chore: Update interdependent dependencies and revise command-line interface

.gitignore

@@ -22,6 +22,7 @@ b000027.txt
 npm-debug.log*
 yarn-debug.log*
 yarn-error.log*
+api.log
 
 # Editor directories and files
 .idea

README.md

@@ -39,7 +39,7 @@ disruptive and wastefully repetitive if performed in each visitor's browser.
    a dotenv (`.env`) file with the database credentials.
    + Some details necessary for this step are found in
      [configuring PostgreSQL](doc/install-postgres.md).
-7. Run backscope: `python manage.py runserver`
+7. Run backscope: `flask run`
    + See also detailed instructions for
      [running backscope](doc/running-backscope.md).
 

doc/directory_descriptions.md

@@ -6,22 +6,6 @@ As of 2022-11-01, this document might be outdated.
 
 Auto generated
 
-##### manage.py
-
-The main entry point into the application
-
-The main usage from this file is:
-
-```bash
-$ python3 manage.py db init
-$ python3 manage.py db migrate
-$ python3 manage.py db upgrade
-
-$ python3 manage.py runserver
-```
-
-Any other target may be considered for future development
-
 ##### api.log
 
 The log file for the flask application
@@ -36,6 +20,9 @@ Logging levels are set in flaskr/config.py
 
 Refer to https://flask.palletsprojects.com/en/1.1.x/logging/ for more information
 
+Note that this file should not be checked into git for versioning; it's now
+in the .gitignore file, which should hopefully prevent that happening.
+
 ##### flaskr
 
 Flaskr is the main application. It contains all entry points to the application. \_\_init\_\_.py contains all the application macros.

doc/install-postgres.md

@@ -70,16 +70,16 @@ character indicates a "shell comment." You don't need to enter this
 character or anything that follows it on a line.
 
 ```
-> python manage.py db init  # initializes tables inside database
+> flask db init  # initializes tables inside database
 ```
 
 The previous command might issue a message about editing
 `alembic.ini`, which is safe to ignore. The default works fine. Then continue
 with:
 
 ```
-> python manage.py db migrate  # migrate data models
-> python manage.py db upgrade  # upgrade changes to database
+> flask db migrate  # migrate data models
+> flask db upgrade  # upgrade changes to database
 > psql -U <backscope database user> -d <database name>  # invokes data browser
 db> \d
             List of relations

doc/resetting-the-database.md

@@ -11,7 +11,7 @@ commands that you have activated the virtual environment
 dropdb <database_name>
 createdb <database_name>
 rm -rf migrations
-python manage.py db init
-python manage.py db migrate
-python manage.py db upgrade
-```
+flask db init
+flask db migrate
+flask db upgrade
+```

doc/running-backscope.md

@@ -4,25 +4,16 @@ Running backscope
 To run the development server:
 
 ```
-python manage.py runserver
-```
-
-(You should also be able to do this via
-
-```bash
-export FLASK_APP=flaskr
 flask run
 ```
 
-if you prefer.)
-
 By enabling debug mode, the server will automatically reload if code
 changes, and will show an interactive debugger in the browser if an
 error occurs during a request. To run the development server in "debug"
 mode:
 
 ```
-python manage.py runserver --debug
+flask run --debug
 ```
 
 In either of these modes, the command should print a serries of messages.

doc/tests.md

@@ -45,9 +45,9 @@ For guidance, consult the basic instructions on how to [set up your environment]
 1. Go into the top-level directory of the Backscope repository.
 2. Activate the Backscope virtual environment.
    + If you're using [`venv`](https://docs.python.org/3/library/venv.html) to manage virtual environments, and you've put Backscope's virtual environment in a directory called `.venv`, use the command `source .venv/bin/activate` to activate.
-3. Call `python manage.py test`.
+3. Execut the command `flask test`.
    + In quiet mode, you'll see a string of characters representing passed (`.`), failed (`F`), and skipped (`s`) tests.
-   + To see the tests' names as well as their outcomes, call `python manage.py test -v` or `python manage.py test --verbose`.
+   + To see the tests' names as well as their outcomes, execute `flask test -v` or `flask test --verbose`.
    + This command is a wrapper for `python -m unittest [-v]` and `python -m unitpytest discover [-v] [-s START] [-p PATTERN] [-t TOP]`. For more options, call `unittest` or `unittest discover` directly.
 
 ### Look at the test output
@@ -57,7 +57,7 @@ Here are some examples of what test results can look like.
 :arrow_down: The `..` below tells us that both tests passed.
 
 ```
-> python manage.py test
+> flask test
 ..
 ----------------------------------------------------------------------
 Ran 2 tests in 1.650s
@@ -68,7 +68,7 @@ OK
 :arrow_down: The `s.` below tells us that one test was skipped and the other passed. Running in verbose mode may print an explanation of why we're skipping the test. This message is passed to the `@unittest.skip()` decorator.
 
 ```
-> python manage.py test
+> flask test
 s.
 ----------------------------------------------------------------------
 Ran 2 tests in 0.934s
@@ -79,7 +79,7 @@ OK (skipped=1)
 :arrow_down: The `F.` below tells us that one test failed and the other passed. A report from the failed test follows.
 
 ```
-> python manage.py test
+> flask test
 F.
 ======================================================================
 FAIL: test_endpoint (flaskr.nscope.test.test_get_oeis_values.TestGetOEISValues)
@@ -99,7 +99,7 @@ FAILED (failures=1)
 :arrow_down: Testing in verbose mode, like below, shows the tests' names as well as their outcomes.
 
 ```
-> python manage.py test -v
+> flask test -v
 test_endpoint (flaskr.nscope.test.test_get_oeis_values.TestGetOEISValues) ... 
   Testing response
   Waiting for background work
@@ -115,4 +115,4 @@ ok
 Ran 2 tests in 2.556s
 
 OK
-```
+```

flaskr/__init__.py

@@ -6,8 +6,9 @@
 from flask import Flask
 import click
 from flask.cli import with_appcontext
-from flask_sqlalchemy import SQLAlchemy
 from flask_cors import CORS
+from flask_migrate import Migrate
+from flask_sqlalchemy import SQLAlchemy
 import logging
 from logging.handlers import RotatingFileHandler
 import sys
@@ -65,7 +66,8 @@ def create_app(environment=None):
 
     # Initialize the application
     db.init_app(app)
-
+    Migrate(app, db)
+
     # Add a command line interface to the application
     app.cli.add_command(init_db_command)
 

requirements-freeze.txt

@@ -1,33 +1,35 @@
 alembic==1.8.1
+blinker==1.6.3
 certifi==2023.7.22
 charset-normalizer==2.1.1
-click==7.1.2
+click==8.1.7
 cypari2==2.1.3
 cysignals==1.11.2
 Cython==0.29.36
-Flask==1.1.4
-flask-cors==3.0.10
-Flask-Executor==0.10.0
+Flask==3.0.0
+Flask-Cors==3.0.10
+Flask-Executor==1.0.0
 Flask-Login==0.5.0
 Flask-Migrate==2.7.0
-Flask-Script==2.0.6
-Flask-SQLAlchemy==2.5.1
+Flask-SQLAlchemy==3.1.1
 Flask-WTF==0.15.1
+greenlet==2.0.2
 idna==3.4
-itsdangerous==1.1.0
-Jinja2==2.11.3
+itsdangerous==2.1.2
+Jinja2==3.1.2
 jsonify==0.5
 Mako==1.2.2
-MarkupSafe==1.1.1
+MarkupSafe==2.1.3
 numpy==1.23.2
 psycopg2-binary==2.9.7
 python-dateutil==2.8.2
 python-dotenv==0.20.0
 python-editor==1.0.4
 requests==2.28.1
 six==1.16.0
-SQLAlchemy==1.4.40
+SQLAlchemy==2.0.22
+typing_extensions==4.8.0
 urllib3==1.26.12
-Werkzeug==1.0.1
+Werkzeug==3.0.0
 wheel==0.41.2
 WTForms==2.3.3

wsgi.py

@@ -1,2 +1,30 @@
+import click
+import unittest
 from flaskr import create_app
+
 app = create_app()
+
+# this is a wrapper for 'unittest discover', and the help messages are copied
+# from there
+#   https://docs.python.org/3/library/unittest.html#test-discovery
+@app.cli.command()
+@click.option('-v', '--verbose', 'verbosity',
+  count=True, default=0,
+  help='Verbose output'
+)
+@click.option('-s', '--start-directory', 'start_dir', default='.',
+  help='Directory to start discovery (. default)'
+)
+@click.option('-p', '--pattern', 'pattern', default='test*.py',
+  help='Pattern to match test files (test*.py default)'
+)
+@click.option('-t', '--top-level-directory', 'top_level_dir',
+  help='Top level directory of project (defaults to start directory)'
+)
+def test(verbosity, start_dir, pattern, top_level_dir):
+  test_suite = unittest.defaultTestLoader.discover(
+    start_dir=start_dir,
+    pattern=pattern,
+    top_level_dir=top_level_dir
+  )
+  unittest.TextTestRunner(verbosity=verbosity+1).run(test_suite)