool, optional
Whether to enforce equal communalities constraint. Defaults to True.

Returns
-------
RS4: Fitted model object from the circe package.
ro.ListVector
Fitted model object from the circe package.

Examples
--------
>>> import soundscapy as sspy
>>> from soundscapy.satp import CircModelE
>>> data = sspy.isd.load()
>>> data_paqs = data[PAQ_IDS]
>>> data_paqs = data_paqs.dropna()
>>> data_cor = data_paqs.corr()
>>> n = data_paqs.shape[0]
>>> circ_model = CircModelE.CIRCUMPLEX
>>> circe_res = bfgs(
... data_cor=data_cor,
... n=n,
... scales=PAQ_IDS,
... m_val=3,
... equal_ang=circ_model.equal_ang,
... equal_com=circ_model.equal_com,
... )
>>> import soundscapy as sspy
>>> from soundscapy.satp import CircModelE
>>> data = sspy.isd.load()
>>> data_paqs = data[PAQ_IDS]
>>> data_paqs = data_paqs.dropna()
>>> data_cor = data_paqs.corr()
>>> n = data_paqs.shape[0]
>>> circ_model = CircModelE.CIRCUMPLEX
>>> circe_res = bfgs(
... data_cor=data_cor,
... n=n,
... scales=PAQ_IDS,
... m_val=3,
... equal_ang=circ_model.equal_ang,
... equal_com=circ_model.equal_com,
... )

"""
r = get_r_session()
Expand Down
5 changes: 3 additions & 2 deletions src/soundscapy/r_wrapper/_r_wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -599,8 +599,9 @@ def install_r_packages(packages: list[str] | None = None) -> None:
packnames_to_install.remove("CircE")
logger.info("Installed R package 'CircE' from GitHub")

utils.install_packages(StrVector(packnames_to_install))
logger.info("Installed missing R packages: %s", packnames_to_install)
if packnames_to_install:
utils.install_packages(StrVector(packnames_to_install))
logger.info("Installed missing R packages: %s", packnames_to_install)
else:
logger.debug("All required R packages are already installed")

Expand Down
6 changes: 3 additions & 3 deletions src/soundscapy/satp/circe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -377,7 +377,7 @@ def to_dict(self) -> dict[str, Any]:
if self.polar_angles is not None:
base.update(self.polar_angles.to_dict())
else:
base.update({paq: None for paq in PAQ_IDS})
base.update(dict.fromkeys(PAQ_IDS))
return base


Expand Down Expand Up @@ -469,7 +469,7 @@ def fit_circe(
if len(data) == 0:
msg = (
"No complete cases found: input DataFrame is empty. "
"Check that data contains valid rows with PAQ1-PAQ8 and participant column."
"Check that data contains valid rows with PAQ1-PAQ8 columns."
)
raise ValueError(msg)
validated = SATPSchema.validate(data, lazy=True)
Expand Down Expand Up @@ -523,7 +523,7 @@ def fit_circe(
"rmsea_l": None,
"rmsea_u": None,
"gdiff": None,
**{paq: None for paq in PAQ_IDS},
**dict.fromkeys(PAQ_IDS),
"error": str(e),
}
)
Expand Down