Some linting things

.gitignore

@@ -2,4 +2,4 @@ __pycache__/
 *.pyc
 .env
 # We want this to be generated within the instance on start
-debug-current-results.csv
+debug-current-results.csv

about.py

@@ -154,7 +154,7 @@ FAQS = {
     ),
 }
 
-SUBMIT_INTRUCTIONS = f"""
+SUBMIT_INSTRUCTIONS = f"""
 # Antibody Developability Submission
 
 You do **not** need to predict all 5 properties — each property has its own leaderboard and prize.

app.py

@@ -7,7 +7,7 @@ import contextlib
 
 load_dotenv()  # Load environment variables from .env file
 
-from about import ABOUT_INTRO, ABOUT_TEXT, FAQS, SUBMIT_INTRUCTIONS
+from about import ABOUT_INTRO, ABOUT_TEXT, FAQS, SUBMIT_INSTRUCTIONS
 from constants import (
     ASSAY_RENAME,  # noqa: F401
     SEQUENCES_FILE_DICT,
@@ -100,6 +100,7 @@ async def periodic_data_fetch(app):
     event.set()
     t.join(3)
 
+
 # Make font size bigger using gradio theme
 with gr.Blocks(theme=gr.themes.Default(text_size=sizes.text_lg)) as demo:
     timer = gr.Timer(3)  # Run every 3 seconds when page is focused
@@ -141,12 +142,13 @@ with gr.Blocks(theme=gr.themes.Default(text_size=sizes.text_lg)) as demo:
                 width="30vw",
             )
             gr.Markdown(ABOUT_TEXT)
-            
+
             # Sequence download buttons
             gr.Markdown(
-            """### 📥 Download Sequences
-            The GDPa1 dataset (with assay data and sequences) is available on Hugging Face [here](https://huggingface.co/datasets/ginkgo-datapoints/GDPa1), 
-            but we provide this and the private test set for convenience.""")
+                """### 📥 Download Sequences
+            The GDPa1 dataset (with assay data and sequences) is available on Hugging Face [here](https://huggingface.co/datasets/ginkgo-datapoints/GDPa1),
+            but we provide this and the private test set for convenience."""
+            )
             with gr.Row():
                 with gr.Column():
                     download_button_cv_about = gr.DownloadButton(
@@ -178,7 +180,7 @@ with gr.Blocks(theme=gr.themes.Default(text_size=sizes.text_lg)) as demo:
             demo.load(fn=refresh_overall_leaderboard, outputs=lb)
 
         with gr.TabItem(SUBMIT_TAB_NAME, elem_id="boundary-benchmark-tab-table"):
-            gr.Markdown(SUBMIT_INTRUCTIONS)
+            gr.Markdown(SUBMIT_INSTRUCTIONS)
 
             with gr.Row():
                 with gr.Column():
@@ -271,6 +273,4 @@ with gr.Blocks(theme=gr.themes.Default(text_size=sizes.text_lg)) as demo:
     )
 
 if __name__ == "__main__":
-    demo.launch(
-        ssr_mode=False, app_kwargs={"lifespan": periodic_data_fetch}
-    )
+    demo.launch(ssr_mode=False, app_kwargs={"lifespan": periodic_data_fetch})

