Merge pull request #156 from labgem/ref_api_in_doc

Fix api reference in readthedoc
labgem · Dec 20, 2023 · f5eadc7 · f5eadc7
2 parents c90dc81 + d896a14
commit f5eadc7
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diff --git a/.github/workflows/check_doc.yml b/.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

diff --git a/.readthedocs.yaml b/.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

diff --git a/docs/Makefile b/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".

diff --git a/docs/api/api_ref.md b/docs/api/api_ref.md
@@ -0,0 +1,8 @@
+# API Reference
+
+```{toctree}
+:maxdepth: 2
+ppanggolin
+indice_and_table
+```
+
diff --git a/docs/api/indice_and_table.md b/docs/api/indice_and_table.md
@@ -0,0 +1,7 @@
+# Indices and tables
+
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`
+
+
diff --git a/docs/api/ppanggolin.formats.md b/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:

diff --git a/docs/index.md b/docs/index.md
@@ -86,13 +86,5 @@ user/metadata
 
 dev/contribute
 dev/buildDoc
+api/api_ref
 ```
-
-# API Reference
-[//]: # (- {ref}`ppanggolin package`)
-
-- {ref}`genindex`
-
-- {ref}`modindex`
-
-- {ref}`search`
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/pyproject.toml b/pyproject.toml
@@ -45,11 +45,24 @@ doc = [
     "sphinx-autobuild==2021.3.14",
     "myst-parser==2",
     "docutils==0.18.1",
-    "sphinxcontrib.mermaid==0.9.2"
+    "sphinxcontrib.mermaid==0.9.2",
 ]
 test = [
     "pytest>=7.0.0"
 ]
+python_deps = [
+    "tqdm>=4.64",
+    "tables>=3.7",
+    "pyrodigal>=3.0.1",
+    "networkx>=3.0",
+    "scipy>=1.10.0",
+    "plotly>=4.14.3",
+    "gmpy2>=2.1.2",
+    "pandas>=2.0",
+    "colorlover>=0.3",
+    "numpy>=1.24",
+    "bokeh>=2.4.2,<3"
+]
 #
 [project.urls]
 Homepage = "https://labgem.genoscope.cns.fr/2023/04/27/ppanggolin/"