Merge branch 'master' of https://github.com/braingeneers/braingeneerspy…

… into maxwell_gpio

.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]
 
@@ -39,7 +39,7 @@ jobs:
           allow-prereleases: true
 
       - name: Install package
-        run: python -m pip install .[test]
+        run: python -m pip install .[dev]
 
       - name: Test package
         run: >-

.readthedocs.yaml

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

README.md

@@ -39,10 +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:
@@ -53,7 +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
 

pyproject.toml

@@ -6,7 +6,12 @@ build-backend = "hatchling.build"
 [project]
 name = "braingeneers"
 authors = [
-  { name = "Braingeneers", email = "[email protected]" },
+  { name = "UCSC Braingeneers", email = "[email protected]" },
+]
+maintainers = [
+  { name = "David", email = "[email protected]" },
+  { name = "Alex", email = "[email protected]" },
+  { name = "Lon", email = "[email protected]" },
 ]
 description = "Braingeneers Python utilities"
 readme = "README.md"
@@ -27,12 +32,25 @@ classifiers = [
 ]
 dynamic = ["version"]
 dependencies = [
-  "typing_extensions >=4.6; python_version<'3.11'",
-  'deprecated',
-  'requests',
-  'numpy',
-  'tenacity',
-  'boto3',
+    'awswrangler==3.*',
+    'boto3',
+    'braingeneers-smart-open==2023.10.6',
+    'deprecated',
+    'h5py',
+    'matplotlib',
+    'nptyping',
+    'numpy',
+    'paho-mqtt',
+    'pandas',
+    'powerlaw',
+    'redis',
+    'requests',
+    'schedule',
+    'scipy>=1.10.0',
+    'tenacity',
+    "typing_extensions>=4.6; python_version<'3.11'",
+    'diskcache',
+    'pytz'
 ]
 
 [tool.hatch.build.hooks.vcs]
@@ -43,35 +61,9 @@ local_scheme = "no-local-version"
 
 [project.optional-dependencies]
 all = [
-  'braingeneers[data]',
-  'braingeneers[analysis]',
   'braingeneers[ml]',
-  'braingeneers[iot]',
   'braingeneers[hengenlab]',
-  'braingeneers[test]',
-  'braingeneers[docs]',
-]
-data = [
-  'h5py',
-  'braingeneers-smart-open==2023.10.6',  # 'smart_open>=5.1.0',  the hash version fixes the bytes from-to range header issue.
-  'awswrangler==3.*',
-  'pandas',
-  'nptyping',
-  'paho-mqtt'
-]
-iot = [
-  'redis',
-  'schedule',
-  'paho-mqtt'
-]
-analysis = [
-  'scipy>=1.10.0',
-  'pandas',
-  'powerlaw',
-  'matplotlib',
-  # Both of these dependencies are required for read_phy_files
-  'awswrangler==3.*',
-  'braingeneers-smart-open==2023.10.6',  # 'smart_open>=5.1.0',  the hash version fixes the bytes from-to range header issue.
+  'braingeneers[dev]',
 ]
 ml = [
   'torch',
@@ -80,11 +72,9 @@ ml = [
 hengenlab = [
   'neuraltoolkit==0.3.1',  # channel mapping information
 ]
-test = [
+dev = [
   "pytest >=6",
   "pytest-cov >=3",
-]
-docs = [
   "sphinx>=4.0",
   "myst_parser>=0.13",
   "sphinx_book_theme>=0.1.0",

src/braingeneers/utils/configure.py

@@ -13,60 +13,6 @@
 CURRENT_ENDPOINT = None
 _open = None  # a reference to the current smart_open function that is configured this should not be used directly
 
-"""
-Define all groups of dependencies here. `minimal` dependencies are always installed with
-the braingeneerspy package, all other groups of dependencies will be installed
-braingeneerspy[all] or braingeneerspy[specific_dependency_group]
-Maintainers are encouraged to move dependencies to specific dependency groups and keep
-`minimal` as small as possible. `minimal` would typically be used in a RaspberryPI
-environment for example, where large dependencies can be very slow to build.
-"""
-DEPENDENCIES = {
-    # Minimal dependencies are always installed with a pip install of the repo
-    'minimal': [
-        'deprecated',
-        'requests',
-        'numpy',
-        'tenacity',
-        # 'sortedcontainers',
-        'boto3',
-        'joblib>=1.3.0,<2',
-        'braingeneers_smart_open',  # 'smart_open>=5.1.0',  the hash version fixes the bytes from-to range header issue.
-        'awswrangler==3.*',
-    ],
-    'data': [
-        'h5py',
-        'pandas',
-        'nptyping',
-        'paho-mqtt',
-    ],
-    # Specific dependency groups allow unnecessary (and often large) dependencies to be skipped
-    # add dependency groups here, changes will be dynamically added to setup(...)
-    'iot': [
-        # 'awsiotsdk==1.6.0',  # dependency issues occur when the current version is installed, that may be resolvable
-        'redis',
-        'schedule',
-        'paho-mqtt',
-        'diskcache',
-        'pytz',
-        'tzlocal',
-    ],
-    'analysis': [
-        'scipy>=1.10.0',
-        'pandas',
-        'powerlaw',
-        'matplotlib',
-    ],
-    'ml': [
-        'torch',
-        'scikit-learn',
-    ],
-    'hengenlab': [
-        'neuraltoolkit @ git+https://github.com/hengenlab/neuraltoolkit.git',  # channel mapping information
-    ],
-}
-
-
 def get_default_endpoint() -> str:
     """
     Returns the current default (S3) endpoint. By default this will point to the standard