Update tqdm for notebook

src/pyobo/getters.py

@@ -25,7 +25,7 @@
 )
 
 import bioregistry
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from .constants import DATABASE_DIRECTORY
 from .identifier_utils import MissingPrefix, wrap_norm_prefix

src/pyobo/reader.py

@@ -10,7 +10,7 @@
 import bioregistry
 import networkx as nx
 from more_itertools import pairwise
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from .constants import DATE_FORMAT, PROVENANCE_PREFIXES
 from .identifier_utils import MissingPrefix, normalize_curie

src/pyobo/sources/antibodyregistry.py

@@ -7,7 +7,7 @@
 
 import bioversions
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo import Obo, Term
 from pyobo.utils.path import ensure_df

src/pyobo/sources/complexportal.py

@@ -6,7 +6,7 @@
 from typing import Iterable, List, Tuple
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo import get_id_name_mapping
 from pyobo.constants import NCBITAXON_PREFIX

src/pyobo/sources/dictybase_gene.py

@@ -9,7 +9,7 @@
 from typing import Iterable
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo.struct import Obo, Reference, Synonym, Term, from_species, has_gene_product
 from pyobo.utils.io import multisetdict

src/pyobo/sources/drugbank.py

@@ -13,7 +13,7 @@
 from xml.etree import ElementTree
 
 import pystow
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import Obo, Reference, Term
 from ..struct.typedef import has_salt

src/pyobo/sources/flybase.py

@@ -6,7 +6,7 @@
 from typing import Iterable, Mapping, Set
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo import Reference
 from pyobo.constants import NCBITAXON_PREFIX

src/pyobo/sources/gwascentral_phenotype.py

@@ -5,7 +5,7 @@
 import json
 from typing import Iterable
 
-from tqdm import tqdm, trange
+from tqdm.auto import tqdm, trange
 
 from pyobo.sources.gwascentral_study import VERSION
 from pyobo.struct import Obo, Reference, Term

src/pyobo/sources/hgnc.py

@@ -11,7 +11,7 @@
 from typing import DefaultDict, Dict, Iterable, Optional
 
 from tabulate import tabulate
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo.struct import (
     Obo,

src/pyobo/sources/hgncgenefamily.py

@@ -6,7 +6,7 @@
 from typing import Iterable, List, Mapping
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import Obo, Reference, Synonym, SynonymTypeDef, Term, from_species
 from ..utils.path import ensure_path

src/pyobo/sources/icd10.py

@@ -10,7 +10,7 @@
 
 import click
 from more_click import verbose_option
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..sources.icd_utils import (
     ICD10_TOP_LEVEL_URL,

src/pyobo/sources/icd11.py

@@ -12,7 +12,7 @@
 
 import click
 from more_click import verbose_option
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..sources.icd_utils import (
     ICD11_TOP_LEVEL_URL,

src/pyobo/sources/icd_utils.py

@@ -17,7 +17,7 @@
 import pystow
 import requests
 from cachier import cachier
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import Term
 

src/pyobo/sources/interpro.py

@@ -5,7 +5,7 @@
 from collections import defaultdict
 from typing import DefaultDict, Iterable, List, Mapping, Set, Tuple
 
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from .utils import get_go_mapping
 from ..struct import Obo, Reference, Term

src/pyobo/sources/kegg/genes.py

@@ -10,7 +10,7 @@
 
 import click
 from more_click import verbose_option
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from .api import (
     KEGG_GENES_PREFIX,

src/pyobo/sources/kegg/genome.py

@@ -10,7 +10,7 @@
 
 import click
 from more_click import verbose_option
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 import pyobo
 from pyobo.constants import NCBITAXON_PREFIX

src/pyobo/sources/kegg/pathway.py

@@ -12,7 +12,7 @@
 
 import click
 from more_click import verbose_option
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo.sources.kegg.api import (
     KEGG_GENES_PREFIX,

src/pyobo/sources/mesh.py

@@ -8,7 +8,7 @@
 from typing import Any, Dict, Iterable, List, Mapping, Optional, Set
 from xml.etree.ElementTree import Element
 
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import Obo, Reference, Synonym, Term
 from ..utils.cache import cached_json, cached_mapping

src/pyobo/sources/mgi.py

@@ -7,7 +7,7 @@
 from typing import Iterable
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import (
     Obo,

src/pyobo/sources/mirbase.py

@@ -6,7 +6,7 @@
 import logging
 from typing import Iterable, List, Mapping
 
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import Obo, Reference, Synonym, Term, from_species
 from ..struct.typedef import has_mature

src/pyobo/sources/mirbase_family.py

@@ -5,7 +5,7 @@
 from typing import Iterable
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from .mirbase_constants import (
     get_premature_df,

src/pyobo/sources/mirbase_mature.py

@@ -4,7 +4,7 @@
 
 from typing import Iterable
 
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from .mirbase_constants import get_mature_df
 from ..struct import Obo, Reference, Synonym, Term

