Release v1.0.0-alpha.1

CHANGELOG.md

@@ -5,5 +5,25 @@ 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.1...HEAD
 
-[Unreleased]: https://github.com/althonos/pronto/compare/v0.7.2...HEAD
+## [1.0.0-alpha.1] - 2019-10-02
+[1.0.0-alpha.1]: https://github.com/althonos/pronto/compare/v0.12.2...v1.0.0-alpha.1
+### Changed
+- Dropped support for Python earlier than `3.6`.
+- Brand new data model that follow the OBO 1.4 object model.
+- Partial OWL XML parser implementation using the OBO 1.4 semantics.
+- New OBO parser implementation based on `fastobo`.
+- Imports are properly separated from the top-level ontology.
+- `Ontology.__getitem__` can also access entities from imports.
+- `Term`, `Relationship`, `Xref`, `SynonymType` compare only based on their ID.
+- `Subset`, `Definition` compare only based on their textual value.
+### Added
+- Support for OBO JSON parser based on `fastobo`.
+- Provisional `mypy` type hints.
+- Type checking for most properties in `__debug__` mode.
+- Proper `repr` implementation that should roundtrip most of the time.
+- Detection of file format and encoding based on buffer content.
+### Removed
+- OBO and JSON serialization support (for now).
+- `Term.rchildren` and `Term.rparents` and stop making direction assumptions on relationships.

setup.cfg

@@ -12,7 +12,7 @@ license-file = COPYING
 platform = any
 keywords = bioinformatics, ontology, OBO, OWL, convert, parse
 classifiers =
-    Development Status :: 4 - Beta
+    Development Status :: 3 - Alpha
     Programming Language :: Python
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3.6

tests/test_issues.py

@@ -22,7 +22,7 @@ class TestIssues(unittest.TestCase):
     def test_parser_consistency(self):
         """Assert several runs on the same file give the same output.
 
-        See (#4)[https://github.com/althonos/pronto/issues/4].
+        See `#4 <https://github.com/althonos/pronto/issues/4>`_.
         Thanks to @winni-genp for issue reporting.
         """
         path = os.path.join(utils.DATADIR, "imagingMS.obo")
@@ -35,7 +35,7 @@ def test_parser_consistency(self):
     def test_unicode_in_term_names(self):
         """Test if unicode characters in term names work.
 
-        See (#6)[https://github.com/althonos/pronto/issues/6].
+        See `#6 <https://github.com/althonos/pronto/issues/6>`_.
         Thanks to @owen-jones-gen for issue reporting.
         """
         ont = pronto.Ontology(os.path.join(utils.DATADIR, "owen-jones-gen.obo"))