Merge pull request #56 from pyt-team/frantzen/docs-github-link

Tweaks to documentation

CODE_OF_CONDUCT.md

@@ -0,0 +1,4 @@
+Our Code of Conduct is at
+https://pyt-team.github.io/toponetx/project/code_of_conduct.html.
+
+The code of conduct lives in the TopoNetX repository under `docs/project/code_of_conduct.rst`.

README.md

@@ -89,14 +89,12 @@ import topoembedx as tex
 import toponetx as tnx
 
 # create a cell complex object with a few cells
-cc = tnx.classes.CellComplex([[1, 2, 3, 4], [3, 4, 5, 6, 7, 8]],ranks=2)
+cc = tnx.CellComplex([[1, 2, 3, 4], [3, 4, 5, 6, 7, 8]], ranks=2)
 
 # create a model
-
 model = tex.Cell2Vec()
 
 # fit the model
-
 model.fit(cc, neighborhood_type="adj", neighborhood_dim={"rank": 1, "via_rank": -1})
 # here neighborhood_dim={"rank": 1, "via_rank": -1} specifies the dimension for
 # which the cell embeddings are going to be computed.
@@ -106,9 +104,7 @@ model.fit(cc, neighborhood_type="adj", neighborhood_dim={"rank": 1, "via_rank":
 
 
 # get the embeddings:
-
 embeddings = model.get_embedding()
-
 ```
 
 ## 🔍 References ##
@@ -147,4 +143,3 @@ Figure from:
 Partially funded by the European Union (ERC, HIGH-HOPeS, 101039827). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.
 
 Partially funded by the National Science Foundation (DMS-2134231, DMS-2134241).
-

docs/conf.py

@@ -1,102 +1,79 @@
 """Sphinx configuration file."""
 
+# -- Project information -----------------------------------------------------
+
 project = "TopoEmbedX"
 copyright = "2022-2023, PyT-Team, Inc."
 author = "PyT-Team Authors"
+language = "en"
+
+# -- General configuration ---------------------------------------------------
 
 extensions = [
     "nbsphinx",
     "nbsphinx_link",
     "numpydoc",
     "sphinx.ext.autodoc",
-    "sphinx.ext.coverage",
-    "sphinx.ext.doctest",
     "sphinx.ext.githubpages",
     "sphinx.ext.intersphinx",
-    "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
+    "sphinx_copybutton",
     "sphinx_gallery.load_style",
 ]
 
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+
+intersphinx_mapping = {
+    "networkx": ("https://networkx.org/documentation/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "python": ("https://docs.python.org/3/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "toponetx": ("https://pyt-team.github.io/toponetx/", None),
+}
+
 # Configure nbsphinx for notebook execution
 nbsphinx_execute_arguments = [
     "--InlineBackend.figure_formats={'svg', 'pdf'}",
     "--InlineBackend.rc={'figure.dpi': 96}",
 ]
 
 nbsphinx_execute = "never"
-
-# To get a prompt similar to the Classic Notebook, use
-nbsphinx_input_prompt = " In [%s]:"
-nbsphinx_output_prompt = " Out [%s]:"
-
 nbsphinx_allow_errors = True
 
-templates_path = ["_templates"]
-
-source_suffix = [".rst"]
-
-master_doc = "index"
-
-language = "en"
-
-nbsphinx_prolog = r"""
-{% set docname = env.doc2path(env.docname, base=None) %}
-
-.. raw:: latex
-    \nbsphinxstartnotebook{\scriptsize\noindent\strut
-    \textcolor{gray}{The following section was generated from
-    \sphinxcode{\sphinxupquote{\strut {{ docname | escape_latex }}}} \dotfill}}
-    """
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
-
-pygments_style = None
+# -- Options for HTML output -------------------------------------------------
 
 html_theme = "pydata_sphinx_theme"
-html_baseurl = "pyt-team.github.io"
-htmlhelp_basename = "pyt-teamdoc"
-html_last_updated_fmt = "%c"
+html_baseurl = "https://pyt-team.github.io/topoembedx/"
 
-latex_elements = {}
+html_context = {
+    "github_user": "pyt-team",
+    "github_repo": "TopoEmbedX",
+    "github_version": "main",
+    "doc_path": "docs",
+}
 
+html_theme_options = {
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/pyt-team/TopoEmbedX",
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
+        }
+    ],
+    "use_edit_page_button": True,
+}
 
-latex_documents = [
-    (
-        master_doc,
-        "topoembedx.tex",
-        "TopoEmbedX Documentation",
-        "PyT-Team",
-        "manual",
-    ),
-]
+html_favicon = "_static/favicon-48.png"
 
-man_pages = [(master_doc, "topoembedx", "TopoEmbedX Documentation", [author], 1)]
-
-texinfo_documents = [
-    (
-        master_doc,
-        "topoembedx",
-        "TopoEmbedX Documentation",
-        author,
-        "topoembedx",
-        "One line description of project.",
-        "Miscellaneous",
-    ),
-]
+html_show_sourcelink = False
 
-epub_title = project
-epub_exclude_files = ["search.html"]
+# Exclude copy button from appearing over notebook cell numbers by using :not()
+# The default copybutton selector is `div.highlight pre`
+# https://github.com/executablebooks/sphinx-copybutton/blob/master/sphinx_copybutton/__init__.py#L82
+copybutton_selector = ":not(.prompt) > div.highlight pre"
 
-# configure intersphinx
-intersphinx_mapping = {
-    "networkx": ("https://networkx.org/documentation/stable/", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
-    "python": ("https://docs.python.org/3/", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
-    "toponetx": ("https://pyt-team.github.io/toponetx/", None),
-}
+# -- Options for EPUB output -------------------------------------------------
 
-# configure numpydoc
-numpydoc_validation_checks = {"all", "GL01", "ES01", "SA01", "EX01"}
-numpydoc_show_class_members = False
-numpydoc_class_members_toctree = False
+epub_exclude_files = ["search.html"]

pyproject.toml

@@ -46,6 +46,7 @@ doc = [
     "nbsphinx_link",
     "numpydoc >= 1.8.0",
     "sphinx",
+    "sphinx-copybutton",
     "sphinx_gallery",
     "pydata-sphinx-theme"
 ]

test/test_tutorials.py

@@ -8,20 +8,20 @@
 
 
 def _exec_tutorial(path):
-    file_name = tempfile.NamedTemporaryFile(suffix=".ipynb").name
-    args = [
-        "jupyter",
-        "nbconvert",
-        "--to",
-        "notebook",
-        "--execute",
-        "--ExecutePreprocessor.timeout=1000",
-        "--ExecutePreprocessor.kernel_name=python3",
-        "--output",
-        file_name,
-        path,
-    ]
-    subprocess.check_call(args)
+    with tempfile.NamedTemporaryFile(suffix=".ipynb") as tmp_file:
+        args = [
+            "jupyter",
+            "nbconvert",
+            "--to",
+            "notebook",
+            "--execute",
+            "--ExecutePreprocessor.timeout=1000",
+            "--ExecutePreprocessor.kernel_name=python3",
+            "--output",
+            tmp_file.name,
+            path,
+        ]
+        subprocess.check_call(args)
 
 
 TUTORIALS_DIR = "tutorials"