v0.9.8 Release

.github/workflows/publish-to-pypi.yml

@@ -51,47 +51,3 @@ jobs:
         path: dist/
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
-
-  github-release:
-    name: >-
-      Sign the Python 🐍 distribution 📦 with Sigstore
-      and upload them to GitHub Release
-    if: startsWith(github.ref, 'refs/tags/')  # only create GitHub releases for tag pushes
-    needs:
-    - publish-to-pypi
-    runs-on: ubuntu-latest
-
-    permissions:
-      contents: write  # IMPORTANT: mandatory for making GitHub Releases
-      id-token: write  # IMPORTANT: mandatory for sigstore
-
-    steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Sign the dists with Sigstore
-      uses: sigstore/[email protected]
-      with:
-        inputs: >-
-          ./dist/*.tar.gz
-          ./dist/*.whl
-    - name: Create GitHub Release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-      run: >-
-        gh release create
-        "$GITHUB_REF_NAME"
-        --repo "$GITHUB_REPOSITORY"
-        --notes ""
-    - name: Upload artifact signatures to GitHub Release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-      # Upload to GitHub Release using the `gh` CLI.
-      # `dist/` contains the built packages, and the
-      # sigstore-produced signatures and certificates.
-      run: >-
-        gh release upload
-        "$GITHUB_REF_NAME" dist/**
-        --repo "$GITHUB_REPOSITORY"

README.md

@@ -35,11 +35,11 @@ If you use ModDotPlot for your research, please cite our software!
 
 ## About
 
-_ModDotPlot_ is a dot plot visualization tool designed for large sequences and whole genomes. _ModDotPlot_ is the spiritual successor to [StainedGlass](https://mrvollger.github.io/StainedGlass/). The core algorithm breaks an input sequence down into intervals of sketched *k*-mers called **mod**imizers, and rapidly approximating the Average Nucleotide Identity between pairwise combinations of these intervals. This significantly reduces the computational time required to produce these plots, enough to view multiple layers of resolution in real time!
+_ModDotPlot_ is a dot plot visualization tool designed to be used at scale, both for smaller sequences and whole genomes. _ModDotPlot_ is the spiritual successor to [StainedGlass](https://mrvollger.github.io/StainedGlass/). The core algorithm breaks an input sequence down into intervals of sketched *k*-mers called **mod**imizers. This enables the rapid approximation of the Average Nucleotide Identity between combinations of intervals! 
 
 ![](images/demo.gif)
 
-If you're interested in learning more about ModDotPlot and tandem repeats, you can watch my in-depth [YouTube video tutorial](https://www.youtube.com/watch?v=_7sQaljB_ys&t=2321s&pp=ygUXYWxleCBzd2VldGVuIG1vZGRvdHBsb3Q%3D) from the [BioDiversity Genomics Academy](https://thebgacademy.org).
+If you're interested in learning more about _ModDotPlot_ and how to visualize tandem repeats, we have an in-depth [YouTube video tutorial](https://www.youtube.com/watch?v=_7sQaljB_ys&t=2321s&pp=ygUXYWxleCBzd2VldGVuIG1vZGRvdHBsb3Q%3D) hosted by the [BioDiversity Genomics Academy](https://thebgacademy.org).
 
 --- 
 
@@ -74,19 +74,19 @@ Finally, confirm that the installation was installed correctly and that your ver
  | |  | | (_) | (_| | | |__| | (_) | |_  | |    | | (_) | |_ 
  |_|  |_|\___/ \__,_| |_____/ \___/ \__| |_|    |_|\___/ \__|
 
- v0.9.7
+ v0.9.8
 
 usage: moddotplot [-h] {interactive,static} ...
 
