bioversions 0.5.513__tar.gz → 0.5.515__tar.gz

{bioversions-0.5.513/src/bioversions.egg-info → bioversions-0.5.515}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.513
+Version: 0.5.515
 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-0.5.513 → bioversions-0.5.515}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-10-15'
-  revision: 812
+  date: '2024-10-16'
+  revision: 814
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -44,6 +44,10 @@ database:
     version: 2024/06
   - retrieved: '2024-10-13'
     version: 2024/09
+  - retrieved: '2024-10-15'
+    version: 2024/06
+  - retrieved: '2024-10-16'
+    version: 2024/09
   vtype: date
 - name: Alzheimer's Disease Ontology
   prefix: ado
@@ -155,6 +159,10 @@ database:
     version: '2024-08-03'
   - retrieved: '2024-10-13'
     version: '2024-09-18'
+  - retrieved: '2024-10-15'
+    version: '2024-08-03'
+  - retrieved: '2024-10-16'
+    version: '2024-09-18'
   vtype: date
 - name: Bambara groundnut ontology
   prefix: co_366
@@ -495,6 +503,10 @@ database:
     version: '2024-04-09'
   - retrieved: '2024-10-13'
     version: '2024-09-26'
+  - retrieved: '2024-10-15'
+    version: '2024-04-09'
+  - retrieved: '2024-10-16'
+    version: '2024-09-26'
   vtype: date
 - name: C. elegans Gross Anatomy Ontology
   prefix: wbbt
@@ -523,6 +535,10 @@ database:
     version: '2024-07-01'
   - retrieved: '2024-10-13'
     version: '2024-09-24'
+  - retrieved: '2024-10-15'
+    version: '2024-07-01'
+  - retrieved: '2024-10-16'
+    version: '2024-09-24'
   vtype: date
 - name: C. elegans phenotype
   prefix: wbphenotype
@@ -567,6 +583,10 @@ database:
     version: '2024-06-05'
   - retrieved: '2024-10-13'
     version: '2024-09-26'
+  - retrieved: '2024-10-15'
+    version: '2024-06-05'
+  - retrieved: '2024-10-16'
+    version: '2024-09-26'
   vtype: date
 - name: Cardiovascular Disease Ontology
   prefix: cvdo
@@ -675,6 +695,10 @@ database:
     version: '2024-08-16'
   - retrieved: '2024-10-13'
     version: '2024-09-26'
+  - retrieved: '2024-10-15'
+    version: '2024-08-16'
+  - retrieved: '2024-10-16'
+    version: '2024-09-26'
   vtype: date
 - name: Cell Type Ontology
   prefix: cl
@@ -1006,6 +1030,10 @@ database:
     version: '2.224'
   - retrieved: '2024-10-13'
     version: '2.227'
+  - retrieved: '2024-10-15'
+    version: '2.224'
+  - retrieved: '2024-10-16'
+    version: '2.227'
   vtype: date
 - name: Clinical Trials Ontology
   prefix: cto
@@ -1209,6 +1237,10 @@ database:
     version: '2023-11-16'
   - retrieved: '2024-10-13'
     version: '2024-09-20'
+  - retrieved: '2024-10-15'
+    version: '2023-11-16'
+  - retrieved: '2024-10-16'
+    version: '2024-09-20'
   vtype: date
 - name: Coronavirus Infectious Disease Ontology
   prefix: cido
@@ -1336,6 +1368,10 @@ database:
     version: 2024c_20240617
   - retrieved: '2024-10-13'
     version: 2024d_20240922
+  - retrieved: '2024-10-15'
+    version: 2024c_20240617
+  - retrieved: '2024-10-16'
+    version: 2024d_20240922
   vtype: other
 - name: Dicty Phenotype Ontology (DDPHENO)
   prefix: ddpheno
@@ -2084,6 +2120,10 @@ database:
     version: '4.179'
   - retrieved: '2024-10-13'
     version: '4.184'
+  - retrieved: '2024-10-15'
+    version: '4.179'
+  - retrieved: '2024-10-16'
+    version: '4.184'
   vtype: date
 - name: Experimental Factor Ontology
   prefix: efo
@@ -2162,6 +2202,10 @@ database:
     version: 3.69.0
   - retrieved: '2024-10-13'
     version: 3.70.0
