rcsb.workflow 0.44__tar.gz → 0.46__tar.gz

{rcsb_workflow-0.44 → rcsb_workflow-0.46}/HISTORY.txt

@@ -36,3 +36,5 @@
                     Make CARDTargetOntologyProvider stashable on Buildlocker
 21-May-2024 - V0.43 Fix pylinting
 20-Aug-2024 - V0.44 Add step for loading target cofactor data to MongoDB
+27-Aug-2024 - V0.45 Update usage of CARDTargetOntologyProvider
+22-Oct-2024 - V0.46 Update requirements and CI/CD (to use python 3.10)

{rcsb_workflow-0.44/rcsb.workflow.egg-info → rcsb_workflow-0.46}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: rcsb.workflow
-Version: 0.44
+Version: 0.46
 Summary: RCSB Python data processing and ETL/ELT workflow entry points
 Home-page: https://github.com/rcsb/py-rcsb_workflow
 Author: John Westbrook
@@ -12,16 +12,17 @@ Classifier: Natural Language :: English
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: OpenEye-toolkits>=2020.2.2
+Requires-Dist: OpenEye-toolkits>=2024.1.1
 Requires-Dist: rcsb.utils.chem>=0.79
-Requires-Dist: rcsb.utils.seq>=0.79
-Requires-Dist: rcsb.utils.targets>=0.80
+Requires-Dist: rcsb.utils.seq>=0.82
+Requires-Dist: rcsb.utils.targets>=0.82
 Requires-Dist: rcsb.utils.seqalign>=0.29
-Requires-Dist: rcsb.exdb>=1.22
-Requires-Dist: rcsb.utils.io>=1.46
+Requires-Dist: rcsb.exdb>=1.24
+Requires-Dist: rcsb.utils.io>=1.48
 Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"
 Provides-Extra: test

{rcsb_workflow-0.44 → rcsb_workflow-0.46}/rcsb/workflow/chem/__init__.py

@@ -2,4 +2,4 @@ __docformat__ = "google en"
 __author__ = "John Westbrook"
 __email__ = "john.westbrook@rcsb.org"
 __license__ = "Apache 2.0"
-__version__ = "0.44"
+__version__ = "0.46"

{rcsb_workflow-0.44 → rcsb_workflow-0.46}/rcsb/workflow/targets/ProteinTargetSequenceWorkflow.py

@@ -16,6 +16,7 @@
 #  12-Jun-2023 dwp Set useTaxonomy filter to False for CARD annotations
 #   6-Jul-2023 aae Don't overwrite Buildlocker files if there is no data
 #  20-Aug-2024 dwp Add step for loading target cofactor data to MongoDB
+#  27-Aug-2024 dwp Update usage of CARDTargetOntologyProvider
 ##
 __docformat__ = "google en"
 __author__ = "John Westbrook"
@@ -359,17 +360,18 @@ class ProteinTargetSequenceWorkflow(object):
                     okB = fP.backup(self.__cfgOb, self.__configName, remotePrefix=remotePrefix, useStash=True, useGit=False)
                     logger.info("%r features backup status (%r)", resourceName, okB)
             elif resourceName == "card":
+                fP = CARDTargetOntologyProvider(cachePath=self.__cachePath, useCache=True)
+                ok = fP.buildOntologyData()
+                fP.reload()
+                if ok and backup and fP.testCache():
+                    okB = fP.backup(self.__cfgOb, self.__configName, remotePrefix=remotePrefix, useStash=True, useGit=False)
+                    logger.info("%r ontology backup status (%r)", resourceName, okB)
                 fP = CARDTargetAnnotationProvider(cachePath=self.__cachePath, useCache=True)
                 ok = fP.buildAnnotationList(resultPath, useTaxonomy=useTaxonomy)
                 fP.reload()
                 if ok and backup and fP.testCache():
                     okB = fP.backup(self.__cfgOb, self.__configName, remotePrefix=remotePrefix, useStash=True, useGit=False)
                     logger.info("%r annotations backup status (%r)", resourceName, okB)
-                fP = CARDTargetOntologyProvider(cachePath=self.__cachePath, useCache=False)
-                ok = fP.reload()
-                if ok and backup and fP.testCache():
-                    okB = fP.backup(self.__cfgOb, self.__configName, remotePrefix=remotePrefix, useStash=True, useGit=False)
-                    logger.info("%r ontology backup status (%r)", resourceName, okB)
             elif resourceName == "imgt":
                 fP = IMGTTargetFeatureProvider(cachePath=self.__cachePath, useCache=True)
                 ok = fP.buildFeatureList(useCache=True)

