Merge pull request #669 from ucbds-infra/beta

.coveragerc

@@ -15,6 +15,3 @@ omit =
 
     # 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
-
-    # The Assign v0 format is deprecated and will be removed in v5
-    otter/assign/v0/*

.github/workflows/release.yml

@@ -15,7 +15,6 @@ jobs:
 
     env:
       TAR: /bin/tar
-      DOCKER_BUILDKIT: 1 
 
     steps:
       - name: Set up Python 3.8
@@ -29,20 +28,6 @@ jobs:
 
       - uses: actions/checkout@v2
 
-      - uses: docker/setup-buildx-action@v1
-        id: buildx
-        with:
-          install: true
-
-      - name: Login to DockerHub
-        uses: docker/login-action@v1
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-
-      - name: Expose GitHub Runtime
-        uses: crazy-max/ghaction-github-runtime@v1
-
       - name: Install dependencies
         run: |
           python3 -m pip install -r requirements.txt twine wheel setuptools
@@ -94,14 +79,3 @@ jobs:
         run: |
           hub pull-request -b ucbds-infra:master -h ucbds-infra:stable -l "release" -r chrispyles \
             -m "Release v${{ github.event.inputs.version }}"$'\n'$'\n'"Updates from the release of version ${{ github.event.inputs.version }}"
-
-      - name: Build Docker image
-        uses: docker/build-push-action@v2
-        with:
-          context: .
-          push: true
-          tags: |
-            ucbdsinfra/otter-grader:v${{ github.event.inputs.version }}
-            ucbdsinfra/otter-grader:latest
-          cache-from: type=gha
-          cache-to: type=gha,mode=max

.github/workflows/run-tests.yml

@@ -20,29 +20,24 @@ jobs:
 
     env:
       TAR: /bin/tar
-      DOCKER_BUILDKIT: 1 
+      DOCKER_BUILDKIT: 1
+      DOCKER_CLI_EXPERIMENTAL: enabled
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: docker/setup-buildx-action@v1
-        id: buildx
+      - uses: docker/setup-buildx-action@v2
         with:
           install: true
 
       - name: Expose GitHub Runtime
         uses: crazy-max/ghaction-github-runtime@v1
 
-      - name: Prepare for Docker image build
-        run: |
-          make docker-test-prepare
-
       - name: Build Docker image
         id: docker_build
         uses: docker/build-push-action@v4
         with:
           context: .
-          file: test-Dockerfile
           load: true
           push: false
           tags: otter-test
@@ -51,11 +46,10 @@ jobs:
           build-args: |
             DOCKER_VERSION=20.10.24
 
-      - name: Clean up Docker image build
-        run: make docker-ci-test-cleanup
-
       - name: Run tests
-        run: docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp otter-test bash -c "cd /home/otter-grader; pip install -r requirements-test.txt -r requirements-export.txt; make testcov && coverage xml -i && cp ./coverage.xml /tmp/coverage.xml" && cp /tmp/coverage.xml ./coverage.xml
+        run: |
+          docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp otter-test /root/otter-grader/bin/run_tests
+          cp /tmp/coverage.xml ./coverage.xml
 
       - uses: codecov/codecov-action@v3
         with:

.gitignore

@@ -19,7 +19,6 @@ gs-testing-stuff
 .OTTER_LOG
 docs/tutorial/dist
 docs/_static/notebooks/html
-arm-Dockerfile
 htmlcov/
 .pytest_cache/
 /sync.sh

.readthedocs.yml

@@ -9,16 +9,8 @@ version: 2
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
-# Optionally set the version of Python and requirements required to build your docs
-python:
-  version: 3.7
-
 conda:
   environment: rtd_environment.yml