data/GDPa1_v1.2_sequences.csv

@@ -244,4 +244,4 @@ GDPa1-242,visilizumab,QVQLVQSGAEVKKPGASVKVSCKASGYTFISYTMHWVRQAPGQGLEWMGYINPRSGYT
 GDPa1-243,xentuzumab,QVELVESGGGLVQPGGSLRLSCAASGFTFTSYWMSWVRQAPGKGLELVSSITSYGSFTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARNMYTHFDSWGQGTLVTVSS,DIVLTQPPSVSGAPGQRVTISCSGSSSNIGSNSVSWYQQLPGTAPKLLIYDNSKRPSGVPDRFSGSKSGTSASLAITGLQSEDEADYYCQSRDTYGYYWVFGGGTKLTVL,DIVLTQP-PSVSGAPGQRVTISCSGSS-SNIGS-----NSVSWYQQLPGTAPKLLIYD--------NSKRPSGVPDRFSGSKSG--TSASLAITGLQSEDEADYYCQSRDTY---------------------GYYWVFGGGTKLTVL-,QVELVES-GGGLVQPGGSLRLSCAASG-FTFTS-----YWMSWVRQAPGKGLELVSSITSY---GSFTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARNMYT----------------------HFDSWGQGTLVTVSS,IgG1,Lambda,4
 GDPa1-244,zalutumumab,QVQLVESGGGVVQPGRSLRLSCAASGFTFSTYGMHWVRQAPGKGLEWVAVIWDDGSYKYYGDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDGITMVRGVMKDYFDYWGQGTLVTVSS,AIQLTQSPSSLSASVGDRVTITCRASQDISSALVWYQQKPGKAPKLLIYDASSLESGVPSRFSGSESGTDFTLTISSLQPEDFATYYCQQFNSYPLTFGGGTKVEIK,AIQLTQSPSSLSASVGDRVTITCRAS--QDIS------SALVWYQQKPGKAPKLLIYD--------ASSLESGVPSRFSGSESG--TDFTLTISSLQPEDFATYYCQQFNS-----------------------YPLTFGGGTKVEIK-,QVQLVES-GGGVVQPGRSLRLSCAASG-FTFST-----YGMHWVRQAPGKGLEWVAVIWDD---GSYKYYGDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDGITMVRG--------------VMKDYFDYWGQGTLVTVSS,IgG1,Kappa,0
 GDPa1-245,zanolimumab,QVQLQQWGAGLLKPSETLSLTCAVYGGSFSGYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARVINWFDPWGQGTLVTVSS,DIQMTQSPSSVSASVGDRVTITCRASQDISSWLAWYQHKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPYTFGQGTKLEIK,DIQMTQSPSSVSASVGDRVTITCRAS--QDIS------SWLAWYQHKPGKAPKLLIYA--------ASSLQSGVPSRFSGSGSG--TDFTLTISSLQPEDFATYYCQQANS-----------------------FPYTFGQGTKLEIK-,QVQLQQW-GAGLLKPSETLSLTCAVYG-GSFSG-----YYWSWIRQPPGKGLEWIGEINH----SGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARVIN-----------------------WFDPWGQGTLVTVSS,IgG1,Kappa,3
-GDPa1-246,zolbetuximab,QVQLQQPGAELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPSDSYTNYNQKFKDKATLTVDKSSSTAYMQLSSPTSEDSAVYYCTRSWRGNSFDYWGQGTTLTVSS,DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLNSGNQKNYLTWYQQKPGQPPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDYSYPFTFGSGTKLEIK,DIVMTQSPSSLTVTAGEKVTMSCKSS--QSLLNSGNQKNYLTWYQQKPGQPPKLLIYW--------ASTRESGVPDRFTGSGSG--TDFTLTISSVQAEDLAVYYCQNDYS-----------------------YPFTFGSGTKLEIK-,QVQLQQP-GAELVRPGASVKLSCKASG-YTFTS-----YWINWVKQRPGQGLEWIGNIYPS---DSYTNYNQKFKDKATLTVDKSSSTAYMQLSSPTSEDSAVYYCTRSWRG---------------------NSFDYWGQGTTLTVSS,IgG1,Kappa,4
+GDPa1-246,zolbetuximab,QVQLQQPGAELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPSDSYTNYNQKFKDKATLTVDKSSSTAYMQLSSPTSEDSAVYYCTRSWRGNSFDYWGQGTTLTVSS,DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLNSGNQKNYLTWYQQKPGQPPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDYSYPFTFGSGTKLEIK,DIVMTQSPSSLTVTAGEKVTMSCKSS--QSLLNSGNQKNYLTWYQQKPGQPPKLLIYW--------ASTRESGVPDRFTGSGSG--TDFTLTISSVQAEDLAVYYCQNDYS-----------------------YPFTFGSGTKLEIK-,QVQLQQP-GAELVRPGASVKLSCKASG-YTFTS-----YWINWVKQRPGQGLEWIGNIYPS---DSYTNYNQKFKDKATLTVDKSSSTAYMQLSSPTSEDSAVYYCTRSWRG---------------------NSFDYWGQGTTLTVSS,IgG1,Kappa,4

