updated docs

.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

.gitignore

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

docs/_static/python_setup.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+export DEBIAN_FRONTEND=noninteractive
+apt-get clean
+apt-get update
+apt-get install -y wget pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic \
+    build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+
+# install conda
+if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
+    then wget -nv https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh \
+        -O /autograder/source/miniconda_install.sh ; \
+    else wget -nv https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+        -O /autograder/source/miniconda_install.sh ; \
+fi
+chmod +x /autograder/source/miniconda_install.sh
+/autograder/source/miniconda_install.sh -b
+echo "export PATH=/root/miniconda3/bin:\$PATH" >> /root/.bashrc
+
+export PATH=/root/miniconda3/bin:$PATH
+export TAR="/bin/tar"
+
+# install dependencies with conda
+conda env create -f /autograder/source/environment.yml
+
+# set conda shell
+conda init --all

docs/_static/r_setup.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+export DEBIAN_FRONTEND=noninteractive
+apt-get clean
+apt-get update
+apt-get install -y wget pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic \
+    build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
+    apt-utils libpoppler-cpp-dev libavfilter-dev  libharfbuzz-dev libfribidi-dev imagemagick \
+    libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic \
+    build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese \
+    libxft-dev
+
+# install conda
+if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
+    then wget -nv https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh \
+        -O /autograder/source/miniconda_install.sh ; \
+    else wget -nv https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+        -O /autograder/source/miniconda_install.sh ; \
+fi
+chmod +x /autograder/source/miniconda_install.sh
+/autograder/source/miniconda_install.sh -b
+echo "export PATH=/root/miniconda3/bin:\$PATH" >> /root/.bashrc
+
+export PATH=/root/miniconda3/bin:$PATH
+export TAR="/bin/tar"
+
+# install dependencies with conda
+conda env create -f /autograder/source/environment.yml
+conda run -n otter-env Rscript /autograder/source/requirements.r
+
+# set conda shell
+conda init --all
+
+# install ottr; not sure why it needs to happen twice but whatever
+conda run -n otter-env Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/ottr/ottr_1.1.5.tar.gz", dependencies=TRUE, repos=NULL)'

docs/conf.py

@@ -14,7 +14,6 @@
 
 import os
 import sys
-import yaml
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -24,6 +23,7 @@
 import nbconvert
 
 from glob import glob
+from jinja2 import Template
 from otter.generate import CondaEnvironment
 from otter.utils import print_full_width
 
@@ -112,7 +112,7 @@
 # a list of builtin themes.
 #
 html_theme = 'sphinx_book_theme'
-html_logo = '../logo/otter-logo-smaller.png'
+html_logo = '../logo/otter-logo-smallest.png'
 
 html_theme_options = {
     'github_url': 'https://github.com/ucbds-infra/otter-grader',
@@ -222,11 +222,29 @@ def convert_static_notebooks():
     print_full_width("=")
 
 
+def make_setup_sh_files():
+    ctx = {
+        "autograder_dir": "/autograder",
+        "otter_env_name": "otter-env",
+        "has_r_requirements": True,
+    }
+
+    for l in ["python", "r"]:
+        with open(f"../otter/generate/templates/{l}/setup.sh") as f:
+            t = Template(f.read())
+        s = t.render(ctx)
+        with open(f"_static/{l}_setup.sh", "w+") as f:
+            f.write(s)
+
+
 # -- Extension configuration -------------------------------------------------
 def setup(app):
     # run nbconvert on all of the notebooks in _static/notebooks
     convert_static_notebooks()
 
+    # convert templates to valid setup.sh files
+    make_setup_sh_files()
+
     with open("_static/grading-environment.yml", "w+") as f:
         f.write(CondaEnvironment(3.7, False, [], False, None).to_str())
 

docs/index.rst

@@ -67,32 +67,18 @@ Installation
 
 Otter is a Python package that is compatible with Python 3.6+. The PDF export internals require 
 either LaTeX and Pandoc or wkhtmltopdf to be installed. Docker is also required to grade assignments 
-locally with containerization, and Postgres only if you're using Otter Service. Otter's Python 
-package can be installed using pip. To install the current stable version, install with
+locally with containerization. Otter's Python package can be installed using pip. To install the
+current stable version, install with
 
 .. code-block:: console
 
     pip install otter-grader
 
-If you are going to be autograding R, you must also install the R package using 
-``devtools::install_github``:
-
-.. code-block:: r
-
-    devtools::install_github("ucbds-infra/ottr@stable")
-
 Installing the Python package will install the ``otter`` binary so that Otter can be called from the 
 command line. You can also call Otter as a Python module with ``python3 -m otter``.
 