{rcsb_workflow-0.44 → rcsb_workflow-0.46/rcsb.workflow.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: rcsb.workflow
-Version: 0.44
+Version: 0.46
 Summary: RCSB Python data processing and ETL/ELT workflow entry points
 Home-page: https://github.com/rcsb/py-rcsb_workflow
 Author: John Westbrook
@@ -12,16 +12,17 @@ Classifier: Natural Language :: English
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: OpenEye-toolkits>=2020.2.2
+Requires-Dist: OpenEye-toolkits>=2024.1.1
 Requires-Dist: rcsb.utils.chem>=0.79
-Requires-Dist: rcsb.utils.seq>=0.79
-Requires-Dist: rcsb.utils.targets>=0.80
+Requires-Dist: rcsb.utils.seq>=0.82
+Requires-Dist: rcsb.utils.targets>=0.82
 Requires-Dist: rcsb.utils.seqalign>=0.29
-Requires-Dist: rcsb.exdb>=1.22
-Requires-Dist: rcsb.utils.io>=1.46
+Requires-Dist: rcsb.exdb>=1.24
+Requires-Dist: rcsb.utils.io>=1.48
 Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"
 Provides-Extra: test

rcsb_workflow-0.46/rcsb.workflow.egg-info/requires.txt

@@ -0,0 +1,13 @@
+OpenEye-toolkits>=2024.1.1
+rcsb.utils.chem>=0.79
+rcsb.utils.seq>=0.82
+rcsb.utils.targets>=0.82
+rcsb.utils.seqalign>=0.29
+rcsb.exdb>=1.24
+rcsb.utils.io>=1.48
+
+[dev]
+check-manifest
+
+[test]
+coverage

rcsb_workflow-0.46/requirements.txt

@@ -0,0 +1,8 @@
+--extra-index-url https://pypi.anaconda.org/OpenEye/simple
+OpenEye-toolkits >= 2024.1.1
+rcsb.utils.chem >= 0.79
+rcsb.utils.seq >= 0.82
+rcsb.utils.targets >= 0.82
+rcsb.utils.seqalign >= 0.29
+rcsb.exdb >= 1.24
+rcsb.utils.io >= 1.48

{rcsb_workflow-0.44 → rcsb_workflow-0.46}/setup.py

@@ -45,7 +45,8 @@ setup(
         "License :: OSI Approved :: Apache Software License",
         "Programming Language :: Python",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
     ],
     # entry_points={"console_scripts": ["cactvs_annotate_mol=rcsb.workflow.cactvsAnnotateMol:main"]},
     #  The following is somewhat flakey --

rcsb_workflow-0.44/rcsb.workflow.egg-info/requires.txt

@@ -1,13 +0,0 @@
-OpenEye-toolkits>=2020.2.2
-rcsb.utils.chem>=0.79
-rcsb.utils.seq>=0.79
-rcsb.utils.targets>=0.80
-rcsb.utils.seqalign>=0.29
-rcsb.exdb>=1.22
-rcsb.utils.io>=1.46
-
-[dev]
-check-manifest
-
-[test]
-coverage

rcsb_workflow-0.44/requirements.txt

@@ -1,8 +0,0 @@
---extra-index-url https://pypi.anaconda.org/OpenEye/simple
-OpenEye-toolkits >= 2020.2.2
-rcsb.utils.chem >= 0.79
-rcsb.utils.seq >= 0.79
-rcsb.utils.targets >= 0.80
-rcsb.utils.seqalign >= 0.29
-rcsb.exdb >= 1.22
-rcsb.utils.io >= 1.46