From 71fbfd2b0f245d88e1ea3f781cf1a5386a7ea15d Mon Sep 17 00:00:00 2001
From: Krishna Kumar <krishnak@utexas.edu>
Date: Tue, 21 Nov 2023 13:06:33 -0600
Subject: [PATCH 1/9] Abstract DS database to a single .py file

---
 .github/workflows/build-test.yml        |  27 ++
 .github/workflows/pypi.yml              |  27 ++
 .gitignore                              | 177 ++++++++++
 LICENSE                                 |   2 +-
 README.md                               |  35 +-
 designsafe_db/__init__.py               |   1 -
 designsafe_db/earthquake_recovery_db.py |  59 ----
 designsafe_db/ngl_db.py                 |  50 ---
 designsafe_db/vp_db.py                  |  50 ---
 dsdatabase/__init__.py                  |   1 +
 dsdatabase/db.py                        |  90 +++++
 poetry.lock                             | 416 ++++++++++++++++++++++++
 pyproject.toml                          |  20 ++
 setup.py                                |   6 +-
 tests/__init__.py                       |   0
 tests/test_db.py                        |  36 ++
 16 files changed, 829 insertions(+), 168 deletions(-)
 create mode 100644 .github/workflows/build-test.yml
 create mode 100644 .github/workflows/pypi.yml
 create mode 100644 .gitignore
 delete mode 100644 designsafe_db/__init__.py
 delete mode 100644 designsafe_db/earthquake_recovery_db.py
 delete mode 100644 designsafe_db/ngl_db.py
 delete mode 100644 designsafe_db/vp_db.py
 create mode 100644 dsdatabase/__init__.py
 create mode 100644 dsdatabase/db.py
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml
 create mode 100644 tests/__init__.py
 create mode 100644 tests/test_db.py

diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
new file mode 100644
index 0000000..df993f1
--- /dev/null
+++ b/.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: ${{ matrix.poetry-version }}
+      - name: Install the project dependencies
+        run: poetry install
+      - name: Lint with black
+        run: poetry run black --check .
+      - name: Run the automated tests
+        run: poetry run pytest -v
\ No newline at end of file
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
new file mode 100644
index 0000000..68f2496
--- /dev/null
+++ b/.github/workflows/pypi.yml
@@ -0,0 +1,27 @@
+name: Publish to PyPI
+on:
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'    
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/dsdatabase
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Poetry image
+        uses: abatilo/actions-poetry@v2
+      - name: Install the project dependencies
+        run: poetry install
+      - name: Build package
+        run: poetry build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..e2afc88
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,177 @@
+# OS temp files
+**/.DS_Store*
+*~*
+*#*
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$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
+
diff --git a/LICENSE b/LICENSE
index da8f155..7306435 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,4 +1,4 @@
-                    MIT License
+MIT License
 
