diff --git a/.gitignore b/.gitignore index f4de6b9..2ec9f5e 100644 --- a/.gitignore +++ b/.gitignore @@ -12,3 +12,4 @@ docs/source/sg_execution_times.rst docs/site docs/generated site +src/osipi.egg-info diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c2429e4..4a2ca8a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -5,25 +5,9 @@ repos: - id: ruff args: [--fix] # Optional: to enable lint fixes - id: ruff-format - - repo: https://github.com/pycqa/flake8 - rev: 7.0.0 - hooks: - - id: flake8 - args: - - --exclude=venv,.git,__pycache__,.eggs,.mypy_cache,.pytest_cache - - --max-line-length=100 - - --ignore=E203 - - --per-file-ignores=__init__.py:F401 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.6.0 hooks: - id: trailing-whitespace - id: end-of-file-fixer - id: check-yaml - - - repo: https://github.com/rstcheck/rstcheck - rev: v6.1.2 # Use the latest version - hooks: - - id: rstcheck - args: ["--ignore-directives=autosummary,autofunction,minigallery,image-sg","--ignore-messages=(Hyperlink target *|Duplicate explicit target name*)"] - additional_dependencies: [sphinx] diff --git a/.rstcheck.cfg b/.rstcheck.cfg deleted file mode 100644 index 19f4a4d..0000000 --- a/.rstcheck.cfg +++ /dev/null @@ -1,5 +0,0 @@ -[rstcheck] -ignore-directives = - autosummary, - image-sg, - minigallery diff --git a/README.md b/README.md index 4546465..d5ce152 100755 --- a/README.md +++ b/README.md @@ -33,7 +33,72 @@ We welcome contributions to OSIPI! To contribute, follow these steps: - Push your changes to your fork. - Submit a pull request to the main OSIPI repository. -For more details on how to contribute, visit the [Developer Guide](https://osipi.github.io/pypi/developers_guide/index.html). +## Development Setup + +We use poetry to manage the dependencies for this project. + +### Using Poetry + +1. If you don't have Poetry installed, you can install it using pip: + + ```bash + pip install poetry + ``` + + Or, if you're using a Unix-based system, you can install it using the following command: + + ```bash + curl -sSL https://install.python-poetry.org | python3 - + ``` + + For more information on installing Poetry, see the [official documentation](https://python-poetry.org/docs/) +2. Clone the repository to your local machine. +3. Navigate to the project directory. +4. Install the project dependencies with Poetry: + + ```bash + poetry install + ``` + +5. Activate the Poetry environment: + + ```bash + poetry shell + ``` + +## Setting up pre-commit + +`pre-commit` is a tool that we use to maintain high-quality code in this project. It runs checks (hooks) on your code each time you commit changes. Here's how to set it up: + +## Pre-Commit Hooks +Pre-commit hooks are scripts that run automatically before a commit is made in a Git repository. They help catch common issues like syntax errors, formatting problems, and other code quality issues. + +### Example hooks +- `flake8` - a linter that checks your code for common errors and style issues. +- `trailing-whitespace` - a hook that removes trailing whitespace from your files. +- `ruff` - also a linter that checks your code for common errors and style issues. +- `end of file fixer` - a hook that ensures that all files end with a newline. +- `check yaml` + +We are using pre-commit configuration file to define our hooks. You can find the configuration file [here](https://github.com/OSIPI/osipi/blob/main/.pre-commit-config.yaml) + +1. In the project directory, run the following command to install the `pre-commit` hooks: + + ```bash + pre-commit install + ``` + +2. You can run all pre-commit hooks on all files with: + + ```bash + pre-commit run --all-files + ``` +**NOTE:** +- Next time you commit changes, `pre-commit` will run the hooks automatically. +- Some hooks automatically fix/format your files to specific standards. If you see that some of your files have been changed after a commit, don't worry! It's just `pre-commit` doing its job. + Add the changes and commit them again. + +For more details on how to contribute, visit the [Developer Guide](https://osipi.github.io/pypi/contribution/#making-a-pull-request-pr-to-the-osipi-package). #### As mentioned before, this project is still in the early stages of development. If you'd like to contribute by adding functionality, we recommend opening an issue first to discuss your proposed functionality and the best ways to implement it. ## Details diff --git a/manage.py b/manage.py deleted file mode 100755 index d7f40f9..0000000 --- a/manage.py +++ /dev/null @@ -1,71 +0,0 @@ -import logging -import os -import sys -import venv - -# logging root configuration -logging.basicConfig( - level=logging.INFO, - format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", -) - - -def set_debug_mode(debug_mode): - if debug_mode: - logging.getLogger().setLevel(logging.DEBUG) - else: - logging.getLogger().setLevel(logging.INFO) - - -def distribute(): - """Create new version on PyPI. - - IMPORTANT! First increment your version number in pyproject.toml: - Increment the MAJOR version - when you make incompatible API changes. - Increment