Adding in CI (#25)

* added install workflow
* update lock file, fix python versions
* lock numpy to 1.26.4
* add status badge

.github/workflows/build-package-install.yaml

@@ -0,0 +1,60 @@
+name: Build and Install
+
+on:
+    push:
+        branches:
+            - '**'
+
+jobs:
+    build-install:
+        runs-on: ${{ matrix.os }}
+        strategy:
+          matrix:
+            os: [ubuntu-latest]
+            python-version: ["3.9", "3.10", "3.11"]
+
+        steps:
+          - name: Checkout repository
+            uses: actions/checkout@v2
+
+          - name: Set up Python
+            uses: actions/setup-python@v2
+            with:
+              python-version: ${{ matrix.python-version }}
+
+          - name: Check python3 == python${{ matrix.python-version }}
+            run: |
+              installed_python=$(python3 --version)
+              echo "Installed Python: $installed_python"
+              if [[ "$installed_python" != *"${{ matrix.python-version }}"* ]]; then
+                echo "Python version mismatch. Expected: ${{ matrix.python-version }}, but got: $installed_python"
+                exit 1
+              else
+                echo "${{ matrix.python-version }}"
+              fi
+
+
+          - name: Install Poetry
+            run: |
+              curl -sSL https://install.python-poetry.org | python3 -
+
+          - name: Install dependencies
+            run: |
+              python3 -m pip install setuptools
+              poetry install --with dev
+
+          - name: Package with Poetry
+            run: |
+              # clear out dist folder first
+              rm -rf dist
+              poetry build
+
+          - name: Install Built Package
+            run: |
+              python3 -m pip install dist/*.whl
+
+          - name: Test Installation
+            run: |
+              petprep_extract_tacs --version
+              merge_tacs --help
+

Makefile

@@ -19,3 +19,10 @@ dockerbuild:
 dockerpush: dockerbuild
 	docker push openneuropet/$(shell cat pyproject.toml | grep name | cut -d '"' -f 2):$(shell cat pyproject.toml | grep version | head -n 1 | cut -d '"' -f 2)
 	docker push openneuropet/$(shell cat pyproject.toml | grep name | cut -d '"' -f 2):latest
+
+# runs github actions ci locally using nektos/act
+# needs to be installed with brew install act on mac
+# install instructions for other platforms can be found here:
+# https://nektosact.com/installation/index.html
+ci:
+	act push

README.md

@@ -1,5 +1,9 @@
 # BIDS App for PETPrep Extract Time Activity Curves Workflow
 
+---
+
+[![Build and Install](https://github.com/mnoergaard/petprep_extract_tacs/actions/workflows/build-package-install.yaml/badge.svg)](https://github.com/mnoergaard/petprep_extract_tacs/actions/workflows/build-package-install.yaml)
+
 ## Overview
 
 This BIDS App is designed to extract time activity curves (TACs) from PET data. The workflow has options to extract TACs from different regions of the brain, and it uses the Brain Imaging Data Structure (BIDS) standard for organizing and describing the data. This README will guide you through how to use the app and the various options available. The workflow requires that freesurfer's recon-all was already executed for these subjects, and exist as a 'freesurfer' directory inside the derivatives directory for the given BIDS dataset.