+  - retrieved: '2024-10-15'
+    version: 3.69.0
+  - retrieved: '2024-10-16'
+    version: 3.70.0
   vtype: semver
 - name: Exposure ontology
   prefix: exo
@@ -2310,6 +2354,10 @@ database:
     version: '2024-09-02'
   - retrieved: '2024-10-13'
     version: '2024-10-07'
+  - retrieved: '2024-10-15'
+    version: '2024-09-02'
+  - retrieved: '2024-10-16'
+    version: '2024-10-07'
   vtype: date
 - name: Flora Phenotype Ontology
   prefix: flopo
@@ -2725,6 +2773,10 @@ database:
     version: '2024-05-21'
   - retrieved: '2024-10-13'
     version: '2024-09-26'
+  - retrieved: '2024-10-15'
+    version: '2024-05-21'
+  - retrieved: '2024-10-16'
+    version: '2024-09-26'
   vtype: semver
 - name: Glycan Naming and Subsumption Ontology (GNOme)
   prefix: gno
@@ -2863,6 +2915,9 @@ 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 +3553,10 @@ database:
     version: '2024-08-08'
   - retrieved: '2024-10-13'
     version: '2024-09-18'
+  - retrieved: '2024-10-15'
+    version: '2024-08-08'
+  - retrieved: '2024-10-16'
+    version: '2024-09-18'
   vtype: date
 - name: Mass Spectrometry Controlled Vocabulary
   prefix: ms
@@ -3540,6 +3599,10 @@ database:
     version: 4.1.173
   - retrieved: '2024-10-13'
     version: 4.1.179
+  - retrieved: '2024-10-15'
+    version: 4.1.173
+  - retrieved: '2024-10-16'
+    version: 4.1.179
   vtype: date
 - name: Mathematical modeling ontology
   prefix: mamo
@@ -3596,6 +3659,10 @@ database:
     version: '2.138'
   - retrieved: '2024-10-13'
     version: '2.141'
+  - retrieved: '2024-10-15'
+    version: '2.138'
+  - retrieved: '2024-10-16'
+    version: '2.141'
   vtype: date
 - name: Medaka Developmental Stages
   prefix: olatdv
@@ -3973,6 +4040,10 @@ database:
     version: '2024-08-06'
   - retrieved: '2024-10-13'
     version: '2024-10-01'
+  - retrieved: '2024-10-15'
+    version: '2024-08-06'
+  - retrieved: '2024-10-16'
+    version: '2024-10-01'
   vtype: date
 - name: MOP
   prefix: mop
@@ -4269,6 +4340,10 @@ database:
     version: '2022-10-05'
   - retrieved: '2024-10-13'
     version: '2024-08-27'
+  - retrieved: '2024-10-15'
+    version: '2022-10-05'
+  - retrieved: '2024-10-16'
+    version: '2024-08-27'
   vtype: date
 - name: NMR-instrument specific component of metabolomics investigations
   prefix: nmr
@@ -4733,6 +4808,9 @@ 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 +5045,10 @@ database:
     version: '2024-06-27'
   - retrieved: '2024-10-13'
     version: '2024-09-12'
+  - retrieved: '2024-10-15'
+    version: '2024-06-27'
+  - retrieved: '2024-10-16'
+    version: '2024-09-12'
   vtype: date
 - name: Ontology of Genetic Susceptibility Factor
   prefix: ogsf
@@ -5075,6 +5157,10 @@ database:
     version: '2024-01-25'
   - retrieved: '2024-10-13'
     version: '2024-09-30'
+  - retrieved: '2024-10-15'
+    version: '2024-01-25'
+  - retrieved: '2024-10-16'
+    version: '2024-09-30'
   vtype: date
 - name: Ontology of Precision Medicine and Investigation
   prefix: opmi
@@ -5426,6 +5512,10 @@ database:
     version: '2024-03-28'
   - retrieved: '2024-10-13'
     version: '2024-09-04'
+  - retrieved: '2024-10-15'
+    version: '2024-03-28'
+  - retrieved: '2024-10-16'
+    version: '2024-09-04'
   vtype: date
 - name: PHI-base Ontology
   prefix: phi
@@ -6087,6 +6177,10 @@ database:
     version: '6.230'
   - retrieved: '2024-10-13'
     version: '6.235'
+  - retrieved: '2024-10-15'
+    version: '6.230'
+  - retrieved: '2024-10-16'
+    version: '6.235'
   vtype: date
 - name: Reactome
   prefix: reactome
@@ -7744,6 +7838,10 @@ database:
     version: '2024-08-06'
   - retrieved: '2024-10-13'
     version: '2024-09-17'
+  - retrieved: '2024-10-15'
+    version: '2024-08-06'
+  - retrieved: '2024-10-16'
+    version: '2024-09-17'
   vtype: date
 - name: The COVID-19 Infectious Disease Ontology
   prefix: idocovid19
@@ -7784,6 +7882,10 @@ database:
     version: '2024-08-07'
   - retrieved: '2024-10-13'
     version: '2024-09-04'
+  - retrieved: '2024-10-15'
+    version: '2024-08-07'
+  - retrieved: '2024-10-16'
+    version: '2024-09-04'
   vtype: date
 - name: The Echinoderm Anatomy and Development Ontology
   prefix: ecao
@@ -7941,6 +8043,10 @@ database:
     version: '2024-08-07'
   - retrieved: '2024-10-13'
     version: '2024-09-03'
+  - retrieved: '2024-10-15'
+    version: '2024-08-07'
+  - retrieved: '2024-10-16'
+    version: '2024-09-03'
   vtype: date
 - name: UBERON
   prefix: uberon
@@ -7975,6 +8081,10 @@ database:
     version: '2017-10-31'
   - retrieved: '2024-10-13'
     version: '2024-09-04'
+  - retrieved: '2024-10-15'
+    version: '2017-10-31'
+  - retrieved: '2024-10-16'
+    version: '2024-09-04'
   vtype: date
 - name: Unified phenotype ontology (uPheno)
   prefix: upheno
@@ -8144,6 +8254,10 @@ database:
     version: '2024-08-11'
   - retrieved: '2024-10-13'
     version: '2024-09-22'
+  - retrieved: '2024-10-15'
+    version: '2024-08-11'
+  - retrieved: '2024-10-16'
+    version: '2024-09-22'
   vtype: semver
 - name: Variation Ontology
   prefix: vario
@@ -8220,6 +8334,10 @@ database:
     version: '2024-08-13'
   - retrieved: '2024-10-13'
     version: '2024-10-02'
+  - retrieved: '2024-10-15'
+    version: '2024-08-13'
+  - retrieved: '2024-10-16'
+    version: '2024-10-02'
   vtype: date
 - name: VEuPathDB Ontology
   prefix: eupath
@@ -8443,6 +8561,10 @@ database:
     version: '2024-08-23'
   - retrieved: '2024-10-13'
     version: '2024-09-03'
+  - retrieved: '2024-10-15'
+    version: '2024-08-23'
+  - retrieved: '2024-10-16'
+    version: '2024-09-03'
   vtype: date
 - name: Xenopus Phenotype Ontology
   prefix: xpo
@@ -10175,6 +10297,8 @@ database:
     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-0.5.515/docs/failures.md

@@ -0,0 +1,5 @@
+# Errors
+
+- failed to resolve DisGeNet
+- failed to resolve Antibody Registry
+- failed to resolve SwissLipids

{bioversions-0.5.513 → bioversions-0.5.515}/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>2024-10-15T01:02:09.800391</dc:date>
+    <dc:date>2024-10-16T01:01:59.694293</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.513 → bioversions-0.5.515}/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>2024-10-15T01:02:09.746710</dc:date>
+    <dc:date>2024-10-16T01:01:59.639305</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.513 → bioversions-0.5.515}/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>2024-10-15T01:02:09.665461</dc:date>
+    <dc:date>2024-10-16T01:01:59.555508</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.513 → bioversions-0.5.515}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = bioversions
-version = 0.5.513
+version = 0.5.515
 description = What's the current version for each biological database?
 long_description = file: README.md
 long_description_content_type = text/markdown

{bioversions-0.5.513 → bioversions-0.5.515}/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