bioversions 0.5.512__tar.gz → 0.5.514__tar.gz

{bioversions-0.5.512/src/bioversions.egg-info → bioversions-0.5.514}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.512
+Version: 0.5.514
 Summary: What's the current version for each biological database?
 Home-page: https://github.com/biopragmatics/bioversions
 Download-URL: https://github.com/biopragmatics/bioversions/releases

{bioversions-0.5.512 → bioversions-0.5.514}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
-  author: runner
-  date: '2024-10-14'
-  revision: 811
+  author: cthoyt
+  date: '2024-10-15'
+  revision: 813
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -44,6 +44,8 @@ database:
     version: 2024/06
   - retrieved: '2024-10-13'
     version: 2024/09
+  - retrieved: '2024-10-15'
+    version: 2024/06
   vtype: date
 - name: Alzheimer's Disease Ontology
   prefix: ado
@@ -155,6 +157,8 @@ database:
     version: '2024-08-03'
   - retrieved: '2024-10-13'
     version: '2024-09-18'
+  - retrieved: '2024-10-15'
+    version: '2024-08-03'
   vtype: date
 - name: Bambara groundnut ontology
   prefix: co_366
@@ -495,6 +499,8 @@ database:
     version: '2024-04-09'
   - retrieved: '2024-10-13'
     version: '2024-09-26'
+  - retrieved: '2024-10-15'
+    version: '2024-04-09'
   vtype: date
 - name: C. elegans Gross Anatomy Ontology
   prefix: wbbt
@@ -523,6 +529,8 @@ database:
     version: '2024-07-01'
   - retrieved: '2024-10-13'
     version: '2024-09-24'
+  - retrieved: '2024-10-15'
+    version: '2024-07-01'
   vtype: date
 - name: C. elegans phenotype
   prefix: wbphenotype
@@ -567,6 +575,8 @@ database:
     version: '2024-06-05'
   - retrieved: '2024-10-13'
     version: '2024-09-26'
+  - retrieved: '2024-10-15'
+    version: '2024-06-05'
   vtype: date
 - name: Cardiovascular Disease Ontology
   prefix: cvdo
@@ -675,6 +685,8 @@ database:
     version: '2024-08-16'
   - retrieved: '2024-10-13'
     version: '2024-09-26'
+  - retrieved: '2024-10-15'
+    version: '2024-08-16'
   vtype: date
 - name: Cell Type Ontology
   prefix: cl
@@ -1006,6 +1018,8 @@ database:
     version: '2.224'
   - retrieved: '2024-10-13'
     version: '2.227'
+  - retrieved: '2024-10-15'
+    version: '2.224'
   vtype: date
 - name: Clinical Trials Ontology
   prefix: cto
@@ -1209,6 +1223,8 @@ database:
     version: '2023-11-16'
   - retrieved: '2024-10-13'
     version: '2024-09-20'
+  - retrieved: '2024-10-15'
+    version: '2023-11-16'
   vtype: date
 - name: Coronavirus Infectious Disease Ontology
   prefix: cido
@@ -1336,6 +1352,8 @@ database:
     version: 2024c_20240617
   - retrieved: '2024-10-13'
     version: 2024d_20240922
+  - retrieved: '2024-10-15'
+    version: 2024c_20240617
   vtype: other
 - name: Dicty Phenotype Ontology (DDPHENO)
   prefix: ddpheno
@@ -2084,6 +2102,8 @@ database:
     version: '4.179'
   - retrieved: '2024-10-13'
     version: '4.184'
+  - retrieved: '2024-10-15'
+    version: '4.179'
   vtype: date
 - name: Experimental Factor Ontology
   prefix: efo
@@ -2162,6 +2182,8 @@ database:
     version: 3.69.0
   - retrieved: '2024-10-13'
     version: 3.70.0
+  - retrieved: '2024-10-15'
+    version: 3.69.0
   vtype: semver
 - name: Exposure ontology
   prefix: exo
@@ -2310,6 +2332,8 @@ database:
     version: '2024-09-02'
   - retrieved: '2024-10-13'
     version: '2024-10-07'
+  - retrieved: '2024-10-15'
+    version: '2024-09-02'
   vtype: date
 - name: Flora Phenotype Ontology
   prefix: flopo
@@ -2725,6 +2749,8 @@ database:
     version: '2024-05-21'
   - retrieved: '2024-10-13'
     version: '2024-09-26'
+  - retrieved: '2024-10-15'
+    version: '2024-05-21'
   vtype: semver
 - name: Glycan Naming and Subsumption Ontology (GNOme)
   prefix: gno
@@ -2863,6 +2889,9 @@ database:
   - homepage: http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/json/hgnc_complete_set_2024-08-23.json
     retrieved: '2024-08-24'
     version: '2024-08-23'
+  - homepage: https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-10-01.json
+    retrieved: '2024-10-15'
+    version: '2024-10-01'
   vtype: date
 - name: Histopathology Ontology
   prefix: hpath
@@ -3498,6 +3527,8 @@ database:
     version: '2024-08-08'
   - retrieved: '2024-10-13'
     version: '2024-09-18'
+  - retrieved: '2024-10-15'
