diff --git a/.readthedocs.yml b/.readthedocs.yml index dddaefae1..4ee8d3aa2 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -4,6 +4,11 @@ # Required version: 2 +build: + os: ubuntu-22.04 + tools: + python: "3.10" + # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py @@ -16,7 +21,6 @@ formats: # Optionally set the version of Python and requirements required to build your docs python: - version: 3.6 install: - requirements: docs/requirements.txt - - requirements: requirements.txt \ No newline at end of file + - path: . diff --git a/.vscode/launch.json b/.vscode/launch.json index 6f5be1f23..e9764ae00 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -1,8 +1,4 @@ { - // Use IntelliSense to learn about possible attributes. - // Hover to view descriptions of existing attributes. - // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 - "version": "0.2.0", "configurations": [ { @@ -19,11 +15,11 @@ "django": true }, { - "name": "Python: Attach Debugger", + "name": "Python: Attach Debugger (Bento)", "type": "python", "request": "attach", "port": 5678, "host": "0.0.0.0" - }, + } ] - } \ No newline at end of file +} diff --git a/README.md b/README.md index 807113845..664665440 100644 --- a/README.md +++ b/README.md @@ -245,6 +245,16 @@ tox coverage html ``` +### Developing and debugging inside a container with VS Code (*Bento*) + +The development Docker image includes metadata for the +[`devcontainer.json`](https://code.visualstudio.com/docs/devcontainers/attach-container) +specification. Using VS Code, you can attach to a running instance of a `*-dev` Katsu container +and launch the `Attach Debugger (Bento)` task to set breakpoints and step through code, as well +as interacting with and Git-committing inside the container via a remote terminal using the +pre-configured `bento_user` user, if the `BENTO_GIT_NAME` and `BENTO_GIT_EMAIL` environment +variables are set. + ### Terminal Commands Katsu ships with a variety of command-line helpers to facilitate common actions diff --git a/bento.Dockerfile b/bento.Dockerfile index fd58cdb67..1efe2c58e 100644 --- a/bento.Dockerfile +++ b/bento.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.27 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.03.22 SHELL ["/bin/bash", "-c"] diff --git a/bento.dev.Dockerfile b/bento.dev.Dockerfile index a07d221ea..59a66eb8e 100644 --- a/bento.dev.Dockerfile +++ b/bento.dev.Dockerfile @@ -1,15 +1,23 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.27 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.03.22 + +LABEL org.opencontainers.image.description="Local development image for Katsu." +LABEL devcontainer.metadata='[{ \ + "remoteUser": "bento_user", \ + "customizations": { \ + "vscode": { \ + "extensions": ["ms-python.python", "eamodio.gitlens"], \ + "settings": {"workspaceFolder": "/app"} \ + } \ + } \ +}]' SHELL ["/bin/bash", "-c"] # Install Postgres client for checking if database is ready # Install Poetry for dependency management -# - For development, install dependencies inside a venv so the developer can interact / change them RUN apt-get update -y && \ apt-get install -y postgresql-client && \ rm -rf /var/lib/apt/lists/* && \ - python -m venv /env && \ - source /env/bin/activate && \ pip install --no-cache-dir "uvicorn[standard]==0.20.0" # Backwards-compatible with old BentoV2 container layout @@ -22,7 +30,7 @@ COPY poetry.toml . # Install production + development dependencies # Without --no-root, we get errors related to the code not being copied in yet. # But we don't want the code here, otherwise Docker cache doesn't work well. -RUN source /env/bin/activate && poetry install --no-root +RUN poetry install --no-root # Create temporary directory for downloading files etc. RUN mkdir -p /app/tmp diff --git a/docs/conf.py b/docs/conf.py index 91a431e2e..2489063e4 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -10,11 +10,12 @@ # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # -import configparser + import datetime import os import sys import django +import toml from pathlib import Path @@ -22,21 +23,19 @@ os.environ['DJANGO_SETTINGS_MODULE'] = 'chord_metadata_service.metadata.settings' django.setup() -config = configparser.ConfigParser() -config.read(os.path.join(Path(os.path.dirname(os.path.realpath(__file__))).parent, - "chord_metadata_service", - "package.cfg")) +with open(Path(__file__).parent.parent / "pyproject.toml", "r") as cfh: + config = toml.load(cfh) # -- Project information ----------------------------------------------------- project = 'Katsu Metadata service' -author = config["package"]["authors"] +author = ", ".join(config["tool"]["poetry"]["authors"]) # noinspection PyShadowingBuiltins copyright = f"{datetime.datetime.now().year} {author}" # The full version, including alpha/beta/rc tags -release = config["package"]["version"] +release = config["tool"]["poetry"]["version"] version = ".".join(release.split(".")