v6 updates (#835)

* remove nbconvert < 6 compat patches * throw error on nbconvert<6 * convert pdf via html exporter to use nbconvert webpdf exporter * removed pdfkit, wkhtmltopdf, cleanup * undo adding nbconvert[webpdf] to grading container image * changelog * add depencies for exporting pdfs via html to grading image * enable pdf via html in grading containers * install only chromium * remove nbconvert < 6 compat patches * throw error on nbconvert<6 * convert pdf via html exporter to use nbconvert webpdf exporter * removed pdfkit, wkhtmltopdf, cleanup * undo adding nbconvert[webpdf] to grading container image * changelog * add depencies for exporting pdfs via html to grading image * enable pdf via html in grading containers * install only chromium * use poetry and pyproject.toml for packaging * update CI to run Docker tests weekly instead of on every push/PR * extras poetry * docs * py3.12 default, migrate to extras for dep mgmt, slim down grading envs * update proj03 example * Update .readthedocs.yml * catch chromium error from nbconvert * changelog * combine export and grading extras * update run-docker-tests.yml * debugging beta branch not reusing cached docker images in tests * update .dockerignore * add matplotlib and numpy to grade test requirements.txt * Handle empty assignment configs in Otter Assign Closes #795 * Clean up JupyterLite support and remove import_or_raise per #511 * Removed variables key of assignment config in favor of generate.serialized_variables in Otter Assign per #628 * Update Otter Assign to add cell metadata so that questions with no check cell have their tests run after the last solution cell per #798 * type hints for functions in otter/assign * cleanup * upgrade setup-buildx-action * Updated Otter Assign to strip type annotations from generated test code per #796 * Updated Otter Grade Docker image to create an empty submission_metadata.json file in the grading image to prevent plugins from erroring per #811 * Otter Grade: Added Progress Monitoring to Queue - When an instance of ``multiprocessing.Queue`` is passed to grade/__init_.py::main, progress messages are written to the ``multiprocessing.Queue` via custom QueueLoggingHandler * Otter Grade: Cleaned Up Progress Monitoring * Otter Grade: Clean Up Progress Monitoring * Otter Grade: Progress Monitoring CHANGELOG updated * Update CHANGELOG.md * Update utils.py * Format code with black and isort (#839) * add black to pyproject.toml * reformat files with black * add isort for import sorting * reformat files with isort * restore test file formatting * fix exclusions and make otter generate render templates correctly * add workflow for checking formatting * use different poetry setup action * pin fica>=0.4.1 * fixing lsp complaints * fix args and kwargs type hints * add student_files to otter assign (#852) * Add pip install cell to Colab notebooks (#862) * Add ability to ignore .OTTER_LOG to Notebook.export and Otter Assign (#863) * add ability to ignore .OTTER_LOG to Notebook.export and Otter Assign * typo * Fix/add support for all_or_nothing test file config (#865) * Add more tests for otter.test_files (#866) * update deps * update cache key * debugging failed builds * add nb_conda_kernels * add note about code formatting to CONTRIBUTING.md * go back an additional frame in Notebook.check for py3.13 for some reason :( * use matrix to cover supported python versions * add coveralls parallel builds for matrix and pin py3.9 for docker tests * docs for all_or_nothing * Auto-ignore test fn calls in assign exception-based test cells (#867) * Add addl packages to otter --version (#868) * add addl packages to otter --version * add addl packages to otter --version * remake poetry.lock * Fix converting indented functions in test cells to doctests (#869) * add question structure to otter assign docs * remove unnecessary passage --------- Co-authored-by: sean-morris <[email protected]>
ucbds-infra · Oct 26, 2024 · e56de20 · e56de20
1 parent 8a946bf
commit e56de20
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Showing 177 changed files with 9,658 additions and 3,367 deletions.
diff --git a/.coveragerc b/.coveragerc
@@ -11,9 +11,15 @@ exclude_lines =
     # Don't complain if tests don't hit defensive assertion code:
     raise NotImplementedError
 
+    # Ignore ellipse statements
+    \.\.\.
+
 omit =
     # This file is just calls otter.cli.cli
     otter/__main__.py
 
     # This file is a copy of an external script and is not tested as part of Otter
     otter/plugins/builtin/gmail_notifications/bin/gmail_oauth2.py
+
+    # ignore templates
+    otter/generate/templates/**/*
diff --git a/.dockerignore b/.dockerignore
@@ -1,22 +1,22 @@
 __pycache__
-.DS_Store
-dist
-build
-*.egg-info
-.ipynb_checkpoints
-test/test-grading-notebook.ipynb
-test/tests
 .coverage
-.vscode
-test/output
-.sos
-docs/_build
-.Rproj.user
-.Rhistory
+.DS_Store
 .ionide
-gs-testing-stuff
+.ipynb_checkpoints
+.git
+.github
 .mypy.cache
+.pytest_cache
 .OTTER_LOG
+.Rproj.user
+.Rhistory
+.sos
+.vscode
+*.egg-info
+build
+dist
 docs
+examples
 logo
-.git
+poetry.lock
+test
diff --git a/.github/workflows/check-formatting.yml b/.github/workflows/check-formatting.yml
@@ -0,0 +1,52 @@
+name: Check formatting
+
+on:
+  push:
+    branches:
+      - master
+      - beta
+      - release
+  pull_request:
+    branches:
+      - master
+      - beta
+      - release
+      - temp
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Check formatting
+    runs-on: ubuntu-latest
+
+    env:
+      TAR: /bin/tar
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          virtualenvs-path: .venv
+          installer-parallel: true
+
+      - name: Install dependencies
+        run: |
+          poetry install --with dev --no-root
+
+      - name: Run formatters
+        run: |
+          source .venv/bin/activate
+          make format CI=true
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -17,20 +17,25 @@ jobs:
       TAR: /bin/tar
 
