bioversions 0.6.9__tar.gz → 0.6.11__tar.gz

{bioversions-0.6.9 → bioversions-0.6.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bioversions
-Version: 0.6.9
+Version: 0.6.11
 Summary: Get the current version for biological databases
 Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
 Project-URL: Homepage, https://github.com/biopragmatics/bioversions

{bioversions-0.6.9 → bioversions-0.6.11}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-12-17'
-  revision: 873
+  date: '2024-12-19'
+  revision: 875
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -5125,6 +5125,12 @@ database:
   - date: '2024-12-13'
     retrieved: '2024-12-15'
     version: December 13, 2024
+  - date: '2024-12-16'
+    retrieved: '2024-12-18'
+    version: December 16, 2024
+  - date: '2024-12-17'
+    retrieved: '2024-12-19'
+    version: December 17, 2024
   vtype: date
 - name: 'OntoAvida: ontology for Avida digital evolution platform'
   prefix: ontoavida
@@ -8179,6 +8185,10 @@ database:
     version: '2024-12-16'
   - retrieved: '2024-12-17'
     version: '2024-12-17'
+  - retrieved: '2024-12-18'
+    version: '2024-12-18'
+  - retrieved: '2024-12-19'
+    version: '2024-12-19'
   vtype: date
 - name: SWO (The Software Ontology)
   prefix: swo
@@ -10908,6 +10918,10 @@ database:
     version: '2024-12-14'
   - retrieved: '2024-12-17'
     version: '2024-12-15'
+  - retrieved: '2024-12-18'
+    version: '2024-12-16'
+  - retrieved: '2024-12-19'
+    version: '2024-12-17'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

{bioversions-0.6.9 → bioversions-0.6.11}/docs/failures.md

@@ -3,7 +3,7 @@
 - DisGeNet - failed to resolve DisGeNet
 - Antibody Registry - failed to resolve Antibody Registry
 - DrugBank - failed to resolve DrugBank
-- Ensembl - failed to resolve Ensembl
+- InterPro - failed to resolve InterPro
 
 ## DisGeNet
 
@@ -144,38 +144,43 @@ requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.d
 
 ```
 
-## Ensembl
+## InterPro
 
-Using class: `EnsemblGetter`
+Using class: `InterProGetter`
 
 ```python-traceback
 Traceback (most recent call last):
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 536, in _make_request
-    response = conn.getresponse()
-               ^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 507, in getresponse
-    httplib_response = super().getresponse()
-                       ^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 1428, in getresponse
-    response.begin()
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 331, in begin
-    version, status, reason = self._read_status()
-                              ^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 292, in _read_status
-    line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
-               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/socket.py", line 720, in readinto
-    return self._sock.recv_into(b)
-           ^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1251, in recv_into
-    return self.read(nbytes, buffer)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1103, in read
-    return self._sslobj.read(len, buffer)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-TimeoutError: The read operation timed out
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 789, in urlopen
+    response = self._make_request(
+               ^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 490, in _make_request
+    raise new_e
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 466, in _make_request
+    self._validate_conn(conn)
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1095, in _validate_conn
+    conn.connect()
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 730, in connect
+    sock_and_verified = _ssl_wrap_socket_and_match_hostname(
+                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 909, in _ssl_wrap_socket_and_match_hostname
+    ssl_sock = ssl_wrap_socket(
+               ^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 469, in ssl_wrap_socket
+    ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
+               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 513, in _ssl_wrap_socket_impl
+    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 455, in wrap_socket
+    return self.sslsocket_class._create(
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1041, in _create
+    self.do_handshake()
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1319, in do_handshake
+    self._sslobj.do_handshake()
+ConnectionResetError: [Errno 104] Connection reset by peer
 
-The above exception was the direct cause of the following exception:
+During handling of the above exception, another exception occurred:
 