the MINOR version when you add functionality - in a backwards compatible manner. - Increment the PATCH version when you make backwards - compatible bug fixes. You need: PyPI username and password. You need to type in the PyPI - password rather than copy-pasting. - - """ - create_venv() - install() - - os.system(activate() + " && " + "pip install --upgrade build") - os.system(activate() + " && " + "python -m build") - os.system(activate() + " && " + "pip install --upgrade twine") - os.system(activate() + " && " + "twine upload dist/*") - - -def create_venv(): - venv_dir = os.path.join(os.getcwd(), ".venv") - if not os.path.exists(venv_dir): - logging.info("Creating virtual environment...") - os.system("py -3 -m venv .venv") - else: - logging.info("Virtual environment already exists.") - - -def activate(): - """Active virtual environment.""" - - venv_dir = os.path.join(os.getcwd(), ".venv") - os.makedirs(venv_dir, exist_ok=True) - venv.create(venv_dir, with_pip=True) - windows = (sys.platform == "win32") or (sys.platform == "win64") or (os.name == "nt") - if windows: - return os.path.join(venv_dir, "Scripts", "activate") - else: # MacOS and Linux - return '. "' + os.path.join(venv_dir, "bin", "activate") - - -def install(): - """Install requirements to a virtual environment.""" - - logging.info("Installing requirements...") - os.system(activate() + " && " + "py -m pip install -r requirements.txt") - - -if __name__ == "__main__": - # install() - set_debug_mode(debug_mode=True) - distribute() diff --git a/mkdocs.yml b/mkdocs.yml index 8c1e0b6..a742a1c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -41,7 +41,9 @@ theme: plugins: - mkdocstrings: - default_handler: python + handlers: + python: + paths: ["src"] - gallery: examples_dirs: docs/examples gallery_dirs: docs/generated/gallery diff --git a/poetry.lock b/poetry.lock index cf9709b..21802f1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -50,17 +50,6 @@ files = [ [package.extras] dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] -[[package]] -name = "backports-strenum" -version = "1.3.1" -description = "Base class for creating enumerated constants that are also subclasses of 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>>> t = np.arange(0, 6*60, 1) + >>> t = np.arange(0, 6 * 60, 1) >>> ca = osipi.aif_parker(t) - >>> plt.plot(t,ca) + >>> plt.plot(t, ca) >>> plt.show() """ @@ -107,9 +107,9 @@ def aif_georgiou(t: np.ndarray, BAT: float = 0.0) -> np.ndarray: Calculate AIF and plot - >>> t = np.arange(0, 6*60, 0.1) + >>> t = np.arange(0, 6 * 60, 0.1) >>> ca = osipi.aif_georgiou(t) - >>> plt.plot(t,ca) + >>> plt.plot(t, ca) >>> plt.show() """ @@ -161,9 +161,9 @@ def aif_weinmann(t: np.ndarray, BAT: float = 0.0) -> np.ndarray: Calculate AIF and plot - >>> t = np.arange(0, 6*60, 0.1) + >>> t = np.arange(0, 6 * 60, 0.1) >>> ca = osipi.aif_weinmann(t) - >>> plt.plot(t,ca) + >>> plt.plot(t, ca) """ diff --git a/src/osipi/_tissue.py b/src/osipi/_tissue.py index 3e9e13d..372b41c 100755 --- a/src/osipi/_tissue.py +++ b/src/osipi/_tissue.py @@ -27,8 +27,7 @@ def tofts( extravascular compartment (e). [OSIPI code Q.PH1.001.[e]] Ta (float, optional): Arterial delay time, - i.e., difference in onset time between tissue curve and AIF in units of sec. - Defaults to 30 seconds. [OSIPI code Q.PH1.007] + i.e., difference in onset time between tissue curve and AIF in units of sec. Defaults to 30 seconds. [OSIPI code Q.PH1.007] discretization_method (str, optional): Defines the discretization method. Options include – 'conv': Numerical convolution (default) [OSIPI code G.DI1.001] @@ -63,15 +62,15 @@ def tofts( Calculate AIF: - >>> t = np.arange(0, 6*60, 1) + >>> t = np.arange(0, 6 * 60, 1) >>> ca = osipi.aif_parker(t) Calculate tissue concentrations and plot: - >>> Ktrans = 0.6 # in units of 1/min - >>> ve = 0.2 # takes values from 0 to 1 + >>> Ktrans = 0.6 # in units of 1/min + >>> ve = 0.2 # takes values from 0 to 1 >>> ct = osipi.tofts(t, ca, Ktrans, ve) - >>> plt.plot(t, ca, 'r', t, ct, 'b') + >>> plt.plot(t, ca, "r", t, ct, "b") """ if not np.allclose(np.diff(t), np.diff(t)[0]): @@ -208,8 +207,7 @@ def extended_tofts( `tofts` References: - - Lexicon url: - https://osipi.github.io/OSIPI_CAPLEX/perfusionModels/#indicator-kinetic-models + - Lexicon url: https://osipi.github.io/OSIPI_CAPLEX/perfusionModels/#indicator-kinetic-models - Lexicon code: M.IC1.005 - OSIPI name: Extended Tofts Model - Adapted from contributions by: LEK_UoEdinburgh_UK, ST_USyd_AUS, MJT_UoEdinburgh_UK @@ -227,16 +225,16 @@ def extended_tofts( Calculate AIF - >>> t = np.arange(0, 6*60, 0.1) + >>> t = np.arange(0, 6 * 60, 0.1) >>> ca = osipi.aif_parker(t) Calculate tissue concentrations and plot - >>> Ktrans = 0.6 # in units of 1/min - >>> ve = 0.2 # takes values from 0 to 1 - >>> vp = 0.3 # takes values from 0 to 1 + >>> Ktrans = 0.6 # in units of 1/min + >>> ve = 0.2 # takes values from 0 to 1 + >>> vp = 0.3 # takes values from 0 to 1 >>> ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp) - >>> plt.plot(t, ca, 'r', t, ct, 'b') + >>> plt.plot(t, ca, "r", t, ct, "b") """