Merge branch 'master' into device_branch

.github/workflows/cd.yml

@@ -31,7 +31,7 @@ jobs:
       - name: Build sdist and wheel
         run: pipx run build
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: dist
 
@@ -45,11 +45,11 @@ jobs:
     permissions:
       id-token: write
     steps:
-      - uses: actions/setup-python@v4.7.0
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: '3.10'
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist
@@ -58,7 +58,7 @@ jobs:
           ls -ltrh
           ls -ltrh dist
       - name: Publish to Test PyPI
-        uses: pypa/[email protected].10
+        uses: pypa/[email protected].14
         with:
           repository-url: https://test.pypi.org/legacy/
           verbose: true
@@ -92,10 +92,10 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist
 
-      - uses: pypa/[email protected].10
+      - uses: pypa/[email protected].14
         if: startsWith(github.ref, 'refs/tags')

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11"]  # add this back later: , "3.12"
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
         experimental: [false, false, true]
 
@@ -33,18 +33,18 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           allow-prereleases: true
 
       - name: Install package
-        run: python -m pip install .[test]
+        run: python -m pip install .[dev]
 
       - name: Test package
         run: >-
           python -m pytest -ra --cov --cov-report=xml --cov-report=term
           --durations=20
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.1.0

.readthedocs.yaml

@@ -15,4 +15,4 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        - docs
+        - dev

README.md

@@ -3,6 +3,7 @@
 [![ssec](https://img.shields.io/badge/SSEC-Project-purple?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAA0AAAAOCAQAAABedl5ZAAAACXBIWXMAAAHKAAABygHMtnUxAAAAGXRFWHRTb2Z0d2FyZQB3d3cuaW5rc2NhcGUub3Jnm+48GgAAAMNJREFUGBltwcEqwwEcAOAfc1F2sNsOTqSlNUopSv5jW1YzHHYY/6YtLa1Jy4mbl3Bz8QIeyKM4fMaUxr4vZnEpjWnmLMSYCysxTcddhF25+EvJia5hhCudULAePyRalvUteXIfBgYxJufRuaKuprKsbDjVUrUj40FNQ11PTzEmrCmrevPhRcVQai8m1PRVvOPZgX2JttWYsGhD3atbHWcyUqX4oqDtJkJiJHUYv+R1JbaNHJmP/+Q1HLu2GbNoSm3Ft0+Y1YMdPSTSwQAAAABJRU5ErkJggg==&style=plastic)](https://escience.washington.edu/wetai/)
 [![MIT License](https://badgen.net/badge/license/MIT/blue)](LICENSE)
 [![Documentation Status](https://readthedocs.org/projects/braingeneers/badge/?version=latest)](https://braingeneers.readthedocs.io/en/latest/?badge=latest)
+[![DOI](https://zenodo.org/badge/166130153.svg)](https://zenodo.org/badge/latestdoi/166130153)
 
 ## Getting Started
 
@@ -38,10 +39,22 @@ pip install --force-reinstall git+https://github.com/braingeneers/braingeneerspy
 
 You can install `braingeneerspy` with specific optional dependencies based on your needs. Use the following command examples:
 
-- Install with IoT, analysis, and data access functions (skips machine learning and lab-specific dependencies):
+- Install with machine-learning dependencies:
 
 ```bash
-pip install "braingeneers[iot,analysis,data]"
+pip install "braingeneers[ml]"
+```
+
+- Install with Hengen lab dependencies:
+
+```bash
+pip install "braingeneers[hengenlab]"
+```
+
+- Install with developer dependencies (running tests and building sphinx docs):
+
+```bash
+pip install "braingeneers[dev]"
 ```
 
 - Install with all optional dependencies:
@@ -52,7 +65,7 @@ pip install "braingeneers[all]"
 
 ## Committing Changes to the Repo
 
-To make changes and publish them on GitHub, please refer to the [CONTRIBUTING.md](https://github.com/braingeneers/braingeneerspy/blob/development/.github/CONTRIBUTING.md) file for up-to-date guidelines.
+To make changes and publish them on GitHub, please refer to the [CONTRIBUTING.md](https://github.com/braingeneers/braingeneerspy/blob/master/.github/CONTRIBUTING.md) file for up-to-date guidelines.
 
 ## Modules and Subpackages
 

braingeneers/data/test_data/maxwell-metadata.expected.json

@@ -172,4 +172,4 @@
             "data_format": "NeurodataWithoutBorders"
         }
     }
-}
+}

braingeneers/data/test_data/maxwell-metadata.old.json

@@ -171,4 +171,4 @@
             ]
         }
     }
-}
+}

src/braingeneers/_version.py

@@ -0,0 +1,2 @@
+__version__ = version = '0.0.0.dev0'
+__version_tuple__ = version_tuple = (0, 0, 0, 'dev0')