Merge pull request #1 from BrkRaw/main

brkraw catchup

.dockerignore

@@ -0,0 +1,19 @@
+.github
+
+*.pyc
+
+env
+
+**/__pycache__
+**/.pytest_cache
+
+.idea/**
+
+**/dist
+**/build
+**/*.egg-info*
+
+tests/*
+paper
+
+.DS_Store

.flake8

@@ -0,0 +1,10 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+	env,
+	venv,
+max-line-length = 127
+max-complexity=10

.github/workflows/autotest.yml

@@ -1,4 +1,4 @@
-name: CI workflow
+name: test
 
 on:
   # this workflow triggered on below condition [push, pull_request]

.github/workflows/main.yml → .github/workflows/flake8.yml

@@ -1,31 +1,32 @@
-name: CI workflow
+name: flake8
 
 on:
   # this workflow triggered on below condition [push, pull_request]
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ '*' ]
+
+# cancel previous similar workflow runs
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.5, 3.6, 3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up python ${{ matrix.python-version }}
+    - name: Set up python
       uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: "3.11"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install flake8
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.github/workflows/validation.yml

@@ -0,0 +1,24 @@
+---
+name: validation
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  validate_cff:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Check whether the citation metadata from CITATION.cff is valid
+      uses: citation-file-format/cffconvert-github-action@2.0.0
+      with:
+        args: --validate
+

CITATION.cff

@@ -0,0 +1,49 @@
+cff-version: 1.2.0
+
+title: "brkraw"
+
+version: "0.3.10"
+
+abstract: Bruker PvDataset Loader
+
+message: "If you use this software, please cite it as below."
+
+repository-code: "https://github.com/BrkRaw/brkraw"
+
+identifiers:
+  - description: This is the collection of archived snapshots of all releases
+    type: doi
+    value: "10.5281/zenodo.245546149"
+
+contact:
+  - email: shlee@unc.edu
+    family-names: SungHo 
+    given-names: Lee
+
+authors:
+  - email: shlee@unc.edu
+    family-names: SungHo 
+    given-names: Lee
+
+  - email: banwoomi@unc.edu
+    family-names: Woomi  
+    given-names: Ban
+
+  - family-names: Dumas 
+    given-names: Jaiden
+
+  - family-names: Devenyi 
+    given-names: Gabriel A.
+
+  - email: shihy@neurology.unc.edu
+    family-names: Yen-Yu
+    given-names: Ian Shih
+
+license: GPL-3.0
+
+keywords:
+  - bruker
+  - data_handler
+  - converter
+  - administrator_tool
+  - brain imaging data structure

CONTRIBUTING.md

@@ -1,3 +1,17 @@
-Here is how to contribute.
+# Contributing
 
-TODO:
+When contributing to this repository, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change. 
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+## Pull Request Process
+
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a 
+   build.
+2. Update the README.md with details of changes to the interface, this includes new environment 
+   variables, exposed ports, useful file locations and container parameters.
+3. Increase the version numbers in any examples files and the README.md to the new version that this
+   Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
+4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you 
+   do not have permission to do that, you may request the second reviewer to merge it for you.

Dockerfile.dev

@@ -1,12 +1,12 @@
 # This docker file build a editable image.
 # You could directly edit the source code at `/home/brkraw to make changes. Or you could mount your brkraw code folder to /home/brkraw
 
-FROM python:3.7
+FROM python:3.11
 WORKDIR /home
 RUN mkdir ./brkraw
 WORKDIR /home/brkraw
 COPY . .
-RUN python -m pip install -e /home/brkraw
+RUN python -m pip install --editable /home/brkraw
 RUN mkdir /data
 WORKDIR /data