From c11fd22a9ed6d9d1698ca38da9451992286d3901 Mon Sep 17 00:00:00 2001
From: Trevor Manz <trevor.j.manz@gmail.com>
Date: Mon, 27 Jan 2025 12:57:32 -0500
Subject: [PATCH 1/4] Document release flow in `README.md`
---
README.md | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/README.md b/README.md
index 481596e..7662e6a 100644
--- a/README.md
+++ b/README.md
@@ -89,3 +89,17 @@ left column and its corresponding action in the right column. The formatting is
clean and easy to read.
Our CI enforces formatting, linting, and tests.
+
+## Changelog
+
+Check the [GitHub Releases](https://github.com/higlass/higlass-python/releases) for a detailed changelog.
+
+## Release
+
+Releases are managed via the GitHub UI:
+
+1. [Draft a new release](https://github.com/higlass/higlass-python/releases/new)
+2. **Create a tag** in the format `v[major].[minor].[patch]`.
+ - *Note:* You can either create the tag in the GitHub UI or select an existing tag created via the Git CLI. The tag triggers publishing to PyPI.
+3. **Generate release notes** to summarize changes from merged PRs, and edit.
+4. Add details for significant changes or migration steps, and ensure titles are clear and consistent.
From 45988e5aa7efb074f7dc7223446f2742081b0736 Mon Sep 17 00:00:00 2001
From: Trevor Manz <trevor.j.manz@gmail.com>
Date: Tue, 28 Jan 2025 13:53:30 -0500
Subject: [PATCH 2/4] Remove `CHANGELOG.md`
Point to GitHub Releases instead and updates PR template with
instructions
---
.github/PULL_REQUEST_TEMPLATE.md | 7 +-
CHANGELOG.md | 153 -------------------------------
2 files changed, 4 insertions(+), 156 deletions(-)
delete mode 100644 CHANGELOG.md
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 8da7db3..5eb7362 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,6 +8,7 @@ Fixes #___
## Checklist
-- [ ] Unit tests added or updated
-- [ ] Documentation added or updated
-- [ ] Updated CHANGELOG.md
+- [ ] **Clear PR title** (used for generating release notes).
+ - Prefer using prefixes like `fix:` or `feat:` to help organize auto-generated notes.
+- [ ] **Unit tests** added or updated.
+- [ ] **Documentation** added or updated.
diff --git a/CHANGELOG.md b/CHANGELOG.md
deleted file mode 100644
index 8e8559e..0000000
--- a/CHANGELOG.md
+++ /dev/null
@@ -1,153 +0,0 @@
-## [v1.2.1](https://github.com/higlass/higlass-python/compare/v1.2.0...v1.2.1)
-
-- Calculate file pointer hash for track uids for tileset tracks
-- Fix view copy behavior to preserve specific plugin track class vars
-
-## [v1.2.0](https://github.com/higlass/higlass-python/compare/v1.1.2...v1.2.0)
-
-- **Breaking**: Migrate to higlass-schema v0.2.0 (pydantic v2)
-- Shorter automatic uids for Tracks and Views
-- Upgrade HiGlass front-end to v1.13
-
-This release does not introduce changes to the `higlass-python` API itself. However, it migrates the core data objects created and modified by the `higlass-python` API from Pydantic v1 to Pydantic v2. We are marking this as a **breaking release**, as some methods and attributes on these objects are now deprecated.
-
-Libraries relying on `higlass-schema` (Pydantic models for Python) may encounter breaking changes if they use methods that have changed between Pydantic v1 and v2. We expect this update to improve compatibility and make it easier to use `higlass-python` in environments that depend on Pydantic v2 (which are increasing).
