Merge dev branch into master to release version 2.2.0

.github/workflows/black_lint.yml

@@ -0,0 +1,10 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable

.github/workflows/main.yml

@@ -139,6 +139,7 @@ jobs:
       shell: bash -l {0}
       run: |
         cd testingDataset
+        cat myannopang/gene_families.tsv | cut -f1,2,4 > clusters.tsv 
         ppanggolin panrgp --anno genomes.gbff.list --cluster clusters.tsv --output readclusterpang  --cpu $NUM_CPUS 
         ppanggolin annotate --anno genomes.gbff.list --output readclusters --cpu $NUM_CPUS
         awk 'BEGIN{FS=OFS="\t"} {$1 = $1 OFS $1} 1' clusters.tsv > clusters_with_reprez.tsv;

VERSION

@@ -1 +1 @@
-2.1.2
+2.2.0

docs/conf.py

@@ -14,12 +14,14 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'PPanGGOLiN'
-copyright = '2023, LABGeM'
-author = 'Jérôme Arnoux'
+project = "PPanGGOLiN"
+copyright = "2023, LABGeM"
+author = "Jérôme Arnoux"
 
 # The full version, including alpha/beta/rc tags
-release = open(Path(__file__).resolve().parents[1]/"VERSION").read().rstrip()  # Get release number in the VERSION file
+release = (
+    open(Path(__file__).resolve().parents[1] / "VERSION").read().rstrip()
+)  # Get release number in the VERSION file
 
 
 # -- General configuration ---------------------------------------------------
@@ -33,21 +35,19 @@
     "sphinx.ext.duration",
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.autodoc",
-    'sphinx_search.extension',
-    'sphinxcontrib.mermaid'
+    "sphinx_search.extension",
+    "sphinxcontrib.mermaid",
 ]
 
 
-source_suffix = {
-    '.md': 'markdown'
-}
+source_suffix = {".md": "markdown"}
 
 # Prefix document path to section labels, to use:
 # `path/to/file:heading` instead of just `heading`
 autosectionlabel_prefix_document = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -60,9 +60,9 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]

docs/dev/contribute.md

@@ -8,35 +8,47 @@ If you have ideas for new features or improvements, initiating a discussion in a
 
 For minor changes like fixing typos or making small edits, feel free to create a new Pull Request (PR) directly with your proposed changes. 
 
+
 ## Setting Up the Development Environment
 
-1. **Fork the Repository:** Start by forking the repository to your GitHub account. 🍴
+1. **Fork the Repository:** 
+    Start by forking the repository to your GitHub account. 🍴
 
-2. **Clone the Forked Repository:** Clone your forked repository to your local machine.
+2. **Clone the Forked Repository:** 
+    Clone your forked repository to your local machine.
 
 3. **Get an Environment:** Create an environment with all PPanGGOLiN prerequisites installed. For that, you can follow installation instructions [here](../user/install.md#installing-from-source-code-github).
 
-4. **Branch from 'dev':** Begin your changes from the 'dev' branch, where we incorporate changes for the upcoming release.
+4. **Branch from 'dev':** 
+    Begin your changes from the 'dev' branch, where we incorporate changes for the upcoming release.
+
+
+5. **Install in Editable Mode:** 
 
-5. **Install in Editable Mode:** To enable seamless code editing and testing of new functionality, install PPanGGOLiN in editable mode using the following command:
+    To enable code editing and testing of new functionality, you can install PPanGGOLiN in editable mode using the following command:
 
     ```bash
     pip install -e .
     ```
 
     This allows you to modify the code and experiment with new features directly. 
 
-    ```{note}
-    Note: Currently, we are not utilizing any auto formatters (like autopep8 or black). Kindly refrain from using them, as it could introduce extensive changes across the project, making code review challenging for us.
+6. **Apply Code Formatting with Black:** 
+    We have integrated [Black](https://github.com/psf/black)  as our code formatter to maintain consistent styling. Code changes are automatically checked via a GitHub Action in our CI, so **ensure your code is formatted with Black before committing**.
+
+
+    ```{tip}
+    Integrate Black with your IDE to automatically format your changes and avoid formatting-related CI failures. 
     ```
 
+
 ## Making Your Changes
 
-We encourage consistency in code formatting; when adding new code, try to follow the existing code structure as closely as possible. Functions should include descriptive docstrings explaining their purpose and detailing the parameters. Ensure that argument types are specified in the function definitions. 
+Keep it consistent! Match the existing code style, add docstrings to describe functions, and specify argument types.
 
 ## Update Documentation
 
-It's essential to update the documentation to reflect your changes. Provide clear descriptions and, if necessary, examples of commands and their respective outputs.
+Update docs to reflect changes—clear descriptions and examples are always helpful!
 
 ## Tests
 

ppanggolin/RGP/__init__.py

@@ -1,3 +1,3 @@
 from .genomicIsland import subparser, launch
 from .spot import *
-from . import rgp_cluster
+from . import rgp_cluster