Merge pull request #21 from gymrek-lab/feat/add-md-docs

feat: add md files to readthedocs
CAST-genomics · Apr 13, 2022 · e290f2e · e290f2e
2 parents 435ef2c + 6bd5ea5
commit e290f2e
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Showing 5 changed files with 159 additions and 14 deletions.
diff --git a/docs/commands/simgenotype.rst b/docs/commands/simgenotype.rst
@@ -0,0 +1,4 @@
+.. _subcommands-simgenotype:
+
+.. include:: ../../haptools/simgenotype/README.md
+   :parser: myst_parser.sphinx_
diff --git a/docs/conf.py b/docs/conf.py
@@ -34,6 +34,7 @@
     "sphinx_rtd_theme",
     "numpydoc",
     "sphinx_click",
+    "myst_parser",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -47,6 +48,8 @@
 # -- Extension configuration -------------------------------------------------
 autosummary_generate = True
 numpydoc_show_class_members = False
+# allow for both rst and md syntax
+source_suffix = ['.rst']
 
 # -- Options for HTML output -------------------------------------------------
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,8 +1,7 @@
 .. _manual-main:
 
-========
-haptools
-========
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
 
 .. toctree::
    :caption: Execution
@@ -12,6 +11,14 @@ haptools
 
    executing/inputs.rst
 
+.. toctree::
+   :caption: Commands
+   :name: commands
+   :hidden:
+   :maxdepth: 1
+
+   commands/simgenotype.rst
+
 .. toctree::
    :caption: API
    :name: api

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -17,22 +17,25 @@ cyvcf2 = "^0.30.14"
 # docs
 # these belong in dev-dependencies, but RTD doesn't support that yet -- see
 # https://github.com/readthedocs/readthedocs.org/issues/4912
-Sphinx = {version = "^4.3.2", optional = true }
-sphinx-autodoc-typehints = {version = "^1.12.0", optional = true }
-sphinx-rtd-theme = {version = "^1.0.0", optional = true }
-numpydoc = {version = "^1.1.0", optional = true }
-sphinx-click = {version = "^3.0.2", optional = true }
+Sphinx = { version = "^4.3.2", optional = true }
+sphinx-autodoc-typehints = { version = "^1.12.0", optional = true }
+sphinx-rtd-theme = { version = "^1.0.0", optional = true }
+numpydoc = { version = "^1.1.0", optional = true }
+sphinx-click = { version = "^3.0.2", optional = true }
+myst-parser = { version = "^0.17.0", optional = true }
 
 [tool.poetry.dev-dependencies]
 
 # docs
 # these belong in dev-dependencies, but RTD doesn't support that yet -- see
 # https://github.com/readthedocs/readthedocs.org/issues/4912
-Sphinx = {version = "^4.3.2" }
-sphinx-autodoc-typehints = {version = "^1.12.0" }
-sphinx-rtd-theme = {version = "^1.0.0" }
-numpydoc = {version = "^1.1.0" }
-sphinx-click = {version = "^3.0.2" }
+Sphinx = { version = "^4.3.2" }
+sphinx-autodoc-typehints = { version = "^1.12.0" }
+sphinx-rtd-theme = { version = "^1.0.0" }
+numpydoc = { version = "^1.1.0" }
+sphinx-click = { version = "^3.0.2" }
+myst-parser = { version = "^0.17.0" }
+
 pytest = "^6.2.5"
 black = "^22.3.0"
 ipython = "^7.30.1"