Add Alex quote

.gitignore

@@ -4,6 +4,10 @@ __pycache__/
 *$py.class
 .DS_Store
 
+
+# Test file
+test.ipynb
+
 # C extensions
 *.so
 

README.md

@@ -29,28 +29,44 @@ functions for handling large datasets, on the order of tens of thousands, of
 In high-throughput analysis using `.cif` files, the research project has
 identified the folowing needs:
 
-- **Format files at once:** `.cif` files parsed from databases often contain
+- **Preprocess files at once:** `.cif` files parsed from databases often contain
   ill-formatted files. We need a tool to standardize, preprocess, and filter out
-  bad files. I also need to copy, move, and sort `.cif` files based on specific
+  bad files. We also need to copy, move, and sort `.cif` files based on specific
   attributes.
+
 - **Visualize coordination geometry:** We are interested in determining the
   coordination geometry and the best site in the supercell for analysis in a
   high-throughput manner. We need to identify the best site for each site label.
 - **Visualize distribution of files:** We want to easily identify and categorize
   a distribution of underlying `.cif` files based on supercell size, tags,
   coordination numbers, elements, etc.
 
+## Quotes
+
+Here is a quote illustrating how `cifkit` addresses one of the challenges mentioned above.
+
+> "I am building an X-Ray diffraction analysis (XRD) pattern visualization
+> script for my lab using `pymatgen`. I feel like `cifkit` integrated really
+> well into my existing stable of libraries, while surpassing some alternatives
+> in preprocessing and parsing. For example, it was often unclear at what stage
+> an error occurred—whether during pre-processing with `CifParser`, or XRD plot
+> generation with `diffraction.core` in `pymatgen`. The pre-processing logic in
+> `cifkit` was communicated clearly, both in documentation and in actual
+> outputs, allowing me to catch errors in my data before it was used in my
+> visualizations. I now use `cifkit` by default for processing CIFs before they
+> pass through the rest of my pipeline." - Alex Vtorov
+
 ## Overview
 
 Designed for individuals with minimal programming experience, `cifkit` provides
 two primary objects: `Cif` and `CifEnsemble`.
 
 ### Cif
 
-**`Cif`** is initialized with a `.cif` file path. It parses the .cif file,
-preprocesses ill-formatted files, generates supercells, and computes nearest
-neighbors. It also determines coordination numbers using four different methods
-and generates polyhedrons for each site.
+**`Cif`** is initialized with a `.cif` file path. It parses the `.cif` file,
+generates supercells, and computes nearest neighbors. It also determines
+coordination numbers using four different methods and generates polyhedrons for
+each site.
 
 ```python
 from cifkit import Cif
@@ -179,11 +195,8 @@ Here is how you can contribute to the `cifkit` project if you found it helpful:
 
 ## Contributors
 
-`cifkit` is made possible with contributions and support from the following
-individuals:
-
 `cifkit` has been greatly enhanced thanks to the contributions from a diverse
-group of developers and researchers. Here are a few notable contributors:
+group of researchers:
 
 - **Anton Oliynyk**: provided original ideation with `.cif` files
 - **Alex Vtorov**: recommended tool for polyhedron visualization
@@ -196,3 +209,5 @@ group of developers and researchers. Here are a few notable contributors:
 
 We welcome all forms of contributions from the community. Your ideas and
 improvements are valued and appreciated.
+
+## Testimonial

docs/notebooks/00_Intro.ipynb

@@ -11,9 +11,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Requirement already satisfied: cifkit in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (1.0.2)\n",
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    }
+   ],
    "source": [
     "pip install cifkit"
    ]
@@ -27,9 +36,40 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Requirement already satisfied: cifkit in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (1.0.2)\n",
+      "Requirement already satisfied: pyvista in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (0.43.10)\n",
+      "Requirement already satisfied: gemmi in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (0.6.6)\n",
+      "Requirement already satisfied: matplotlib>=3.0.1 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from pyvista) (3.9.0)\n",
+      "Requirement already satisfied: numpy>=1.21.0 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from pyvista) (1.26.4)\n",
+      "Requirement already satisfied: pillow in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from pyvista) (10.3.0)\n",
+      "Requirement already satisfied: pooch in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from pyvista) (1.8.2)\n",
+      "Requirement already satisfied: scooby>=0.5.1 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from pyvista) (0.10.0)\n",
+      "Requirement already satisfied: vtk in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from pyvista) (9.3.1)\n",
+      "Requirement already satisfied: contourpy>=1.0.1 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista) (1.2.1)\n",
+      "Requirement already satisfied: cycler>=0.10 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista) (0.12.1)\n",
+      "Requirement already satisfied: fonttools>=4.22.0 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista) (4.53.0)\n",
+      "Requirement already satisfied: kiwisolver>=1.3.1 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista) (1.4.5)\n",
+      "Requirement already satisfied: packaging>=20.0 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista) (24.1)\n",
+      "Requirement already satisfied: pyparsing>=2.3.1 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista) (3.1.2)\n",
+      "Requirement already satisfied: python-dateutil>=2.7 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista) (2.9.0.post0)\n",
+      "Requirement already satisfied: platformdirs>=2.5.0 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from pooch->pyvista) (4.2.2)\n",
+      "Requirement already satisfied: requests>=2.19.0 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from pooch->pyvista) (2.32.3)\n",
+      "Requirement already satisfied: six>=1.5 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from python-dateutil>=2.7->matplotlib>=3.0.1->pyvista) (1.16.0)\n",
+      "Requirement already satisfied: charset-normalizer<4,>=2 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from requests>=2.19.0->pooch->pyvista) (3.3.2)\n",
+      "Requirement already satisfied: idna<4,>=2.5 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from requests>=2.19.0->pooch->pyvista) (3.7)\n",
+      "Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from requests>=2.19.0->pooch->pyvista) (2.2.2)\n",
+      "Requirement already satisfied: certifi>=2017.4.17 in /Users/imac/miniconda3/envs/cifkit-test/lib/python3.12/site-packages (from requests>=2.19.0->pooch->pyvista) (2024.6.2)\n",
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    }
+   ],
    "source": [
     " pip install cifkit pyvista gemmi"
    ]
@@ -68,7 +108,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,