Merge pull request #80 from Exabyte-io/feat/SOF-6720-1-style

SOF-6720:  reformat `qe_scf_calculation.ipynb` notebook

README.md

@@ -79,15 +79,25 @@ NOTE: The Materials Project API key should be obtained from [https://legacy.mate
 
 This is an open-source repository and we welcome contributions for other use cases. The original set of examples is only meant to demonstrate the capabilities and can be extended.
 
-We suggest forking this repository and introducing the adjustments there. The changes in the fork can further be considered for merging into this repository as it is commonly used on Github. This process is explained in more details elsewhere online [[4](#links)].
+We suggest forking this repository and introducing the adjustments there. The changes in the fork can further be considered for merging into this repository as it is commonly used on GitHub. This process is explained in more details elsewhere online [[4](#links)].
 
 If you would like to add new examples or adjust existing ones, please consider the following:
 
 1. Put examples into the corresponding directories by domain.
 
-2. Walk the readers through the examples by providing step-by-step explanation similar to [this](examples/material/get_materials_by_formula.ipynb).
+2. Walk the readers through the examples by providing step-by-step explanation similar to [this](examples/material/get_materials_by_formula.ipynb) example.
 
-3. We use post-save hooks to automatically convert notebooks to python scripts. See [config](examples/config.py) file for more information. In order to facilitate code review, we exclude notebook sources from version control and store them in Git LFS [[3](#links)]. Please follow this convention.
+3. We use post-save hooks to automatically convert notebooks to python scripts. See [config](examples/config.py) file for more information. In order to facilitate code review, we exclude notebook sources in the `other/` directory from version control and store them in Git LFS [[3](#links)]. Please follow this convention.
+
+4. Apply code formatting by installing development requirements as follows:
+
+    ```bash
+    pip install -e ."[dev]"
+    pre-commit install
+    pre-commit run --all-files
+    ```
+
+    Check more details about `pre-commit` [here](https://pre-commit.com/).
 
 ## Links
 

examples/workflow/qe_scf_calculation.ipynb

@@ -1,13 +1,74 @@
 {
  "cells": [
   {
+   "attachments": {},
+   "cell_type": "markdown",
+   "id": "e5d1a592",
+   "metadata": {},
+   "source": [
+    "<a href=\"https://colab.research.google.com/github/Exabyte-io/api-examples/blob/dev/examples/workflow/qe_scf_calculation.ipynb\" target=\"_parent\">\n",
+    "<img alt=\"Open in Google Colab\" src=\"https://user-images.githubusercontent.com/20477508/128780728-491fea90-9b23-495f-a091-11681150db37.jpeg\" width=\"150\" border=\"0\">\n",
+    "</a>"
+   ]
+  },
+  {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "92673fc2-8999-415b-a866-7692a3e7d682",
    "metadata": {},
    "source": [
     "# Quantum Espresso SCF calcuation via API\n"
    ]
   },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "id": "41378265",
+   "metadata": {},
+   "source": [
+    "# Complete Authorization Form and Initialize Settings\n",
+    "\n",
+    "This will also determine environment and set all environment variables. We determine if we are using Jupyter Notebooks or Google Colab to run this tutorial.\n",
+    "\n",
+    "If you are running this notebook from Google Colab, Colab takes ~1 min to execute the following cell.\n",
+    "\n",
+    "ACCOUNT_ID and AUTH_TOKEN - Authentication parameters needed for when making requests to [Mat3ra.com's API Endpoints](https://docs.mat3ra.com/rest-api/endpoints/).\n",
+    "\n",
+    "MATERIALS_PROJECT_API_KEY - Authentication parameter needed for when making requests to [Material Project's API](https://materialsproject.org/open)\n",
+    "\n",
+    "ORGANIZATION_ID - Authentication parameter needed for when working with collaborative accounts https://docs.mat3ra.com/collaboration/organizations/overview/\n",
+    "\n",
+    "> <span style=\"color: orange\">**NOTE**</span>: If you are running this notebook from Jupyter, the variables ACCOUNT_ID, AUTH_TOKEN, MATERIALS_PROJECT_API_KEY, and ORGANIZATION_ID should be set in the file [settings.json](../../utils/settings.json) if you need to use these variables. To obtain API token parameters, please see the following link to the documentation explaining how to get them: https://docs.mat3ra.com/accounts/ui/preferences/api/"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "62f59cb7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# @title Authorization Form\n",
+    "ACCOUNT_ID = \"ACCOUNT_ID\"  # @param {type:\"string\"}\n",
+    "AUTH_TOKEN = \"AUTH_TOKEN\"  # @param {type:\"string\"}\n",
+    "MATERIALS_PROJECT_API_KEY = \"MATERIALS_PROJECT_API_KEY\"  # @param {type:\"string\"}\n",
+    "ORGANIZATION_ID = \"ORGANIZATION_ID\"  # @param {type:\"string\"}\n",
+    "\n",
+    "import os\n",
+    "\n",
+    "if \"COLAB_JUPYTER_IP\" in os.environ:\n",
+    "    os.environ.update(\n",
+    "        dict(\n",
+    "            ACCOUNT_ID=ACCOUNT_ID,\n",
+    "            AUTH_TOKEN=AUTH_TOKEN,\n",
+    "            MATERIALS_PROJECT_API_KEY=MATERIALS_PROJECT_API_KEY,\n",
+    "            ORGANIZATION_ID=ORGANIZATION_ID,\n",
+    "        )\n",
+    "    )\n",
+    "\n",
+    "    !GIT_BRANCH=\"dev\"; export GIT_BRANCH; curl -s \"https://raw.githubusercontent.com/Exabyte-io/api-examples/${GIT_BRANCH}/scripts/env.sh\" | bash"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