-ModDotPlot: Visualization of Complex Repeat Structures
+ModDotPlot: Visualization of Tandem Repeats
 
 positional arguments:
   {interactive,static}  Choose mode: interactive or static
     interactive         Interactive mode commands
     static              Static mode commands
 
 options:
-  -h, --help            show this help message and exit`
+  -h, --help            show this help message and exit
   ```
 --- 
 
@@ -119,7 +119,7 @@ _ModDotPlot_ supports highly customizable plotting features in static mode. See
 moddotplot interactive <ARGS>
 ```
 
-Running _ModDotPlot_ in interactive mode will launch a [Dash application](https://plotly.com/dash/) on your machine's localhost. Open any web browser and go to `http://127.0.0.1:<PORT_NUMBER>` to view the interactive plot (this should happen automatically, but depending on your environment you might need to copy and paste this URL into your web browser). Running `Ctrl+C` on the command line will exit the Dash application. The default port number used by Dash is `8050`, but this can be customized using the `--port` command (see [interactive mode commands](#interactive-mode-commands) for further info).
+Running _ModDotPlot_ in interactive mode will launch a [Dash application](https://plotly.com/dash/) on your machine's localhost. Open any web browser and go to `http://127.0.0.1:<PORT_NUMBER>` to view the interactive plot (this should happen automatically, but depending on your environment you might need to copy and paste this URL into your web browser). Running `Ctrl+C` on the command line will exit the Dash application. The default port number used by Dash is `8050`, but this can be customized using the `--port` command (see [interactive mode commands](#interactive-mode-commands) for further info, and [Sample run - Port Forwarding](#sample-run---port-forwarding) for tips on running interactive mode on an HPC environment).
 
 --- 
 
@@ -223,9 +223,17 @@ By default, vectorized outputs rasterize the actual dotplot (not the axis). This
 
 Window size. Unlike interactive mode, only one matrix will be created, so this represents the *only* window size. Default is set to `n/1000` (eg. 3000bp for a 3Mbp sequence). 
 
+`--region <list of strs>`
+
+Plot only a particular range for a given sequence. Syntax is UCSC style (chr:start-end).
+
 `--palette <str>`
 
-List of accepted palettes can be found [here](https://jiffyclub.github.io/palettable/colorbrewer/). The syntax is to have the name of the palette, followed by an underscore with the number of colors, eg. `OrRd_8`. Default is `Spectral_11`.
+List of accepted palettes can be found [here](https://jiffyclub.github.io/palettable/colorbrewer/). Palettes are segregated into 3 types: _Diverging_, _Qualitative_, and _Sequential_. Syntax is the name of the palette, followed by an underscore and the number of colors, eg. `OrRd_8`. Default is  `Spectral_11`.
+
+`--breakpoints <list of ints>`
+
+Add custom identity threshold breakpoints. Note that the number of breakpoints must be equal to the number of colors + 1, otherwise an error will occur. 
 
 `--palette-orientation <bool>`
 
@@ -235,10 +243,6 @@ Flip sequential order of color palette. Set to `-` by default for divergent pale
 
 List of custom colors in hexcode format can be entered sequentially, mapped from low to high identity. 
 
-`--breakpoints <list of ints>`
-
-Add custom identity threshold breakpoints. Note that the number of breakpoints must be equal to the number of colors + 1.
-
 `-t / --axes-ticks <list of ints>`
 
 Custom tickmarks for x and y axis. Values outside of the `--axes-limits` will not be shown. 
@@ -463,3 +467,5 @@ For bug reports or general usage questions, please raise a GitHub issue, or emai
 - Mac users might encounter the following unexpected command line output: `/bin/sh: lscpu: command not found`. This is a known issue with Plotnine, the Python plotting library used by ModDotPlot. This can be safely ignored.
 
 - If you encounter an error with the following traceback: `rv = reductor(4) TypeError: cannot pickle 'generator' object`, ths means that you have a newer version of Plotnine that is incompatible with ModDotPlot. Please uninstall plotnine and reinstall version 0.12.4 `pip install plotnine==0.12.4`. 
+
+- The error ` UserWarning: h5py is running against HDF5 1.xx.x when it was built against 1.xx.x, this may cause problems` is due to the h5py library used by cooler having conflicting versions in the dependency tree. This can also be safely ignored, but if you want to remove this message run `pip uninstall -y h5py` `pip install --no-binary=h5py h5py`