Merge branch 'BrkRaw:main' into main

.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/dependabot.yml

@@ -0,0 +1,9 @@
+---
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+-   package-ecosystem: github-actions
+    directory: /
+    schedule:
+        interval: monthly

.github/workflows/autotest.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 }}
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up python
+      uses: actions/setup-python@v5
       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/test.yml

@@ -0,0 +1,81 @@
+name: test
+
+on:
+  # this workflow triggered on below condition [push, pull_request]
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ "*" ]
+
+# cancel previous similar workflow runs
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test_cli:
+
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+      fail-fast: false
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+
+    - uses: actions/checkout@v4
+
+    - name: Set up python ${{ matrix.python-version }}
+
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+
+    - name: Version and help
+      run: |
+        brkraw --version
+        brkraw --help
+
+    - name: "smoke end-to-end test: use CLI on tutorial data"
+      run: make demo
+
+
+  test_tutorial:
+
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+      fail-fast: false
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+
+    - uses: actions/checkout@v4
+
+    - name: Set up python ${{ matrix.python-version }}
+
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[dev]
+
+    - name: Install tutorial
+      run: make tests/tutorials
+
+    - name: Test tutorial notebook
+      run: |
+        python -m pytest --nbmake tests/tutorials/JupyterNotebooks/01_GettingStarted.ipynb
+        tree tests/tutorials/raw

.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@v4
+    - name: Check whether the citation metadata from CITATION.cff is valid
+      uses: citation-file-format/cffconvert-github-action@2.0.0
+      with:
+        args: --validate
+

.gitignore

@@ -8,8 +8,7 @@ ui/styles/*.css
 dist
 build
 *.pid
-test
-test/*
 *.egg-info
 *.egg-info/*
-.DS_Store
+.DS_Store
+tests/tutorials

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
 

Makefile

@@ -0,0 +1,21 @@
+clean:
+	rm -rf tests/tutorials
+
+tests/tutorials:
+	git clone https://github.com/BrkRaw/tutorials.git tests/tutorials
+
+tests/tutorials/SampleData/20190724_114946_BRKRAW_1_1: tests/tutorials
+	unzip -uq tests/tutorials/SampleData/20190724_114946_BRKRAW_1_1.zip -d tests/tutorials/SampleData/
+
+tests/tutorials/bids_map.csv: tests/tutorials/SampleData/20190724_114946_BRKRAW_1_1
+	brkraw bids_helper tests/tutorials/SampleData/20190724_114946_BRKRAW_1_1 \
+						tests/tutorials/bids_map
+
+tests/tutorials/raw: tests/tutorials/bids_map.csv
+	brkraw bids_convert tests/tutorials/SampleData/20190724_114946_BRKRAW_1_1 \
+						tests/tutorials/bids_map.csv \
+						--output tests/tutorials/raw
+
+demo: tests/tutorials
+	brkraw info tests/tutorials/SampleData/20190724_114946_BRKRAW_1_1.zip
+	make tests/tutorials/raw

brkraw/lib/pvobj.py

@@ -37,8 +37,8 @@ def _update_studyinfo(self):
             subject = self._subject
             self.user_account   = subject.headers['OWNER']
             self.subj_id        = get_value(subject, 'SUBJECT_id')
-            self.study_id       = get_value(subject, 'SUBJECT_study_nr')
-            self.session_id     = get_value(subject, 'SUBJECT_study_name')
+            self.study_id       = get_value(subject, 'SUBJECT_study_name')
+            self.session_id     = get_value(subject, 'SUBJECT_study_nr')
 
             # [20210820] Add-paravision 360 related.
             title = subject.headers['TITLE']