Setup infrastructure for coverage based testing and linting with black

.github/workflows/lint.yml

@@ -0,0 +1,40 @@
+name: Formatting
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+  merge_group:
+
+permissions:
+  contents: read
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    concurrency:
+      group: lint-${{ github.ref }}
+      cancel-in-progress: true
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python -
+          echo "$HOME/.poetry/bin" >> $GITHUB_PATH
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.9"
+          cache: poetry
+      - name: Install dependencies
+        run: |
+          poetry install --with dev
+      - name: Run black
+        uses: psf/black@stable
+        with:
+          options: "--check"
+          src: "."
+          version: "23.3.0" # Black version to use for formatting, since yearly they change the style, this keeps it stable

.github/workflows/tests.yml

@@ -1,4 +1,3 @@
-
 name: Tests
 
 on:
@@ -68,35 +67,39 @@ jobs:
 
   tests:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        # Minimum supported; Maybe add in some newer version to test things won't break if used on newer versions of python?
-        python_version: ["3.9"] #, "3.x"] 
     concurrency:
-      group: tests-${{ github.ref }}-${{ matrix.python_version }}
+      group: tests-${{ github.ref }}
       cancel-in-progress: true
     steps:
       - uses: actions/checkout@v3
       - name: Install Poetry
         run: |
           curl -sSL https://install.python-poetry.org | python -
           echo "$HOME/.poetry/bin" >> $GITHUB_PATH
-      - name: Set up Python ${{ matrix.python_version }}
+      - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: ${{ matrix.python_version }}
+          python-version: "3.9"
           cache: poetry
       - name: Install dependencies
         run: |
           poetry install --with dev
       - name: Run tests
         run: |
-          poetry run pytest tests
+          poetry run pytest --cov-report=xml:coverage.xml -rFxX tests/
       - name: Upload generated files
         if: failure()
         uses: actions/upload-artifact@v3
         with:
-          name: test-generated-files-${{ github.event_name }}-${{ matrix.python_version }}
+          name: test-generated-files-${{ github.event_name }}
           path: tests/test_question_templates/question_generated_outputs/
           if-no-files-found: ignore
           retention-days: 5
+      # - name: Upload coverage report to codecov
+      #   if: always()
+      #   uses: codecov/codecov-action@v3
+      #   with:
+      #     # Needed for private repos, publi repos don't, but it is a good
+      #     #  fallback for if codecov fails to identify it properly as public
+      #     # token: ${{ secrets.CODECOV_TOKEN }}
+      #     files: ./coverage1.xml

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/psf/black
+    rev: 'refs/tags/23.3.0:refs/tags/23.3.0'
+    hooks:
+    -   id: black

README.md

@@ -3,6 +3,7 @@
 [![Python](https://img.shields.io/badge/python-3.9-blue)]()
 [![codecov](https://codecov.io/gh/open-resources/problem_bank_scripts/branch/main/graph/badge.svg)](https://codecov.io/gh/open-resources/problem_bank_scripts)
 [![Documentation Status](https://readthedocs.org/projects/problem_bank_scripts/badge/?version=latest)](https://problem_bank_scripts.readthedocs.io/en/latest/?badge=latest)
+[![Tests](https://github.com/open-resources/problem_bank_scripts/actions/workflows/tests.yml/badge.svg)](https://github.com/open-resources/problem_bank_scripts/actions/workflows/tests.yml)
 
 
 ## Installation

docs/source/conf.py

@@ -6,9 +6,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u"Problem Bank Scripts"
-copyright = u"2021, Open Problem Bank Team"
-author = u"Open Problem Bank Team"
+project = "Problem Bank Scripts"
+copyright = "2021, Open Problem Bank Team"
+author = "Open Problem Bank Team"
 
 # -- General configuration ---------------------------------------------------
 

pyproject.toml

@@ -20,7 +20,7 @@ mdformat = "^0.7.14"
 sympy = "^1.8"
 problem-bank-helpers = "^0.1.14"
 
-[tool.poetry.dev-dependencies]
+[tool.poetry.group.dev.dependencies]
 Sphinx = "^4.4"
 nbsphinx = "^0.8.5"
 ipykernel = "^5.5.5"
@@ -30,10 +30,18 @@ sphinxcontrib-napoleon = "^0.7"
 pytest = "^6.2.4"
 myst-nb = "^0.15"
 myst-parser = "^0.17"
+pytest-cov = "^4.1.0"
+black = {extras = ["jupyter"], version = "^23.3.0"}
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.pytest.ini_options]
 filterwarnings = ["ignore::DeprecationWarning"]
+addopts = "--cov=src/problem_bank_scripts --cov-report=term --cov-branch"
+
+[tool.black]
+required_version = "23" # Black version to use for formatting, since yearly they change the style
+force-exclude = "/tests/test_question_templates"
+line-length = 100

src/problem_bank_scripts/prairielearn.py

@@ -1,16 +1,19 @@
 # This file has been copied directly from the PL repo: https://github.com/PrairieLearn/PrairieLearn/blob/master/lib/python_helper_sympy.py
 
 import sympy
+
 # import ast
 # import sys
 
 # import lxml.html
 # import html
 # import to_precision
 import numpy as np
+
 # import uuid
 # import sympy
 import pandas
+
 # from python_helper_sympy import convert_string_to_sympy
 # from python_helper_sympy import sympy_to_json
 # from python_helper_sympy import json_to_sympy
@@ -22,45 +25,47 @@
 # import os
 import collections
 
