bioversions 0.5.451__tar.gz → 0.5.453__tar.gz

{bioversions-0.5.451/src/bioversions.egg-info → bioversions-0.5.453}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.451
+Version: 0.5.453
 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-0.5.451 → bioversions-0.5.453}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-08-12'
-  revision: 751
+  date: '2024-08-14'
+  revision: 753
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -1631,6 +1631,9 @@ database:
   - date: '2022-02-01'
     retrieved: '2022-02-03'
     version: 2022-Feb
+  - date: '2024-06-01'
+    retrieved: '2024-08-14'
+    version: 2024-Jun
   vtype: month
 - name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
   prefix: dideo
@@ -3936,6 +3939,9 @@ database:
   - homepage: https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.2
     retrieved: '2023-10-21'
     version: '2023.2'
+  - homepage: https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2024.1
+    retrieved: '2024-08-13'
+    version: '2024.1'
   vtype: year_minor
 - name: Mungbean ontology
   prefix: co_346
@@ -5759,6 +5765,8 @@ database:
     version: '2024-05-10'
   - retrieved: '2024-05-21'
     version: Found<-title>
+  - retrieved: '2024-08-13'
+    version: '2024-08-09'
   vtype: date
 - name: Rat Strain Ontology
   prefix: rs
@@ -9717,6 +9725,10 @@ database:
     version: '2024-08-09'
   - retrieved: '2024-08-12'
     version: '2024-08-10'
+  - retrieved: '2024-08-13'
+    version: '2024-08-11'
+  - retrieved: '2024-08-14'
+    version: '2024-08-12'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

{bioversions-0.5.451 → bioversions-0.5.453}/docs/failures.md

@@ -1,8 +1,7 @@
 # Errors
 
-- issue parsing Drug Gene Interaction Database: 
 - failed to resolve DisGeNet
-- issue parsing Online Mendelian Inheritance in Man: Issue parsing OMIMGetter version Augu 9, 2024 with fmt %B %d, %Y
+- issue parsing Online Mendelian Inheritance in Man: Issue parsing OMIMGetter version Augu 12, 2024 with fmt %B %d, %Y
 - failed to resolve Antibody Registry
 - failed to resolve PathBank
 - failed to resolve SwissLipids

{bioversions-0.5.451 → bioversions-0.5.453}/docs/img/has_release_url.svg

@@ -6,11 +6,11 @@
   <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>2024-08-12T00:57:16.187623</dc:date>
+    <dc:date>2024-08-14T00:55:56.200644</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>
-      <dc:title>Matplotlib v3.9.1.post1, https://matplotlib.org/</dc:title>
+      <dc:title>Matplotlib v3.9.2, https://matplotlib.org/</dc:title>
      </cc:Agent>
     </dc:creator>
    </cc:Work>

{bioversions-0.5.451 → bioversions-0.5.453}/docs/img/version_date_types.svg

@@ -6,11 +6,11 @@
   <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>2024-08-12T00:57:16.134485</dc:date>
+    <dc:date>2024-08-14T00:55:56.147186</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>
-      <dc:title>Matplotlib v3.9.1.post1, https://matplotlib.org/</dc:title>
+      <dc:title>Matplotlib v3.9.2, https://matplotlib.org/</dc:title>
      </cc:Agent>
     </dc:creator>
    </cc:Work>

{bioversions-0.5.451 → bioversions-0.5.453}/docs/img/version_types.svg

@@ -6,11 +6,11 @@
   <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>2024-08-12T00:57:16.053563</dc:date>
+    <dc:date>2024-08-14T00:55:56.066886</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>
-      <dc:title>Matplotlib v3.9.1.post1, https://matplotlib.org/</dc:title>
+      <dc:title>Matplotlib v3.9.2, https://matplotlib.org/</dc:title>
      </cc:Agent>
     </dc:creator>
    </cc:Work>

