Remove Flask and example database models (#4)

* Add Chainlit

* Sort imports and remove tests

* Formatting and linting

* Remove Flask and example data models

* Restore pull request template

* Update Trivyignore

* Add ignore to markdown linting

* Update ignore pattern

* Update ignore pattern

* Remove outdated API documentation

.github/pull_request_template.md

@@ -1,14 +1,27 @@
+- [ ] Update PR Title to follow this pattern: `[INTENT]: [MESSAGE]`
+
+> The title will become a one-line commit message in the git log, so be as concise and specific as possible -- refer to [How to Write a Git Commit Message](https://cbea.ms/git-commit/). Prepend [Conventional Commit](https://www.conventionalcommits.org/en/v1.0.0/#summary) intent (`fix:`, `feat:`, `chore:`, `ci:`, `docs:`, `style:`, `refactor:`, `perf:`, `test:`).
+
 ## Ticket
 
-Resolves #{TICKET NUMBER OR URL}
+https://navalabs.atlassian.net/browse/DST-<TICKET_NUMBER_HERE>
+
 
 ## Changes
 
 > What was added, updated, or removed in this PR.
+> Prefer small PRs; try to limit to 300 lines of code changes
+> * https://blog.logrocket.com/using-stacked-pull-requests-in-github/
+> * https://opensource.com/article/18/6/anatomy-perfect-pull-request
+> * https://developers.google.com/blockly/guides/modify/contribute/write_a_good_pr
+
 
 ## Context for reviewers
 
-> Testing instructions, background context, more in-depth details of the implementation, and anything else you'd like to call out or ask reviewers.
+> Background context, more in-depth details of the implementation, and anything else you'd like to call out or ask reviewers.
+> Add comments to your code under the "Files Changed" tab to explain complex logic or code
+> * https://betterprogramming.pub/how-to-make-a-perfect-pull-request-3578fb4c112
+
 
 ## Testing
 

.github/workflows/markdownlint-config.json

@@ -8,6 +8,9 @@
         },
         {
             "pattern": "127.0.0.1"
+        },
+        {
+            "pattern": "https://navalabs.atlassian.net/browse/DST-"
         }
     ],
     "replacementPatterns": [

.trivyignore

@@ -6,4 +6,5 @@
 #                 Link to the dependencies for ease of checking for updates
 #  Issue:         Why there is a finding and why this is here or not been removed
 #  Last checked:  Date last checked in scans
-#The-CVE-or-vuln-id # Remove comment at start of line
+#The-CVE-or-vuln-id # Remove comment at start of line
+jwt-token

app/Makefile

@@ -39,8 +39,6 @@ else
 PY_RUN_CMD := docker compose run $(DOCKER_EXEC_ARGS) --rm $(APP_NAME) poetry run
 endif
 
-FLASK_CMD := $(PY_RUN_CMD) flask --env-file local.env
-
 # Docker user configuration
 # This logic is to avoid issues with permissions and mounting local volumes,
 # which should be owned by the same UID for Linux distros. Mac OS can use root,
@@ -211,23 +209,6 @@ lint-security: # https://bandit.readthedocs.io/en/latest/index.html
 	$(PY_RUN_CMD) bandit -c pyproject.toml -r . --number 3 --skip B101 -ll -x ./.venv
 
 
-##################################################
-# CLI Commands
-##################################################
-
-cmd: ## Run Flask app CLI command (Run `make cli args="--help"` to see list of CLI commands)
-	$(FLASK_CMD) $(args)
-
-cmd-user-create-csv: ## Create a CSV of the useres in the database (Run `make cli-user-create-csv args="--help"` to see the command's options)
-	$(FLASK_CMD) user create-csv $(args)
-
-# Set init-db as pre-requisite since there seems to be a race condition
-# where the DB can't yet receive connections if it's starting from a
-# clean state (e.g. after make stop, make clean-volumes, make openapi-spec)
-openapi-spec: init-db ## Generate OpenAPI spec
-	$(FLASK_CMD) spec --format yaml --output ./openapi.generated.yml
-
-
 ##################################################
 # Miscellaneous Utilities
 ##################################################

app/local.env

@@ -15,8 +15,6 @@ PYTHONPATH=/app/
 # commands that can run in or out
 # of the Docker container - defaults to outside
 
-FLASK_APP=src.app:create_app
-
 ############################
 # Logging
 ############################