[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,20 +2,20 @@ fail_fast: false
 default_language_version:
     python: python3
 default_stages:
-    - commit
-    - push
+    - pre-commit
+    - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 24.4.2
+      rev: 24.10.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
       rev: v4.0.0-alpha.8
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.18.0
+      rev: 1.19.1
       hooks:
           - id: blacken-docs
     - repo: https://github.com/PyCQA/isort
@@ -34,7 +34,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.6.0
+      rev: v5.0.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -53,7 +53,7 @@ repos:
                 - --remove-unused-variable
                 - --ignore-init-module-imports
     - repo: https://github.com/PyCQA/flake8
-      rev: 7.1.0
+      rev: 7.1.1
       hooks:
           - id: flake8
             additional_dependencies:
@@ -64,7 +64,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.16.0
+      rev: v3.19.1
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]

docs/CONDUCT.md

@@ -8,19 +8,19 @@ In the interest of fostering an open and welcoming environment, we as contributo
 
 Examples of behavior that contributes to creating a positive environment include:
 
--   Using welcoming and inclusive language
--   Being respectful of differing viewpoints and experiences
--   Gracefully accepting constructive criticism
--   Focusing on what is best for the community
--   Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
--   The use of sexualized language or imagery and unwelcome sexual attention or advances
--   Trolling, insulting/derogatory comments, and personal or political attacks
--   Public or private harassment
--   Publishing others' private information, such as a physical or electronic address, without explicit permission
--   Other conduct which could reasonably be considered inappropriate in a professional setting
+- The use of sexualized language or imagery and unwelcome sexual attention or advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
 
 ## Our Responsibilities
 

docs/CONTRIBUTING.md

@@ -9,9 +9,9 @@ Report bugs using GitHub issues.
 
 If you are reporting a bug, please include:
 
--   Your operating system name and version.
--   Any details about your local setup that might be helpful in troubleshooting.
--   Detailed steps to reproduce the bug.
+- Your operating system name and version.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug.
 
 ## Fix Bugs
 
@@ -35,10 +35,10 @@ The best way to send feedback is to file an issue on GitHub.
 
 If you are proposing a feature:
 
--   Explain in detail how it would work.
--   Keep the scope as narrow as possible, to make it easier to implement.
--   Remember that this is a volunteer-driven project, and that contributions
-    are welcome :)
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
 
 ## Get Started
 

docs/README.md

@@ -8,10 +8,10 @@ ALLCools documentation
 
 If you'd like to develop on and build the ALLCools book, you should:
 
--   Clone this repository and run
--   Run `pip install -r requirements.txt` (it is recommended you do this within a virtual environment)
--   (Recommended) Remove the existing `ALLCools/_build/` directory
--   Run `jupyter-book build ALLCools/`
+- Clone this repository and run
+- Run `pip install -r requirements.txt` (it is recommended you do this within a virtual environment)
+- (Recommended) Remove the existing `ALLCools/_build/` directory
+- Run `jupyter-book build ALLCools/`
 
 A fully-rendered HTML version of the book will be built in `ALLCools/_build/html/`.
 
@@ -21,8 +21,8 @@ The html version of the book is hosted on the `gh-pages` branch of this repo. A
 
 If you wish to disable this automation, you may remove the GitHub actions workflow and build the book manually by:
 
--   Navigating to your local build; and running,
--   `ghp-import -n -p -f ALLCools/_build/html`
+- Navigating to your local build; and running,
+- `ghp-import -n -p -f ALLCools/_build/html`
 
 This will automatically push your build to the `gh-pages` branch. More information on this hosting process can be found [here](https://jupyterbook.org/publish/gh-pages.html#manually-host-your-book-with-github-pages).
 

docs/allcools/cell_level/basic/intro_basic_clustering.md

@@ -14,19 +14,19 @@ The dataset we used for 100Kb clustering documentation comes from the hippocampu
 
 #### Download Input Files
 
--   Cell metadata: ADD DOWNLOAD URL
--   single-cell ALLC files: ADD DOWNLOAD URL
--   MCDS files: ADD DOWNLOAD URL
+- Cell metadata: ADD DOWNLOAD URL
+- single-cell ALLC files: ADD DOWNLOAD URL
+- MCDS files: ADD DOWNLOAD URL
 
 ### For 5Kb bins clustering
 
 The dataset we used for 5Kb clustering documentation comes from human PBMC (ADD REFERENCE).
 