+    version: '2024-08-08'
   vtype: date
 - name: Mass Spectrometry Controlled Vocabulary
   prefix: ms
@@ -3540,6 +3571,8 @@ database:
     version: 4.1.173
   - retrieved: '2024-10-13'
     version: 4.1.179
+  - retrieved: '2024-10-15'
+    version: 4.1.173
   vtype: date
 - name: Mathematical modeling ontology
   prefix: mamo
@@ -3596,6 +3629,8 @@ database:
     version: '2.138'
   - retrieved: '2024-10-13'
     version: '2.141'
+  - retrieved: '2024-10-15'
+    version: '2.138'
   vtype: date
 - name: Medaka Developmental Stages
   prefix: olatdv
@@ -3973,6 +4008,8 @@ database:
     version: '2024-08-06'
   - retrieved: '2024-10-13'
     version: '2024-10-01'
+  - retrieved: '2024-10-15'
+    version: '2024-08-06'
   vtype: date
 - name: MOP
   prefix: mop
@@ -4269,6 +4306,8 @@ database:
     version: '2022-10-05'
   - retrieved: '2024-10-13'
     version: '2024-08-27'
+  - retrieved: '2024-10-15'
+    version: '2022-10-05'
   vtype: date
 - name: NMR-instrument specific component of metabolomics investigations
   prefix: nmr
@@ -4733,6 +4772,9 @@ database:
   - date: '2024-10-11'
     retrieved: '2024-10-13'
     version: October 11, 2024
+  - date: '2024-10-14'
+    retrieved: '2024-10-15'
+    version: October 14, 2024
   vtype: date
 - name: 'OntoAvida: ontology for Avida digital evolution platform'
   prefix: ontoavida
@@ -4967,6 +5009,8 @@ database:
     version: '2024-06-27'
   - retrieved: '2024-10-13'
     version: '2024-09-12'
+  - retrieved: '2024-10-15'
+    version: '2024-06-27'
   vtype: date
 - name: Ontology of Genetic Susceptibility Factor
   prefix: ogsf
@@ -5075,6 +5119,8 @@ database:
     version: '2024-01-25'
   - retrieved: '2024-10-13'
     version: '2024-09-30'
+  - retrieved: '2024-10-15'
+    version: '2024-01-25'
   vtype: date
 - name: Ontology of Precision Medicine and Investigation
   prefix: opmi
@@ -5426,6 +5472,8 @@ database:
     version: '2024-03-28'
   - retrieved: '2024-10-13'
     version: '2024-09-04'
+  - retrieved: '2024-10-15'
+    version: '2024-03-28'
   vtype: date
 - name: PHI-base Ontology
   prefix: phi
@@ -6087,6 +6135,8 @@ database:
     version: '6.230'
   - retrieved: '2024-10-13'
     version: '6.235'
+  - retrieved: '2024-10-15'
+    version: '6.230'
   vtype: date
 - name: Reactome
   prefix: reactome
@@ -7744,6 +7794,8 @@ database:
     version: '2024-08-06'
   - retrieved: '2024-10-13'
     version: '2024-09-17'
+  - retrieved: '2024-10-15'
+    version: '2024-08-06'
   vtype: date
 - name: The COVID-19 Infectious Disease Ontology
   prefix: idocovid19
@@ -7784,6 +7836,8 @@ database:
     version: '2024-08-07'
   - retrieved: '2024-10-13'
     version: '2024-09-04'
+  - retrieved: '2024-10-15'
+    version: '2024-08-07'
   vtype: date
 - name: The Echinoderm Anatomy and Development Ontology
   prefix: ecao
@@ -7941,6 +7995,8 @@ database:
     version: '2024-08-07'
   - retrieved: '2024-10-13'
     version: '2024-09-03'
+  - retrieved: '2024-10-15'
+    version: '2024-08-07'
   vtype: date
 - name: UBERON
   prefix: uberon
@@ -7975,6 +8031,8 @@ database:
     version: '2017-10-31'
   - retrieved: '2024-10-13'
     version: '2024-09-04'
+  - retrieved: '2024-10-15'
+    version: '2017-10-31'
   vtype: date
 - name: Unified phenotype ontology (uPheno)
   prefix: upheno
@@ -8144,6 +8202,8 @@ database:
     version: '2024-08-11'
   - retrieved: '2024-10-13'
     version: '2024-09-22'
+  - retrieved: '2024-10-15'
+    version: '2024-08-11'
   vtype: semver
 - name: Variation Ontology
   prefix: vario
@@ -8220,6 +8280,8 @@ database:
     version: '2024-08-13'
   - retrieved: '2024-10-13'
     version: '2024-10-02'
+  - retrieved: '2024-10-15'
+    version: '2024-08-13'
   vtype: date
 - name: VEuPathDB Ontology
   prefix: eupath
@@ -8443,6 +8505,8 @@ database:
     version: '2024-08-23'
   - retrieved: '2024-10-13'
     version: '2024-09-03'
+  - retrieved: '2024-10-15'
+    version: '2024-08-23'
   vtype: date
 - name: Xenopus Phenotype Ontology
   prefix: xpo
@@ -10173,6 +10237,10 @@ database:
     version: '2024-10-10'
   - retrieved: '2024-10-14'
     version: '2024-10-12'
+  - retrieved: '2024-10-15'
+    version: '2024-10-13'
+  - retrieved: '2024-10-15'
+    version: '2024-10-14'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

