chore: Update pyproject.toml to work with Poetry 2.x (#241)

* update pre-commit config

* Pin the ruff version used in Actions

* Update to latest dev.sh script

* Update pyproject.toml to new format
Update poetry.lock with updated dependencies
Update project to require Python >= 3.9

* Move container files to product-agnostic file names
Update README
Add .containerignore file
Update to a more standard Containerfile

* move from green to pytest for unit testing

Author: coreone

.containerignore

@@ -0,0 +1,8 @@
+.[a-z]*
+.venv/*
+*.sh
+*.xml
+CHANGELOG.md
+Dockerfile
+tests/*
+tmp/*

.github/workflows/checks.yaml

@@ -12,9 +12,12 @@ jobs:
   linting:
     uses: broadinstitute/shared-workflows/.github/workflows/[email protected]
     with:
+      ruff_version: '0.8.6'
       use_pylama: false
       use_ruff: true
   unit-tests:
     uses: broadinstitute/shared-workflows/.github/workflows/[email protected]
     with:
       python_package_name: cert_manager
+      run_coverage: false
+      test_runner: pytest

.green

@@ -1,7 +1,7 @@
 ---
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -28,12 +28,12 @@ repos:
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.14
+    rev: v0.8.6
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.33.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
         args:

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+FROM docker.io/node:bookworm AS prettier-install
+RUN yarn add prettier@3
+
+FROM python:3.11-slim-bookworm
+
+ARG LOCAL_BIN=/root/.local/bin
+ENV PATH=$LOCAL_BIN:$PATH
+
+# Install prettier
+RUN mkdir -p $LOCAL_BIN
+COPY --from=prettier-install /usr/local/bin/node $LOCAL_BIN
+COPY --from=prettier-install /node_modules/prettier /prettier
+RUN ln -s /prettier/bin/prettier.cjs $LOCAL_BIN/prettier
+
+COPY . /working/
+
+WORKDIR /working
+
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get install -yq --no-install-recommends curl make \
+    && curl -sSL https://install.python-poetry.org | python3 - \
+    && poetry install \
+    && rm -rf /tmp/* \
+    && rm -rf /var/cache/apt/* \
+    && rm -rf /var/tmp/*
+
+ENTRYPOINT ["poetry", "run"]
+
+CMD ["bash"]

Containerfile

@@ -6,7 +6,7 @@ This library provides a [Python][1] interface to the [Sectigo][2] Certificate Ma
 
 ## Basics
 
-`cert_manager` runs on [Python][1] >= 3.7
+`cert_manager` runs on [Python][1] >= 3.9
 
 ## Features
 
@@ -109,15 +109,15 @@ Pull requests to add functionality and fix bugs are always welcome.  Please chec
 
 ### Testing
 
-We try to have a high level of test coverage on the code.  Therefore, when adding anything to the repo, tests should be written to test a new feature or to test a bug fix so that there won't be a regression.  This library is setup to be pretty simple to build a working development environment using [Docker][4].  Therefore, it is suggested that you have [Docker][4] installed where you clone this repository to make development easier.
+We try to have a high level of test coverage on the code.  Therefore, when adding anything to the repo, tests should be written to test a new feature or to test a bug fix so that there won't be a regression.  This library is setup to be pretty simple to build a working development environment using [Docker][4]. Therefore, it is suggested that you have [Docker][4] installed where you clone this repository to make development easier.
 
-To start a development environment, you should be able to just run the `dev.sh` script.  This script will use the `Dockerfile` in this repository to build a [Docker][4] container with all the dependencies for development installed using [Pipenv][3].
+To start a development environment, you should be able to just run the `dev.bash` script.  This script will use the `Containerfile` in this repository to build a [Docker][4] container with all the dependencies for development installed using [Poetry][3].
 
 ```sh
-./dev.sh
+./dev.bash
 ```
 
-The first time you run the script, it should build the [Docker][4] image and then drop you into the container's shell.  The directory where you cloned this repository should be volume mounted in to `/usr/src`, which should also be the current working directory.  From there, you can make changes as you see fit.  Tests can be run from the `/usr/src` directory by simply typing `green` as [green][5] has been setup to with the correct parameters.
+The first time you run the script, it should build the [Docker][4] image and then drop you into the container's shell.  The directory where you cloned this repository should be volume mounted in to `/working`, which should also be the current working directory.  From there, you can make changes as you see fit.  Tests can be run from the `/working` directory by simply typing `pytest` as [pytest][5] has been setup to with the correct parameters.
 
 ## Changelog
 
@@ -162,7 +162,7 @@ git push --tags
 
 [1]: https://www.python.org/ "Python"
 [2]: https://sectigo.com/ "Sectigo"
-[3]: https://pipenv.readthedocs.io/en/latest/ "Pipenv"
+[3]: https://python-poetry.org/ "Poetry"
 [4]: https://www.docker.com/ "Docker"
-[5]: https://github.com/CleanCut/green "green"
+[5]: https://docs.pytest.org/en/stable/ "pytest"
 [6]: https://pypi.org/project/bump2version/ "bump2version"

Dockerfile

@@ -0,0 +1,89 @@
+#!/usr/bin/env bash
+
+declare -g CHECKSUM_APP
+declare -g CONTAINER_APP
+declare -g CONTAINER_IMAGE='cert_manager:dev'
+declare -g LABEL_PREFIX='org.broadinstitute.cert-manager'
+declare -g SCRIPT_DIR
+declare -ga TRACK_FILES=( Containerfile poetry.lock pyproject.toml )
+declare -ga SUDO
+declare -ag TTY
+
+SCRIPT_DIR="$( cd -P "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+if hash sha256sum 2>/dev/null; then
+    CHECKSUM_APP='sha256sum'
+elif hash shasum 2>/dev/null; then
+    CHECKSUM_APP='shasum -a 256'
+elif hash md5sum 2>/dev/null; then
+    CHECKSUM_APP='md5sum'
+else
+    echo 'Could not find a checksumming program. Exiting!'
+    exit 1
+fi
+
+if hash docker 2>/dev/null; then
+    CONTAINER_APP='docker'
+elif hash podman 2>/dev/null; then
+    CONTAINER_APP='podman'
+else
+    echo 'Container environment cannot be found. Exiting!'
+    exit 2
+fi
+
+if [[ "${TERM}" != 'dumb' ]]; then
+    TTY=( -it )
+fi
+
+if [[ "${CONTAINER_APP}" = 'docker' ]] && [[ "$( uname -s )" != 'Darwin' ]]; then
+    if [[ ! -w "${DOCKER_SOCKET}" ]]; then
+        SUDO=( sudo )
+    fi
+fi
+
+function build() {
+    if [[ -z "$1" ]]; then
+        echo 'Image name not provided to build. Exiting!'
+        exit 1
+    fi
+    CONTAINER_IMAGE=$1
+
+    if ! git diff --quiet; then
+        echo 'Branch is dirty.  The build can only happen on an unmodified branch.'
+        exit 2
+    fi
+
+    local -a labels
+    for tfile in "${TRACK_FILES[@]}"; do
+        label="$( "${CHECKSUM_APP}" "${tfile}" | awk -v PREFIX="${LABEL_PREFIX}" '{print PREFIX"."$2"="$1}' )"
+        labels+=( --label "${label}" )
+    done
+
+    "${SUDO[@]}" "${CONTAINER_APP}" build --pull -t "${CONTAINER_IMAGE}" "${labels[@]}" .
+}
+
+pushd "${SCRIPT_DIR}" >/dev/null || exit 1
+if ! "${SUDO[@]}" "${CONTAINER_APP}" image ls | awk '{print $1":"$2}' | grep --quiet -E "^(localhost\/)*${CONTAINER_IMAGE}"; then
+    build "${CONTAINER_IMAGE}"
+fi
+
+rebuild='0'
+for tfile in "${TRACK_FILES[@]}"; do
+    current="$( "${CHECKSUM_APP}" "${tfile}" | cut -d' ' -f1 )"
+    stored="$( "${CONTAINER_APP}" image inspect --format="{{index .Config.Labels \"${LABEL_PREFIX}.${tfile}\"}}" "${CONTAINER_IMAGE}" )"
+
+    if [[ "${current}" != "${stored}" ]]; then
+        echo "${tfile} changed.  Rebuilding."
+        rebuild='1'
+    fi
+done
+
+if [[ "${rebuild}" == '1' ]]; then
+    build "${CONTAINER_IMAGE}"
+fi
+
+"${SUDO[@]}" "${CONTAINER_APP}" run "${TTY[@]}" --rm \
+    -v "${SCRIPT_DIR}:/working" \
+    "${CONTAINER_IMAGE}" "$@"
+
+popd >/dev/null || exit 1