From f3c1a26b0d7c2503de9b206ae4146b3403091bba Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Fri, 25 Oct 2024 16:23:33 +0200
Subject: [PATCH] bump to v0.4.0

---
 CHANGES.md     | 22 +++++++++++++++++-----
 pyproject.toml |  2 +-
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 3ce03f7..e1a3b9f 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,14 +1,21 @@
 ## Unreleased
 
-*Date: On going*
+## [v0.3.0](https://github.com/js2264/momics/releases/tag/0.4.0)
+
+*Date: 2024-10-25*
 
 ### API changes
 
-* All ranges are now 0-based half-open intervals, as in `pyranges` and BED files.
+* `MultiRangeQuery` -> `MomicsQuery`.
+* `manifest` method to output the whole configuration of a `Momics` instance.
+* `consolidate` method to consolidate a `Momics` repository.
+* No submodules are imported in `__init__.py` anymore.
+* All export functions are now `Momics` methods.
 * All ingestion methods for `Momics` now start with `ingest_*`.
 
 ### New features
 
+* `aggregate` submodule to merge dictionaries of partial coverage tracks (over pyranges) into genome-wide tracks.
 * Relatively basic `ChromNN` CNN `TensorFlow` model.
 * `MomicsDataset` class to pass data to `TensorFlow` models.
 * `MomicsStreamer` class to stream data from `Momics` repositories.
@@ -17,14 +24,17 @@
 
 ### Enhancements
 
+* CLI is now partially based on `cloup` to improve user experience.
+* `seq(label = "...)` now returns the sequence for an entire chromosome.
 * `tracks(label = "...)` now returns the genome-wide track.
-* `MultiRangeQuery` queries now rely on `pyranges` for range queries.
-* `MultiRangeQuery` queries can extract only a subset of the tracks.
+* `MomicsQuery` queries now rely on `pyranges` for range queries.
+* `MomicsQuery` queries can extract only a subset of the tracks.
 * `add_track` and `remove` methods for `Momics` class.
-* `to_npz` and `to_json` methods for `MultiRangeQuery` class.
+* `to_npz` and `to_json` methods for `MomicsQuery` class.
 
 ### Maintenance
 
+* Support jupyter notebooks in documentation.
 * Add changelog.
 * Improve docs.
 * Logging system updates.
@@ -33,6 +43,8 @@
 
 ### Bug fixes
 
+* Ensure that queries are done per chromosome, even if provided ranges are stranded.
+* All ranges are now 0-based half-open intervals, as in `pyranges` and BED files.
 * Parallelization for queries only relies on `TileDB` internal system.
 * Filters used in `Momics` tables.
 * Removal of `Azure`-hosted repositories.
diff --git a/pyproject.toml b/pyproject.toml
index 556b799..c8361ae 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "momics"
-version = "0.3.0"
+version = "0.4.0"
 description = "A package to create and manage genome-related TileDB arrays"
 requires-python = ">=3.8"
 license = {text = "CC BY-NC 4.0"}