data/heldout-set-sequences.csv

@@ -78,4 +78,4 @@ P907-A14-unary-estuary-9ae8d,EVQLVESGGGLVQPGGSLRLSCAASGFTFSRYWMSWVRQAPGKGLEWVANI
 P907-A14-undirected-hull-8daff,QMQLVQSGAEVRKPGASVKVSCKASGYTFTGHYIHWVRQAPGRGPEWMGWINPNSGGTNSSQSFQGRVTMTRDTSISTAYMELSRLTSDDTAVYSCARARYGDYYYFDSWGQGTLVTVSS,DIQMTQSPSSLSASVGDRVTITCRASQDISSYLAWYQQKPEKAPKSLIYAASSLQGGVPSRFSGSGSGTHFTLTISSLQPEDFATYYCQQYYSYPVTFGPGTKVDIK,QMQLVQS-GAEVRKPGASVKVSCKASG-YTFTG-----HYIHWVRQAPGRGPEWMGWINPN---SGGTNSSQSFQGRVTMTRDTSISTAYMELSRLTSDDTAVYSCARARYGD-------------------YYYFDSWGQGTLVTVSS,DIQMTQSPSSLSASVGDRVTITCRAS--QDIS------SYLAWYQQKPEKAPKSLIYA--------ASSLQGGVPSRFSGSGSG--THFTLTISSLQPEDFATYYCQQYYS-----------------------YPVTFGPGTKVDIK-,IgG1,Kappa
 P907-A14-vain-bucket-0f231,QVQLQQWGAGLLKPSETLSLTCAVYNGSSSAHYWSWVRQPPGKGLEWIGEISHGGSTTYNPSLKGRVSISVDTPKNQFSLNLSSVTAADTAVYYCATRAIHFRNRNFYSFYVEVWGKGTTVTVSS,EIVLTQSPGTLSLSPGERATLSCRASQSVSSSKLVWYQQRPGQAPRPLIYGASSRATGIPDRFSGSGSETDFTLTISWLEPEDFAVYYCHQYGSSPRTFGQGTKVEIK,QVQLQQW-GAGLLKPSETLSLTCAVYN-GSSSA-----HYWSWVRQPPGKGLEWIGEISH----GGSTTYNPSLKGRVSISVDTPKNQFSLNLSSVTAADTAVYYCATRAIHFRNR-------------NFYSFYVEVWGKGTTVTVSS,EIVLTQSPGTLSLSPGERATLSCRAS--QSVSS-----SKLVWYQQRPGQAPRPLIYG--------ASSRATGIPDRFSGSGSE--TDFTLTISWLEPEDFAVYYCHQYGS-----------------------SPRTFGQGTKVEIK-,IgG1,Kappa
 P907-A14-wintry-couple-24188,QVQLQQWGAGLLKPSETLSVTCAVYGGSFIGSSWIWIRQPPEKGLEWIGEINHGGSTTYNPSLKSRVTISLDMSKNQFSLNLTSVTAADTAVYYCATDRGSLAAVDWGQGTLVTVSS,DIQMTQSPSSLSASVGDRVTITCRASQAISSYLAWYQQKPGKVPKLLIYAASTLQSGVASRFTGSGSGTDFTLTISSLQPEDVATYYCQKYNSAPRTFGQGTRVEIK,QVQLQQW-GAGLLKPSETLSVTCAVYG-GSFIG-----SSWIWIRQPPEKGLEWIGEINH----GGSTTYNPSLKSRVTISLDMSKNQFSLNLTSVTAADTAVYYCATDRGS---------------------LAAVDWGQGTLVTVSS,DIQMTQSPSSLSASVGDRVTITCRAS--QAIS------SYLAWYQQKPGKVPKLLIYA--------ASTLQSGVASRFTGSGSG--TDFTLTISSLQPEDVATYYCQKYNS-----------------------APRTFGQGTRVEIK-,IgG1,Kappa