[:2]) @@ -53,7 +52,7 @@ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**/site-packages/*'] # -- Options for HTML output ------------------------------------------------- diff --git a/docs/index.rst b/docs/index.rst index 04fbfee21..79825a6a9 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -4,7 +4,7 @@ contain the root `toctree` directive. Welcome to Katsu Metadata service's documentation! -============================================ +================================================== .. toctree:: :maxdepth: 2 diff --git a/docs/requirements.txt b/docs/requirements.txt index 719cd8299..83c5a4e27 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,12 +1,27 @@ alabaster==0.7.12 +asgiref==3.6.0 +Babel==2.12.1 +certifi==2022.12.7 +charset-normalizer==3.1.0 +Django==4.1.7 docutils==0.16 -jinja2<3.1 -setuptools==65.5.1 +idna==3.4 +imagesize==1.4.1 +Jinja2==3.0.3 +MarkupSafe==2.1.2 +packaging==23.0 +Pygments==2.14.0 +requests==2.28.2 +snowballstemmer==2.2.0 Sphinx==2.4.4 -sphinx-rtd-theme==0.4.3 -sphinxcontrib-applehelp==1.0.2 +sphinx-rtd-theme==1.2.0 +sphinxcontrib-applehelp==1.0.4 sphinxcontrib-devhelp==1.0.2 -sphinxcontrib-htmlhelp==1.0.3 +sphinxcontrib-htmlhelp==2.0.1 +sphinxcontrib-jquery==4.1 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 -sphinxcontrib-serializinghtml==1.1.4 \ No newline at end of file +sphinxcontrib-serializinghtml==1.1.5 +sqlparse==0.4.3 +toml==0.10.2 +urllib3==1.26.15 diff --git a/entrypoint.bash b/entrypoint.bash index 3f31c6250..2b7f11b96 100644 --- a/entrypoint.bash +++ b/entrypoint.bash @@ -11,9 +11,6 @@ mkdir -p /app/tmp # Fix permissions on /app/tmp and /env chown -R bento_user:bento_user /app/tmp chmod -R o-rwx /app/tmp # Remove all access from others -if [[ -d /env ]]; then - chown -R bento_user:bento_user /env -fi # Drop into bento_user from root and execute the CMD specified for the image exec gosu bento_user "$@" diff --git a/poetry.lock b/poetry.lock index 7f3a22d5c..6bb664b2e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -356,100 +356,87 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.0.1" +version = "3.1.0" description = "The Real First Universal Charset Detector. 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["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "virtualenv" -version = "20.19.0" +version = "20.21.0" description = "Virtual Python Environment builder" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.19.0-py3-none-any.whl", hash = "sha256:54eb59e7352b573aa04d53f80fc9736ed0ad5143af445a1e539aada6eb947dd1"}, - {file = "virtualenv-20.19.0.tar.gz", hash = "sha256:37a640ba82ed40b226599c522d411e4be5edb339a0c0de030c0dc7b646d61590"}, + {file = "virtualenv-20.21.0-py3-none-any.whl", hash = "sha256:31712f8f2a17bd06234fa97fdf19609e789dd4e3e4bf108c3da71d710651adbc"}, + {file = "virtualenv-20.21.0.tar.gz", hash = "sha256:f50e3e60f990a0757c9b68333c9fdaa72d7188caa417f96af9e52407831a3b68"}, ] [package.dependencies] @@ -1943,19 +1911,19 @@ multidict = ">=4.0" [[package]] name = "zipp" -version = "3.13.0" +version = "3.15.0" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "zipp-3.13.0-py3-none-any.whl", hash = "sha256:e8b2a36ea17df80ffe9e2c4fda3f693c3dad6df1697d3cd3af232db680950b0b"}, - {file = "zipp-3.13.0.tar.gz", hash = "sha256:23f70e964bc11a34cef175bc90ba2914e1e4545ea1e3e2f67c079671883f9cb6"}, + {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"}, + {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"}, ] [package.extras] docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [metadata] lock-version = "2.0" diff --git a/pyproject.toml b/pyproject.toml index 2378876f4..8ba833d0f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "chord_metadata_service" # can be renamed to katsu if inner module directory is renamed too -version = "2.18.0" +version = "2.18.1" description = "An implementation of a clin/pheno metadata store for the Bento platform." authors = [ "Ksenia Zaytseva", diff --git a/run.bash b/run.bash index ced3c7204..6f3e78d4e 100644 --- a/run.bash +++ b/run.bash @@ -7,11 +7,8 @@ python manage.py makemigrations admin auth python manage.py migrate -# Set the internal port unless it's been externally configured -if [ -z "${INTERNAL_PORT}" ]; then - # Set default internal port to 8000 - INTERNAL_PORT=8000 -fi +# Set default internal port to 8000 +: "${INTERNAL_PORT:=8000}" # Run the ASGI server uvicorn chord_metadata_service.metadata.asgi:application \ diff --git a/run.dev.bash b/run.dev.bash index e726dc552..3fa0fdf55 100644 --- a/run.dev.bash +++ b/run.dev.bash @@ -3,11 +3,8 @@ # Set .gitconfig for development /set_gitconfig.bash -# Source the development virtual environment -source /env/bin/activate - -# Update dependencies and install module locally (similar to pip install -e: "editable mode") -poetry install +# Update dependencies and install module locally +/poetry_user_install_dev.bash # Wait for database to start ./wait_for_db.bash @@ -16,10 +13,7 @@ poetry install python manage.py makemigrations admin auth python manage.py migrate -# Set the internal port unless it's been externally configured -if [[ -z "${INTERNAL_PORT}" ]]; then - # Set default internal port to 8000 - INTERNAL_PORT=8000 -fi +# Set default internal port to 8000 +: "${INTERNAL_PORT:=8000}" python manage.py runserver "0.0.0.0:${INTERNAL_PORT}"