ov.bulk.geneset_enrichment function error in Cell interaction with CellPhoneDB part

[WeiQin2001]

Run the following code:
enr=ov.bulk.geneset_enrichment(gene_list=enrichr_genes,
pathways_dict=pathway_dict,
pvalue_type='auto',
organism='human')

The errors will be found:

AttributeError Traceback (most recent call last)
/tmp/ipykernel_1445/3054788131.py in ?()
1 #deg_genes=dds.result.loc[dds.result['sig']!='normal'].index.tolist()
----> 2 enr=ov.bulk.geneset_enrichment(gene_list=enrichr_genes,
3 pathways_dict=pathway_dict,
4 pvalue_type='auto',
5 organism='human')

~/miniconda3/envs/omicverse/lib/python3.10/site-packages/omicverse/bulk/_Enrichment.py in ?(gene_list, pathways_dict, pvalue_threshold, pvalue_type, organism, description, background, outdir, cutoff)
207 background='mmusculus_gene_ensembl'
208 elif (organism == 'Human') or (organism == 'human') or (organism == 'hs'):
209 background='hsapiens_gene_ensembl'
210
--> 211 enr = gp.enrichr(gene_list=gene_list,
212 gene_sets=pathways_dict,
213 organism=organism, # don't forget to set organism to the one you desired! e.g. Yeast
214 description=description,

~/miniconda3/envs/omicverse/lib/python3.10/site-packages/gseapy/enrichr.py in ?(gene_list, gene_sets, organism, description, outdir, background, cutoff, format, figsize, top_term, no_plot, verbose)
516 enr = Enrichr(gene_list, gene_sets, organism, description, outdir,
517 cutoff, background, format, figsize, top_term, no_plot, verbose)
518 # set organism
519 enr.set_organism()
--> 520 enr.run()
521
522 return enr

~/miniconda3/envs/omicverse/lib/python3.10/site-packages/gseapy/enrichr.py in ?(self)
423 shortID, res = self.get_results(genes_list)
424 # Remember gene set library used
425 res.insert(0, "Gene_set", self._gs)
426 # Append to master dataframe
--> 427 self.results = self.results.append(res, ignore_index=True)
428 self.res2d = res
429 if self._outdir is None: continue
430 self._logger.info('Save file of enrichment results: Job Id:' + str(shortID))

~/miniconda3/envs/omicverse/lib/python3.10/site-packages/pandas/core/generic.py in ?(self, name)
6295 and name not in self._accessors
6296 and self._info_axis._can_hold_identifiers_and_holds_name(name)
6297 ):
6298 return self[name]
-> 6299 return object.getattribute(self, name)

AttributeError: 'DataFrame' object has no attribute 'append'

[WeiQin2001]

sorry，this error happen in the Pathway analysis with AUCell part in fact.

[WeiQin2001]

But in Cell interaction with CellPhoneDB part, the similar error can be found :
enr=ov.bulk.geneset_enrichment(gene_list=enrichr_genes,
pathways_dict=pathway_dict,
pvalue_type='auto',
organism='human')

error:

AttributeError Traceback (most recent call last)
/tmp/ipykernel_1445/3054788131.py in ?()
1 #deg_genes=dds.result.loc[dds.result['sig']!='normal'].index.tolist()
----> 2 enr=ov.bulk.geneset_enrichment(gene_list=enrichr_genes,
3 pathways_dict=pathway_dict,
4 pvalue_type='auto',
5 organism='human')

~/miniconda3/envs/omicverse/lib/python3.10/site-packages/omicverse/bulk/_Enrichment.py in ?(gene_list, pathways_dict, pvalue_threshold, pvalue_type, organism, description, background, outdir, cutoff)
207 background='mmusculus_gene_ensembl'
208 elif (organism == 'Human') or (organism == 'human') or (organism == 'hs'):
209 background='hsapiens_gene_ensembl'
210
--> 211 enr = gp.enrichr(gene_list=gene_list,
212 gene_sets=pathways_dict,
213 organism=organism, # don't forget to set organism to the one you desired! e.g. Yeast
214 description=description,

~/miniconda3/envs/omicverse/lib/python3.10/site-packages/gseapy/enrichr.py in ?(gene_list, gene_sets, organism, description, outdir, background, cutoff, format, figsize, top_term, no_plot, verbose)
516 enr = Enrichr(gene_list, gene_sets, organism, description, outdir,
517 cutoff, background, format, figsize, top_term, no_plot, verbose)
518 # set organism
519 enr.set_organism()
--> 520 enr.run()
521
522 return enr

~/miniconda3/envs/omicverse/lib/python3.10/site-packages/gseapy/enrichr.py in ?(self)
423 shortID, res = self.get_results(genes_list)
424 # Remember gene set library used
425 res.insert(0, "Gene_set", self._gs)
426 # Append to master dataframe
--> 427 self.results = self.results.append(res, ignore_index=True)
428 self.res2d = res
429 if self._outdir is None: continue
430 self._logger.info('Save file of enrichment results: Job Id:' + str(shortID))

~/miniconda3/envs/omicverse/lib/python3.10/site-packages/pandas/core/generic.py in ?(self, name)
6295 and name not in self._accessors
6296 and self._info_axis._can_hold_identifiers_and_holds_name(name)
6297 ):
6298 return self[name]
-> 6299 return object.getattribute(self, name)

AttributeError: 'DataFrame' object has no attribute 'append'

[Starlitnightly]

I have fixed this error in nightly version

[WeiQin2001]

Thank you for your great work!