update sphinx

DataForScience · Apr 15, 2024 · 6d45ed0 · 6d45ed0
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diff --git a/docs/Makefile b/docs/Makefile
@@ -5,8 +5,8 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

diff --git a/docs/conf.py b/docs/conf.py
@@ -0,0 +1,32 @@
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../src/epidemik/'))
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'epidemik'
+copyright = '2024, Bruno Goncalves'
+author = 'Bruno Goncalves'
+release = '0.0.20'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
diff --git a/docs/epidemik.rst b/docs/epidemik.rst
@@ -0,0 +1,45 @@
+epidemik package
+================
+
+Submodules
+----------
+
+epidemik.EpiModel module
+------------------------
+
+.. automodule:: epidemik.EpiModel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epidemik.MetaEpiModel module
+----------------------------
+
+.. automodule:: epidemik.MetaEpiModel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epidemik.NetworkEpiModel module
+-------------------------------
+
+.. automodule:: epidemik.NetworkEpiModel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epidemik.utils module
+---------------------
+
+.. automodule:: epidemik.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: epidemik
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/index.rst b/docs/index.rst
@@ -0,0 +1,20 @@
+.. epidemik documentation master file, created by
+   sphinx-quickstart on Mon Apr 15 09:20:13 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to epidemik's documentation!
+====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/make.bat b/docs/make.bat
@@ -7,10 +7,8 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=source
-set BUILDDIR=build
-
-if "%1" == "" goto help
+set SOURCEDIR=.
+set BUILDDIR=_build
 
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
@@ -21,10 +19,12 @@ if errorlevel 9009 (
 	echo.may add the Sphinx directory to PATH.
 	echo.
 	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
+	echo.https://www.sphinx-doc.org/
 	exit /b 1
 )
 
+if "%1" == "" goto help
+
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 goto end
 

diff --git a/docs/modules.rst b/docs/modules.rst
@@ -0,0 +1,7 @@
+epidemik
+========
+
+.. toctree::
+   :maxdepth: 4
+
+   epidemik
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,2 +1,6 @@
-sphinx==7.1.2
-sphinx-rtd-theme==1.3.0rc1
+matplotlib>=3.3
+networkx>=3
+numpy>=1.2
+pandas>=2.0
+scipy>=1.10
+tqdm>=4
diff --git a/docs/source/conf.py b/docs/source/conf.py
diff --git a/docs/source/index.rst b/docs/source/index.rst
diff --git a/tests/tests_MetaEpiModel.py b/tests/tests_MetaEpiModel.py
@@ -5,8 +5,8 @@
 
 class MetaEpiModelTestCase(unittest.TestCase):
 	def setUp(self):
-		self.travel = pd.DataFrame({'A': [0.9, 0.1], 'B':[0.1, 0.9]}, index=["A", "B"])
-		self.population = pd.DataFrame({'Population':[100000, 10000]}, index=["A", "B"])
+		self.travel = pd.DataFrame({'A': [0.99, 0.1], 'B':[0.01, 0.9]}, index=["A", "B"])
+		self.population = pd.DataFrame({'Population':[100_000, 10_000]}, index=["A", "B"])
 
 		self.SIR = MetaEpiModel(self.travel, self.population)
 		self.beta = 0.3