bioversions-0.5.514/docs/failures.md

@@ -0,0 +1,6 @@
+# Errors
+
+- failed to resolve DisGeNet
+- failed to resolve Antibody Registry
+- failed to resolve PathBank
+- failed to resolve SwissLipids

{bioversions-0.5.512 → bioversions-0.5.514}/docs/img/has_release_url.svg

@@ -6,7 +6,7 @@
   <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-10-14T01:03:44.733386</dc:date>
+    <dc:date>2024-10-15T01:02:09.800391</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.512 → bioversions-0.5.514}/docs/img/version_date_types.svg

@@ -6,7 +6,7 @@
   <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-10-14T01:03:44.677219</dc:date>
+    <dc:date>2024-10-15T01:02:09.746710</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.512 → bioversions-0.5.514}/docs/img/version_types.svg

@@ -6,7 +6,7 @@
   <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-10-14T01:03:44.592827</dc:date>
+    <dc:date>2024-10-15T01:02:09.665461</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.512 → bioversions-0.5.514}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = bioversions
-version = 0.5.512
+version = 0.5.514
 description = What's the current version for each biological database?
 long_description = file: README.md
 long_description_content_type = text/markdown

{bioversions-0.5.512 → bioversions-0.5.514}/src/bioversions/resources/update.py

@@ -7,6 +7,7 @@ import sys
 from datetime import datetime
 
 import click
+from tqdm import tqdm
 from tqdm.contrib.logging import logging_redirect_tqdm
 
 from bioversions.resources import (
@@ -83,7 +84,7 @@ def _update(force: bool):
             v["releases"].append(append_dict)
 
     if not changes and not force:
-        click.secho(f"No changes to {EXPORT_PATH}", fg="yellow", bold=True)
+        tqdm.write(click.style(f"No changes to {EXPORT_PATH}", fg="yellow", bold=True))
     else:
         rv_database = sorted(versions.values(), key=lambda version: version["name"].lower())
         rv = {
@@ -94,7 +95,7 @@ def _update(force: bool):
             },
             "database": rv_database,
         }
-        click.secho(f"Writing new {EXPORT_PATH}", fg="green", bold=True)
+        tqdm.write(click.style(f"Writing new {EXPORT_PATH}", fg="green", bold=True))
         write_export(rv)
         write_versions(rv)
 
