Release v*.*.*

.gitignore

@@ -187,7 +187,7 @@ dev_scripts/
 /notes/
 /my_tests/
 /data
-
+*data/
 
 _version.py
 
@@ -196,4 +196,6 @@ _version.py
 
 /papers/
 
-sphinx/_build/
+sphinx/_build/
+
+pyrightconfig.json

README.md

@@ -1,6 +1,8 @@
 # MatGraphDB
 
-**MatGraphDB** is a Python package designed to simplify graph-based data management and analysis in materials and molecular science. It enables researchers to efficiently transform complex theoretical data into structured graph representations, leveraging:
+[Documentation][docs] | [PyPI][pypi] | [GitHub][github]
+
+**MatGraphDB** is a Python package designed to simplify graph-based data management and analysis in materials and molecular science. It is built on top of `ParquetGraphDB` [ParquetDB][parquetdb], which is a graph database which uses Apache Parquet for storage. It enables researchers to efficiently transform complex theoretical data into structured graph representations, leveraging:
 
 - **High-performance storage:** Utilizes Apache Parquet for scalable and rapid data access.
 - **Automated workflows:** Converts theoretical and computational data into graph structures.
@@ -9,16 +11,11 @@
 ## Table of Contents
 - [MatGraphDB](#matgraphdb)
     - [Table of Contents](#table-of-contents)
-    - [Documentation](#documentation)
     - [Installing](#installing)
     - [Usage](#usage)
     - [Contributing](#contributing)
     - [License](#license)
-
-
-## Documentation
-
-Check out the [docs](https://matgraphdb.readthedocs.io/en/latest/)
+    - [Authors](#authors)
 
 
 ## Installing
@@ -175,11 +172,11 @@ materials = mgdb.delete_materials(ids=[0])
 
 ## Contributing
 
-Contributions are welcome! Please open an issue or submit a pull request on GitHub. More information can be found in the [CONTRIBUTING.md](https://github.com/lllangWV/ParquetDB/blob/main/CONTRIBUTING.md) file.
+Contributions are welcome! Please open an issue or submit a pull request on GitHub. More information can be found in the [CONTRIBUTING][contributing] file.
 
 ## License
 
-This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.
+This project is licensed under the MIT License. See the [LICENSE][license] file for details.
 
 
 ## Authors
@@ -194,3 +191,9 @@ Eduardo Hernandez,
 
 
 
+[docs]: https://matgraphdb.readthedocs.io/en/latest/
+[pypi]: https://pypi.org/project/matgraphdb/
+[github]: https://github.com/romerogroup/MatGraphDB
+[contributing]: https://github.com/romerogroup/MatGraphDB/blob/main/CONTRIBUTING.md
+[license]: https://github.com/romerogroup/MatGraphDB/blob/main/LICENSE
+[parquetdb]: https://github.com/lllangWV/ParquetDB

docs/source/_static/notebook.css

@@ -0,0 +1,6 @@
+/* cap all output at ~15 lines, then scroll */
+/* targets nbsphinx output areas too */
+.output_area pre {
+    max-height: calc(1.2em * 15) !important;
+    overflow-y: auto         !important;
+  }

docs/source/conf.py

@@ -14,6 +14,7 @@
 import shutil
 import sys
 from distutils.sysconfig import get_python_lib
+from pathlib import Path
 
 from matgraphdb._version import version
 
@@ -25,17 +26,25 @@
 
 sys.path.insert(0, os.path.abspath("."))
 
-repo_root = os.path.abspath(os.path.join(os.path.dirname(__file__), "../.."))
-src_examples_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "examples"))
-if os.path.exists(src_examples_path):
-    shutil.rmtree(src_examples_path)
+SRC_DIR = Path(__file__).parent
+REPO_ROOT = SRC_DIR.parent.parent
+SRC_EXAMPLES_PATH = SRC_DIR / "examples"
+REPO_EXAMPLES_PATH = REPO_ROOT / "examples"
+CONTRIBUTING_PATH = REPO_ROOT / "CONTRIBUTING.md"
 
-shutil.copytree(os.path.join(repo_root, "examples"), src_examples_path)
-print(repo_root)
-print(src_examples_path)
 
-# examples_path = os.path.join(repo_root, "examples")
-# sys.path.insert(0, examples_path)
+print(f"REPO_ROOT: {REPO_ROOT}")
+print(f"SRC_DIR: {SRC_DIR}")
+print(f"SRC_EXAMPLES_PATH: {SRC_EXAMPLES_PATH}")
+
+
+# Copy Repo Examples to docs source directory
+if SRC_EXAMPLES_PATH.exists():
+    shutil.rmtree(SRC_EXAMPLES_PATH)
+shutil.copytree(REPO_EXAMPLES_PATH, SRC_EXAMPLES_PATH)
+
+shutil.copy(CONTRIBUTING_PATH, SRC_DIR / "CONTRIBUTING.md")
+
 
 
 if os.environ.get("READTHEDOCS") == "True":
@@ -88,6 +97,7 @@
     "numpydoc",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
+    "myst_parser",
     # "sphinx-nbexamples",
     # "sphinx_gallery.gen_gallery",
     # 'sphinx.youtube',
@@ -96,6 +106,11 @@
 nbsphinx_allow_errors = True
 pygments_style = "sphinx"
 
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'markdown',
+    '.md': 'markdown',
+}
 
 # sphinx_gallery_conf = {
 #     # convert rst to md for ipynb
@@ -175,7 +190,8 @@
     "logo_link": "index.html",  # Specify the link for the logo if needed
 }
 
-html_css_files = ["css/custom.css"]
+html_css_files = ["css/custom.css", "notebook.css"]
+
 
 html_js_files = ["js/custom.js"]
 

docs/source/index.rst

@@ -89,7 +89,7 @@ Index
     :glob:
 
 
-    01_tutorials/index
+    examples/01_tutorials/index
     02_internal/index
     examples/index.rst
     03_api/index