bioregistry 0.13.17__tar.gz → 0.13.19__tar.gz

{bioregistry-0.13.17 → bioregistry-0.13.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioregistry
-Version: 0.13.17
+Version: 0.13.19
 Summary: Integrated registry of biological databases and nomenclatures
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases,persistent identifiers
 Author: Charles Tapley Hoyt
@@ -53,11 +53,11 @@ Requires-Dist: tabulate ; extra == 'align'
 Requires-Dist: defusedxml ; extra == 'align'
 Requires-Dist: class-resolver ; extra == 'align'
 Requires-Dist: fairsharing-client>=0.1.0 ; extra == 'align'
-Requires-Dist: pandas ; extra == 'align'
+Requires-Dist: pandas<3.0 ; extra == 'align'
 Requires-Dist: matplotlib ; extra == 'charts'
 Requires-Dist: matplotlib-venn ; extra == 'charts'
 Requires-Dist: seaborn ; extra == 'charts'
-Requires-Dist: pandas ; extra == 'charts'
+Requires-Dist: pandas<3.0 ; extra == 'charts'
 Requires-Dist: jinja2 ; extra == 'charts'
 Requires-Dist: sphinx>=8 ; extra == 'docs'
 Requires-Dist: sphinx-rtd-theme>=3.0 ; extra == 'docs'
@@ -70,13 +70,13 @@ Requires-Dist: rdflib-jsonld ; extra == 'export'
 Requires-Dist: ndex2 ; extra == 'export'
 Requires-Dist: more-itertools ; extra == 'gha'
 Requires-Dist: click-default-group ; extra == 'health'
-Requires-Dist: pandas ; extra == 'health'
+Requires-Dist: pandas<3.0 ; extra == 'health'
 Requires-Dist: tabulate ; extra == 'health'
 Requires-Dist: pyyaml ; extra == 'health'
 Requires-Dist: jinja2 ; extra == 'health'
-Requires-Dist: pandas ; extra == 'mapping-checking'
+Requires-Dist: pandas<3.0 ; extra == 'mapping-checking'
 Requires-Dist: sentence-transformers ; extra == 'mapping-checking'
-Requires-Dist: pandas ; extra == 'paper-ranking'
+Requires-Dist: pandas<3.0 ; extra == 'paper-ranking'
 Requires-Dist: scikit-learn ; extra == 'paper-ranking'
 Requires-Dist: tabulate ; extra == 'paper-ranking'
 Requires-Dist: pubmed-downloader>=0.0.12 ; extra == 'paper-ranking'
@@ -102,9 +102,9 @@ Maintainer: Charles Tapley Hoyt
 Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 Requires-Python: >=3.10
 Project-URL: Bug Tracker, https://github.com/biopragmatics/bioregistry/issues
-Project-URL: Documentation, https://bioregistry.readthedocs.io
 Project-URL: Homepage, https://github.com/biopragmatics/bioregistry
 Project-URL: Repository, https://github.com/biopragmatics/bioregistry.git
+Project-URL: Documentation, https://bioregistry.readthedocs.io
 Provides-Extra: align
 Provides-Extra: charts
 Provides-Extra: docs

{bioregistry-0.13.17 → bioregistry-0.13.19}/pyproject.toml

@@ -10,7 +10,7 @@ markers = [
 
 [project]
 name = "bioregistry"
-version = "0.13.17"
+version = "0.13.19"
 description = "Integrated registry of biological databases and nomenclatures"
 readme = "README.md"
 authors = [
@@ -88,7 +88,7 @@ align = [
     "defusedxml",
     "class-resolver",
     "fairsharing-client>=0.1.0",
-    "pandas",
+    "pandas<3.0",
 ]
 export = [
     "pyyaml",
@@ -100,12 +100,12 @@ charts = [
     "matplotlib",
     "matplotlib_venn",
     "seaborn",
-    "pandas",
+    "pandas<3.0",
     "jinja2",
 ]
 health = [
     "click_default_group",
-    "pandas",
+    "pandas<3.0",
     "tabulate",
     "pyyaml",
     "jinja2",
@@ -126,13 +126,13 @@ web = [
     "api-analytics[fastapi]",
 ]
 paper-ranking = [
-    "pandas",
+    "pandas<3.0",
     "scikit-learn",
     "tabulate",
     "pubmed-downloader>=0.0.12",
 ]
 mapping-checking = [
-    "pandas",
+    "pandas<3.0",
     "sentence_transformers",
 ]
 
@@ -254,7 +254,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.13.17"
+current_version = "0.13.19"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{bioregistry-0.13.17 → bioregistry-0.13.19}/src/bioregistry/analysis/paper_ranking.py

@@ -24,6 +24,7 @@ import logging
 import textwrap
 from collections import defaultdict
 from pathlib import Path
+from time import sleep
 from typing import TYPE_CHECKING, NamedTuple, TypeAlias, cast
 
 import click
@@ -213,6 +214,7 @@ def _search(
         ):
             if pubmed_id not in pubmed_ids_to_filter:
                 pubmed_to_terms[pubmed_id].append(term)
+            sleep(1)
     return dict(pubmed_to_terms)