Merge pull request #17 from PixelgenTechnologies/release/0.14.0

Release/0.14.0

.flake8

@@ -3,7 +3,7 @@ extend-ignore = E501,E402,W503,E203,D213,D203,DOC301
 exclude = .git,__pycache__,docs/source/conf.py,old,build,dist,cue.mod
 docstring-convention = all
 style = sphinx
-require-return-section-when-returning-none = False
+require-return-section-when-returning-nothing = False
 arg-type-hints-in-signature = True
 arg-type-hints-in-docstring = False
 # Ignore documentation linting in tests

.pre-commit-config.yaml

@@ -7,6 +7,7 @@ repos:
       - id: check-yaml
         exclude: '^(conda-recipe)/(.*)$'
       - id: end-of-file-fixer
+        exclude: '^(.*)/webreport/template.html$'
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black

CHANGELOG.md

@@ -5,6 +5,34 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.14.0] - 2023-10-05
+
+### Added
+
+* Lazy option for edge list loading (`pixeldataset.edgelist_lazy`), which returns a
+  `polars` `LazyFrame` that can be used to operate on the edge list without reading
+  all of it into memory.
+* Option (`ignore_edgelists`) to skip the edge lists when aggregating files. This defaults
+  to `False`.
+
+
+### Changed
+
+* Types on the edge list in memory will utilize the `pandas` `category` type for string, and
+  `uint16` for numeric values to lower the memory consumption when working with the
+  edge list
+* Remove `--pbs1` and `--pbs2` commandline arguments to `pixelator single-cell adapterqc`.
+* Restructure report figures.
+* Improve metric names and tooltips in the report.
+* Synchronize zoom level between the scatter plots in cell annotations section of the report.
+* Add report placeholder for missing cell annotation data
+* Add `Fraction of discarded UMIs` and `Avg. Reads per Molecule` metrics to the report.
+
+### Fixed
+
+* Fix an issue where pixelator --version would return 0.0.0 when installing in editable mode.
+
+
 ## [0.13.1] - 2023-09-15
 
 ### Added
@@ -23,6 +51,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
+* `clr` and `relative` transformation options for the colocalization computations in `analysis`
+
 
 ## [0.13.0] - 2023-09-13
 

README.md

@@ -69,7 +69,7 @@ pip install .
 
 ### Using docker
 
-The `pixelator`` command-line tool can be run with docker images available on
+The `pixelator` command-line tool can be run with docker images available on
 the [GitHub container registry](https://github.com/PixelgenTechnologies/pixelator/pkgs/container/pixelator).
 
 ```shell
@@ -99,7 +99,7 @@ Pixelator is developed and maintained by the [developers](https://github.com/Pix
 
 When using pixelator in your research, please cite the following publication:
 
-> Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770.
+> Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, _et al._ “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770.
 
 
 Main development happened thanks to: