Create project structure

98916d37 · nguyed99 · c1d033fd · 98916d37 · 98916d37 · 98916d37
Commit 98916d37 authored 1 year ago by nguyed99
--- a/.gitignore
+++ b/.gitignore
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
+stages:
+  - build
+  - test
+  - deploy
+build:
+  stage: build
+  script:
+    - docker build -t myproject .
+test:
+  stage: test
+  script:
+    - docker run myproject pytest
+ script:
+    - echo "Deploying the application..."
+    # Add deployment scripts here
+    - scp docker-compose.yml $DEPLOY_USER@$DEPLOY_SERVER:/path/to/deployment
+    - ssh $DEPLOY_USER@$DEPLOY_SERVER 'docker-compose down && docker-compose up -d'
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
+repos:
+  # we're managing our tools with poetry, no need to have pre-commit install them again
+  - repo: local
+    hooks:
+      # https://github.com/charliermarsh/ruff-pre-commit/blob/main/.pre-commit-hooks.yaml
+      - id: ruff
+        name: linter
+        language: system
+        entry: poetry run ruff check
+        args: [--force-exclude, --fix, --exit-non-zero-on-fix]
+        types_or: [python, pyi]
+        require_serial: true
+      # https://github.com/google/yapf/blob/main/.pre-commit-hooks.yaml
+      - id: yapf
+        name: code format 
+        language: system
+        entry: poetry run yapf
+        args: [-i]
+        types: [python]
+        require_serial: true
--- a/Makefile
+++ b/Makefile
+.PHONY: help
+help:
+	@echo ""
+	@echo "make clean     - remove .pyc + __pycache__ fragments"
+	@echo "make format    - format source code"
+	@echo "make lint      - lint source code"
+	@echo "make lint-fix  - lint source code and fix auto-fixable problems"
+	@echo ""
+init:
+	poetry install						#  install the dependencies specified in `pyproject.toml` 
+	poetry run pre-commit install
+clean:
+	find . -type f -name "*.py[co]" -delete
+	find . -type d -name "__pycache__" -delete
+format:
+	poetry run yapf -i -r -p .
+lint:
+	poetry run ruff .
+lint-fix:
+	poetry run ruff . --fix
\ No newline at end of file
--- a/README.md
+++ b/README.md
-# comp-sci-project
+## Repository structure
+All folders are isolated projects. `cd` into the folder to run/build them.
+- `jobs`: jobs to be built as docker images (`build/build_image.sh` in each job)
+- `tasks`: a task can be composed of many jobs
-## Getting started
+## Getting Started
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+[poetry](https://python-poetry.org/docs/) is used as package manager. Ensure you've it! Also please have Python 3.11 installed.
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+#### Do this once
-## Add your files
+    curl -sSL https://install.python-poetry.org | python3 -
- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
+To get started you need Poetry's bin directory (~/.local/bin) in your `PATH` environment variable. Add `export PATH="~/.local/bin:$PATH"` to your shell configuration file.
- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-```
+    make init
-cd existing_repo
-git remote add origin https://git.imp.fu-berlin.de/nguyed99/comp-sci-project.git
-git branch -M main
-git push -uf origin main
-```
-## Integrate with your tools
+#### Do this happily ever after
- [ ] [Set up project integrations](https://git.imp.fu-berlin.de/nguyed99/comp-sci-project/-/settings/integrations)
+    poetry shell
-## Collaborate with your team
+We are storing Docker images at GitLab's integrated container registry. Make sure Docker is aware of your GitLab token. If you do not have one, make one [here](https://docs.gitlab.com/ee/security/token_overview.html) (with scope `read_registry` and `write_registry`). Then enter:
- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
+    docker login registry.example.com -u <username> -p <token>
- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-## Test and Deploy
+## Local development
+### jobs
-Use the built-in continuous integration in GitLab.
+Jobs are run inside of docker containers. Each job has a docker build script and can be run in `dev` mode via `docker run`. Please be aware it can take a while to build the initial image.
- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
+    cd jobs/a-job
- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
+    build/build_image.sh
- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-***
+The image is built now and ready to be used by tasks. This image can be sanity-checked via (test implementation without minio-s3-parameter transport):
-# Editing this README
+    docker run -it --rm registry.example.com/group/project/image:local sanity-check
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
+If you change code in `src`, you need to rebuild the image with `build/build_image.sh`. The `src` folder can also be mounted in the image, but the assumption is that life is already difficult as it is...
-## Suggestions for a good README
+### tasks
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
+Tasks are python scripts that can spawn jobs which run in docker containers. Before calling a task, make sure you have built the related job-image. 
-## Name
+    python -B src/a-task.py local --config=docker.yaml --IN0 demo-inputs/system.json --OUT /tmp/test-a-task
-Choose a self-explaining name for your project.
\ No newline at end of file
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-## License
-For open source projects, say how it is licensed.
