Merge pull request #1 from camsai/chore/2024-12-12/initial-notebooks

chore/2024 12 12/initial notebooks

.github/workflows/cicd.yml

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+# Work in progress, needs `camsai/actions` repository to be present
+name: Continuous Testing and Publication
+
+on: [push]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  run-py-linter:
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python-version:
+            - 3.10.x
+
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Checkout actions repository
+        uses: actions/checkout@v4
+        with:
+          repository: camsai/actions
+          token: ${{ secrets.GITHUB_TOKEN }}
+          path: actions
+
+      - name: Run ruff linter
+        uses: ./actions/py/lint
+        with:
+          python-version: ${{ matrix.python-version }}
+
+  run-py-tests:
+    needs: run-py-linter
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python-version:
+          - 3.10.x
+          - 3.11.x
+
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Checkout actions repository
+        uses: actions/checkout@v4
+        with:
+          repository: camsai/actions
+          token: ${{ secrets.GITHUB_TOKEN }}
+          path: actions
+
+      - name: Run python unit tests
+        uses: ./actions/py/pytest
+        with:
+          python-version: ${{ matrix.python-version }}
+          unit-test-directory: tests/
+
+  publish-py-package:
+    needs:
+      - run-py-tests
+      - run-py-linter
+    runs-on: ubuntu-latest
+    if: (github.ref_name == 'main')
+
+    steps:
+      -   name: Checkout this repository
+          uses: actions/checkout@v4
+          with:
+            lfs: true
+
+      -   name: Checkout actions repository
+          uses: actions/checkout@v4
+          with:
+            repository: camsai/actions
+            token: ${{ secrets.GITHUB_TOKEN }}
+            path: actions
+
+      -   name: Publish python release
+          uses: ./actions/py/publish
+          with:
+            python-version: 3.10.12
+            github-token: ${{ secrets.GITHUB_TOKEN }}
+            pypi-api-token: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+.python-version

README.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# CAMSAI Notebooks\n",
+    "\n",
+    "## 1. Overview.\n",
+    "\n",
+    "This repository contains a collection of Jupyter notebooks that demonstrate how to use the CAMSAI toolchain.\n",
+    "\n",
+    "## 2. Generic Functionality.\n",
+    "\n",
+    "The following notebooks are available:\n",
+    "\n",
+    "- [validate_data](validate_data.ipynb): This notebook provides an introduction to data standards.\n",
+    "\n",
+    "## 3. Specific Functionality.\n",
+    "\n",
+    "Below, we list the contents per provider.\n",
+    "\n",
+    "| File                                               | Description |\n",
+    "|----------------------------------------------------|---------------------------------------------------- |\n",
+    "| [mat3ra/introduction](mat3ra/introduction.ipynb)   | Mat3ra Introduction.\n",
+    "| [Examples/Workflow](jarvisnist/introduction.ipynb) | JARVIS NIST Introduction. |\n",
+    "\n",
+    "\n",
+    "## Links\n",
+    "\n",
+    "- [Mat3ra API Documentation](https://docs.mat3ra.com/)\n",
+    "- [JARVIS NIST](https://jarvis.nist.gov/)\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "ca988675356058"
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

config.yml

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+# This manifest file is used to install the required packages for the corresponding notebook.
+# The following types of kernels are supported:
+# 1. python
+# 2. pyodide
+# Accordingly, the packages are installed using the kernel type, e.g., packages_pyodide.
+# The default packages are installed for all the notebooks.
+default:
+  packages_common: []
+  packages_python: []
+  packages_pyodide: []
+notebooks:
+  - name: validate_data.ipynb
+    packages_common:
+      - mat3ra-esse

jarvisnist/introduction.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Introduction\n",
+    "\n",
+    "## 1. Overview.\n",
+    "\n",
+    "A brief overview of the notebooks in this folder.\n",
+    "\n",
+    "TBA."
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "ca988675356058"
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}