Merge branch 'dev' into devForPanorama

.github/workflows/check_doc.yml

@@ -4,19 +4,27 @@ on:
   push:
     paths:
       - 'docs/**'
+      - '.readthedocs.yaml'
+      - '.github/workflows/check_doc.yml'
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
-    # Standard drop-in approach that should work for most people.
-    - uses: ammaraskar/sphinx-action@master
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
-        docs-folder: "docs/"
-        build-command: "sphinx-build -b html . build/"
+        python-version: '3.8'
+    - name: install ppanggolin with python deps and doc deps
+      run: pip install .[doc,python_deps]
+
+    - name: Complete workflow
+      shell: bash -l {0}
+      run: |
+        cd docs/
+        sphinx-build -b html . build/
     # Great extra actions to compose with:
     # Create an artifact of the html output.
     - uses: actions/upload-artifact@v1

.readthedocs.yaml

@@ -6,18 +6,19 @@
 version: 2
 python:
   install:
-    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
+        - python_deps
 
 # Set the OS, Python version and other tools you might need
 build:
   os: ubuntu-22.04
   tools:
     python: "3.8"
-    # You can also specify other tool versions:
-    # nodejs: "19"
-    # rust: "1.64"
-    # golang: "1.19"
 
+
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
    configuration: docs/conf.py

VERSION

@@ -1 +1 @@
-1.2.194
+2.0.0-alpha1

docs/Makefile

@@ -5,7 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
+SOURCEDIR     = .
 BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".

docs/api/api_ref.md

@@ -0,0 +1,8 @@
+# API Reference
+
+```{toctree}
+:maxdepth: 2
+ppanggolin
+indice_and_table
+```
+

docs/api/indice_and_table.md

@@ -0,0 +1,7 @@
+# Indices and tables
+
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`
+
+

docs/api/ppanggolin.formats.md

@@ -29,10 +29,19 @@
    :show-inheritance:
 ```
 
-## ppanggolin.formats.writeFlat module
+## ppanggolin.formats.writeFlatGenomes module
 
 ```{eval-rst}
-.. automodule:: ppanggolin.formats.writeFlat
+.. automodule:: ppanggolin.formats.writeFlatGenomes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
+
+## ppanggolin.formats.writeFlatPangenome module
+
+```{eval-rst}
+.. automodule:: ppanggolin.formats.writeFlatPangenome
    :members:
    :undoc-members:
    :show-inheritance:

docs/conf.py

@@ -34,8 +34,14 @@
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.autodoc",
     'sphinx_search.extension',
+    'sphinxcontrib.mermaid'
 ]
 
+
+source_suffix = {
+    '.md': 'markdown'
+}
+
 # Prefix document path to section labels, to use:
 # `path/to/file:heading` instead of just `heading`
 autosectionlabel_prefix_document = True