CHANGELOG.md

@@ -1,5 +1,27 @@
 # Changelog
 
+**Unreleased (beta):**
+
+* Converted all dependency management in the autograder configuration zip file to Conda per [#501](https://github.com/ucbds-infra/otter-grader/issues/501)
+* Removed deprecated Otter Assign format v0
+* Disabled editing for question prompt cells in the notebooks generated by Otter Assign per [#431](https://github.com/ucbds-infra/otter-grader/issues/431)
+* Removed `ucbdsinfra/otter-grader` Docker image and made default image for Otter Grade `ubuntu:22.04` per [#534](https://github.com/ucbds-infra/otter-grader/issues/534)
+* Make `xeCJK` opt-in behavior for exporting notebooks via LaTeX per [#548](https://github.com/ucbds-infra/otter-grader/issues/548)
+* Convert from use of deprecated `PyPDF2` package to `pypdf`
+* Add configuration to submit blank PDF to manual-grading Gradescope assignment if PDF generation fails per [#551](https://github.com/ucbds-infra/otter-grader/issues/551)
+* Removed the `after_execution` event from the plugin lifecycle
+* Updated execution internals to use `nbconvert.preprocessors.ExecutePreprocessor` instead of the `exec` function to execute submissions per [#604](https://github.com/ucbds-infra/otter-grader/issues/604)
+* Deprecated the `variables` key of the assignment config in favor of `generate.serialized_variables`
+* Enabled Otter Generate for all assignments created with Otter Assign
+* Updated Otter Assign to use Otter Run to validate that all tests in the assignment pass, allowing tests to be run for R assignments as well as Python, per [#427](https://github.com/ucbds-infra/otter-grader/issues/427)
+* Allow Markdown cells to be used instead of raw cells for Otter Assign per [#592](https://github.com/ucbds-infra/otter-grader/issues/592)
+* Use Otter Grade CLI flags to update `otter_config.json` values in the grading container per [#395](https://github.com/ucbds-infra/otter-grader/issues/395)
+* Removed `linux/amd64` platform specification for Docker images in Otter Grade
+* Updated Otter Assign to normalize notebooks before writing them with `nbformat.validator.normalize` per [#658](https://github.com/ucbds-infra/otter-grader/issues/658)
+* Added summary of assignment questions to Otter Assign logging per [#564](https://github.com/ucbds-infra/otter-grader/issues/564)
+* Converted to Mamba from Conda for package management in grading containers per [#660](https://github.com/ucbds-infra/otter-grader/issues/660)
+* Upgraded default Python version in grading containers from 3.7 to 3.9
+
 **v4.4.1:**
 
 * Update Otter Grade to close file handles before copying files out of Docker containers to fix bug on Windows