@@ -106,7 +107,7 @@ def _log_update(bv) -> None:
     if bv.homepage:
         text += f". See {bv.homepage}"
 
-    click.secho(text, fg="green", bold=True)
+    tqdm.write(click.style(text, fg="green", bold=True))
 
     try:
         from .. import slack_client

{bioversions-0.5.512 → bioversions-0.5.514}/src/bioversions/resources/versions.json

@@ -1,8 +1,8 @@
 {
   "annotations": {
-    "revision": 811,
-    "date": "2024-10-14",
-    "author": "runner"
+    "revision": 813,
+    "date": "2024-10-15",
+    "author": "cthoyt"
   },
   "database": [
     {
@@ -82,6 +82,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024/09"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024/06"
         }
       ],
       "vtype": "date"
@@ -293,6 +297,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-18"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-03"
         }
       ],
       "vtype": "date"
@@ -910,6 +918,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-26"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-04-09"
         }
       ],
       "name": "C. elegans development ontology",
@@ -967,6 +979,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-24"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-07-01"
         }
       ],
       "vtype": "date"
@@ -1052,6 +1068,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-26"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-06-05"
         }
       ],
       "name": "C. elegans phenotype",
@@ -1261,6 +1281,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-26"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-16"
         }
       ],
       "prefix": "cl",
@@ -1847,6 +1871,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2.227"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2.224"
         }
       ],
       "vtype": "date"
@@ -2216,6 +2244,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-20"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2023-11-16"
         }
       ],
       "vtype": "date"
@@ -2460,6 +2492,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024d_20240922"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024c_20240617"
         }
       ],
       "vtype": "other"
@@ -3804,6 +3840,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "4.184"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "4.179"
         }
       ],
       "vtype": "date"
@@ -3959,6 +3999,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "3.70.0"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "3.69.0"
         }
       ],
       "vtype": "semver"
@@ -4251,6 +4295,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-10-07"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-09-02"
         }
       ],
       "vtype": "date"
@@ -4981,6 +5029,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-26"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-05-21"
         }
       ],
       "name": "Glycan Naming and Subsumption Ontology",
@@ -5213,6 +5265,11 @@
           "retrieved": "2024-08-24",
           "version": "2024-08-23",
           "homepage": "http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/json/hgnc_complete_set_2024-08-23.json"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-10-01",
+          "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-10-01.json"
         }
       ],
       "name": "HGNC",
@@ -6341,6 +6398,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-18"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-08"
         }
       ],
       "vtype": "date"
@@ -6421,6 +6482,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "4.1.179"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "4.1.173"
         }
       ],
       "name": "Mass spectrometry ontology",
@@ -6532,6 +6597,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2.141"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2.138"
         }
       ],
       "vtype": "date"
@@ -7225,6 +7294,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-10-01"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-06"
         }
       ],
       "vtype": "date"
@@ -7755,6 +7828,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-08-27"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2022-10-05"
         }
       ],
       "name": "Next Generation Biobanking Ontology",
@@ -8550,6 +8627,11 @@
           "retrieved": "2024-10-13",
           "version": "October 11, 2024",
           "date": "2024-10-11"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "October 14, 2024",
+          "date": "2024-10-14"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -9001,6 +9083,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-12"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-06-27"
         }
       ],
       "vtype": "date"
@@ -9208,6 +9294,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-30"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-01-25"
         }
       ],
       "name": "Ontology of Organizational Structures of Trauma centers and Trauma systems",
@@ -9830,6 +9920,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-04"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-03-28"
         }
       ],
       "prefix": "pato",
@@ -11026,6 +11120,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "6.235"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "6.230"
         }
       ],
       "vtype": "date"
@@ -14240,6 +14338,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-17"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-06"
         }
       ],
       "vtype": "date"
@@ -14318,6 +14420,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-04"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-07"
         }
       ],
       "vtype": "date"
@@ -14616,6 +14722,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-03"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-07"
         }
       ],
       "name": "Uber Anatomy Ontology",
@@ -14681,6 +14791,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-04"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2017-10-31"
         }
       ],
       "name": "Unified Phenotype Ontology",
@@ -14978,6 +15092,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-22"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-11"
         }
       ],
       "vtype": "semver"
@@ -15124,6 +15242,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-10-02"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-13"
         }
       ],
       "vtype": "date"
@@ -15487,6 +15609,10 @@
         {
           "retrieved": "2024-10-13",
           "version": "2024-09-03"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-08-23"
         }
       ],
       "vtype": "date"
@@ -18660,6 +18786,14 @@
         {
           "retrieved": "2024-10-14",
           "version": "2024-10-12"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-10-13"
+        },
+        {
+          "retrieved": "2024-10-15",
+          "version": "2024-10-14"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.5.512 → bioversions-0.5.514}/src/bioversions/sources/dgi.py

