Release v3.5.0

Author: althonos

CHANGELOG.md

@@ -6,7 +6,25 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyrodigal/compare/v3.4.0...HEAD
+[Unreleased]: https://github.com/althonos/pyrodigal/compare/v3.5.0...HEAD
+
+
+## [v3.5.0] - 2024-07-17
+[v3.5.0]: https://github.com/althonos/pyrodigal/compare/v3.4.1...v3.5.0
+
+### Added
+- Support for reading from `stdin` in CLI ([#35](https://github.com/althonos/pyrodigal/issues/35)).
+- Flag for changing parallel computation to use `Pool` instead of `ThreadPool` ([#57](https://github.com/althonos/pyrodigal/issues/57)).
+- Better documentation of command line interface ([#56](https://github.com/althonos/pyrodigal/issues/56)).
+- Allow changing the formatter class in `pyrodigal.cli.argument_parser`.
+
+### Changed
+- Migrate documentation to `pydata-sphinx-theme`.
+
+### Fixed
+- Cython warnings with unused `except *` statements in `MetagenomicBins`.
+- Signatures of `__init__` methods missing from all Cython types after the `v3.0` update.
+- Small typos in documentation.
 
 
 ## [v3.4.1] - 2024-05-23

docs/_static/json/switcher.json

@@ -1,4 +1,9 @@
 [
+    {
+        "name": "v3.5 (stable)",
+        "version": "3.5.0",
+        "url": "https://pyrodigal.readthedocs.io/en/v3.5.0/"
+    },
     {
         "name": "v3.4 (stable)",
         "version": "3.4.1",
@@ -34,4 +39,4 @@
         "version": "1.1.2",
         "url": "https://pyrodigal.readthedocs.io/en/v1.1.2/"
     }
-]
+]

docs/guide/cli.rst

@@ -51,6 +51,8 @@ of Pyrodigal, such as multi-threading or smaller gene prediction:
     --max-overlap MAX_OVERLAP      The maximum number of nucleotides that can overlap between two genes on the same strand.
                                    This must be lower or equal to the minimum gene length.
     --no-stop-codon                Disables translation of stop codons into star characters (*) for complete genes.
+      --pool {thread,process}      The sort of pool to use to process genomes in parallel. Processes may be faster than
+                                   threads on some machines, refer to documentation. (default: thread)
 
 Piping
 ------

pyrodigal/_version.py

@@ -1 +1 @@
-__version__ = "3.4.1"
+__version__ = "3.5.0"