+If you are going to be autograding R, you must also install the R package ``ottr``:
 
-Docker
-++++++
-
-Otter uses Docker to create containers in which to run the students' submissions. **Docker and our 
-Docker image are only required if using Otter Grade.** Please make sure that you 
-install Docker and pull our Docker image, which is used to grade the notebooks. To get the Docker 
-image, run
-
-.. code-block:: console
+.. code-block:: r
 
-    docker pull ucbdsinfra/otter-grader
+    install.packages("ottr")

docs/requirements.txt

@@ -1,4 +1,5 @@
 sphinx_markdown_tables
-sphinx-book-theme==0.1.7
+sphinx-book-theme==0.3.3
 sphinxcontrib-apidoc
 sphinx-click
+jinja2

docs/tutorial.rst

@@ -44,12 +44,7 @@ Otter Assign on this notebook, run
 
 .. code-block:: console
 
-    $ otter assign demo.ipynb dist
-    Generating views...
-    Generating solutions PDF...
-    Generating autograder zipfile...
-    Running tests...
-    All tests passed!
+    otter assign demo.ipynb dist
 
 Otter Assign should create a ``dist`` directory which contains two further subdirectories: 
 ``autograder`` and ``student``. The ``autograder`` directory contains the Gradescope autograder, 
@@ -101,16 +96,15 @@ machine. You can also grade on Gradescope or without containerization, as descri
 
 Let's now construct a call to Otter that will grade these notebooks. We will use 
 ``dist/autograder/autograder.zip`` from running Otter Assign to configure our grading image. Our notebooks 
-are in the ``ipynbs`` subdirectory, so we'll need to use the ``-p`` flag. The notebooks also contain 
-a couple of written questions, and the :ref:`filtering <pdfs>` is implemented using HTML comments, so 
+are in the ``ipynbs`` subdirectory and contain a couple of written questions, so 
 we'll specify the ``--pdfs`` flag to indicate that Otter should grab the PDFs out of the Docker 
-containers.
+containers. Lastly, we'll name the assignment ``demo`` with the ``-n`` flag.
 
 Let's run Otter on the notebooks:
 
 .. code-block:: console
 
-    otter grade -p submissions/ipynbs -a dist/autograder/demo-autograder_*.zip --pdfs -v
+    otter grade -n demo -a dist/autograder/demo-autograder_*.zip --pdfs -v submissions/ipynbs
 
 (The ``-v`` flag so that we get verbose output.) After this finishes running, there 
 should be a new file and a new folder in the working directory: ``final_grades.csv`` and 
@@ -168,16 +162,16 @@ The latter, the ``submission_pdfs`` directory, should contain the filtered PDFs
 Otter Grade can also grade the zip file exports provided by the ``Notebook.export`` method. Before 
 grading the zip files, you must edit your ``autograder.zip`` to indicate that you're doing so. To 
 do this, open ``demo.ipynb`` (the file we used with Otter Assign) and edit the first cell of the 
-notebook (beginning with ``BEGIN ASSIGNMENT``) so that the ``zips`` key under ``generate`` is 
+notebook (beginning with ``# ASSIGNMENT CONFIG``) so that the ``zips`` key under ``generate`` is 
 ``true`` in the YAML and rerun Otter Assign.
 
-Now, all we need to do is add the ``-z`` flag to the call to indicate that you're grading these zip 
-files. We have provided some, with the same notebooks as above, in the ``zips`` directory, so let's 
-grade those:
+Now, all we need to do is add the ``--ext`` flag to indicate that the submissions are zip files.
+We have provided some example submissions, with the same notebooks as above, in the ``zips``
+directory, so let's grade those:
 
 .. code-block:: console
 
-    otter grade -p submissions/zips -a dist/autograder/demo-autograder_*.zip -vz
+    otter grade -n demo -a dist/autograder/demo-autograder_*.zip -v --ext zip submissions/zips
 
 This should have the same CSV output as above but no ``submission_pdfs`` directory since we didn't 
 tell Otter to generate PDFs.