 Copyright (c) 2021 Scott J. Brandenberg
 
diff --git a/README.md b/README.md
index 816f155..8aec79c 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,33 @@
-# 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 |
+|----------|--------|
+| NGL | sjbrande_ngl_db |
+| Earthake Recovery | sjbrande_vpdb |
+| Vp | sjbrande_vpdb |
+
+
+## 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:
\ No newline at end of file
diff --git a/designsafe_db/__init__.py b/designsafe_db/__init__.py
deleted file mode 100644
index c617616..0000000
--- a/designsafe_db/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-name = 'designsafe_db'
diff --git a/designsafe_db/earthquake_recovery_db.py b/designsafe_db/earthquake_recovery_db.py
deleted file mode 100644
index 1b4551d..0000000
--- a/designsafe_db/earthquake_recovery_db.py
+++ /dev/null
@@ -1,59 +0,0 @@
-# Establishes connection to NGL database from MySQL Workbench
-#import pymysql
-#def connect():
-#    try:
-#        return(pymysql.connect(user='dspublic', password='R3ad0nlY', host='129.114.52.174', port=3306, db='post_earthquake_recovery'))
-#    except:
-#        pass
-
-    
-import pymysql
-import pandas as pd
-import sqlalchemy
-from sqlalchemy import exc, text
-
-def connect():
-    try:
-        print('We have phased out the earthquake_recovery_db.connect() command in favor of the earthquake_recovery_db.read_sql(sql, output) command.')
-    except:
-        pass
-    
-def read_sql(*args):
-    if(len(args)<1):
-        print('You must specify a sql string in the read_sql function')
-        return
-    if(len(args)>2):
-        print('You must only specify sql and type in the read_sql function')
-        return
-    sql = args[0]
-    if(len(args)==1):
-        output = 'DataFrame'
-    else:
-        if(args[1] in ['DataFrame','dict']):
-            output = args[1]
-        else:
-            print('type "' + str(args[1]) + '" is not a valid option. Must be either "DataFrame" or "dict". Using "DataFrame" type as default.')
-            
-    if(output=='DataFrame'):
-        try:
-            engine = sqlalchemy.create_engine('mysql+pymysql://dspublic:R3ad0nlY@129.114.52.174:3306/post_earthquake_recovery')
-            data = pd.DataFrame(engine.connect().execute(text(sql)))
-            engine.dispose()
-            return(data)
-        except exc.SQLAlchemyError as e:
-            print(e)
-            pass
-    elif(output=='dict'):
-        try:
-            cnx = pymysql.connect(user='dspublic', password='R3ad0nlY', host='129.114.52.174', port=3306, db='post_earthquake_recovery')
-            cur = cnx.cursor(pymysql.cursors.DictCursor)
-            cur.execute(sql)
-            data = cur.fetchall()
-            cnx.close()
-            return(data)
-        except pymysql.Error as e:
-            print("Error %d: %s" % (e.args[0], e.args[1]))
-            pass
-    else:
-        print('In earthquake_recovery_db.read_sql(text(sql), output), output must be either "DataFrame" or "dict", not "' + output + '"')
-        return
diff --git a/designsafe_db/ngl_db.py b/designsafe_db/ngl_db.py
deleted file mode 100644
index e71a429..0000000
--- a/designsafe_db/ngl_db.py
+++ /dev/null
@@ -1,50 +0,0 @@
-import pymysql
-import pandas as pd
-import sqlalchemy
-from sqlalchemy import exc
-
-def connect():
-    try:
-        print('We have phased out the ngl_db.connect() command in favor of the ngl_db.read_sql(sql, output) command. Please see https://ngl-tools.readthedocs.io/en/latest/ for details.')
-    except:
-        pass
-    
-def read_sql(*args):
-    if(len(args)<1):
-        print('You must specify a sql string in the read_sql function')
-        return
-    if(len(args)>2):
-        print('You must only specify sql and type in the read_sql function')
-        return
-    sql = args[0]
-    if(len(args)==1):
-        output = 'DataFrame'
-    else:
-        if(args[1] in ['DataFrame','dict']):
-            output = args[1]
-        else:
-            print('type "' + str(args[1]) + '" is not a valid option. Must be either "DataFrame" or "dict". Using "DataFrame" type as default.')
-    
-    if(output=='DataFrame'):
-        try:
-            engine = sqlalchemy.create_engine('mysql+pymysql://dspublic:R3ad0nlY@129.114.52.174:3306/sjbrande_ngl_db')
-            data = pd.read_sql_query(sql, con=engine)
-            engine.dispose()
-            return(data)
-        except exc.SQLAlchemyError as e:
-            print(e)
-            pass
-    elif(output=='dict'):
-        try:
-            cnx = pymysql.connect(user='dspublic', password='R3ad0nlY', host='129.114.52.174', port=3306, db='sjbrande_ngl_db')
-            cur = cnx.cursor(pymysql.cursors.DictCursor)
-            cur.execute(sql)
-            data = cur.fetchall()
-            cnx.close()
-            return(data)
-        except pymysql.Error as e:
-            print("Error %d: %s" % (e.args[0], e.args[1]))
-            pass
-    else:
-        print('In ngl_db.read_sql(sql, output), output must be either "DataFrame" or "dict", not "' + output + '"')
-        return
diff --git a/designsafe_db/vp_db.py b/designsafe_db/vp_db.py
deleted file mode 100644
index 5a638be..0000000
--- a/designsafe_db/vp_db.py
+++ /dev/null
@@ -1,50 +0,0 @@
-import pymysql
-import pandas as pd
-import sqlalchemy
-from sqlalchemy import exc
-
-def connect():
-    try:
-        print('We have phased out the vp_db.connect() command in favor of the vp_db.read_sql(sql, output) command.')
-    except:
-        pass
-    
-def read_sql(*args):
-    if(len(args)<1):
-        print('You must specify a sql string in the read_sql function')
-        return
-    if(len(args)>2):
-        print('You must only specify sql and type in the read_sql function')
-        return
-    sql = args[0]
-    if(len(args)==1):
-        output = 'DataFrame'
-    else:
-        if(args[1] in ['DataFrame','dict']):
-            output = args[1]
-        else:
