Merge pull request #13 from SFB-ELAINE/LeadDBS_integration

Lead-DBS integration

.github/workflows/ci.yml

@@ -0,0 +1,54 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+jobs:
+  check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          # if running a cron job, we add the --pre flag to test against pre-releases
+          python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+# TODO add release

.gitignore

@@ -10,18 +10,22 @@ dist/
 *.egg-info/
 _build/
 docs/._*
+Results*/
+.idea/
+.ipynb_checkpoints/
 
 # Ignore file
+*.vol.gz
 *.pyc
 .coverage
 .coveragerc
 *.vtu
 .DS_Store
-
-case*/
 ng.ini
-
 *.swp
-test_cases/input_case2/micro_probes_SNEX100_custom.json
-input_files/impedance.csv
+impedance.csv
 *checkpoints.ipynb
+*.nii.gz
+*.nii
+success_*.txt
+fail_*.txt

.gitlab-ci.yml

@@ -10,17 +10,18 @@ stages:
     - pip install virtualenv
     - virtualenv venv
     - source venv/bin/activate
-    - pip install tox
-    - tox -e $PYTHONVERSION
+    - pip install ".[test]"
+    - pytest
 
 .run:
   script:
    - pip install virtualenv
    - virtualenv venv
    - source venv/bin/activate
-   - pip install .
+   - pip install "."
    - cd input_files
    - ossdbs 'inputTest.json'
+   - ossdbs 'input_cc.json'
 
 test-3.8:
    extends: ".test"

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+# enable pre-commit.ci at https://pre-commit.ci/
+# it adds:
+# 1. auto fixing pull requests
+# 2. auto updating the pre-commit configuration
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.13
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.282
+    hooks:
+      - id: ruff
+        args: [--fix]
+
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black

MANIFEST.in

@@ -1 +1,19 @@
-include requirements.txt
+recursive-include docs *.dia
+recursive-include docs *.ipynb
+recursive-include docs *.md
+recursive-include docs *.py
+recursive-include docs *.rst
+recursive-include docs *.svg
+recursive-include docs *.txt
+recursive-include docs Makefile
+recursive-include examples *.ipynb
+recursive-include examples *.json
+recursive-include examples *.md
+recursive-include examples *.py
+recursive-include input_files *.gz
+recursive-include input_files *.h5
+recursive-include input_files *.json
+recursive-include input_test_cases *.json
+recursive-include input_test_cases *.md
+recursive-include input_test_cases *.sh
+recursive-include ossdbs *.py

README.md

@@ -1,7 +1,9 @@
 OSS-DBSv2
 =========
 
-This is a first draft of the OSS-DBS rebuild.
+This is the development version of the OSS-DBS rewrite.
+Use with caution and please wait for the first official release before deploying it.
+Bug reports are highly welcome, though!
 
 
 Installation
@@ -16,6 +18,30 @@ To install OSS-DBS, clone it into a local directory,
 pip install -e .
 ```
 
+To also run the test suite of OSS-DBS, run
+
+```
+pip install -e ".[test]"
+```
+
+To develop OSS-DBS, run
+
+```
+pip install -e ".[dev]"
+```
+
+To locally build the docs of OSS-DBS, run
+
+```
+pip install -e ".[doc]"
+```
+
+To do everything of the above, run
+
+```
+pip install -e ".[all]"
+```
+
 Run OSS-DBS
 -----------
 
@@ -26,4 +52,21 @@ and start the simulation with
 ossdbs input.json
 ```
 
-Also check out the `examples` directory and the documentation.
+Also check out the `examples` directory and the documentation.
+
+Development
+-----------
+
+The code uses the `input_files` and `tests` directories to check the functionality
+upon each commit. If you add a new feature, please add a test to `tests`.
+Make sure that the test does not run long and does not consume much memory.
+It shall be rather a unit test than a full simulation run.
+Likewise, only change `input_files` after opening an issue.
+
+The `examples` directory is meant for users to understand what has been implemented.
+Place heavy and/or experimental code there (e.g., code that may crash or consume many resources).
+
+The code development follows different coding styles that are checked
+by git pre-commit hooks.
+Install `pre-commit` via `pip install pre-commit` and run
+`pre-commit install` to activate it.