Fix neurosyth download_abstracts example; inc biopython (#753)

* DOC: fix neurosyth download_abstracts example; inc biopython * example 01_*/02: imporrt Bio; not biopython * comment: Bio from pip install biopython * Update examples/01_datasets/02_download_neurosynth.py Co-authored-by: Taylor Salo <[email protected]> * typo: install Co-authored-by: Taylor Salo <[email protected]>
neurostuff · Dec 7, 2022 · c5f18ee · c5f18ee
1 parent abb8feb
commit c5f18ee
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/examples/01_datasets/02_download_neurosynth.py b/examples/01_datasets/02_download_neurosynth.py
@@ -39,6 +39,10 @@
 from nimare.extract import download_abstracts, fetch_neuroquery, fetch_neurosynth
 from nimare.io import convert_neurosynth_to_dataset
 
+# biopython is unnecessary here, but is required by download_abstracts.
+# We import it here only to document the dependency and cause an early failure if it's missing.
+import Bio  # pip install biopython
+
 ###############################################################################
 # Download Neurosynth
 # -----------------------------------------------------------------------------
@@ -74,7 +78,7 @@
 # This is only possible because Neurosynth uses PMIDs as study IDs.
 #
 # Make sure you replace the example email address with your own.
-neurosynth_dset = extract.download_abstracts(neurosynth_dset, "[email protected]")
+neurosynth_dset = download_abstracts(neurosynth_dset, "[email protected]")
 neurosynth_dset.save(os.path.join(out_dir, "neurosynth_dataset_with_abstracts.pkl.gz"))
 
 ###############################################################################