-            print('type "' + str(args[1]) + '" is not a valid option. Must be either "DataFrame" or "dict". Using "DataFrame" type as default.')
-            
-    if(output=='DataFrame'):
-        try:
-            engine = sqlalchemy.create_engine('mysql+pymysql://dspublic:R3ad0nlY@129.114.52.174:3306/sjbrande_vpdb')
-            data = pd.read_sql_query(sql, con=engine)
-            engine.dispose()
-            return(data)
-        except exc.SQLAlchemyError as e:
-            print(e)
-            pass
-    elif(output=='dict'):
-        try:
-            cnx = pymysql.connect(user='dspublic', password='R3ad0nlY', host='129.114.52.174', port=3306, db='sjbrande_vpdb')
-            cur = cnx.cursor(pymysql.cursors.DictCursor)
-            cur.execute(sql)
-            data = cur.fetchall()
-            cnx.close()
-            return(data)
-        except pymysql.Error as e:
-            print("Error %d: %s" % (e.args[0], e.args[1]))
-            pass
-    else:
-        print('In vp_db.read_sql(sql, output), output must be either "DataFrame" or "dict", not "' + output + '"')
-        return
diff --git a/dsdatabase/__init__.py b/dsdatabase/__init__.py
new file mode 100644
index 0000000..e7c972d
--- /dev/null
+++ b/dsdatabase/__init__.py
@@ -0,0 +1 @@
+name = "designsafe_db"
diff --git a/dsdatabase/db.py b/dsdatabase/db.py
new file mode 100644
index 0000000..51c0562
--- /dev/null
+++ b/dsdatabase/db.py
@@ -0,0 +1,90 @@
+import os
+import pandas as pd
+from sqlalchemy import create_engine, exc
+from sqlalchemy.orm import sessionmaker
+from sqlalchemy import text
+
+
+class DSDatabase:
+    """A database utility class for connecting to a DesignSafe SQL database.
+
+    This class provides functionality to connect to a MySQL database using
+    SQLAlchemy and PyMySQL. It supports executing SQL queries and returning
+    results in different formats.
+
+    Attributes:
+        user (str): Database username, defaults to 'dspublic'.
+        password (str): Database password, defaults to 'R3ad0nlY'.
+        host (str): Database host address, defaults to '129.114.52.174'.
+        port (int): Database port, defaults to 3306.
+        db (str): Database name, can be 'sjbrande_ngl_db', 'sjbrande_vpdb', or 'post_earthquake_recovery'.
+        recycle_time (int): Time in seconds to recycle database connections.
+        engine (Engine): SQLAlchemy engine for database connection.
+        Session (sessionmaker): SQLAlchemy session maker bound to the engine.
+    """
+
+    def __init__(self, dbname="sjbrande_ngl_db"):
+        """Initializes the DSDatabase instance with environment variables and creates the database engine.
+
+        Args:
+            dbname (str): Database name. Must be one of 'sjbrande_ngl_db', 'sjbrande_vpdb', or 'post_earthquake_recovery'.
+        """
+        allowed_dbnames = [
+            "sjbrande_ngl_db",
+            "sjbrande_vpdb",
+            "post_earthquake_recovery",
+        ]
+        if dbname not in allowed_dbnames:
+            raise ValueError(
+                f"Invalid database name '{dbname}'. Allowed names are: {', '.join(allowed_dbnames)}"
+            )
+
+        self.user = os.getenv("DB_USER", "dspublic")
+        self.password = os.getenv("DB_PASSWORD", "R3ad0nlY")
+        self.host = os.getenv("DB_HOST", "129.114.52.174")
+        self.port = os.getenv("DB_PORT", 3306)
+        self.db = dbname
+        self.recycle_time = 3600  # 1 hour in seconds
+
+        # Setup the database connection
+        self.engine = create_engine(
+            f"mysql+pymysql://{self.user}:{self.password}@{self.host}:{self.port}/{self.db}",
+            pool_recycle=self.recycle_time,
+        )
+        self.Session = sessionmaker(bind=self.engine)
+
+    def read_sql(self, sql, output_type="DataFrame"):
+        """Executes a SQL query and returns the results.
+
+        Args:
+            sql (str): The SQL query string to be executed.
+            output_type (str, optional): The format for the query results. Defaults to 'DataFrame'.
+                Possible values are 'DataFrame' for a pandas DataFrame, or 'dict' for a list of dictionaries.
+
+        Returns:
+            pandas.DataFrame or list of dict: The result of the SQL query.
+
+        Raises:
+            ValueError: If the SQL query string is empty or if the output type is not valid.
+            SQLAlchemyError: If an error occurs during query execution.
+        """
+        if not sql:
+            raise ValueError("SQL query string is required")
+
+        if output_type not in ["DataFrame", "dict"]:
+            raise ValueError('Output type must be either "DataFrame" or "dict"')
+
+        session = self.Session()
+
+        try:
+            if output_type == "DataFrame":
+                return pd.read_sql_query(sql, session.bind)
+            else:
+                # Convert SQL string to a text object
+                sql_text = text(sql)
+                result = session.execute(sql_text)
+                return [dict(row) for row in result]
+        except exc.SQLAlchemyError as e:
+            raise Exception(f"SQLAlchemyError: {e}")
+        finally:
+            session.close()
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..9ba91e9
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,416 @@
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+description = "Cross-platform colored terminal text."
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
+]
+
+[[package]]
+name = "greenlet"
+version = "3.0.1"
+description = "Lightweight in-process concurrent programming"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "greenlet-3.0.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f89e21afe925fcfa655965ca8ea10f24773a1791400989ff32f467badfe4a064"},
+    {file = "greenlet-3.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:28e89e232c7593d33cac35425b58950789962011cc274aa43ef8865f2e11f46d"},
+    {file = "greenlet-3.0.1-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:b8ba29306c5de7717b5761b9ea74f9c72b9e2b834e24aa984da99cbfc70157fd"},
+    {file = "greenlet-3.0.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:19bbdf1cce0346ef7341705d71e2ecf6f41a35c311137f29b8a2dc2341374565"},
+    {file = "greenlet-3.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:599daf06ea59bfedbec564b1692b0166a0045f32b6f0933b0dd4df59a854caf2"},
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+    {file = "SQLAlchemy-2.0.23-cp38-cp38-win32.whl", hash = "sha256:42ede90148b73fe4ab4a089f3126b2cfae8cfefc955c8174d697bb46210c8306"},
+    {file = "SQLAlchemy-2.0.23-cp38-cp38-win_amd64.whl", hash = "sha256:964971b52daab357d2c0875825e36584d58f536e920f2968df8d581054eada4b"},
+    {file = "SQLAlchemy-2.0.23-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:616fe7bcff0a05098f64b4478b78ec2dfa03225c23734d83d6c169eb41a93e55"},
+    {file = "SQLAlchemy-2.0.23-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:0e680527245895aba86afbd5bef6c316831c02aa988d1aad83c47ffe92655e74"},
+    {file = "SQLAlchemy-2.0.23-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9585b646ffb048c0250acc7dad92536591ffe35dba624bb8fd9b471e25212a35"},
+    {file = "SQLAlchemy-2.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4895a63e2c271ffc7a81ea424b94060f7b3b03b4ea0cd58ab5bb676ed02f4221"},
+    {file = "SQLAlchemy-2.0.23-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:cc1d21576f958c42d9aec68eba5c1a7d715e5fc07825a629015fe8e3b0657fb0"},
+    {file = "SQLAlchemy-2.0.23-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:967c0b71156f793e6662dd839da54f884631755275ed71f1539c95bbada9aaab"},
+    {file = "SQLAlchemy-2.0.23-cp39-cp39-win32.whl", hash = "sha256:0a8c6aa506893e25a04233bc721c6b6cf844bafd7250535abb56cb6cc1368884"},
+    {file = "SQLAlchemy-2.0.23-cp39-cp39-win_amd64.whl", hash = "sha256:f3420d00d2cb42432c1d0e44540ae83185ccbbc67a6054dcc8ab5387add6620b"},
+    {file = "SQLAlchemy-2.0.23-py3-none-any.whl", hash = "sha256:31952bbc527d633b9479f5f81e8b9dfada00b91d6baba021a869095f1a97006d"},
+    {file = "SQLAlchemy-2.0.23.tar.gz", hash = "sha256:c1bda93cbbe4aa2aa0aa8655c5aeda505cd219ff3e8da91d1d329e143e4aff69"},
+]
+
+[package.dependencies]
+greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""}
+typing-extensions = ">=4.2.0"
+
+[package.extras]
+aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
+aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
+aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
+asyncio = ["greenlet (!=0.4.17)"]
+asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
+mssql = ["pyodbc"]
+mssql-pymssql = ["pymssql"]
+mssql-pyodbc = ["pyodbc"]
+mypy = ["mypy (>=0.910)"]
+mysql = ["mysqlclient (>=1.4.0)"]
+mysql-connector = ["mysql-connector-python"]
+oracle = ["cx-oracle (>=8)"]
+oracle-oracledb = ["oracledb (>=1.0.1)"]
+postgresql = ["psycopg2 (>=2.7)"]
+postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
+postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
+postgresql-psycopg = ["psycopg (>=3.0.7)"]
+postgresql-psycopg2binary = ["psycopg2-binary"]
+postgresql-psycopg2cffi = ["psycopg2cffi"]
+postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
+pymysql = ["pymysql"]
+sqlcipher = ["sqlcipher3-binary"]
+
+[[package]]
+name = "typing-extensions"
+version = "4.8.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
+    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
+]
+
+[[package]]
+name = "tzdata"
+version = "2023.3"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+files = [
+    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
+    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.11"
+content-hash = "b0ee5a78da466971435f48193795ff01158a67ca7052a7bc1219a8c597dd47b4"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..c25c247
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,20 @@
+[tool.poetry]
+name = "dsdatabase"
+version = "0.1.0"
+description = "DesignSafe relational database connection scripts"
+authors = ["Scott Brandenberg <sjbrandenberg@ucla.edu>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.11"
+pandas = "^2.1.3"
+pymysql = "^1.1.0"
+sqlalchemy = "^2.0.23"
+
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.4.3"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/setup.py b/setup.py
index 216dd30..06408a4 100644
--- a/setup.py
+++ b/setup.py
@@ -18,9 +18,5 @@
         "License :: OSI Approved :: GNU Public License version 3",
         "Operating System :: OS Independent",
     ],
-    install_requires=[
-        'pymysql',
-        'pandas',
-        'sqlalchemy'
-      ],
+    install_requires=["pymysql", "pandas", "sqlalchemy"],
 )
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test_db.py b/tests/test_db.py
new file mode 100644
index 0000000..5e3aa08
--- /dev/null
+++ b/tests/test_db.py
@@ -0,0 +1,36 @@
+import unittest
+from unittest.mock import MagicMock, patch
+import pandas as pd
+from dsdatabase.db import DSDatabase
+
+
+class MockRowProxy:
+    def __init__(self, row_data, column_names):
+        self._row_data = row_data
+        self._column_names = column_names
+
+    def __getitem__(self, key):
+        if isinstance(key, int):
+            return self._row_data[key]
+        elif isinstance(key, str):
+            return self._row_data[self._column_names.index(key)]
+
+
+class TestDSDatabase(unittest.TestCase):
+    def setUp(self):
+        self.mock_connection = MagicMock()
+        self.db = DSDatabase(dbname="sjbrande_ngl_db")
+        self.db.engine.connect = MagicMock(return_value=self.mock_connection)
+
+    @patch("pandas.read_sql_query")
+    def test_read_sql_returns_dataframe(self, mock_read_sql_query):
+        sql = "SELECT * FROM table"
+        mock_df = pd.DataFrame([{"id": 1, "name": "Test"}])
+        mock_read_sql_query.return_value = mock_df
+        result = self.db.read_sql(sql)
+        self.assertIsInstance(result, pd.DataFrame)
+        pd.testing.assert_frame_equal(result, mock_df)
+
+
+if __name__ == "__main__":
+    unittest.main()

From 6fa799d93c29a1986ceb9f5f0a847304a7b1dff6 Mon Sep 17 00:00:00 2001
From: Krishna Kumar <krishnak@utexas.edu>
Date: Tue, 21 Nov 2023 13:32:28 -0600
Subject: [PATCH 2/9] Config for 3 databases

---
 README.md        | 17 +++++++++++++----
 dsdatabase/db.py | 40 ++++++++++++++++++++++++----------------
 tests/test_db.py | 29 ++++++++++++++++++++++++++++-
 3 files changed, 65 insertions(+), 21 deletions(-)

diff --git a/README.md b/README.md
index 8aec79c..4906bb5 100644
--- a/README.md
+++ b/README.md
@@ -11,9 +11,9 @@ Connects to SQL databases on DesignSafe:
 
 | Database | dbname |
 |----------|--------|
-| NGL | sjbrande_ngl_db |
-| Earthake Recovery | sjbrande_vpdb |
-| Vp | sjbrande_vpdb |
+| NGL | `ngl`|
+| Earthake Recovery | `eq` |
+| Vp | `vp` |
 
 
 ## Installation
@@ -30,4 +30,13 @@ To install the current development version of the library use:
 pip install git+https://github.com/DesignSafe-CI/dsdatabase.git --quiet
 ```
 
-## Example usage:
\ No newline at end of file
+## Example usage:
+```
+db = DSDatabase(dbname="mydatabase")
+with db.Session() as session:
+    # Perform database operations
+    pass  # replace with actual operations
+
+# Optionally, close the database connection when done
+db.close()
+```
\ No newline at end of file
diff --git a/dsdatabase/db.py b/dsdatabase/db.py
index 51c0562..9de99b6 100644
--- a/dsdatabase/db.py
+++ b/dsdatabase/db.py
@@ -23,33 +23,37 @@ class DSDatabase:
         Session (sessionmaker): SQLAlchemy session maker bound to the engine.
     """
 
-    def __init__(self, dbname="sjbrande_ngl_db"):
+    def __init__(self, dbname="ngl"):
         """Initializes the DSDatabase instance with environment variables and creates the database engine.
 
         Args:
-            dbname (str): Database name. Must be one of 'sjbrande_ngl_db', 'sjbrande_vpdb', or 'post_earthquake_recovery'.
+            dbname (str): Shorthand for the database name. Must be one of 'ngl', 'vp', or 'eq'.
         """
-        allowed_dbnames = [
-            "sjbrande_ngl_db",
-            "sjbrande_vpdb",
-            "post_earthquake_recovery",
-        ]
-        if dbname not in allowed_dbnames:
+        # Mapping of shorthand names to actual database names and environment prefixes
+        db_config = {
+            "ngl": {"dbname": "sjbrande_ngl_db", "env_prefix": "NGL_"},
+            "vp": {"dbname": "sjbrande_vpdb", "env_prefix": "VP_"},
+            "eq": {"dbname": "post_earthquake_recovery", "env_prefix": "EQ_"},
+        }
+
+        if dbname not in db_config:
             raise ValueError(
-                f"Invalid database name '{dbname}'. Allowed names are: {', '.join(allowed_dbnames)}"
+                f"Invalid database shorthand '{dbname}'. Allowed shorthands are: {', '.join(db_config.keys())}"
             )
 
-        self.user = os.getenv("DB_USER", "dspublic")
-        self.password = os.getenv("DB_PASSWORD", "R3ad0nlY")
-        self.host = os.getenv("DB_HOST", "129.114.52.174")
-        self.port = os.getenv("DB_PORT", 3306)
-        self.db = dbname
-        self.recycle_time = 3600  # 1 hour in seconds
+        config = db_config[dbname]
+        env_prefix = config["env_prefix"]
+
+        self.user = os.getenv(f"{env_prefix}DB_USER", "dspublic")
+        self.password = os.getenv(f"{env_prefix}DB_PASSWORD", "R3ad0nlY")
+        self.host = os.getenv(f"{env_prefix}DB_HOST", "129.114.52.174")
+        self.port = os.getenv(f"{env_prefix}DB_PORT", 3306)
+        self.db = config["dbname"]
 
         # Setup the database connection
         self.engine = create_engine(
             f"mysql+pymysql://{self.user}:{self.password}@{self.host}:{self.port}/{self.db}",
-            pool_recycle=self.recycle_time,
+            pool_recycle=3600,  # 1 hour in seconds
         )
         self.Session = sessionmaker(bind=self.engine)
 
@@ -88,3 +92,7 @@ def read_sql(self, sql, output_type="DataFrame"):
             raise Exception(f"SQLAlchemyError: {e}")
         finally:
             session.close()
+
+    def close(self):
+        """Close the database connection."""
+        self.engine.dispose()
diff --git a/tests/test_db.py b/tests/test_db.py
index 5e3aa08..4bc278b 100644
--- a/tests/test_db.py
+++ b/tests/test_db.py
@@ -19,9 +19,36 @@ def __getitem__(self, key):
 class TestDSDatabase(unittest.TestCase):
     def setUp(self):
         self.mock_connection = MagicMock()
-        self.db = DSDatabase(dbname="sjbrande_ngl_db")
+        self.db = DSDatabase(dbname="ngl")
         self.db.engine.connect = MagicMock(return_value=self.mock_connection)
 
+    @patch.dict(
+        "os.environ", {"NGL_DB_USER": "ngl_user", "NGL_DB_PASSWORD": "ngl_pass"}
+    )
+    def test_init_with_valid_dbname_ngl(self):
+        db = DSDatabase(dbname="ngl")
+        self.assertEqual(db.user, "ngl_user")
+        self.assertEqual(db.password, "ngl_pass")
+        self.assertEqual(db.db, "sjbrande_ngl_db")
+
+    @patch.dict("os.environ", {"VP_DB_USER": "vp_user", "VP_DB_PASSWORD": "vp_pass"})
+    def test_init_with_valid_dbname_vp(self):
+        db = DSDatabase(dbname="vp")
+        self.assertEqual(db.user, "vp_user")
+        self.assertEqual(db.password, "vp_pass")
+        self.assertEqual(db.db, "sjbrande_vpdb")
+
+    @patch.dict("os.environ", {"EQ_DB_USER": "eq_user", "EQ_DB_PASSWORD": "eq_pass"})
+    def test_init_with_valid_dbname_eq(self):
+        db = DSDatabase(dbname="eq")
+        self.assertEqual(db.user, "eq_user")
+        self.assertEqual(db.password, "eq_pass")
+        self.assertEqual(db.db, "post_earthquake_recovery")
+
+    def test_init_with_invalid_dbname(self):
+        with self.assertRaises(ValueError):
+            DSDatabase(dbname="invalid")
+
     @patch("pandas.read_sql_query")
     def test_read_sql_returns_dataframe(self, mock_read_sql_query):
         sql = "SELECT * FROM table"

From dce2378c6eaebf8657edaa2a2e5a6433dd4056f3 Mon Sep 17 00:00:00 2001
From: Krishna Kumar <krishnak@utexas.edu>
Date: Tue, 21 Nov 2023 13:33:57 -0600
Subject: [PATCH 3/9] Fix min python version to 3.8

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index c25c247..46c215e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ authors = ["Scott Brandenberg <sjbrandenberg@ucla.edu>"]
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "^3.11"
+python = "^3.8"
 pandas = "^2.1.3"
 pymysql = "^1.1.0"
 sqlalchemy = "^2.0.23"

From 59f530e53dd21703d880c3533e3471ace63382df Mon Sep 17 00:00:00 2001
From: Krishna Kumar <krishnak@utexas.edu>
Date: Tue, 21 Nov 2023 13:35:37 -0600
Subject: [PATCH 4/9] Fix python dependencies

---
 poetry.lock    | 125 ++++++++++++++++++++++++++++++++++++++++++++++++-
 pyproject.toml |   3 +-
 2 files changed, 125 insertions(+), 3 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9ba91e9..4a02d43 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,61 @@
 # This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
+[[package]]
+name = "black"
+version = "23.11.0"
+description = "The uncompromising code formatter."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "black-23.11.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dbea0bb8575c6b6303cc65017b46351dc5953eea5c0a59d7b7e3a2d2f433a911"},
+    {file = "black-23.11.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:412f56bab20ac85927f3a959230331de5614aecda1ede14b373083f62ec24e6f"},
+    {file = "black-23.11.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d136ef5b418c81660ad847efe0e55c58c8208b77a57a28a503a5f345ccf01394"},
+    {file = "black-23.11.0-cp310-cp310-win_amd64.whl", hash = "sha256:6c1cac07e64433f646a9a838cdc00c9768b3c362805afc3fce341af0e6a9ae9f"},
+    {file = "black-23.11.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:cf57719e581cfd48c4efe28543fea3d139c6b6f1238b3f0102a9c73992cbb479"},
+    {file = "black-23.11.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:698c1e0d5c43354ec5d6f4d914d0d553a9ada56c85415700b81dc90125aac244"},
+    {file = "black-23.11.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:760415ccc20f9e8747084169110ef75d545f3b0932ee21368f63ac0fee86b221"},
+    {file = "black-23.11.0-cp311-cp311-win_amd64.whl", hash = "sha256:58e5f4d08a205b11800332920e285bd25e1a75c54953e05502052738fe16b3b5"},
+    {file = "black-23.11.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:45aa1d4675964946e53ab81aeec7a37613c1cb71647b5394779e6efb79d6d187"},
+    {file = "black-23.11.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:4c44b7211a3a0570cc097e81135faa5f261264f4dfaa22bd5ee2875a4e773bd6"},
+    {file = "black-23.11.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2a9acad1451632021ee0d146c8765782a0c3846e0e0ea46659d7c4f89d9b212b"},
+    {file = "black-23.11.0-cp38-cp38-win_amd64.whl", hash = "sha256:fc7f6a44d52747e65a02558e1d807c82df1d66ffa80a601862040a43ec2e3142"},
+    {file = "black-23.11.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:7f622b6822f02bfaf2a5cd31fdb7cd86fcf33dab6ced5185c35f5db98260b055"},
+    {file = "black-23.11.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:250d7e60f323fcfc8ea6c800d5eba12f7967400eb6c2d21ae85ad31c204fb1f4"},
+    {file = "black-23.11.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5133f5507007ba08d8b7b263c7aa0f931af5ba88a29beacc4b2dc23fcefe9c06"},
+    {file = "black-23.11.0-cp39-cp39-win_amd64.whl", hash = "sha256:421f3e44aa67138ab1b9bfbc22ee3780b22fa5b291e4db8ab7eee95200726b07"},
+    {file = "black-23.11.0-py3-none-any.whl", hash = "sha256:54caaa703227c6e0c87b76326d0862184729a69b73d3b7305b6288e1d830067e"},
+    {file = "black-23.11.0.tar.gz", hash = "sha256:4c68855825ff432d197229846f971bc4d6666ce90492e5b02013bcaca4d9ab05"},
+]
+
+[package.dependencies]
+click = ">=8.0.0"
+mypy-extensions = ">=0.4.3"
+packaging = ">=22.0"
+pathspec = ">=0.9.0"
+platformdirs = ">=2"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+colorama = ["colorama (>=0.4.3)"]
+d = ["aiohttp (>=3.7.4)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+uvloop = ["uvloop (>=0.15.2)"]
+
+[[package]]
+name = "click"
+version = "8.1.7"
+description = "Composable command line interface toolkit"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
+    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -11,6 +67,20 @@ files = [
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
+[[package]]
+name = "exceptiongroup"
+version = "1.2.0"
+description = "Backport of PEP 654 (exception groups)"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"},
+    {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"},
+]
+
+[package.extras]
+test = ["pytest (>=6)"]
+
 [[package]]
 name = "greenlet"
 version = "3.0.1"
@@ -92,6 +162,17 @@ files = [
     {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
 ]
 
+[[package]]
+name = "mypy-extensions"
+version = "1.0.0"
+description = "Type system extensions for programs checked with the mypy type checker."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
+    {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
+]
+
 [[package]]
 name = "numpy"
 version = "1.26.2"
@@ -184,6 +265,7 @@ files = [
 
 [package.dependencies]
 numpy = [
+    {version = ">=1.22.4,<2", markers = "python_version < \"3.11\""},
     {version = ">=1.23.2,<2", markers = "python_version == \"3.11\""},
     {version = ">=1.26.0,<2", markers = "python_version >= \"3.12\""},
 ]
@@ -215,6 +297,32 @@ sql-other = ["SQLAlchemy (>=1.4.36)"]
 test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)"]
 xml = ["lxml (>=4.8.0)"]
 
+[[package]]
+name = "pathspec"
+version = "0.11.2"
+description = "Utility library for gitignore style pattern matching of file paths."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pathspec-0.11.2-py3-none-any.whl", hash = "sha256:1d6ed233af05e679efb96b1851550ea95bbb64b7c490b0f5aa52996c11e92a20"},
+    {file = "pathspec-0.11.2.tar.gz", hash = "sha256:e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3"},
+]
+
+[[package]]
+name = "platformdirs"
+version = "4.0.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "platformdirs-4.0.0-py3-none-any.whl", hash = "sha256:118c954d7e949b35437270383a3f2531e99dd93cf7ce4dc8340d3356d30f173b"},
+    {file = "platformdirs-4.0.0.tar.gz", hash = "sha256:cb633b2bcf10c51af60beb0ab06d2f1d69064b43abf4c185ca6b28865f3f9731"},
+]
+
+[package.extras]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
+
 [[package]]
 name = "pluggy"
 version = "1.3.0"
@@ -258,9 +366,11 @@ files = [
 
 [package.dependencies]
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
+exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
 pluggy = ">=0.12,<2.0"
+tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
@@ -388,6 +498,17 @@ postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
 pymysql = ["pymysql"]
 sqlcipher = ["sqlcipher3-binary"]
 
+[[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+]
+
 [[package]]
 name = "typing-extensions"
 version = "4.8.0"
@@ -412,5 +533,5 @@ files = [
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.11"
-content-hash = "b0ee5a78da466971435f48193795ff01158a67ca7052a7bc1219a8c597dd47b4"
+python-versions = ">=3.9"
+content-hash = "07a3c04e4018dbc8df494a25ba3b4f18f2391c49e45bf9e2a415dd0019426b5b"
diff --git a/pyproject.toml b/pyproject.toml
index 46c215e..2f5c608 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ authors = ["Scott Brandenberg <sjbrandenberg@ucla.edu>"]
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = ">=3.9"
 pandas = "^2.1.3"
 pymysql = "^1.1.0"
 sqlalchemy = "^2.0.23"
@@ -14,6 +14,7 @@ sqlalchemy = "^2.0.23"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.3"
+black = "^23.11.0"
 
 [build-system]
 requires = ["poetry-core"]

From 3603c12a86521e2f4f9695d5805a9e9ac58dbf7a Mon Sep 17 00:00:00 2001
From: Krishna Kumar <krishnak@utexas.edu>
Date: Tue, 21 Nov 2023 13:44:53 -0600
Subject: [PATCH 5/9] Fixing numpy version

---
 README.md              | 7 ++-----
 dsdatabase/__init__.py | 1 +
 poetry.lock            | 2 +-
 pyproject.toml         | 1 +
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 4906bb5..691c20b 100644
--- a/README.md
+++ b/README.md
@@ -31,11 +31,8 @@ pip install git+https://github.com/DesignSafe-CI/dsdatabase.git --quiet
 ```
 
 ## Example usage:
-```
-db = DSDatabase(dbname="mydatabase")
-with db.Session() as session:
-    # Perform database operations
-    pass  # replace with actual operations
+```python
+db = DSDatabase(dbname="ngl")
 
 # Optionally, close the database connection when done
 db.close()
diff --git a/dsdatabase/__init__.py b/dsdatabase/__init__.py
index e7c972d..d69811a 100644
--- a/dsdatabase/__init__.py
+++ b/dsdatabase/__init__.py
@@ -1 +1,2 @@
 name = "designsafe_db"
+from .db import DSDatabase
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index 4a02d43..b887a8b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -534,4 +534,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9"
-content-hash = "07a3c04e4018dbc8df494a25ba3b4f18f2391c49e45bf9e2a415dd0019426b5b"
+content-hash = "930b48bbcda504f3be306e82243f2f780de5ac4b0acfced6a165e707693b98f6"
diff --git a/pyproject.toml b/pyproject.toml
index 2f5c608..f7dfe96 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,6 +10,7 @@ python = ">=3.9"
 pandas = "^2.1.3"
 pymysql = "^1.1.0"
 sqlalchemy = "^2.0.23"
+numpy = "^1.24.0"
 
 
 [tool.poetry.group.dev.dependencies]

From caece5cb494a15d2474b669107071a6c65dc0a4b Mon Sep 17 00:00:00 2001
From: Krishna Kumar <krishnak@utexas.edu>
Date: Tue, 21 Nov 2023 13:50:51 -0600
Subject: [PATCH 6/9] DSDatabase example usage

---
 README.md | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 691c20b..b317c8f 100644
--- a/README.md
+++ b/README.md
@@ -32,7 +32,12 @@ pip install git+https://github.com/DesignSafe-CI/dsdatabase.git --quiet
 
 ## Example usage:
 ```python
-db = DSDatabase(dbname="ngl")
+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()

From c6f61efad7243865b50c414a90d58d2e2f2b171f Mon Sep 17 00:00:00 2001
From: Krishna Kumar <krishnak@utexas.edu>
Date: Tue, 21 Nov 2023 14:20:44 -0600
Subject: [PATCH 7/9] Refactor to db config.py

---
 dsdatabase/__init__.py | 2 +-
 dsdatabase/config.py   | 6 ++++++
 dsdatabase/db.py       | 8 ++------
 3 files changed, 9 insertions(+), 7 deletions(-)
 create mode 100644 dsdatabase/config.py

diff --git a/dsdatabase/__init__.py b/dsdatabase/__init__.py
index d69811a..4e5e730 100644
--- a/dsdatabase/__init__.py
+++ b/dsdatabase/__init__.py
@@ -1,2 +1,2 @@
 name = "designsafe_db"
-from .db import DSDatabase
\ No newline at end of file
+from .db import DSDatabase
diff --git a/dsdatabase/config.py b/dsdatabase/config.py
new file mode 100644
index 0000000..4dc35bb
--- /dev/null
+++ b/dsdatabase/config.py
@@ -0,0 +1,6 @@
+# Mapping of shorthand names to actual database names and environment prefixes
+db_config = {
+    "ngl": {"dbname": "sjbrande_ngl_db", "env_prefix": "NGL_"},
+    "vp": {"dbname": "sjbrande_vpdb", "env_prefix": "VP_"},
+    "eq": {"dbname": "post_earthquake_recovery", "env_prefix": "EQ_"},
+}
diff --git a/dsdatabase/db.py b/dsdatabase/db.py
index 9de99b6..04d60ef 100644
--- a/dsdatabase/db.py
+++ b/dsdatabase/db.py
@@ -4,6 +4,8 @@
 from sqlalchemy.orm import sessionmaker
 from sqlalchemy import text
 
+from config import db_config
+
 
 class DSDatabase:
     """A database utility class for connecting to a DesignSafe SQL database.
@@ -29,12 +31,6 @@ def __init__(self, dbname="ngl"):
         Args:
             dbname (str): Shorthand for the database name. Must be one of 'ngl', 'vp', or 'eq'.
         """
-        # Mapping of shorthand names to actual database names and environment prefixes
-        db_config = {
-            "ngl": {"dbname": "sjbrande_ngl_db", "env_prefix": "NGL_"},
-            "vp": {"dbname": "sjbrande_vpdb", "env_prefix": "VP_"},
-            "eq": {"dbname": "post_earthquake_recovery", "env_prefix": "EQ_"},
-        }
 
         if dbname not in db_config:
             raise ValueError(

From e1f9ce82fb4f25ea50ecc41c0ecde5840ad7e600 Mon Sep 17 00:00:00 2001
From: Krishna Kumar <krishnak@utexas.edu>
Date: Tue, 21 Nov 2023 14:25:47 -0600
Subject: [PATCH 8/9] Add instructions on env variables

---
 README.md | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index b317c8f..43ba971 100644
--- a/README.md
+++ b/README.md
@@ -9,12 +9,21 @@
 
 Connects to SQL databases on DesignSafe:
 
-| Database | dbname |
-|----------|--------|
-| NGL | `ngl`|
-| Earthake Recovery | `eq` |
-| Vp | `vp` |
+| 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
 

From f3114640e55d9b9194da17708857e55eabefd296 Mon Sep 17 00:00:00 2001
From: Krishna Kumar <krishnak@utexas.edu>
Date: Tue, 21 Nov 2023 14:31:51 -0600
Subject: [PATCH 9/9] Fix imports

---
 dsdatabase/db.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dsdatabase/db.py b/dsdatabase/db.py
index 04d60ef..344ccbb 100644
--- a/dsdatabase/db.py
+++ b/dsdatabase/db.py
@@ -4,7 +4,7 @@
 from sqlalchemy.orm import sessionmaker
 from sqlalchemy import text
 
-from config import db_config
+from .config import db_config
 
 
 class DSDatabase: