use poetry and pyproject.toml for packaging

.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
 
       - 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

.github/workflows/run-tests.yml

@@ -41,6 +41,11 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - uses: liskin/gh-pipx@v1
+        with:
+          packages: >-
+            poetry
+
       - uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment.yml
@@ -49,6 +54,11 @@ jobs:
           cache-environment: true
           cache-environment-key: requirements-${{ hashFiles('requirements*.txt') }}
 
+      - name: Install dependencies
+        run: |
+          micromamba activate otter-grader
+          poetry install --with test
+
       - name: Install ottr
         run: |
           micromamba run -n otter-grader Rscript -e 'install.packages("ottr", dependencies=TRUE, repos="https://cran.r-project.org/")'

.readthedocs.yml

@@ -18,4 +18,15 @@ conda:
 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

CONTRIBUTING.md

@@ -6,19 +6,24 @@ 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
+```
 
 
 ## Running Tests

environment.yml

@@ -3,13 +3,8 @@ channels:
     - conda-forge
     - defaults
 dependencies:
-    - python>=3.6,<3.11
+    - python>=3.8
     - r-base>=4.0.0
     - r-essentials
     - r-devtools
     - pip
-    - pip:
-        - -r requirements.txt
-        - -r requirements-export.txt
-        - -r requirements-test.txt
-        - -r docs/requirements.txt

pyproject.toml

@@ -0,0 +1,87 @@
+[tool.poetry]
+name = "otter-grader"
+version = "5.6.0"
+description = "A Python and R autograding solution"
+authors = ["Christopher Pyles <[email protected]>"]
+license = "BSD-3-Clause"
+readme = "README.md"
+homepage = "https://otter-grader.readthedocs.io/"
+repository = "https://github.com/ucbds-infra/otter-grader"
+documentation = "https://otter-grader.readthedocs.io/"
+classifiers = [
+		"Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+]
+packages = [
+  { include = "otter" },
+]
+include = [
+  { path = "otter/export/exporters/templates/**/*" },
+  { path = "otter/generate/templates/**/*" },
+  { path = "otter/grade/Dockerfile" },
+]
+
+[tool.poetry.scripts]
+otter = "otter.cli:cli"
+gmail_oauth2 = "otter.plugins.builtin.gmail_notifications.bin.gmail_oauth2:main"
+
+[tool.poetry.dependencies]
+python = "^3.9"
+astunparse = "^1.6.3"
+click = "^8.1.7"
+dill = "^0.3.8"
+fica = ">=0.3.1"
+google-api-python-client = { version = "*", optional = true }
+google-auth-oauthlib = { version = "*", optional = true }
+six = { version = "*", optional = true }
+gspread = { version = "*", optional = true }
+ipylab = "^1.0.0"
+ipython = "*"
+ipywidgets = "^8.1.5"
+jinja2 = "^3.1.4"
+jupytext = "^1.16.4"
+nbconvert = { version = ">=6.0.0", extras = ["webpdf"], markers = "sys_platform != 'emscripten' and sys_platform != 'wasi'" }
+nbformat = ">=5.0.0"
+pandas = ">=2.0.0"
+python-on-whales = "^0.72.0"
+pyyaml = "^6.0.2"
+requests = "^2.32.3"
+rpy2 = { version = "^3.5.16", optional = true }
+setuptools = "^74.0.0"
+wrapt = "^1.16.0"
+
+[tool.poetry.extras]
+plugins = ["google-api-python-client", "google-auth-oauthlib", "gspread", "six"]
+r = ["rpy2"]
+
+[tool.poetry.group.dev.dependencies]
+ipykernel = "*"
+jupyter_client = "*"
+matplotlib = "*"
+pypdf = "*"
+scikit-learn = "*"
+tqdm = "*"
+
+[tool.poetry.group.test]
+optional = true
+
+[tool.poetry.group.test.dependencies]
+coverage = "^7.2.0"
+pytest = "^8.2.2"
+pytest-html = "*"
+responses = "^0.25.3"
+
+[tool.poetry.group.docs]
+optional = true
+
+[tool.poetry.group.docs.dependencies]
+sphinx = ">=5.0.0"
+sphinx-book-theme = "1.1.0"
+sphinx-click = "*"
+sphinx_markdown_tables = "*"
+sphinxcontrib-apidoc = "*"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

release.py

@@ -90,6 +90,20 @@
     with open("otter/version.py", "w") as f:
         f.write(contents)
 
+    # fix pyproject.toml
+    with open("pyproject.toml") as f:
+        contents = f.read()
+
+    if args.new_version is not None:
+        contents = re.sub(
+            r"version = \"\d+\.\d+\.\d+(?:\.\w+)?\"",
+            f"version = \"{new_version_number}\"",
+            contents
+        )
+
+    with open("pyproject.toml", "w") as f:
+        f.write(contents)
+
     # fix CITATION.cff
     with open("CITATION.cff") as f:
         contents = f.read()