Metadata GDSC annotation improvements (#625)

* Small metadata cell line fixes

* Check that queried GDSC dataset is either 1 or 2

* gdsc_dataset must be specified as a string

* Doc String update

pertpy/metadata/_cell_line.py

@@ -228,10 +228,8 @@ def annotate(
  if query_id == "DepMap_ID":
  query_id = "stripped_cell_line_name"
  logger.error(
- "`stripped_cell_line_name` is used as reference and query identifier ",
- " to annotate cell line metadata from Cancerrxgene. "
- "Ensure that stripped cell line names are available in 'adata.obs.' ",
- "or use the DepMap as `cell_line_source` to annotate the cell line first ",
+ "`stripped_cell_line_name` is used as reference and query identifier to annotate cell line metadata from Cancerrxgene. "
+ "Ensure that stripped cell line names are available in 'adata.obs.' or use the DepMap as `cell_line_source` to annotate the cell line first."
  )
  if self.cancerxgene is None:
  self._download_cell_line(cell_line_source="Cancerrxgene")
@@ -485,7 +483,7 @@ def annotate_from_gdsc(
  reference_id: Literal["cell_line_name", "sanger_model_id", "cosmic_id"] = "cell_line_name",
  query_perturbation: str = "perturbation",
  reference_perturbation: Literal["drug_name", "drug_id"] = "drug_name",
- gdsc_dataset: Literal[1, 2] = 1,
+ gdsc_dataset: Literal["gdsc_1", "gdsc_2"] = "gdsc_1",
  verbosity: int | str = 5,
  copy: bool = False,
  ) -> AnnData:
@@ -500,7 +498,7 @@ def annotate_from_gdsc(
  reference_id: The type of cell line identifier in the metadata, cell_line_name, sanger_model_id or cosmic_id.
  query_perturbation: The column of `.obs` with perturbation information.
  reference_perturbation: The type of perturbation in the metadata, drug_name or drug_id.
- gdsc_dataset: The GDSC dataset, 1 or 2.
+ gdsc_dataset: The GDSC dataset, 1 or 2, specified as 'gdsc_1' or 'gdsc_2'.
  The GDSC1 dataset updates previous releases with additional drug screening data from the
  Sanger Institute and Massachusetts General Hospital.
  It covers 970 Cell lines and 403 Compounds with 333292 IC50s.
@@ -528,14 +526,16 @@ def annotate_from_gdsc(
  "This ensures that the required query ID is included in your data."
  )
  # Lazily download the GDSC data
- if gdsc_dataset == 1:
+ if gdsc_dataset == "gdsc_1":
  if self.drug_response_gdsc1 is None:
  self._download_gdsc(gdsc_dataset=1)
  gdsc_data = self.drug_response_gdsc1
- else:
+ elif gdsc_dataset == "gdsc_2":
  if self.drug_response_gdsc2 is None:
  self._download_gdsc(gdsc_dataset=2)
  gdsc_data = self.drug_response_gdsc2
+ else:
+ raise ValueError("The GDSC dataset specified in `gdsc_dataset` must be either 'gdsc_1' or 'gdsc_2'.")
 
  identifier_num_all = len(adata.obs[query_id].unique())
  not_matched_identifiers = list(set(adata.obs[query_id]) - set(gdsc_data[reference_id]))
@@ -552,7 +552,7 @@ def annotate_from_gdsc(
  adata.obs = (
  adata.obs.reset_index()
  .set_index([query_id, query_perturbation])
- .assign(ln_ic50=self.drug_response_gdsc1.set_index([reference_id, reference_perturbation]).ln_ic50)
+ .assign(ln_ic50=gdsc_data.set_index([reference_id, reference_perturbation]).ln_ic50)
  .reset_index()
  .set_index(old_index_name)
  )

pertpy/tools/_differential_gene_expression/_statsmodels.py

@@ -29,7 +29,8 @@ def fit(
 
  Examples:
  >>> import statsmodels.api as sm
- >>> model = StatsmodelsDE(adata, design="~condition")
+ >>> import pertpy as pt
+ >>> model = pt.tl.Statsmodels(adata, design="~condition")
  >>> model.fit(sm.GLM, family=sm.families.NegativeBinomial(link=sm.families.links.Log()))
  >>> results = model.test_contrasts(np.array([0, 1]))
  """