updated changelong

Author: sbooeshaghi

docs/CHANGELOG.md

@@ -1,27 +1,65 @@
 ---
 title: Changelog
-date: 2024-06-25
+date: 2024-10-08
 authors:
   - name: A. Sina Booeshaghi
 ---
 
 # Changelog
 
-## [0.2.x] - XXXX-XX-XX
+## [0.3.0] - XXXX-XX-XX (Unreleased)
+
+### Added
+
+- Added typing hints to many `Assay` and `Region` functions
+- Added `'k key` to `seqspec info` to display one of `meta` for metadata, `sequence_spec` for sequence spec, and `library_spec` for library spec
+- Added `-f format` to `seqspec info` to enable multiple formats for displaying info
+- Added support for 0 length regions in the specification
+- Added ability to modify reads using `seqspec modify`
+- `seqspec init` now accepts read information
+- Added templates and updated documentation to myst, website
+- Added new examples (e.g., dogmaseq-dig)
+- Added File object to Read
+- Added SeqKit, SeqProtocol, LibKit, and LibProtocol attributes
+- Added option to specify multiple SeqKit, SeqProtocol, LibKit, LibProtocol for each modality
+- Added name validation against known list of SeqKit, SeqProtocol, LibKit, LibProtocol
+- Added new attributes to Onlist object (Onlist now contains a File object):
+  - filetype
+  - filesize
+  - url
+- Added "file_id" to the File object
+- Added `seqspec file` command to return the list of files in the spec as paired across reads or interleaved
+- Added `seqspec upgrade` hidden feature to upgrade v0.2.x seqspec files to v0.3.0.
 
 ### Changed
 
+- Updated `seqspec index` to read strands for chromap
+- Updated `seqspec split` to correctly split sequence_spec
+- Modified `seqspec` string to use min_len instead of max_len to accommodate nanopore reads
+- Updated documentation on how to propose new vocabulary
 - Modified the internals of `seqspec onlist` to manage saving the joined onlist to the `-o` location when specified (otherwise saves to path where spec lives).
+- Renamed "location" to "urltype" in Onlist object
+- Replaced `-r` with `-i` id type for all functions (deprecated `-r`)
+- Multiple seqspec commands now require the addition of a `-s selector [read, region, file]`
+- `seqspec index` can now take in reads, regions, or files and index
+- `seqspec modify` can now add files to the template
+- Updated splitseq template
 
-### Added
+### Fixed
 
-- Add typing hints to many `Assay` and `Region` functions
-- Add `'k key` to `seqspec info` to display one of `meta` for metadata, `sequence_spec` for sequence spec, and `library_spec` for library spec
-- Add `-f format` to `seqspec info` to enable multiple formats for displaying info
+- Fixed `seqspec onlist` functionality
+- Fixed error enumeration in seqspec check
 
 ### Removed
 
-### Fixed
+TODO:
+
+- Remove `lib_struct`
+- Remove `parent_id`
+
+### Breaking Changes
+
+- File elements are now required in Read objects and Onlist objects in version 0.3.0
 
 ## [0.2.0] - 2024-04-17
 
@@ -47,22 +85,22 @@ authors:
 - Update `seqspec print` command to use the replacement `assay_id` attribute instead of `assay`
 - Implement downloading onlists via URLs and transparently decompress gzip files
 - Change `read_list` function to take the `onlist` object for handling local and remote files
-- Add `onlist` argument to specify combined barcode list file format (kallisto's multi-file format and default cartesian product format)
+- Added `onlist` argument to specify combined barcode list file format (kallisto's multi-file format and default cartesian product format)
 