@@ -21,7 +21,7 @@ class DGIGetter(Getter):
     def get(self):
         """Get the latest DGI version number."""
         res = requests.get(GITHUB_PAGE)
-        soup = bs4.BeautifulSoup(res.content)
+        soup = bs4.BeautifulSoup(res.content, features="html.parser")
         time_tag = soup.find("relative-time")
         if time_tag is None:
             raise ValueError

bioversions-0.5.514/src/bioversions/sources/hgnc.py

@@ -0,0 +1,43 @@
+# -*- coding: utf-8 -*-
+
+"""A getter for HGNC."""
+
+import datetime
+import logging
+
+import requests
+
+from bioversions.utils import Getter, VersionType
+
+__all__ = [
+    "HGNCGetter",
+]
+
+logger = logging.getLogger(__name__)
+
+PATH = "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/"
+PREFIX = "hgnc_complete_set_"
+SUFFIX = ".json"
+
+
+class HGNCGetter(Getter):
+    """A getter for HGNC."""
+
+    bioregistry_id = "hgnc"
+    name = "HGNC"
+    homepage_fmt = PATH + "hgnc_complete_set_{version}.json"
+
+    version_type = VersionType.date
+
+    def get(self) -> str:
+        """Get the latest HGNC version number."""
+        today = datetime.date.today()
+        maybe = today.strftime("%Y-%m-01")
+        res = requests.head(self.homepage_fmt.format(version=maybe))
+        if res.status_code == 200:
+            return maybe
+        raise ValueError(f"HGNC hasn't posted new data for this month under version {maybe}")
+
+
+if __name__ == "__main__":
+    HGNCGetter.print()

{bioversions-0.5.512 → bioversions-0.5.514}/src/bioversions/version.py

@@ -9,7 +9,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.512"
+VERSION = "0.5.514"
 
 
 def get_git_hash() -> str:

{bioversions-0.5.512 → bioversions-0.5.514/src/bioversions.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.512
+Version: 0.5.514
 Summary: What's the current version for each biological database?
 Home-page: https://github.com/biopragmatics/bioversions
 Download-URL: https://github.com/biopragmatics/bioversions/releases

bioversions-0.5.512/docs/failures.md

@@ -1,6 +0,0 @@
-# Errors
-
-- failed to resolve DisGeNet
-- failed to resolve Antibody Registry
-- issue parsing HGNC: max() arg is an empty sequence
-- failed to resolve SwissLipids

bioversions-0.5.512/src/bioversions/sources/hgnc.py

@@ -1,43 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""A getter for HGNC."""
-
-import logging
-
-from bioversions.utils import Getter, VersionType, get_soup
-
-__all__ = [
-    "HGNCGetter",
-]
-
-logger = logging.getLogger(__name__)
-
-PATH = "https://ftp.ebi.ac.uk/pub/databases/genenames/new/archive/monthly/json/"
-PREFIX = "hgnc_complete_set_"
-SUFFIX = ".json"
-
-
-class HGNCGetter(Getter):
-    """A getter for HGNC."""
-
-    bioregistry_id = "hgnc"
-    name = "HGNC"
-    homepage_fmt = (
-        "http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/"
-        "archive/monthly/json/hgnc_complete_set_{version}.json"
-    )
-
-    version_type = VersionType.date
-
-    def get(self) -> str:
-        """Get the latest HGNC version number."""
-        soup = get_soup(PATH)
-        return max(
-            anchor.attrs["href"][len(PREFIX) : -len(SUFFIX)]
-            for anchor in soup.find_all("a")
-            if anchor.attrs["href"].startswith(PREFIX)
-        )
-
-
-if __name__ == "__main__":
-    HGNCGetter.print()