diff --git a/.github/workflows/test-and-lint.yml b/.github/workflows/test-and-lint.yml new file mode 100644 index 0000000..2a7b127 --- /dev/null +++ b/.github/workflows/test-and-lint.yml @@ -0,0 +1,38 @@ +name: Test and Lint + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + test_lint: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.7, 3.8] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install poetry + poetry config virtualenvs.in-project true + poetry install + - name: Testing + run: | + poetry run poe test + - name: Linting + run: | + poetry run poe ci_check + - name: "Upload coverage to Codecov" + uses: codecov/codecov-action@v2 + with: + fail_ci_if_error: true diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..eef1cbb --- /dev/null +++ b/.gitignore @@ -0,0 +1,243 @@ + +# Created by https://www.toptal.com/developers/gitignore/api/jupyternotebooks,linux,macos,python,windows +# Edit at https://www.toptal.com/developers/gitignore?templates=jupyternotebooks,linux,macos,python,windows + +### JupyterNotebooks ### +# gitignore template for Jupyter Notebooks +# website: http://jupyter.org/ + +.ipynb_checkpoints +*/.ipynb_checkpoints/* + +# IPython +profile_default/ +ipython_config.py + +# Remove previous ipynb_checkpoints +# git rm -r .ipynb_checkpoints/ + +### Linux ### +*~ + +# temporary files which can be created if a process still has a handle open of a deleted file +.fuse_hidden* + +# KDE directory preferences +.directory + +# Linux trash folder which might appear on any partition or disk +.Trash-* + +# .nfs files are created when an open file is removed but is still being accessed +.nfs* + +### macOS ### +# General +.DS_Store +.AppleDouble +.LSOverride + +# Icon must end with two \r +Icon + + +# Thumbnails +._* + +# Files that might appear in the root of a volume +.DocumentRevisions-V100 +.fseventsd +.Spotlight-V100 +.TemporaryItems +.Trashes +.VolumeIcon.icns +.com.apple.timemachine.donotpresent + +# Directories potentially created on remote AFP share +.AppleDB +.AppleDesktop +Network Trash Folder +Temporary Items +.apdisk + +### Python ### +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook + +# IPython + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +### Windows ### +# Windows thumbnail cache files +Thumbs.db +Thumbs.db:encryptable +ehthumbs.db +ehthumbs_vista.db + +# Dump file +*.stackdump + +# Folder config file +[Dd]esktop.ini + +# Recycle Bin used on file shares +$RECYCLE.BIN/ + +# Windows Installer files +*.cab +*.msi +*.msix +*.msm +*.msp + +# Windows shortcuts +*.lnk + +# End of https://www.toptal.com/developers/gitignore/api/jupyternotebooks,linux,macos,python,windows + +# Virtual env +.venv + +# vscode (full) +.vscode + +# PyCharm +.idea + +# The data folder. Remove that line, if you want to store your data in git as well. +data + + + +# Pyenv +.python-version diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000..88668ca --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,25 @@ +stages: + - testing + +.python_base: &python_base + tags: + - docker + image: python:3.8 + before_script: + - git config --global credential.helper store + - echo "https://gitlab-ci-token:${CI_JOB_TOKEN}@mad-srv.informatik.uni-erlangen.de" > ~/.git-credentials + - pip install pip --upgrade + - pip install poetry + - poetry install + +test: + stage: testing + <<: *python_base + script: + - poetry run poe test + +lint: + stage: testing + <<: *python_base + script: + - poetry run poe ci_check diff --git a/.ruff.toml b/.ruff.toml new file mode 100644 index 0000000..494250e --- /dev/null +++ b/.ruff.toml @@ -0,0 +1,108 @@ +line-length = 120 +update-check = true +target-version = "py38" + +select = [ + # pyflakes + "F", + # pycodestyle + "E", + "W", + # mccabe + "C90", + # isort + "I", + # pydocstyle + "D", + # pyupgrade + "UP", + # pep8-naming + "N", + # flake8-blind-except + "BLE", + # flake8-2020 + "YTT", + # flake8-builtins + "A", + # flake8-comprehensions + "C4", + # flake8-debugger + "T10", + # flake8-errmsg + "EM", + # flake8-implicit-str-concat + "ISC", + # flake8-pytest-style + "PT", + # flake8-return + "RET", + # flake8-simplify + "SIM", + # flake8-unused-arguments + "ARG", + # pandas-vet + "PD", + # pygrep-hooks + "PGH", + # flake8-bugbear + "B", + # flake8-quotes + "Q", + # pylint + "PL", + # flake8-pie + "PIE", + # flake8-type-checking + "TCH", + # tryceratops + "TRY", + # flake8-use-pathlib + "PTH", + "RUF" +] + +ignore = [ + # controversial + "B006", + # controversial + "B008", + "B010", + # Magic constants + "PLR2004", + # Strings in error messages + "EM101", + "EM102", + "EM103", + # Multiline docstring summary + "D213", + # Varaibles before return + "RET504", + # Abstract raise into inner function + "TRY301", + # Use type-checking block + "TCH001", + "TCH002", + "TCH003", + # df as varaible name + "PD901", + # melt over stack + "PD013" +] + + +exclude = [ + "doc/sphinxext/*.py", + "doc/build/*.py", + "doc/temp/*.py", + ".eggs/*.py", + "example_data", + "examples" +] + + +[pydocstyle] +convention = "numpy" + +[pyupgrade] +# Preserve types, even if a file imports `from __future__ import annotations`. +keep-runtime-typing = true \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..0f19722 --- /dev/null +++ b/README.md @@ -0,0 +1,110 @@ +# emrad-analysis + + + + +## Project structure + +``` +emrad_analysis +│ README.md +├── emrad_analysis # The core library folder. All project-wide helper