-
-## [v1.1.2](https://github.com/higlass/higlass-python/compare/v1.1.1...v1.1.2)
-
-- Pin higlass-schema version upper bound for <v1.2
-
-## [v1.1.1](https://github.com/higlass/higlass-python/compare/v1.1.0...v1.1.1)
-
-- Upgrade anywidget version
-- Add vertical track variants for auto layout
-
-## [v1.1.0](https://github.com/higlass/higlass-python/compare/v1.0.3...v1.1.0)
-
-- Add bedlike file support
-
-## [v1.0.3](https://github.com/higlass/higlass-python/compare/v1.0.2...v1.0.3)
-
-- Ensure JS is included in PyPI wheel
-
-## [v1.0.2](https://github.com/higlass/higlass-python/compare/v1.0.1...v1.0.2)
-
-- Added docs on passing in an auth header
-- Ensure JS is included in PyPI wheel
-
-## [v1.0.1](https://github.com/higlass/higlass-python/compare/v1.0.1...v1.0.0)
-
-- Pass kwargs in to Viewconf.widget() so that they can be passed on to the higlass widget and potentially make their way to the higlass component
-
-## [v0.4.8](https://github.com/higlass/higlass-python/compare/v0.4.8...v0.4.7)
-
-- Bumped higlass version
-
-## [v0.4.7](https://github.com/higlass/higlass-python/compare/v0.4.7...v0.4.6)
-
-- Bumped pillow version
-
-## [v0.4.6](https://github.com/higlass/higlass-python/compare/v0.4.6...v0.4.5)
-
-- Added inline_tile support for bed-like items
-- Bumped React version dependency to ensure compatibility with latest Juptyerlab
-- Bumped higlass version to v1.11.8
-- Bumped matplotlib version and added pillow dependency version
-
-## [v0.4.5](https://github.com/higlass/higlass-python/compare/v0.4.5...v0.4.4)
-
-- Add constructor for multivec tilesets
-- Added wrapper for bam tileset generator
-- Updated docs to include examples for bam and multivec tilesets
-- Add proxy support
-- Add support for listening on a unix socket
-
-## [v0.4.4](https://github.com/higlass/higlass-python/compare/v0.4.4...v0.4.3)
-
-- Added default positions for non `horizontal-` tracks
-- Update docs to include Views import in simple example
-- Bump HiGlass to v1.11
-
-## [v0.4.2](https://github.com/higlass/higlass-python/compare/v0.4.2...v0.4.1)
-
-- Only load FUSE python package when it is called to avoid libfuse missing error
-
-## [v0.4.1](https://github.com/higlass/higlass-python/compare/v0.4.1...v0.4.0)
-
-- Add missing `pixi.js` dependency from `higlass-jupyter`
-- Update `@jupyter-widgets/base` to support Jupyter Lab v2
-- Update simple-httpfs to fix the missing `boto3` error
-
-## [v0.4.0](https://github.com/higlass/higlass-python/compare/v0.4.0...v0.3.0)
-
-- API for adding genome position search box within python
-- Removed default log file creation. Servers now log to in-memory stream by default.
-- Copied Python docs over from the higlass repo
-- Added `save_as_png` function
-- Added section on track types and multiple views to the docs
-- Overloaded '+' operator to for combining tracks and creating CombinedTracks
-- Added `ViewProjection` track
-- Remove the higlass-python.log files that are created everywhere
-- Overloaded the '/' operator to create divided tracks
-- Added support using matplotlib colormaps
-- Created simplified view creation API
-- Add auth_token parameter to higlass.display
-- Use higlass v1.8.1
-- Parameters for turning on the genome position search box
-
-## [v0.3.0](https://github.com/higlass/higlass-python/compare/v0.2.1...v0.3.0)
-
-- Support multiple overlays and allow to set the `uid` and `type` options manually
-- Add support for value locks via the new `value_scale_syncs` argument of `display()` and `ViewConf`
-- Allow not starting FUSE by passing `no_fuse=True` to `display()`
-- Update the HiGlass JavaScript library to `v1.7`
-
-## [v0.2.1](https://github.com/higlass/higlass-python/compare/v0.2.0...v0.2.1)
-
-- Fixed #30: Example working again
-- Fixed `overlay` property by making it a property of `Views`. Also updated HiGlass to v1.6.11 to properly render overlays.
-
-## [v0.2.0](https://github.com/higlass/higlass-python/compare/v0.1.13...v0.2.0)
-
-- Implement two-way data bindings via traitlets. See [notebooks/two-way-data-binding.ipynb](notebooks/two-way-data-binding.ipynb) for an example
-- Add `overlays` to `display` and `ViewConf` to be able to define overlays
-- Store HiGlass' JavaScript API on the widget's root container. This container can be found via a random ID that is stored in `widget.dom_element_id`
-
-## [v0.1.14](https://github.com/higlass/higlass-python/compare/v0.1.13...v0.1.14)
-
-- Add compatibility with JupyterLab `v1` and ipywidgets `v7.5`
-- Bumped HiGlass to `v1.6`
-
-## [v0.1.13](https://github.com/higlass/higlass-python/compare/v0.1.12...v0.1.13)
-
-- Added top-level exports of `view`, `display`, `Tileset`, `Server`, `Track`, `CombinedTrack`, `View`, and `ViewConf`
-
-## [v0.1.12](https://github.com/higlass/higlass-python/compare/v0.1.11...v0.1.12)
-
-- Expose dark mode in `higlass.display(dark_mode=True)`
-- Do not mutate track objects in `higlass.display()` for reusability
-- Further API cleaning. `ViewConf.views` is a list of views now
-
-## [v0.1.11](https://github.com/higlass/higlass-python/compare/v0.1.10...v0.1.11)
-
-- Convenience function for loading 2d labeled points from a dataframe.