examples/workflow/qe_scf_calculation.py

@@ -1,9 +1,51 @@
 #!/usr/bin/env python
 # coding: utf-8
 
+# <a href="https://colab.research.google.com/github/Exabyte-io/api-examples/blob/dev/examples/workflow/qe_scf_calculation.ipynb" target="_parent">
+# <img alt="Open in Google Colab" src="https://user-images.githubusercontent.com/20477508/128780728-491fea90-9b23-495f-a091-11681150db37.jpeg" width="150" border="0">
+# </a>
+
 # # Quantum Espresso SCF calcuation via API
 # 
 
+# # Complete Authorization Form and Initialize Settings
+# 
+# This will also determine environment and set all environment variables. We determine if we are using Jupyter Notebooks or Google Colab to run this tutorial.
+# 
+# If you are running this notebook from Google Colab, Colab takes ~1 min to execute the following cell.
+# 
+# ACCOUNT_ID and AUTH_TOKEN - Authentication parameters needed for when making requests to [Mat3ra.com's API Endpoints](https://docs.mat3ra.com/rest-api/endpoints/).
+# 
+# MATERIALS_PROJECT_API_KEY - Authentication parameter needed for when making requests to [Material Project's API](https://materialsproject.org/open)
+# 
+# ORGANIZATION_ID - Authentication parameter needed for when working with collaborative accounts https://docs.mat3ra.com/collaboration/organizations/overview/
+# 
+# > <span style="color: orange">**NOTE**</span>: If you are running this notebook from Jupyter, the variables ACCOUNT_ID, AUTH_TOKEN, MATERIALS_PROJECT_API_KEY, and ORGANIZATION_ID should be set in the file [settings.json](../../utils/settings.json) if you need to use these variables. To obtain API token parameters, please see the following link to the documentation explaining how to get them: https://docs.mat3ra.com/accounts/ui/preferences/api/
+
+# In[ ]:
+
+
+# @title Authorization Form
+ACCOUNT_ID = "ACCOUNT_ID"  # @param {type:"string"}
+AUTH_TOKEN = "AUTH_TOKEN"  # @param {type:"string"}
+MATERIALS_PROJECT_API_KEY = "MATERIALS_PROJECT_API_KEY"  # @param {type:"string"}
+ORGANIZATION_ID = "ORGANIZATION_ID"  # @param {type:"string"}
+
+import os
+
+if "COLAB_JUPYTER_IP" in os.environ:
+    os.environ.update(
+        dict(
+            ACCOUNT_ID=ACCOUNT_ID,
+            AUTH_TOKEN=AUTH_TOKEN,
+            MATERIALS_PROJECT_API_KEY=MATERIALS_PROJECT_API_KEY,
+            ORGANIZATION_ID=ORGANIZATION_ID,
+        )
+    )
+
+    get_ipython().system('GIT_BRANCH="dev"; export GIT_BRANCH; curl -s "https://raw.githubusercontent.com/Exabyte-io/api-examples/${GIT_BRANCH}/scripts/env.sh" | bash')
+
+
 # In[1]:
 
 

pyproject.toml

@@ -28,7 +28,7 @@ localhost = [
 ]
 dev = [
   "pre-commit>=3.3.3",
-  "pip-compile>=6.13.0",
+  "pip-tools>=6.13.0",
 ]
 docs = [
   "mkdocs>=1.4.3",