 #### Download Input Files
 
--   Cell metadata: ADD DOWNLOAD URL
--   single-cell ALLC files: ADD DOWNLOAD URL
--   MCDS files: ADD DOWNLOAD URL
+- Cell metadata: ADD DOWNLOAD URL
+- single-cell ALLC files: ADD DOWNLOAD URL
+- MCDS files: ADD DOWNLOAD URL
 
 ## Prepare your own datasets
 

docs/allcools/intro.md

@@ -21,10 +21,10 @@ ALLCools documentation organization.
 
 ## Authors
 
--   Hanqing Liu, developer, initial conception
--   Jingtian Zhou, developer, 5kb clustering algorithms
--   Wei Tian
--   Jiaying Xu
+- Hanqing Liu, developer, initial conception
+- Jingtian Zhou, developer, 5kb clustering algorithms
+- Wei Tian
+- Jiaying Xu
 
 ## Support
 
@@ -37,10 +37,10 @@ figclass: margin
 Click on this to create a page specific issue.
 ```
 
--   The source code is on [github](https://github.com/lhqing/ALLCools);
--   For releases and changelog, please check out the [github releases page](https://github.com/lhqing/ALLCools/releases);
--   For bugs and feature requests, please use the [issue tracker](https://github.com/lhqing/ALLCools/issues).
--   For page-specific issues, please use the "open issue" button on the top-right toggle.
+- The source code is on [github](https://github.com/lhqing/ALLCools);
+- For releases and changelog, please check out the [github releases page](https://github.com/lhqing/ALLCools/releases);
+- For bugs and feature requests, please use the [issue tracker](https://github.com/lhqing/ALLCools/issues).
+- For page-specific issues, please use the "open issue" button on the top-right toggle.
 
 ## Citing ALLCools
 

docs/allcools/start/analysis_steps.md

@@ -20,11 +20,11 @@ In general, the **cellular analysis** is focused on individual cells' overall di
 
 ### Sections
 
--   [Basic walk-through of the clustering analysis](../cell_level/basic/intro_basic_clustering.md).
--   [Step-by-step description of the clustering analysis](../cell_level/step_by_step/intro_step_by_step_clustering.md).
--   [Identification of Differentially Methylated Genes clusters](../cell_level/dmg/intro_dmg.md).
--   [Cell-level data integration](../cell_level/integration/intro_integration.md).
--   [Potential cell doublets identification](../cell_level/doublets/intro_doublets.md).
+- [Basic walk-through of the clustering analysis](../cell_level/basic/intro_basic_clustering.md).
+- [Step-by-step description of the clustering analysis](../cell_level/step_by_step/intro_step_by_step_clustering.md).
+- [Identification of Differentially Methylated Genes clusters](../cell_level/dmg/intro_dmg.md).
+- [Cell-level data integration](../cell_level/integration/intro_integration.md).
+- [Potential cell doublets identification](../cell_level/doublets/intro_doublets.md).
 
 ### Input
 
@@ -49,12 +49,12 @@ Specifically, this strategy starts from a cell-by-5kb-bin hypo-methylation score
 
 ### Sections
 
--   [Prepare pseudo-bulk ALLC files](../cluster_level/intro.md)
--   [Call Differentially Methylated Region (DMR)](../cluster_level/RegionDS/01a.call_dmr)
--   [DMR annotation](../cluster_level/RegionDS/02.annotation.ipynb)
--   [DMR motif analysis (finding upstream regulators of DMRs)](../cluster_level/RegionDS/intro_motif.md)
--   [DMR - Gene correlation analysis (finding downstream targets of DMRs)](../cluster_level/Correlation/intro_corr)
--   [Enhancer prediction with REPTILE algorithm](../cluster_level/REPTILE/intro_reptile.md)
+- [Prepare pseudo-bulk ALLC files](../cluster_level/intro.md)
+- [Call Differentially Methylated Region (DMR)](../cluster_level/RegionDS/01a.call_dmr)
+- [DMR annotation](../cluster_level/RegionDS/02.annotation.ipynb)
+- [DMR motif analysis (finding upstream regulators of DMRs)](../cluster_level/RegionDS/intro_motif.md)
+- [DMR - Gene correlation analysis (finding downstream targets of DMRs)](../cluster_level/Correlation/intro_corr)
+- [Enhancer prediction with REPTILE algorithm](../cluster_level/REPTILE/intro_reptile.md)
 
 ### Basic process of genomic analysis
 

docs/allcools/start/installation.md

@@ -123,8 +123,8 @@ conda deactivate
 
 Here are some optional packages which might be hard to install on some old systems.
 
--   `rpy2` (R and the R package pvclust) is used for the cluster dendrogram.
--   `tpot` is used in REPTILE model.
+- `rpy2` (R and the R package pvclust) is used for the cluster dendrogram.
+- `tpot` is used in REPTILE model.
 
 ```shell
 mamba install -n allcools rpy2