Release v1.0.0-alpha.3

althonos · Oct 10, 2019 · 5a9c0d8 · 5a9c0d8
1 parent 1649800
commit 5a9c0d8
Show file tree

Hide file tree

Showing 6 changed files with 39 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,30 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.2...HEAD
+[Unreleased]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.3...HEAD
+
+## [1.0.0-alpha.3] - 2019-10-10
+[1.0.0-alpha.2]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.2...v1.0.0-alpha.3
+### Added
+- Extraction of `oboInOwl:consider` annotation in `RdfXMLParser`.
+- Extraction of `oboInOwl:savedBy` annotation in `RdfXMLParser`.
+- Extraction of `subsetdef` and `synonymtypedef` as annotation properties in
+  `RdfXMLParser`.
+- Support for `doap:Version` instead of `owl:VersionIri` for specification
+  of ontology data version.
+- Proper comparison of `PropertyValue` classes, based on the lexicographic order
+  of their serialization.
+- `Ontology.dump` and `Ontology.dumps` methods to serialize an ontology in
+  **obo** or **obojson** format.
+### Fixed
+- `Metadata` not storing optional description of ID spaces if any.
+- Wrong type hints in `RelationshipData.equivalent_to_chain`.
+### Changed
+- Added type checking to some more property setters.
+- Avoid using `networkx` in `Term.subclasses`.
+- `fastobo`-derived parsers will not create a new entity if one exists in the
+  graph of dependencies already.
+- Exposed `pronto.warnings` and the complete warnings hierarchy.
 
 ## [1.0.0-alpha.2] - 2019-10-03
 [1.0.0-alpha.2]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.1...v1.0.0-alpha.2

diff --git a/pronto/_version.txt b/pronto/_version.txt
@@ -1 +1 @@
-1.0.0-alpha.2
+1.0.0-alpha.3
diff --git a/pronto/parsers/base.py b/pronto/parsers/base.py
@@ -28,6 +28,7 @@ def process_imports(
             imports: Set[str],
             import_depth: int = -1,
             basepath: str = "",
+            timeout: int = 5,
     ) -> Dict[str, Ontology]:
         # check we did not reach the maximum import depth
         resolved = {}
@@ -47,9 +48,10 @@ def process_imports(
                 else:
                     id_ = f"{ref}.obo" if not os.path.splitext(ref)[1] else ref
                     url = f"http://purl.obolibrary.org/obo/{id_}"
-
             resolved[ref] = Ontology(
-                url, max(import_depth - 1, 0), self.ont.timeout
+                url,
+                max(import_depth - 1, 0),
+                timeout
             )
 
         # return the resolved imports

diff --git a/pronto/parsers/obo.py b/pronto/parsers/obo.py
@@ -1,3 +1,5 @@
+import os
+
 import fastobo
 
 from .base import BaseParser
@@ -18,10 +20,11 @@ def parse_from(self, handle):
 
         # Extract metadata from the OBO header and resolve imports
         self.ont.metadata = self._extract_metadata(doc.header())
-        self.ont.medata.imports.update(self.process_imports(
+        self.ont.imports.update(self.process_imports(
             self.ont.metadata.imports,
             self.ont.import_depth,
             os.path.dirname(self.ont.path or str()),
+            self.ont.timeout,
         ))
 
         # Extract frames from the current document.

diff --git a/pronto/parsers/obojson.py b/pronto/parsers/obojson.py
@@ -1,3 +1,5 @@
+import os
+
 import fastobo
 
 from .base import BaseParser
@@ -18,10 +20,11 @@ def parse_from(self, handle):
 
         # Extract metadata from the graph metadata and resolve imports
         self.ont.metadata = self._extract_metadata(doc.header)
-        self.ont.medata.imports.update(self.process_imports(
+        self.ont.imports.update(self.process_imports(
             self.ont.metadata.imports,
             self.ont.import_depth,
             os.path.dirname(self.ont.path or str()),
+            self.ont.timeout,
         ))
 
         # Extract frames from the current document.

diff --git a/pronto/parsers/rdfxml.py b/pronto/parsers/rdfxml.py
@@ -89,10 +89,11 @@ def parse_from(self, handle):
         self.ont.metadata = self._extract_meta(owl_ontology)
 
         # Process imports
-        self.ont.medata.imports.update(self.process_imports(
+        self.ont.imports.update(self.process_imports(
             self.ont.metadata.imports,
             self.ont.import_depth,
             os.path.dirname(self.ont.path or str()),
+            self.ont.timeout,
         ))
 
         # Parse typedef first to handle OBO shorthand renaming