Fix ploty graphs not displaying in documentation (#461)

Author: gsheni

.github/workflows/docs.yml

@@ -9,9 +9,9 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
     - name: Build

INSTALL.md

@@ -57,5 +57,4 @@ git checkout -b <your-branch-name>
 make install-develp
 ```
 
-For more details about how to contribute to the project please visit the [Contributing Guide](
-CONTRIBUTING.rst).
+For more details about how to contribute to the project please visit the [Contributing Guide](https://github.com/sdv-dev/copulas/blob/main/CONTRIBUTING.rst).

docs/conf.py

@@ -31,15 +31,15 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
-    'm2r',
     'nbsphinx',
     'sphinx.ext.autodoc',
     'sphinx.ext.githubpages',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
-    'sphinx.ext.mathjax'
+    'sphinx.ext.mathjax',
+    'myst_parser',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -78,7 +78,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -97,7 +97,6 @@
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Readthedocs additions
 html_context = {
@@ -113,7 +112,7 @@
 # documentation.
 html_theme_options = {
     'collapse_navigation': False,
-    'display_version': False,
+    'version_selector': False,
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

docs/history.rst

@@ -1 +1,2 @@
-.. mdinclude:: ../HISTORY.md
+.. include:: ../HISTORY.md
+   :parser: myst_parser.sphinx_

docs/index.rst

@@ -1,4 +1,5 @@
-.. mdinclude:: ../README.md
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
    :end-line: 48
 
 .. toctree::
@@ -21,7 +22,7 @@
    :caption: Advanced Usage
    :maxdepth: 2
 
-   tutorials/04_Syntehtic_Data_for_Machine_Learning
+   tutorials/04_Synthetic_Data_for_Machine_Learning
 
 .. toctree::
    :caption: Resources

docs/install.rst

@@ -1 +1,2 @@
-.. mdinclude:: ../INSTALL.md
+.. include:: ../INSTALL.md
+   :parser: myst_parser.sphinx_

pyproject.toml

@@ -54,61 +54,59 @@ version = {attr = 'copulas.__version__'}
 
 [project.optional-dependencies]
 tutorials = [
-    'markupsafe<=2.0.1',
-    "scikit-learn>=0.24;python_version<'3.12'",
-    "scikit-learn>=1.3.1;python_version>='3.12'",
-    'jupyter>=1.0.0,<2',
+    'markupsafe >= 2.0.1',
+    "scikit-learn >= 0.24;python_version<'3.12'",
+    "scikit-learn >= 1.3.1;python_version >= '3.12'",
+    'jupyter >= 1.0.0',
 ]
 test = [
     'copulas[tutorials]',
-    'pytest>=6.2.5,<7',
-    'pytest-cov>=2.6.0,<3',
-    'pytest-rerunfailures>=10.3,<15',
-    'rundoc>=0.4.3,<0.5',
-    'tomli>=2.0.0,<3',
+    'pytest >= 6.2.5',
+    'pytest-cov >= 2.6.0',
+    'pytest-rerunfailures >= 10.3',
+    'rundoc >= 0.4.3',
+    'tomli >= 2.0.0',
 ]
 dev = [
     'copulas[tutorials, test]',
 
     # general
-    'pip>=9.0.1',
-    'build>=1.0.0,<2',
-    'bump-my-version>=0.18.3,<1',
-    'watchdog>=1.0.1,<5',
+    'pip >= 9.0.1',
+    'build >= 1.0.0',
+    'bump-my-version >= 0.18.3',
+    'watchdog >= 1.0.1',
 
     # docs
-    'm2r>=0.2.0,<0.3',
-    'nbsphinx>=0.5.0,<0.7',
-    'Sphinx>=1.7.1,<3',
-    'sphinx_rtd_theme>=0.2.4,<0.5',
-    'sphinxcontrib_applehelp<1.0.8',
-    'sphinxcontrib-devhelp<1.0.6',
-    'sphinxcontrib-htmlhelp<2.0.5',
-    'sphinxcontrib_serializinghtml<1.1.10',
-    'sphinxcontrib_qthelp<1.0.7',
-    'alabaster<0.7.13',
-
-    # Jinja2>=3 makes the sphinx theme fail
-    "Jinja2>=2,<3;python_version<'3.12'",
-    "Jinja2>=2,<4;python_version>='3.12'",
+    'nbsphinx >= 0.9.7, <0.10',
+    'Sphinx >= 7.4.7, <7.5',
+    'sphinx_rtd_theme >= 3.0.2, <3.1',
+    'sphinxcontrib_applehelp >= 2.0.0, <2.1',
+    'sphinxcontrib-devhelp >= 2.0.0, <2.1',
+    'sphinxcontrib-htmlhelp >= 2.1.0, <2.2',
+    'sphinxcontrib_serializinghtml >= 2.0.0, <2.1',
+    'sphinxcontrib_qthelp >= 2.0.0, <2.1',
+    'alabaster >= 0.7.16, <0.8',
+    'lxml-html-clean >= 0.4.1, <0.5',
+    'Jinja2 >= 3.1.6, <3.2',
+    'myst_parser >= 3.0.1, <4.1',
 
     # style check
-    'ruff>=0.3.2,<1',
+    'ruff >= 0.3.2, <1',
 
     # distribute on PyPI
-    'twine>=1.10.0,<4',
-    'wheel>=0.30.0',
+    'twine >= 1.10.0, <4',
+    'wheel >= 0.30.0',
 
     # Advanced testing
-    'coverage>=4.5.1,<6',
-    'tox>=2.9.1,<4',
+    'coverage >= 7.7.1, <7.8',
+    'tox >= 2.9.1,<4',
     'invoke',
 
     # Large scale evaluation
-    'urllib3>=1.20,<1.26',
-    'tabulate>=0.8.3,<0.9',
-    'boto3>=1.7.47,<1.10',
-    'docutils>=0.10,<0.15'
+    'urllib3 >= 1.26.20, <2.4',
+    'tabulate >= 0.9.0, <0.10',
+    'boto3 >= 1.37.18, <1.38',
+    'docutils >= 0.21.2, <0.22'
 ]
 
 [tool.isort]

tutorials/00_Quickstart.ipynb

@@ -11290,13 +11290,6 @@
    "source": [
     "new_samples = new_copula.sample(num_samples)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -11315,7 +11308,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.9.20"
   }
  },
  "nbformat": 4,

tutorials/01_Introduction_to_Copulas.ipynb

@@ -59,9 +59,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -77824,20 +77822,6 @@
     "\n",
     "compare_2d(df, synthetic)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -77856,7 +77840,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.9.20"
   }
  },
  "nbformat": 4,

tutorials/02_Univariate_Distributions.ipynb

@@ -14233,9 +14233,7 @@
   {
    "cell_type": "code",
    "execution_count": 24,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "synth_data = pd.DataFrame()\n",
@@ -14386,9 +14384,7 @@
   {
    "cell_type": "code",
    "execution_count": 27,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -35147,13 +35143,6 @@
     "\n",
     "univariate.to_dict()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -35172,7 +35161,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.9.20"
   }
  },
  "nbformat": 4,