Update to match neurodatascience/nipoppy:main (#53)

.flake8

@@ -8,7 +8,14 @@ exclude =
 	venv,
 per-file-ignores =
     # - docstrings rules that should not be applied to tests
-	tests/*: D100, D103, D104
+	**/test_*: D100, D103, D104
+    __init__.py:F401
     # allow "weird indentation"
 	tests/test_workflow_*.py: D100, D103, D104, E131, E127, E501
-max-line-length = 90
+docstring-convention = numpy
+max_complexity = 12
+max_function_length = 150
+# for compatibility with black
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8
+max-line-length = 88
+extend-ignore = D105, E203, E704

.github/workflows/run_tests_new.yml

@@ -0,0 +1,49 @@
+---
+name: Run tests
+
+on:
+  push:
+    branches: ['*']
+  pull_request:
+    branches: ['*']
+
+# cancel previous runs if new one is triggered
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  test:
+
+    runs-on: ubuntu-latest
+
+    # only trigger on upstream repo
+    if: github.repository_owner == 'neurodatascience' && github.event.repository.name == 'nipoppy'
+
+    steps:
+
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install package
+      run: |
+        cd nipoppy_cli
+        pip install -U pip
+        pip install .[tests]
+
+    - name: Run tests
+      run: |
+        python -m pytest nipoppy_cli --cov=nipoppy_cli/nipoppy --cov-report=xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        name: codecov-umbrella
+        token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -30,3 +30,6 @@ htmlcov
 
 
 env/
+
+# VS Code
+.vscode/

.pre-commit-config.yaml

@@ -3,9 +3,8 @@
 # See https://pre-commit.com/hooks.html for more hooks
 
 repos:
-
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: check-ast
     -   id: check-case-conflict
@@ -15,9 +14,23 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
     -   id: check-toml
-
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.12.1
+    hooks:
+    -   id: black
+        args: [--config=pyproject.toml]
+-   repo: https://github.com/pyCQA/flake8
+    rev: 7.0.0
+    hooks:
+    -   id: flake8
+        args: [--verbose, --config, .flake8]
+        additional_dependencies: [flake8-docstrings]
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
     -   id: codespell
         args: [--toml=pyproject.toml]

nipoppy_cli/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 NeuroDataScience
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

nipoppy_cli/README.md

@@ -0,0 +1,26 @@
+![License](https://img.shields.io/badge/license-MIT-blue.svg)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8084759.svg)](https://doi.org/10.5281/zenodo.8084759)
+![https://github.com/psf/black](https://img.shields.io/badge/code%20style-black-000000.svg)
+
+# Nipoppy
+
+A framework for standardized organization and processing of neuroimaging-clinical datasets.
+
+## Developer setup
+
+Clone this repo:
+
+```bash
+git clone https://github.com/neurodatascience/nipoppy.git
+```
+
+Install `nipoppy` in editable mode with `dev` dependencies:
+```bash
+cd nipoppy
+pip install -e .[dev]
+```
+
+Set up `pre-commit`:
+```bash
+pre-commit install
+```

nipoppy_cli/nipoppy/__init__.py

@@ -0,0 +1 @@
+"""Nipoppy."""

nipoppy_cli/nipoppy/base.py

@@ -0,0 +1,71 @@
+"""Base class."""
+
+import inspect
+from abc import ABC
+from typing import Optional, Sequence
+
+
+class Base(ABC):
+    """Base class with utilities for pretty string representations."""
+
+    def _str_helper(
+        self,
+        components: Optional[Sequence] = None,
+        names: Optional[Sequence[str]] = None,
+        sep=", ",
+    ) -> str:
+        """Generate a custom string representation of an object.
+
+        The output string is of the form: ClassName(component1[sep]component2[sep]...)
+
+        Parameters
+        ----------
+        components : Sequence, optional
+            Components to concatenate, by default None
+        names : Sequence[str], optional
+            Name of attributes to be added to the components as key-value pairs,
+            by default None
+        sep : str, optional
+            Separator between components, by default ", "
+
+        Returns
+        -------
+        str
+            String representation of the object.
+        """
+        if components is None:
+            components = []
+
+        if names is not None:
+            for name in names:
+                components.append(f"{name}={getattr(self, name)}")
+
+        return f"{type(self).__name__}({sep.join([str(c) for c in components])})"
+
+    def __str__(self) -> str:
+        """Return a string representation of the object based on its __init__ arguments.
+
+        Raises
+        ------
+        RuntimeError
+            If the parameter names obtained from the __init__ method do not match the
+            attributes of the object.
+        """
+        signature = inspect.signature(type(self))
+        names = [
+            name
+            for name, parameter in signature.parameters.items()
+            if parameter.kind is inspect.Parameter.POSITIONAL_OR_KEYWORD
+        ]
+        try:
+            return self._str_helper(names=names)
+        except AttributeError:
+            raise RuntimeError(
+                f"The __init__ method of the {type(self)} class has positional and/or"
+                " keyword arguments that are not set as attributes of the object"
+                ". Failed to build string representation: need to override the"
+                " __str__ method"
+            )
+
+    def __repr__(self) -> str:
+        return self.__str__()

nipoppy_cli/nipoppy/cli/__init__.py

@@ -0,0 +1 @@
+"""Parsers and entrypoint for the command-line interface."""