Merge my dataset updates into main

.github/ISSUE_TEMPLATE/release-checklist.md

@@ -15,6 +15,7 @@ assignees: ''
 ### Preparing for the release
 - [ ] Does this release require an update to the CHANGELOG because there will be changes to downloadable files? If so, please create an issue tracking the CHANGELOG update and mark it as blocking this issue.
 - [ ] Are all other issues planned for this release resolved? If any issues are unresolved, mark this issue as blocked by those on ZenHub.
+- [ ] All `TODO`s and `STUB` links have been filled in with their correct values, or commented out.
 - [ ] Optional: If not all changes in `development` are ready to be released, create a feature branch off `main` and cherry pick commits from `development` to that feature branch.
 - [ ] File a PR from the `development` branch (or the new feature branch) to the `main` branch. This should include all of the changes that will be associated with the next release.
   - [ ] If a CHANGELOG entry was required, add the date to the entry's header as part of this PR.

.github/workflows/spell-check.yml

@@ -6,7 +6,6 @@ on:
     branches:
       - main
       - development
-      - "the-manuscript"
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:

components/dictionary.txt

@@ -105,6 +105,7 @@ submitter
 submitters
 Tian
 transcriptome
+transcriptomic
 transcriptomics
 TSV
 UMAP

docs/CHANGELOG.md

@@ -5,13 +5,26 @@ As of November 2023, the `CHANGELOG` is a feature of our documentation we'll use
 You can find more information about how and when your download was prepared in the following places:
 
 * The date your download was packaged (`Generated on: {date}`) is included at the top of the README in your download.
-* The version of the [`AlexsLemonade/scpca-nf`](https://github.com/alexsLemonade/scpca-nf) pipeline used to process data in your download is included in the `workflow_version` column of the `single_cell_metadata.tsv` or `bulk_metadata.tsv` file in your download.
+* The version of the [`AlexsLemonade/scpca-nf`](https://github.com/alexsLemonade/scpca-nf) pipeline used to process data in your download is included in the `workflow_version` column of the `single_cell_metadata.tsv`, `bulk_metadata.tsv`, or `spatial_metadata.tsv` file in your download.
 For more information about `AlexsLemonade/scpca-nf` versions, please see [the releases page on GitHub](https://github.com/AlexsLemonade/scpca-nf/releases).
 
 <!-------------------------------------------------->
 <!-- PUT THE NEW CHANGELOG ENTRY RIGHT BELOW THIS -->
 <!-------------------------------------------------->
 
+## 2026.01.08
+
+* Data on the Portal can now be downloaded in three different ways: 
+  * By selecting a {ref}`single project<download_files:project downloads>` to download.
+  * By creating a {ref}`custom dataset<download_files:custom datasets>` with a selection of projects and/or samples. 
+  Custom datasets are referred to as `My Dataset` on the Portal. 
+  * By choosing one of the {ref}`Portal-wide download options<download_files:portal-wide downloads>`. 
+* Although the content of the data included in each download has not changed, the download file structures have changed. 
+See the {ref}`Downloadable Files page for more information<download_files:downloadable files>`.
+* A new section of the documentation describing possible {ref}`download options<download_options:download options>` has been added.
+* The previously named `single_cell_metadata.tsv` files that are included with each download have been renamed to `single-cell_metadata.tsv`.
+
+
 ## 2025.12.04
 
 All data on the Portal has been updated to include a number of new features.
@@ -40,11 +53,11 @@ This has now been fixed so that all merged objects have the `cell_id` formatted
 
 ## 2025.04.24
 
-* Consensus cell type annotations are now available in all processed `SingleCellExperiment` and `AnnData` objects and merged objects. 
-  * The labels obtained from `SingleR` and `CellAssign` are used to assign an ontology-aware consensus cell type label. 
-  * See our {ref}`documentation on cell type annotation<processing_information:cell type annotation>` to learn more about how consensus cell types are assigned. 
+* Consensus cell type annotations are now available in all processed `SingleCellExperiment` and `AnnData` objects and merged objects.
+  * The labels obtained from `SingleR` and `CellAssign` are used to assign an ontology-aware consensus cell type label.
+  * See our {ref}`documentation on cell type annotation<processing_information:cell type annotation>` to learn more about how consensus cell types are assigned.
   * See {ref}`the single-cell gene expression file contents page<sce_file_contents:singlecellexperiment cell metrics>` and {ref}`the merged object file contents page<merged_objects:singlecellexperiment cell metrics>` for more information on obtaining these cell type annotations from the downloaded objects.
-* All assays within a merged object are now saved as a sparse matrix (`CsparseMatrix`), whereas previously these assays were saved as a `DelayedArray`. 
+* All assays within a merged object are now saved as a sparse matrix (`CsparseMatrix`), whereas previously these assays were saved as a `DelayedArray`.
 
 ## 2024.11.14