src/pyobo/sources/msigdb.py

@@ -8,7 +8,7 @@
 
 import click
 from more_click import verbose_option
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import Obo, Reference, Term, has_part
 from ..utils.path import ensure_path

src/pyobo/sources/ncbigene.py

@@ -6,7 +6,7 @@
 from typing import Iterable, List, Mapping, Set
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..api import get_id_name_mapping
 from ..constants import NCBITAXON_PREFIX

src/pyobo/sources/npass.py

@@ -6,7 +6,7 @@
 from typing import Iterable
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import Obo, Reference, Synonym, Term
 from ..utils.path import ensure_df

src/pyobo/sources/pathbank.py

@@ -7,7 +7,7 @@
 from typing import Iterable, Mapping, Set
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import Obo, Reference, Term
 from ..struct.typedef import has_part

src/pyobo/sources/pfam.py

@@ -5,7 +5,7 @@
 from typing import Iterable
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..struct import Obo, Reference, Term
 from ..utils.path import ensure_df

src/pyobo/sources/pfam_clan.py

@@ -4,7 +4,7 @@
 
 from typing import Iterable
 
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from .pfam import get_pfam_clan_df
 from ..struct import Obo, Reference, Term

src/pyobo/sources/pombase.py

@@ -7,7 +7,7 @@
 from typing import Iterable
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 import pyobo
 from pyobo import Reference

src/pyobo/sources/pubchem.py

@@ -7,7 +7,7 @@
 
 import bioversions
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..api import get_name_id_mapping
 from ..struct import Obo, Reference, Synonym, Term

src/pyobo/sources/reactome.py

@@ -8,7 +8,7 @@
 from typing import Iterable, Mapping, Set
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from ..api import get_id_multirelations_mapping, get_name_id_mapping
 from ..constants import NCBITAXON_PREFIX, SPECIES_REMAPPING

src/pyobo/sources/rgd.py

@@ -6,7 +6,7 @@
 from typing import Iterable, Optional
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo.struct import (
     Obo,

src/pyobo/sources/slm.py

@@ -5,7 +5,7 @@
 from typing import Iterable
 
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo import Obo, SynonymTypeDef, Term
 from pyobo.utils.path import ensure_df

src/pyobo/sources/umls/umls.py

@@ -12,7 +12,7 @@
 
 import bioregistry
 import pandas as pd
-from tqdm import tqdm
+from tqdm.auto import tqdm
 from umls_downloader import open_umls
 
 from pyobo import Obo, Reference, Synonym, SynonymTypeDef, Term

src/pyobo/sources/uniprot/uniprot.py

@@ -6,7 +6,7 @@
 from typing import Iterable, Optional
 
 import bioversions
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo import Obo, Reference
 from pyobo.constants import NCBITAXON_PREFIX, RAW_MODULE

src/pyobo/sources/uniprot/uniprot_ptm.py

@@ -24,11 +24,12 @@
 //         Terminator                      Once; ends an entr
 
 """
+
 import itertools as itt
 from collections import defaultdict
 from typing import DefaultDict, Iterable, List, Mapping, Optional, Tuple
 
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo import Obo, Reference, Term
 from pyobo.utils.path import ensure_path

src/pyobo/sources/zfin.py

@@ -6,7 +6,7 @@
 from collections import defaultdict
 from typing import Iterable, Optional
 
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo.struct import (
     Obo,

src/pyobo/ssg/__init__.py

@@ -9,7 +9,7 @@
 import bioregistry
 from bioregistry.constants import BIOREGISTRY_DEFAULT_BASE_URL
 from jinja2 import Environment, FileSystemLoader
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo import Obo
 from pyobo.struct import part_of

src/pyobo/struct/struct.py

@@ -34,7 +34,7 @@
 import pandas as pd
 from more_click import force_option, verbose_option
 from networkx.utils import open_file
-from tqdm import tqdm
+from tqdm.auto import tqdm
 from typing_extensions import Literal
 
 from .reference import Reference, Referenced

src/pyobo/utils/io.py

@@ -14,7 +14,7 @@
 from xml.etree import ElementTree
 from xml.etree.ElementTree import Element
 
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 __all__ = [
     "open_map_tsv",

src/pyobo/utils/ndex_utils.py

@@ -7,7 +7,7 @@
 from typing import Any, Iterable, List, Mapping, Tuple
 
 import requests
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from .path import prefix_directory_join
 

src/pyobo/xrefdb/bengo.py

@@ -6,7 +6,7 @@
 
 import bioregistry
 import networkx as nx
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from pyobo import get_hierarchy
 from pyobo.getters import SKIP

src/pyobo/xrefdb/canonicalizer.py

@@ -9,7 +9,7 @@
 import networkx as nx
 import pandas as pd
 from more_itertools import pairwise
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from .priority import DEFAULT_PRIORITY_LIST
 from .xrefs_pipeline import get_graph_from_xref_df