and algorithms go here +| +├── experiments # The main folder for all experiements. Each experiment has its own subfolder +| ├── experiment_1 # A single experiment (can be created with `poe experiment experiment_name`) +| | ├── notebooks # All narrative notebooks belonging to the experiment. +| | ├── scripts # Python scripts for this experiment +| | ├── helper # A Python module with experiment specific helper functions +| | +| ├── experiment_2 +| ├── ... +| +├── tests # Unit tests for the `emrad_analysis` library +| +├── data # The main data folder. This is ignored in the `.gitignore` by default. +| +| pyproject.toml # The required python dependencies for the project +| poetry.lock # The frozen python dependencies to reproduce exact results +| +``` + +## Usage + +This project was created using the mad-cookiecutter ds-base template. + +To work with the project you need to install: + +- [poetry](https://python-poetry.org/docs/#installation) +- [poethepoet](https://github.com/nat-n/poethepoet) in your global python env (`pip install poethepoet`) + +Afterwards run: + +``` +poetry install +``` + +Then you can create a new experiment using: + +``` +poe experiment experiment_name +``` + + +### Dependency management + +All dependencies are manged using `poetry`. +Poetry will automatically create a new venv for the project, when you run `poetry install`. +Check out the [documentation](https://python-poetry.org/docs/basic-usage/) on how to add and remove dependencies. + + +### Jupyter Notebooks + +To use jupyter notebooks with the project you need to add a jupyter kernel pointing to the venv of the project. +This can be done by running: + +``` +poe conf_jupyter +``` + +Afterwards a new kernel called `emrad_analysis` should be available in the jupyter lab / jupyter notebook interface. +Use that kernel for all notebooks related to this project. + + + +All jupyter notebooks should go into the `notebooks` subfolder of the respective experiment. +To make best use of the folder structure, the parent folder of each notebook should be added to the import path. +This can be done by adding the following lines to your first notebook cell: + +```python +# Optional: Auto reloads the helper and the main emrad_analysis module +%load_ext autoreload +%autoreload 2 + +from emrad_analysis import conf_rel_path +conf_rel_path() +``` + +This allows to then import the helper and the script module belonging to a specific experiment as follows: + +``` +import helper +# or +from helper import ... +``` + +### Format and Linting + +To ensure consistent code structure this project uses prospector, black, and ruff to automatically check (and fix) the code format. + +``` +poe format # runs black and ruff with the autofix flag +poe lint # runs ruff without autofix (will show issues that can not automatically be fixed) +``` + +If you want to check if all code follows the code guidelines, run `poe ci_check`. +This can be useful in the CI context + + +### Tests + +All tests are located in the `tests` folder and can be executed by using `poe test`. diff --git a/_tasks.py b/_tasks.py new file mode 100644 index 0000000..ea77a1c --- /dev/null +++ b/_tasks.py @@ -0,0 +1,48 @@ +import platform +import re +import shutil +import subprocess +import sys +from pathlib import Path + +HERE = Path(__file__).parent + + +def update_version_strings(file_path, new_version): + # taken from: + # https://stackoverflow.com/questions/57108712/replace-updated-version-strings-in-files-via-python + version_regex = re.compile(r"(^_*?version_*?\s*=\s*\")(\d+\.\d+\.\d+-?\S*)\"", re.M) + with open(file_path, "r+") as f: + content = f.read() + f.seek(0) + f.write(re.sub(version_regex, lambda match: '{}{}"'.format(match.group(1), new_version), content,)) + f.truncate() + + +def update_version(version): + subprocess.run(["poetry", "version", version], shell=False, check=True) + new_version = ( + subprocess.run(["poetry", "version"], shell=False, check=True, capture_output=True) + .stdout.decode() + .strip() + .split(" ", 1)[1] + ) + update_version_strings(HERE.joinpath("emrad_analysis/__init__.py"), new_version) + + +def task_update_version(): + update_version(sys.argv[1]) + + +def task_new_experiment(): + name = sys.argv[1] + files = ["__init__.py", "helper/__init__.py", "notebooks/.gitkeep", "scripts/.gitkeep", "README.md"] + + base_path: Path = HERE / "experiments" / name + if base_path.is_file() or base_path.is_dir(): + raise ValueError(f"Experiment with name {name} already exists at {base_path}") + + for f in files: + path = HERE / "experiments" / name / f + path.parent.mkdir(exist_ok=True, parents=True) + path.touch(exist_ok=True) diff --git a/emrad_analysis/__init__.py b/emrad_analysis/__init__.py new file mode 100644 index 0000000..9c9e24d --- /dev/null +++ b/emrad_analysis/__init__.py @@ -0,0 +1,14 @@ +# -*- coding: utf-8 -*- + +__version__ = "0.1.0" + + +def conf_rel_path(): + """Configure relative path imports for the experiments folder.""" + + from pathlib import Path + import sys + + parent_folder = str(Path("..").resolve()) + if parent_folder not in sys.path: + sys.path.append(parent_folder) diff --git a/experiments/__init__.py b/experiments/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..d863f07 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1665 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "appnope" +version = "0.1.3" 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