 Traceback (most recent call last):
   File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 667, in send
@@ -187,16 +192,37 @@ Traceback (most recent call last):
   File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/retry.py", line 474, in increment
     raise reraise(type(error), error, _stacktrace)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/util.py", line 39, in reraise
-    raise value
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/util.py", line 38, in reraise
+    raise value.with_traceback(tb)
   File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 789, in urlopen
     response = self._make_request(
                ^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 538, in _make_request
-    self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 369, in _raise_timeout
-    raise ReadTimeoutError(
-urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='useast.ensembl.org', port=443): Read timed out. (read timeout=15)
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 490, in _make_request
+    raise new_e
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 466, in _make_request
+    self._validate_conn(conn)
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1095, in _validate_conn
+    conn.connect()
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 730, in connect
+    sock_and_verified = _ssl_wrap_socket_and_match_hostname(
+                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 909, in _ssl_wrap_socket_and_match_hostname
+    ssl_sock = ssl_wrap_socket(
+               ^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 469, in ssl_wrap_socket
+    ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
+               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 513, in _ssl_wrap_socket_impl
+    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 455, in wrap_socket
+    return self.sslsocket_class._create(
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1041, in _create
+    self.do_handshake()
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1319, in do_handshake
+    self._sslobj.do_handshake()
+urllib3.exceptions.ProtocolError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
 
 During handling of the above exception, another exception occurred:
 
@@ -228,27 +254,21 @@ Traceback (most recent call last):
   File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
     cls._cache = cls().get()
                  ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/ensembl.py", line 23, in get
-    soup = get_soup(URL)
-           ^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 62, in get_soup
-    res = requests.get(url, verify=verify, timeout=timeout or 15, headers=headers)
-          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
-    return request("get", url, params=params, **kwargs)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 59, in request
-    return session.request(method=method, url=url, **kwargs)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/interpro.py", line 28, in get
+    res = session.get(
+          ^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 602, in get
+    return self.request("GET", url, **kwargs)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
     resp = self.send(prep, **send_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
     r = adapter.send(request, **kwargs)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 713, in send
-    raise ReadTimeout(e, request=request)
-requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='useast.ensembl.org', port=443): Read timed out. (read timeout=15)
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 682, in send
+    raise ConnectionError(err, request=request)
+requests.exceptions.ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
 
 ```
 

{bioversions-0.6.9 → bioversions-0.6.11}/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>2024-12-17T01:07:21.409484</dc:date>
+    <dc:date>2024-12-19T01:05:15.034275</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.9 → bioversions-0.6.11}/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>2024-12-17T01:07:21.313364</dc:date>
+    <dc:date>2024-12-19T01:05:14.918357</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.9 → bioversions-0.6.11}/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>2024-12-17T01:07:21.240918</dc:date>
+    <dc:date>2024-12-19T01:05:14.842043</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.9 → bioversions-0.6.11}/docs/source/conf.py

@@ -26,7 +26,7 @@ copyright = f"{date.today().year}, Charles Tapley Hoyt"
 author = "Charles Tapley Hoyt"
 
 # The full version, including alpha/beta/rc tags.
-release = "0.6.9"
+release = "0.6.11"
 
 # The short X.Y version.
 parsed_version = re.match(

{bioversions-0.6.9 → bioversions-0.6.11}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bioversions"
-version = "0.6.9"
+version = "0.6.11"
 description = "Get the current version for biological databases"
 readme = "README.md"
 authors = [
@@ -222,7 +222,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.6.9"
+current_version = "0.6.11"
 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}",

{bioversions-0.6.9 → bioversions-0.6.11}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 873,
-    "date": "2024-12-17",
+    "revision": 875,
+    "date": "2024-12-19",
     "author": "runner"
   },
   "database": [
@@ -9251,6 +9251,16 @@
           "retrieved": "2024-12-15",
           "version": "December 13, 2024",
           "date": "2024-12-13"
+        },
+        {
+          "retrieved": "2024-12-18",
+          "version": "December 16, 2024",
+          "date": "2024-12-16"
+        },
+        {
+          "retrieved": "2024-12-19",
+          "version": "December 17, 2024",
+          "date": "2024-12-17"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -15026,6 +15036,14 @@
         {
           "retrieved": "2024-12-17",
           "version": "2024-12-17"
+        },
+        {
+          "retrieved": "2024-12-18",
+          "version": "2024-12-18"
+        },
+        {
+          "retrieved": "2024-12-19",
+          "version": "2024-12-19"
         }
       ],
       "name": "SwissLipids",
@@ -20030,6 +20048,14 @@
         {
           "retrieved": "2024-12-17",
           "version": "2024-12-15"
+        },
+        {
+          "retrieved": "2024-12-18",
+          "version": "2024-12-16"
+        },
+        {
+          "retrieved": "2024-12-19",
+          "version": "2024-12-17"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.6.9 → bioversions-0.6.11}/src/bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.6.9"
+VERSION = "0.6.11"
 
 
 def get_git_hash() -> str: