refactor: align repo with new ETL template

.editorconfig

@@ -0,0 +1,5 @@
+root = true
+[*]
+indent_style = space
+indent_size = 4
+max_line_length = 80

.github/workflows/cape.yml

@@ -0,0 +1,15 @@
+name: CAPE
+on:
+    push:
+        branches: [main]
+    pull_request:
+
+jobs:
+    python:
+        name: Python
+        uses: cape-ph/.github/.github/workflows/python_checks.yml@main
+        with:
+            pytest: false
+    general:
+        name: General
+        uses: cape-ph/.github/.github/workflows/general_checks.yml@main

.github/workflows/release.yml

@@ -0,0 +1,14 @@
+name: Release
+
+on:
+    push:
+        tags: ["**"]
+    workflow_dispatch:
+
+permissions:
+    contents: write
+
+jobs:
+    Release:
+        uses: cape-ph/.github/.github/workflows/release.yml@main
+        secrets: inherit

.gitignore

@@ -1,13 +1,198 @@
-# OS
-# ===========
-.DS_Store
-ehthumbs.db
-Icon?
-Thumbs.db
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-# General
-# =======
+# 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/
+
+# JetBrains
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+.idea/**/aws.xml
+.idea/**/contentModel.xml
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+.idea/**/gradle.xml
+.idea/**/libraries
+cmake-build-*/
+.idea/**/mongoSettings.xml
+*.iws
+out/
+.idea_modules/
+atlassian-ide-plugin.xml
+.idea/replstate.xml
+.idea/sonarlint/
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+.idea/httpRequests
+.idea/caches/build_file_checksums.ser
+
+# Vagrant/Ansible/CI
+.vagrant
+playbook.retry
+.vault
+ansible.out
+
+# General
 *.dat
 *.out
 *.pid
@@ -19,23 +204,12 @@ Thumbs.db
 logs/
 build/
 
-# IDEs
-# ====
-*.iml
-*.idea
-.vscode
-*.code-workspace
-
-# Vagrant/Ansible/CI related
-# ==========================
-.vagrant
-playbook.retry
-.vault
-ansible.out
+# OS
+.DS_Store
+ehthumbs.db
+Icon?
+Thumbs.db
 
 # Other
-# =====
 sslcerts.pfx
 scripts/*gz
-__pycache__/
-*.py[cod]

.prettierrc.yaml

@@ -0,0 +1,8 @@
+proseWrap: always
+tabWidth: 4
+useTabs: false
+
+overrides:
+    - files: "*.md"
+      options:
+          parser: "markdown"

etl_gphl_cre_alert.py → main.py

@@ -2,6 +2,7 @@
 
 import io
 import sys
+from pathlib import Path
 
 import boto3 as boto3
 import dateutil.parser as dparser
@@ -42,7 +43,7 @@
 # NOTE: for now we'll take the alert object key and change out the file
 #       extension for the clean data (leaving all namespacing and such). this
 #       will probably need to change
-clean_obj_key = alert_obj_key.replace(".docx", ".csv")
+clean_obj_key = str(Path(alert_obj_key).with_suffix(".csv"))
 
 # NOTE: May need some creds here
 s3_client = boto3.client("s3")
@@ -105,7 +106,9 @@
 #             include it in the AR query, but we still have it if we end up
 #             needing it for anything else
 interim = pd.DataFrame()
-interim["Mechanism (*Submitters Report)"] = data["Anti-Microbial Resistance RT-PCR"]
+interim["Mechanism (*Submitters Report)"] = data[
+    "Anti-Microbial Resistance RT-PCR"
+]
 interim["Organism"] = data["Organism ID"]
 interim["Date Received"] = date_received
 interim["Date Reported"] = date_received
@@ -119,7 +122,7 @@
 interim["Facility of Origin"] = data["Received from"]
 interim["State_Lab_ID"] = data["Lab ID"]
 
-# write out the transofrmed data
+# write out the transformed data
 with io.StringIO() as csv_buff:
     interim.to_csv(csv_buff, index=False)
 

pyproject.toml

@@ -0,0 +1,9 @@
+[tool.black]
+line-length = 80
+
+[tool.isort]
+profile = "black"
+line_length = 80
+
+[tool.ruff]
+line-length = 80

pyrightconfig.json

@@ -0,0 +1,4 @@
+{
+    "autoImportCompletions": true,
+    "typeCheckingMode": "basic"
+}