+
 # Create a new instance of this class to access the member dictionaries. This
 # is to avoid accidentally modifying these dictionaries.
 class _Constants:
     def __init__(self):
         self.helpers = {
-            '_Integer': sympy.Integer,
+            "_Integer": sympy.Integer,
         }
         self.variables = {
-            'pi': sympy.pi,
-            'e': sympy.E,
+            "pi": sympy.pi,
+            "e": sympy.E,
         }
         self.hidden_variables = {
-            '_Exp1': sympy.E,
+            "_Exp1": sympy.E,
         }
         self.complex_variables = {
-            'i': sympy.I,
-            'j': sympy.I,
+            "i": sympy.I,
+            "j": sympy.I,
         }
         self.hidden_complex_variables = {
-            '_ImaginaryUnit': sympy.I,
+            "_ImaginaryUnit": sympy.I,
         }
         self.functions = {
             # These are shown to the student
-            'cos': sympy.cos,
-            'sin': sympy.sin,
-            'tan': sympy.tan,
-            'arccos': sympy.acos,
-            'arcsin': sympy.asin,
-            'arctan': sympy.atan,
-            'acos': sympy.acos,
-            'asin': sympy.asin,
-            'atan': sympy.atan,
-            'arctan2': sympy.atan2,
-            'atan2': sympy.atan2,
-            'exp': sympy.exp,
-            'log': sympy.log,
-            'sqrt': sympy.sqrt,
+            "cos": sympy.cos,
+            "sin": sympy.sin,
+            "tan": sympy.tan,
+            "arccos": sympy.acos,
+            "arcsin": sympy.asin,
+            "arctan": sympy.atan,
+            "acos": sympy.acos,
+            "asin": sympy.asin,
+            "atan": sympy.atan,
+            "arctan2": sympy.atan2,
+            "atan2": sympy.atan2,
+            "exp": sympy.exp,
+            "log": sympy.log,
+            "sqrt": sympy.sqrt,
         }
 
+
 # # Safe evaluation of user input to convert from string to sympy expression.
 # #
 # # Adapted from:
@@ -276,6 +281,7 @@ def __init__(self):
 #     w_right = min(ind+w, len(s)) - ind
 #     return s[ind-w_left:ind+w_right] + '\n' + ' '*w_left + '^' + ' '*w_right
 
+
 def sympy_to_json(a, allow_complex=True):
     const = _Constants()
 
@@ -289,14 +295,22 @@ def sympy_to_json(a, allow_complex=True):
     for k in reserved.keys():
         for v in variables:
             if k == v:
-                raise ValueError('sympy expression has a variable with a reserved name: {:s}'.format(k))
+                raise ValueError(
+                    "sympy expression has a variable with a reserved name: {:s}".format(k)
+                )
 
     # Apply substitutions for hidden variables
     a = a.subs([(const.hidden_variables[key], key) for key in const.hidden_variables.keys()])
     if allow_complex:
-        a = a.subs([(const.hidden_complex_variables[key], key) for key in const.hidden_complex_variables.keys()])
+        a = a.subs(
+            [
+                (const.hidden_complex_variables[key], key)
+                for key in const.hidden_complex_variables.keys()
+            ]
+        )
+
+    return {"_type": "sympy", "_value": str(a), "_variables": variables}
 
-    return {'_type': 'sympy', '_value': str(a), '_variables': variables}
 
 # def json_to_sympy(a, allow_complex=True):
 #     if not '_type' in a:
@@ -310,6 +324,7 @@ def sympy_to_json(a, allow_complex=True):
 
 #     return convert_string_to_sympy(a['_value'], a['_variables'], allow_hidden=True, allow_complex=allow_complex)
 
+
 # Added to_json() from this file: https://github.com/PrairieLearn/PrairieLearn/blob/master/question-servers/freeformPythonLib/prairielearn.py
 def to_json(v):
     """to_json(v)
@@ -328,12 +343,16 @@ def to_json(v):
     returned without change.
     """
     if np.isscalar(v) and np.iscomplexobj(v):
-        return {'_type': 'complex', '_value': {'real': v.real, 'imag': v.imag}}
+        return {"_type": "complex", "_value": {"real": v.real, "imag": v.imag}}
     elif isinstance(v, np.ndarray):
         if np.isrealobj(v):
-            return {'_type': 'ndarray', '_value': v.tolist(), '_dtype': str(v.dtype)}
+            return {"_type": "ndarray", "_value": v.tolist(), "_dtype": str(v.dtype)}
         elif np.iscomplexobj(v):
-            return {'_type': 'complex_ndarray', '_value': {'real': v.real.tolist(), 'imag': v.imag.tolist()}, '_dtype': str(v.dtype)}
+            return {
+                "_type": "complex_ndarray",
+                "_value": {"real": v.real.tolist(), "imag": v.imag.tolist()},
+                "_dtype": str(v.dtype),
+            }
     elif isinstance(v, sympy.Expr):
         return sympy_to_json(v)
     elif isinstance(v, sympy.Matrix) or isinstance(v, sympy.ImmutableMatrix):
@@ -345,8 +364,20 @@ def to_json(v):
             for j in range(0, num_cols):
                 row.append(str(v[i, j]))
             M.append(row)
-        return {'_type': 'sympy_matrix', '_value': M, '_variables': s, '_shape': [num_rows, num_cols]}
+        return {
+            "_type": "sympy_matrix",
+            "_value": M,
+            "_variables": s,
+            "_shape": [num_rows, num_cols],
+        }
     elif isinstance(v, pandas.DataFrame):
-        return {'_type': 'dataframe', '_value': {'index': list(v.index), 'columns': list(v.columns), 'data': v.values.tolist()}}
+        return {
+            "_type": "dataframe",
+            "_value": {
+                "index": list(v.index),
+                "columns": list(v.columns),
+                "data": v.values.tolist(),
+            },
+        }
     else:
-        return v
+        return v