CONTRIBUTING.md

@@ -51,33 +51,6 @@ make testcov
 ```
 
 
-### Test Docker Images
-
-To build a Docker image suitable for testing, use the Makefile target `docker-test`. This will
-build a Docker image tagged `otter-test` which includes the development version of Otter in your 
-local copy of the repo as the installed version of Otter.
-
-```
-make docker-test
-```
-
-If you need to build testing images for grading assignments, use the `docker-grade-test` target to 
-edit the Dockerfile in `otter/grade` and then install your local copy of the rpeo:
-
-```
-make docker-grade-test
-pip install .
-```
-
-**Do not commit any changes made by this Makefile target.**
-
-Once you finish, make sure to run the `cleanup-docker-grade-test` target to undo your changes. 
-
-```
-make cleanup-docker-grade-test
-```
-
-
 ## Building the Documentation
 
 To build a local copy of the documentation, use the `docs` target of the Makefile.

Dockerfile

@@ -1,56 +1,33 @@
-# Dockerfile forked from https://github.com/jeffheaton/docker-jupyter-python-r/blob/master/Dockerfile
-FROM ubuntu:20.04
-
-# common packages
-RUN export DEBIAN_FRONTEND=noninteractive && \
-    apt-get update && \
-    apt-get upgrade -y && \
-    apt-get install -y tzdata git vim wget libssl-dev nano && \
-    rm -rf /var/lib/apt/lists/*
-
-# miniconda
-RUN echo 'export PATH=/opt/conda/bin:$PATH' >> /root/.bashrc && \
-    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
-    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
-    rm ~/miniconda.sh && \
-    rm -rf /var/lib/apt/lists/*
-
-ENV PATH /opt/conda/bin:$PATH
-
-# R pre-reqs 
-RUN apt-get clean && \
-    apt-get update && \
-    apt-get install -y --no-install-recommends fonts-dejavu gfortran gcc && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
-
-# R
-RUN apt-get clean && \
-    apt-get update && \
-    conda install -y "r-base>=4.0.0" r-essentials && \
-    conda install -c r r-irkernel r-essentials r-devtools -c conda-forge && \
-    rm -rf /var/lib/apt/lists/*
-
-# install wkhtmltopdf for otter export
-RUN apt-get clean && \
-    apt-get update && \ 
-    apt-get install -y pandoc && \
-    apt-get install -y -f texlive-xetex texlive-fonts-recommended texlive-lang-chinese && \
-    wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.focal_amd64.deb && \
-    apt-get install -y /tmp/wkhtmltopdf.deb && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
-
-# Set the locale to UTF-8 to ensure that Unicode output is encoded correctly
-ENV LANG C.UTF-8
-ENV LC_ALL C.UTF-8
-
-# create dir for autograder
-RUN mkdir /autograder
-
-# Python requirements
-ADD requirements.txt /tmp/requirements.txt
-RUN pip install -r /tmp/requirements.txt
-
-RUN pip install otter-grader==4.4.1
-RUN Rscript -e "install.packages('ottr', dependencies=TRUE, repos='http://cran.us.r-project.org')"
+# Docker image for setting up a development environment and Otter's automated tests.
+
+FROM docker/buildx-bin as buildx
+
+FROM ubuntu:latest
+
+# Make docker buildx available in the container
+COPY --from=buildx /buildx /usr/libexec/docker/cli-plugins/docker-buildx
+
+# Install apt packages
+RUN apt-get update && apt-get upgrade -y && apt-get install -y wget make build-essential
+
+# Install mamba
+RUN if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
+        then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+            -O /tmp/mamba_install.sh ; \
+        else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+            -O /tmp/mamba_install.sh ; \
+    fi && \
+    chmod +x /tmp/mamba_install.sh && \
+    /tmp/mamba_install.sh -b
+ENV PATH=/root/mambaforge/bin:$PATH
+
+# Create mamba environment
+COPY environment.yml requirements.txt requirements-export.txt requirements-test.txt /tmp/
+RUN mkdir -p /tmp/docs && touch /tmp/docs/requirements.txt
+RUN mamba env create -f /tmp/environment.yml
+RUN mamba run -n otter-grader Rscript -e 'install.packages("ottr", dependencies=TRUE, repos="https://cran.r-project.org")'
+ADD . /root/otter-grader
+RUN mamba run -n otter-grader pip install /root/otter-grader
+
+# Make script executable
+RUN chmod +x /root/otter-grader/bin/run_tests

Makefile

@@ -4,7 +4,6 @@ PYTESTOPTS       = -v
 COVERAGE         = coverage
 DOCKER           = true
 SLOW             = true
-OS              := $(shell uname -s)
 
 ifeq ($(DOCKER), false)
 	PYTESTOPTS := $(PYTESTOPTS) -m "not docker"
@@ -28,45 +27,8 @@ htmlcov: testcov
 docs:
 	$(MAKE) -C docs html
 
-docker-test-prepare: 
-	cp -r Dockerfile test-Dockerfile
-	printf "\nADD . /home/otter-grader\nRUN pip install /home/otter-grader" >> test-Dockerfile
-	printf "\nARG DOCKER_VERSION" >> test-Dockerfile
-	printf "\nRUN cd /tmp && curl -sSL -O https://download.docker.com/linux/static/stable/x86_64/docker-$$%s.tgz && tar zxf docker-$$%s.tgz && mv ./docker/docker /usr/local/bin && chmod +x /usr/local/bin/docker && rm -rf /tmp/*" "{DOCKER_VERSION}" "{DOCKER_VERSION}" >> test-Dockerfile
-	printf "\nCOPY --from=docker/buildx-bin /buildx /usr/libexec/docker/cli-plugins/docker-buildx" >> test-Dockerfile
-	printf "\nENV PYTHONUNBUFFERED 1" >> test-Dockerfile
-
-docker-test: docker-test-prepare
-	docker build . -t otter-test -f test-Dockerfile --cache-from ucbdsinfra/otter-grader:latest
-	rm test-Dockerfile
-
-docker-ci-test-cleanup:
-	rm test-Dockerfile
-
 tutorial:
 	cd docs/tutorial; \
 	zip -r tutorial.zip submissions demo.ipynb requirements.txt -x "*.DS_Store"; \
 	cp tutorial.zip ../_static; \
 	rm tutorial.zip
-
-docker-grade-test:
-	cp otter/generate/templates/python/setup.sh otter/generate/templates/python/old-setup.sh
-	printf "\nconda run -n otter-env pip install /home/otter-grader" >> otter/generate/templates/python/setup.sh
-ifeq ($(OS), Darwin)
-	sed -i '' -e "s+ucbdsinfra/otter-grader+otter-test+" otter/generate/templates/python/setup.sh
-	sed -i '' -e "s+ucbdsinfra/otter-grader+otter-test+" otter/generate/templates/python/run_autograder
-else
-	sed -i "s+ucbdsinfra/otter-grader+otter-test+" otter/generate/templates/python/setup.sh
-	sed -i "s+ucbdsinfra/otter-grader+otter-test+" otter/generate/templates/python/run_autograder
-endif
-
-cleanup-docker-grade-test:
-	rm otter/generate/templates/python/setup.sh
-	mv otter/generate/templates/python/old-setup.sh otter/generate/templates/python/setup.sh
-ifeq ($(OS), Darwin)
-	sed -i '' -e "s+otter-test+ucbdsinfra/otter-grader+" otter/generate/templates/python/setup.sh
-	sed -i '' -e "s+otter-test+ucbdsinfra/otter-grader+" otter/generate/templates/python/run_autograder
-else
-	sed -i "s+otter-test+ucbdsinfra/otter-grader+" otter/generate/templates/python/setup.sh
-	sed -i "s+otter-test+ucbdsinfra/otter-grader+" otter/generate/templates/python/run_autograder
-endif

bin/run_tests

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# Runs Otter's tests and copies the resulting coverage.xml file into the /tmp directory. This script
+# should only be used inside a Docker container created by /Dockerfile.
+
+export PATH="/root/mambaforge/bin:$PATH"
+source /root/mambaforge/etc/profile.d/conda.sh
+source /root/mambaforge/etc/profile.d/mamba.sh
+cd /root/otter-grader
+mamba activate otter-grader
+make testcov PYTESTOPTS="-vv" && coverage xml -i && cp ./coverage.xml /tmp/coverage.xml