 ### Added
 
-- Add `sequence_spec` in the `Assay` object
-- Add `Read` object in the `sequence_spec` object
-- Add `sequence_spec` to the seqspec json schema
-- Add `Read` object to specification document
-- Add `Read` generator to website GUI
-- Add pattern matching to `date` in `Assay` (expected date format: DAY MONTH YEAR, where day is one or two numbers, month is the full named month starting with a Capital letter and year is the full year)
-- Add `library_kit` to `Assay` object (kit that adds seq adapters)
-- Add `library_protocol` to `Assay` object (library that generates insert)
-- Add `sequence_kit` to `Assay` object
-- Add website to view example `seqspec` objects
-- Add `get_seqspec` to assay returns sequence structure for a given modality
-- Add multiple checks to `seqspec check`
+- Added `sequence_spec` in the `Assay` object
+- Added `Read` object in the `sequence_spec` object
+- Added `sequence_spec` to the seqspec json schema
+- Added `Read` object to specification document
+- Added `Read` generator to website GUI
+- Added pattern matching to `date` in `Assay` (expected date format: DAY MONTH YEAR, where day is one or two numbers, month is the full named month starting with a Capital letter and year is the full year)
+- Added `library_kit` to `Assay` object (kit that adds seq adapters)
+- Added `library_protocol` to `Assay` object (library that generates insert)
+- Added `sequence_kit` to `Assay` object
+- Added website to view example `seqspec` objects
+- Added `get_seqspec` to assay returns sequence structure for a given modality
+- Added multiple checks to `seqspec check`
   - check read modalities exist in assay modalities
   - check primer ids from seqspec are unique and exists as region ids in libspec
   - check that the primer id exists as an atomic region (currently a strong assumption that may be relaxed in the future)
@@ -75,14 +113,14 @@ authors:
   - check that the min len is less than or equal to the max len
   - check that the length of the sequence is between min and max len
   - Note a strong assumption in `seqspec print` is that the sequence have a length equal to the `max_len` for visualization purposes
-- Add `RegionCoordinate` object that maps `Region` min/max lengths to 0-indexed positions
+- Added `RegionCoordinate` object that maps `Region` min/max lengths to 0-indexed positions
 - `seqspec onlist` searches for onlists in a `Region` based on `--region` flag
-- Add type annotations for `join_onlists` to clarify it needs a list of `Onlist` objects
-- Add minimal tests for `RegionCoordinate`, `project_regions_to_coordinates`, `run_onlist_region`, `run_onlist_read`, and seqspec print functions
-- Add list of options to CLI for `-f FORMAT` within `seqspec onlist` and `seqspec print`
-- Add `-s SEQTYPE` to `seqspec print` to disambiguate printing `sequence`, `library`, or `libseq` objects. TODO wrap `seqspec info` into `seqspec print -f info`.
-- Add `-s SPECOBJECT` to `seqspec onlist`. Specify specific object `read`, `region`, or `region-type` for finding the `onlist`.
-- Add fetching ability for seqspec onlist from remote with IGVF credentials (credit to @detrout)
+- Added type annotations for `join_onlists` to clarify it needs a list of `Onlist` objects
+- Added minimal tests for `RegionCoordinate`, `project_regions_to_coordinates`, `run_onlist_region`, `run_onlist_read`, and seqspec print functions
+- Added list of options to CLI for `-f FORMAT` within `seqspec onlist` and `seqspec print`
+- Added `-s SEQTYPE` to `seqspec print` to disambiguate printing `sequence`, `library`, or `libseq` objects. TODO wrap `seqspec info` into `seqspec print -f info`.
+- Added `-s SPECOBJECT` to `seqspec onlist`. Specify specific object `read`, `region`, or `region-type` for finding the `onlist`.
+- Added fetching ability for seqspec onlist from remote with IGVF credentials (credit to @detrout)
 
 ### Removed
 
@@ -95,6 +133,6 @@ TODO:
 
 - Sequencing overlapping pairs now supported
 - `seqspec check` correctly handles sequences lengths longer than the stated min/max range
-- Fix test for `project_regions_to_coordinates`
+- Fixed test for `project_regions_to_coordinates`
 - Get the test of seqspec check working again by updating the schema for the refactored example specification YAML files and mocking fastq and barcode files
 - Only return the onlist filename if it's a local file, downloading remote lists when needed