{bioversions-0.5.451 → bioversions-0.5.453}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = bioversions
-version = 0.5.451
+version = 0.5.453
 description = What's the current version for each biological database?
 long_description = file: README.md
 long_description_content_type = text/markdown

{bioversions-0.5.451 → bioversions-0.5.453}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 751,
-    "date": "2024-08-12",
+    "revision": 753,
+    "date": "2024-08-14",
     "author": "runner"
   },
   "database": [
@@ -2964,6 +2964,11 @@
           "retrieved": "2022-02-03",
           "version": "2022-Feb",
           "date": "2022-02-01"
+        },
+        {
+          "retrieved": "2024-08-14",
+          "version": "2024-Jun",
+          "date": "2024-06-01"
         }
       ],
       "name": "Drug Gene Interaction Database",
@@ -7155,6 +7160,11 @@
           "retrieved": "2023-10-21",
           "version": "2023.2",
           "homepage": "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.2"
+        },
+        {
+          "retrieved": "2024-08-13",
+          "version": "2024.1",
+          "homepage": "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2024.1"
         }
       ],
       "vtype": "year_minor"
@@ -10434,6 +10444,10 @@
         {
           "retrieved": "2024-05-21",
           "version": "Found<-title>"
+        },
+        {
+          "retrieved": "2024-08-13",
+          "version": "2024-08-09"
         }
       ],
       "name": "Rat Genome Database",
@@ -17823,6 +17837,14 @@
         {
           "retrieved": "2024-08-12",
           "version": "2024-08-10"
+        },
+        {
+          "retrieved": "2024-08-13",
+          "version": "2024-08-11"
+        },
+        {
+          "retrieved": "2024-08-14",
+          "version": "2024-08-12"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.5.451 → bioversions-0.5.453}/src/bioversions/sources/dgi.py

@@ -2,14 +2,13 @@
 
 """A getter for the `Drug Gene Interaction Database (DGI-DB) <http://www.dgidb.org>`_."""
 
-import os
-
 import bs4
+import dateutil.parser
 import requests
 
 from bioversions.utils import Getter, VersionType
 
-DOWNLOADS_PAGE = "https://www.dgidb.org/downloads"
+GITHUB_PAGE = "https://github.com/dgidb/dgidb-v5"
 
 
 class DGIGetter(Getter):
@@ -21,14 +20,14 @@ class DGIGetter(Getter):
 
     def get(self):
         """Get the latest DGI version number."""
-        res = requests.get(DOWNLOADS_PAGE)
-        soup = bs4.BeautifulSoup(res.content, parser="lxml", features="lxml")
-        cells = list(soup.select("table#tsv_downloads tbody tr:first-child td:nth-child(2) a"))
-        if 1 != len(cells):
+        res = requests.get(GITHUB_PAGE)
+        soup = bs4.BeautifulSoup(res.content)
+        time_tag = soup.find("relative-time")
+        if time_tag is None:
             raise ValueError
-        cell = cells[0]
-        href = cell["href"]
-        version = os.path.dirname(os.path.relpath(href, "data/monthly_tsvs"))
+        datetime_str = time_tag.attrs["datetime"]
+        dt_obj = dateutil.parser.parse(datetime_str)
+        version = dt_obj.strftime(self.date_version_fmt)
         return version
 
 

{bioversions-0.5.451 → bioversions-0.5.453}/src/bioversions/sources/rgd.py

@@ -10,7 +10,7 @@ __all__ = [
     "RGDGetter",
 ]
 
-URL = "https://download.rgd.mcw.edu/data_release/GENES.RAT.txt"
+URL = "https://download.rgd.mcw.edu/data_release/GENES_RAT.txt"
 
 
 class RGDGetter(Getter):

{bioversions-0.5.451 → bioversions-0.5.453}/src/bioversions/version.py

@@ -9,7 +9,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.451"
+VERSION = "0.5.453"
 
 
 def get_git_hash() -> str:

{bioversions-0.5.451 → bioversions-0.5.453/src/bioversions.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.451
+Version: 0.5.453
 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