-- Remove Flask-related debugging and uninformative logs
-- Add `__repr__` to `ViewConf` for convenience
-
-## [v0.1.10](https://github.com/higlass/higlass-python/compare/v0.1.8...v0.1.10)
-
-- Synchronized Python and node package versions
-
-## [v0.1.8](https://github.com/higlass/higlass-python/compare/v0.1.7...v0.1.8)
-
-- Fix installation
-
-## [v0.1.7](https://github.com/higlass/higlass-python/compare/v0.1.1...v0.1.7)
-
-- Bumped higlass version to `v1.5`
-- Added CombinedTrack
-- Added change_atributes and change_options functions
-
-## [v0.1.1](https://github.com/higlass/higlass-python/releases/tag/v0.1.1)
-
-- First release
From 90e29c91742d694bfc7d1648e33be08cc5ff7880 Mon Sep 17 00:00:00 2001
From: Trevor Manz <trevor.j.manz@gmail.com>
Date: Tue, 28 Jan 2025 13:55:55 -0500
Subject: [PATCH 3/4] Add note about docs
---
README.md | 1 +
1 file changed, 1 insertion(+)
diff --git a/README.md b/README.md
index 7662e6a..8733e58 100644
--- a/README.md
+++ b/README.md
@@ -102,4 +102,5 @@ Releases are managed via the GitHub UI:
2. **Create a tag** in the format `v[major].[minor].[patch]`.
- *Note:* You can either create the tag in the GitHub UI or select an existing tag created via the Git CLI. The tag triggers publishing to PyPI.
3. **Generate release notes** to summarize changes from merged PRs, and edit.
+ - Documentation and CI changes don't belong in release notes
4. Add details for significant changes or migration steps, and ensure titles are clear and consistent.
From 71db13f2611133f08093491cfa75333fe124d3eb Mon Sep 17 00:00:00 2001
From: Trevor Manz <trevor.j.manz@gmail.com>
Date: Tue, 28 Jan 2025 19:01:47 -0500
Subject: [PATCH 4/4] Update instructions
---
README.md | 23 +++++++++++++++--------
1 file changed, 15 insertions(+), 8 deletions(-)
diff --git a/README.md b/README.md
index 8733e58..b98e7cb 100644
--- a/README.md
+++ b/README.md
@@ -96,11 +96,18 @@ Check the [GitHub Releases](https://github.com/higlass/higlass-python/releases)
## Release
-Releases are managed via the GitHub UI:
-
-1. [Draft a new release](https://github.com/higlass/higlass-python/releases/new)
-2. **Create a tag** in the format `v[major].[minor].[patch]`.
- - *Note:* You can either create the tag in the GitHub UI or select an existing tag created via the Git CLI. The tag triggers publishing to PyPI.
-3. **Generate release notes** to summarize changes from merged PRs, and edit.
- - Documentation and CI changes don't belong in release notes
-4. Add details for significant changes or migration steps, and ensure titles are clear and consistent.
+Releases are managed via the GitHub UI.
+
+[Draft a new release](https://github.com/higlass/higlass-python/releases/new):
+
+1. **Create a tag**
+ - Click _"Choose a tag"_, then **type a new tag** in the format `v[major].[minor].[patch]` to create it.
+ - _Note_: The UI is not obvious about this. You can create a tag here, not just select one. Tag creation triggers a [workflow](.github/workflows/ci.yml) to publish to PyPI.
+
+2. **Generate release notes**
+ - Click _"Generate Release Notes"_ to auto-summarize changes from merged PRs.
+ - Edit to exclude irrelevant changes for end users (e.g., docs or CI).
+
+3. **Document significant changes**
+ - Add migration steps or noteworthy updates.
+ - Ensure PR titles are clear and consistent.