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
--- a/jobs/a-job/build/Dockerfile
+++ b/jobs/a-job/build/Dockerfile
--- a/jobs/a-job/build/build-image.sh
+++ b/jobs/a-job/build/build-image.sh
--- a/poetry.lock
+++ b/poetry.lock
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+[[package]]
+name = "cfgv"
+version = "3.4.0"
+description = "Validate configuration and produce human readable error messages."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
+    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
+]
+[[package]]
+name = "distlib"
+version = "0.3.7"
+description = "Distribution utilities"
+optional = false
+python-versions = "*"
+files = [
+    {file = "distlib-0.3.7-py2.py3-none-any.whl", hash = "sha256:2e24928bc811348f0feb63014e97aaae3037f2cf48712d51ae61df7fd6075057"},
+    {file = "distlib-0.3.7.tar.gz", hash = "sha256:9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8"},
+]
+[[package]]
+name = "filelock"
+version = "3.13.1"
+description = "A platform independent file lock."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "filelock-3.13.1-py3-none-any.whl", hash = "sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c"},
+    {file = "filelock-3.13.1.tar.gz", hash = "sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e"},
+]
+[package.extras]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+typing = ["typing-extensions (>=4.8)"]
+[[package]]
+name = "identify"
+version = "2.5.33"
+description = "File identification library for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "identify-2.5.33-py2.py3-none-any.whl", hash = "sha256:d40ce5fcd762817627670da8a7d8d8e65f24342d14539c59488dc603bf662e34"},
+    {file = "identify-2.5.33.tar.gz", hash = "sha256:161558f9fe4559e1557e1bff323e8631f6a0e4837f7497767c1782832f16b62d"},
+]
+[package.extras]
+license = ["ukkonen"]
+[[package]]
+name = "nodeenv"
+version = "1.8.0"
+description = "Node.js virtual environment builder"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
+files = [
+    {file = "nodeenv-1.8.0-py2.py3-none-any.whl", hash = "sha256:df865724bb3c3adc86b3876fa209771517b0cfe596beff01a92700e0e8be4cec"},
+    {file = "nodeenv-1.8.0.tar.gz", hash = "sha256:d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2"},
+]
+[package.dependencies]
+setuptools = "*"
+[[package]]
+name = "platformdirs"
+version = "4.1.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "platformdirs-4.1.0-py3-none-any.whl", hash = "sha256:11c8f37bcca40db96d8144522d925583bdb7a31f7b0e37e3ed4318400a8e2380"},
+    {file = "platformdirs-4.1.0.tar.gz", hash = "sha256:906d548203468492d432bcb294d4bc2fff751bf84971fbb2c10918cc206ee420"},
+]
+[package.extras]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
+[[package]]
+name = "pre-commit"
+version = "3.6.0"
+description = "A framework for managing and maintaining multi-language pre-commit hooks."
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "pre_commit-3.6.0-py2.py3-none-any.whl", hash = "sha256:c255039ef399049a5544b6ce13d135caba8f2c28c3b4033277a788f434308376"},
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+[package.dependencies]
+cfgv = ">=2.0.0"
+identify = ">=1.0.0"
+nodeenv = ">=0.11.1"
+pyyaml = ">=5.1"
+virtualenv = ">=20.10.0"
+[[package]]
+name = "pyyaml"
+version = "6.0.1"
+description = "YAML parser and emitter for Python"
+optional = false
+python-versions = ">=3.6"
+files = [
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+[[package]]
+name = "virtualenv"
+version = "20.25.0"
+description = "Virtual Python Environment builder"
+optional = false
+python-versions = ">=3.7"
+files = [
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+platformdirs = ">=3.9.1,<5"
+[package.extras]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
+[[package]]
+name = "yapf"
+version = "0.32.0"
+description = "A formatter for Python code."
+optional = false
+python-versions = "*"
+files = [
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+python-versions = "~3.11"
+content-hash = "79e1810a3524adfaaf1d9aa0a659f9dc3c9f35f46f7daa71963d06e011323054"
--- a/pyproject.toml
+++ b/pyproject.toml
+[tool.poetry]
+name = "comp-sci-project"
+version = "0.1.0"
+description = ""
+authors = []
+readme = "README.md"
+[tool.poetry.dependencies]
+python = "~3.11"
+[tool.poetry.group.dev.dependencies]
+ruff = "^0.0.267"
+pre-commit = "^3.3.1"
+yapf = "^0.32.0"
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+[tool.ruff]
+# disable line-length lint since it is handled by yapf
+ignore = ["E501"]
+line-length = 118
+# pyflakes, pycodestyle, isort
+#select = ["F", "E", "W", "I001"]
+[tool.yapf]
+based_on_style = "pep8"
+column_limit = 120
+allow_split_before_dict_value = false
--- a/tasks/docker.yaml
+++ b/tasks/docker.yaml
+backend:
+  name: docker
+  kind: docker
+  release: local
+  transport:
+    name: minio
+    kind: s3
+    url: s3+http://minioadmin:minioadmin@127.0.0.1:9000/test
+    remoteUrl: s3+http://minioadmin:minioadmin@127.0.0.1:9000/test
+  defaultSpecs:
+    network_mode: host
+    maxCpu: 4
+    environment:
+      NUMPROCS: 3  # no cpu+1
+numJobs: 3
--- a/tasks/src/a-task.py
+++ b/tasks/src/a-task.py