     steps:
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.10
 
       - name: Only allow releases off of master (or temp for patches)
         run: |
           python3 -c 'import os, sys; sys.exit(os.environ["GITHUB_REF"] != "refs/heads/master" and os.environ["GITHUB_REF"] != "refs/heads/temp")'
 
+      - uses: liskin/gh-pipx@v1
+        with:
+          packages: >-
+            poetry
+
       - uses: actions/checkout@v2
 
       - name: Install dependencies
         run: |
-          python3 -m pip install -r requirements.txt twine wheel setuptools
+          poetry install --with dev --no-root
 
       - name: Update versions
         run: |
@@ -53,7 +58,7 @@ jobs:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
         run: |
-          python3 setup.py sdist bdist_wheel
+          poetry build
           python3 -m twine upload dist/*
 
       - name: Create a release on GitHub

diff --git a/.github/workflows/run-docker-tests-beta.yml b/.github/workflows/run-docker-tests-beta.yml
@@ -44,7 +44,7 @@ jobs:
         with:
           ref: beta
 
-      - uses: docker/setup-buildx-action@v2
+      - uses: docker/setup-buildx-action@v3
         if: ${{ steps.check-branch.outputs.run == 'true' }}
         with:
           install: true
@@ -65,16 +65,18 @@ jobs:
         if: ${{ steps.check-branch.outputs.run == 'true' }}
         with:
           environment-file: environment.yml
+          create-args: >-
+            python=3.9
           init-shell: >-
             bash
           cache-environment: true
-          cache-environment-key: requirements-${{ hashFiles('pyproject.toml') }}
+          cache-environment-key: requirements-${{ hashFiles('environment.yml') }}
 
       - name: Install dependencies
         if: ${{ steps.check-branch.outputs.run == 'true' }}
         run: |
           micromamba activate otter-grader
-          poetry install --with test --all-extras
+          poetry install --with dev,test --all-extras
 
       - name: Install ottr
         if: ${{ steps.check-branch.outputs.run == 'true' }}

diff --git a/.github/workflows/run-docker-tests.yml b/.github/workflows/run-docker-tests.yml
@@ -33,21 +33,33 @@ jobs:
         with:
           ref: ${{ matrix.branch }}
 
-      - uses: docker/setup-buildx-action@v2
+      - uses: docker/setup-buildx-action@v3
         with:
           install: true
 
       - uses: r-lib/actions/setup-tinytex@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - uses: liskin/gh-pipx@v1
+        with:
+          packages: >-
+            poetry
+
       - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment.yml
+          create-args: >-
+            python=3.9
           init-shell: >-
             bash
           cache-environment: true
-          cache-environment-key: requirements-${{ hashFiles('requirements*.txt') }}
+          cache-environment-key: requirements-${{ hashFiles('environment.yml') }}
+
+      - name: Install dependencies
+        run: |
+          micromamba activate otter-grader
+          poetry install --with dev,test --all-extras
 
       - name: Install ottr
         run: |

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -21,6 +21,10 @@ jobs:
     name: Test suite
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        python_version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
     env:
       TAR: /bin/tar
 
@@ -35,13 +39,26 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - uses: liskin/gh-pipx@v1
+        with:
+          packages: >-
+            poetry
+
       - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment.yml
+          create-args: >-
+            python=${{ matrix.python_version }}
           init-shell: >-
             bash
           cache-environment: true
-          cache-environment-key: requirements-${{ hashFiles('requirements*.txt') }}
+          cache-environment-key: mamba-${{ hashFiles('environment.yml') }}
+
+      - name: Install dependencies
+        run: |
+          micromamba activate otter-grader
+          poetry env info
+          poetry install --with dev,test --all-extras
 
       - name: Install ottr
         run: |
@@ -54,3 +71,15 @@ jobs:
 
       - name: Coveralls
         uses: coverallsapp/github-action@v2
+        with:
+          parallel: true
+          flag-name: run ${{ join(matrix.*, ' - ') }}
+
+  finish:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          parallel-finished: true
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -12,10 +12,18 @@ sphinx:
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
-conda:
-  environment: rtd_environment.yml
-
 build:
   os: ubuntu-22.04
   tools:
-    python: "mambaforge-22.9"
+    python: "3.10"
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-manually
+      - pip install poetry
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
+      # VIRTUAL_ENV needs to be set manually for now.
+      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,35 @@
 # Changelog
 
+**v6.0.0 (unreleased):**
+
+* Switched to [poetry](https://python-poetry.org/) for packaging
+* Removed compatibility patches for nbconvert < 6 per [#777](https://github.com/ucbds-infra/otter-grader/issues/777)
+* Updated Otter Export to throw an error if nbconvert<6.0.0 is found
+* Converted Otter Export's PDF via HTML exporter to use nbconvert's WebPDF exporter per [#781](https://github.com/ucbds-infra/otter-grader/issues/781)
+* Removed pdfkit from dependencies
+* Added ability to export PDFs via HTML in grading containers per [#782](https://github.com/ucbds-infra/otter-grader/issues/782)
+* Set default Python version for grading images to 3.12
+* Remove support for Python versions < 3.9 per [#668](https://github.com/ucbds-infra/otter-grader/issues/668)
+* Removed `setuptools` and `pkg_resources` dependencies
+* Remove dependencies not strictly required by Otter in the grading environment per [#739](https://github.com/ucbds-infra/otter-grader/issues/739)
+* Handle empty assignment configs in Otter Assign per [#795](https://github.com/ucbds-infra/otter-grader/issues/795)
+* Removed `Notebook` `colab` and `jupyterlite` arguments, switching to always determining the interpreter automatically
+* Made `dill` a required dependency
+* Removed `variables` key of assignment config in favor of `generate.serialized_variables` in Otter Assign per [#628](https://github.com/ucbds-infra/otter-grader/issues/628)
+* Update Otter Assign to add cell metadata so that questions with no check cell have their tests run after the last solution cell per [#798](https://github.com/ucbds-infra/otter-grader/issues/798)
+* Updated Otter Assign to strip type annotations from generated test code per [#796](https://github.com/ucbds-infra/otter-grader/issues/796)
+* Updated Otter Grade Docker image to create an empty `submission_metadata.json` file in the grading image to prevent plugins from erroring per [#811](https://github.com/ucbds-infra/otter-grader/issues/811)
+* Added ability to monitor grading progress to Otter Grade per [#827](https://github.com/ucbds-infra/otter-grader/issues/827)
+* Added handling of student-created files with the `student_files` configuration in Otter Assign per [#737](https://github.com/ucbds-infra/otter-grader/issues/737)
+* Updated Otter Assign to add a cell to install Otter at the top of Colab notebooks per [#861](https://github.com/ucbds-infra/otter-grader/issues/861)
+* Added the ability to ignore the `.OTTER_LOG` file to `Notebook.export` and Otter Assign per [#857](https://github.com/ucbds-infra/otter-grader/issues/857)
+* Fixed OK-test support for the `all_or_nothing` config per [#751](https://github.com/ucbds-infra/otter-grader/issues/751)
+* Added exception-based test support for the `all_or_nothing` config per [#751](https://github.com/ucbds-infra/otter-grader/issues/751)
+* Added Otter Assign support for the `all_or_nothing` config per [#751](https://github.com/ucbds-infra/otter-grader/issues/751)
+* Updated Otter Assign to only allow a function definition and statement to call the test function in exception-based test cells and automatically ignore the latter statement instead of requiring an explicit `# IGNORE` comment per [#516](https://github.com/ucbds-infra/otter-grader/issues/516)
+* Added additional package versions to the output of `otter --version` per [#843](https://github.com/ucbds-infra/otter-grader/issues/843)
+* Fixed bug in converting test cells containing indented functions to doctests in Otter Assign per [#840](https://github.com/ucbds-infra/otter-grader/issues/840)
+
 **v5.7.1:**
 
 * Removed testing code unintentioanlly committed in v5.7.0 per [#849](https://github.com/ucbds-infra/otter-grader/issues/849)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -6,19 +6,33 @@ any updates. Make sure to update the changelog with any information about the co
 
 ## Environment Setup
 
-To set up an environment for working on Otter, we recommend using 
-[Conda](https://docs.conda.io/en/latest/miniconda.html). This repo contains an 
+To set up an environment for working on Otter, we recommend using [Mamba](https://mamba.readthedocs.io/en/latest/) (or Conda). This repo contains an 
 [`environment.yml`](environment.yml) file which defines all of the requirements for an environment
 used to work on Otter.
 
 Running
 
 ```
-conda env create -f environment.yml
+mamba env create -f environment.yml
 ```
 
-will create a conda environment called `otter-grader` with the necessary packages installed for both
-Python and R.
+will create a conda environment called `otter-grader` with the necessary Python and R versions.
+
+To install development dependencies, use [`poetry`](https://python-poetry.org/) to update the environment:
+
+```
+mamba activate otter-grader
+poetry install --with dev,test
+```
+
+
+## Code Formatting
+
+The Python files in this repo are formatted with isort and black. Installing the `dev` dependencies
+with poetry will install these as well. You can run `make format` with your conda/virtual environment
+activated to format the files in-place.
+
+Note that code formatting is enforced by a CI test.
 
 
 ## Running Tests

diff --git a/MANIFEST.in b/MANIFEST.in