Merge pull request #1 from kks32/main

Abstract DS database to a single .py file

.github/workflows/build-test.yml

@@ -0,0 +1,27 @@
+name: Build, Lint, and Test
+
+on: [push, pull_request]
+jobs:
+  ci:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.11"]
+        poetry-version: ["1.6.1"]
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Run image
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ matrix.poetry-version }}
+      - name: Install the project dependencies
+        run: poetry install
+      - name: Lint with black
+        run: poetry run black --check .
+      - name: Run the automated tests
+        run: poetry run pytest -v

.github/workflows/pypi.yml

@@ -0,0 +1,27 @@
+name: Publish to PyPI
+on:
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'    
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/dsdatabase
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Poetry image
+        uses: abatilo/actions-poetry@v2
+      - name: Install the project dependencies
+        run: poetry install
+      - name: Build package
+        run: poetry build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -0,0 +1,177 @@
+# OS temp files
+**/.DS_Store*
+*~*
+*#*
+
+# 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/#use-with-ide
+.pdm.toml
+
+# 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/
+
+
+# IntelliJ / PyCharm artifacts
+.idea/
+
+# VS Code artifacts
+.vscode/
+
+# Logs and databases
+*.log
+*.sqlite
+

LICENSE

@@ -1,4 +1,4 @@
-                    MIT License
+MIT License
 
 Copyright (c) 2021 Scott J. Brandenberg
 

README.md

@@ -1,2 +1,53 @@
-# DesignSafe_db_scripts
-Connection scripts to databases set up in DesignSafe
+# DS Database
+
+[![build and test](https://github.com/DesignSafe-CI/dsdatabase/actions/workflows/build-test.yml/badge.svg)](https://github.com/DesignSafe-CI/dsdatabase/actions/workflows/build-test.yml)
+[![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.md)
+
+`dsdatabase` is a library that simplifies accessing databases on [DesignSafe](https://designsafe-ci.org) via [Jupyter Notebooks](https://jupyter.designsafe-ci.org).
+
+## Features
+
+Connects to SQL databases on DesignSafe:
+
+| Database | dbname | env_prefix |
+|----------|--------|------------|
+| NGL | `ngl`| `NGL_` |
+| Earthake Recovery | `eq` | `EQ_` |
+| Vp | `vp` | `VP_` |
+
+Define the following environment variables:
+```
+{env_prefix}DB_USER
+{env_prefix}DB_PASSWORD
+{env_prefix}DB_HOST
+{env_prefix}DB_PORT
+```
+
+For e.g., to add the environment variable `NGL_DB_USER` edit `~/.bashrc`, `~/.zshrc`, or a similar shell-specific configuration file for the current user and add `export NGL_DB_USER="dspublic"`.
+
+## Installation
+
+Install `dsdatabase` via pip
+
+```shell
+pip3 install dsdatabase
+```
+
+To install the current development version of the library use:
+
+```shell
+pip install git+https://github.com/DesignSafe-CI/dsdatabase.git --quiet
+```
+
+## Example usage:
+```python
+from dsdatabase.db import DSDatabase
+
+db = DSDatabase("ngl")
+sql = 'SELECT * FROM SITE'
+df = db.read_sql(sql)
+print(df)
+
+# Optionally, close the database connection when done
+db.close()
+```