-P907-A14-witty-fugue-86932,EVQLVESGGGLVQPGRSLRLSCTASGFTFGDYAMNWVRQAPGKGLEWLGFIESKGYGGTTEYAASVKGRFIISRDDSKSIAYLQMNSLKTEDTAVYYCTPGDYWGQGTLVTVSS,SYELTQPPSVSVSPGQTARITCSGDALPKKYAYWYQQKSGQAPVQVIYEDSGRPSGIPERFSGSSSGTMATLTISGAQVEDEADYYCYSIDSSGNHRVFGGGTKLTVL,EVQLVES-GGGLVQPGRSLRLSCTASG-FTFGD-----YAMNWVRQAPGKGLEWLGFIESKG-YGGTTEYAASVKGRFIISRDDSKSIAYLQMNSLKTEDTAVYYCTPG---------------------------DYWGQGTLVTVSS,SYELTQP-PSVSVSPGQTARITCSGD---ALPK-----KYAYWYQQKSGQAPVQVIYE--------DSGRPSGIPERFSGSSSG--TMATLTISGAQVEDEADYYCYSIDSS---------------------GNHRVFGGGTKLTVL-,IgG1,Lambda
+P907-A14-witty-fugue-86932,EVQLVESGGGLVQPGRSLRLSCTASGFTFGDYAMNWVRQAPGKGLEWLGFIESKGYGGTTEYAASVKGRFIISRDDSKSIAYLQMNSLKTEDTAVYYCTPGDYWGQGTLVTVSS,SYELTQPPSVSVSPGQTARITCSGDALPKKYAYWYQQKSGQAPVQVIYEDSGRPSGIPERFSGSSSGTMATLTISGAQVEDEADYYCYSIDSSGNHRVFGGGTKLTVL,EVQLVES-GGGLVQPGRSLRLSCTASG-FTFGD-----YAMNWVRQAPGKGLEWLGFIESKG-YGGTTEYAASVKGRFIISRDDSKSIAYLQMNSLKTEDTAVYYCTPG---------------------------DYWGQGTLVTVSS,SYELTQP-PSVSVSPGQTARITCSGD---ALPK-----KYAYWYQQKSGQAPVQVIYE--------DSGRPSGIPERFSGSSSG--TMATLTISGAQVEDEADYYCYSIDSS---------------------GNHRVFGGGTKLTVL-,IgG1,Lambda

utils.py

@@ -66,9 +66,8 @@ def fetch_hf_results():
     df.loc[df["user"].isin(BASELINE_USERNAMES), "user"] = "Baseline"
     # Note: Could optionally add a column "is_baseline" to the dataframe to indicate whether the model is a baseline model or not. If things get crowded.
     # Anonymize the user column at this point (so note: users can submit anonymous / non-anonymous and we'll show their latest submission regardless)
-    df.loc[df["anonymous"] != False, "user"] = "anon-" + df.loc[
-        df["anonymous"] != False, "user"
-    ].apply(readable_hash)
+    anon_rows = df["anonymous"].fillna(True)
+    df.loc[anon_rows, "user"] = "anon-" + df.loc[anon_rows, "user"].apply(readable_hash)
 
     # Compare to previous dataframe
     if os.path.exists("debug-current-results.csv"):