update environment

.github/workflows/ci.yml

@@ -2,7 +2,7 @@ name: CI
 on:
   push:
     branches:
-      - "master"
+      - "*"
   pull_request:
     branches:
       - "*"

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.6.0
   hooks:
     - id: trailing-whitespace
     - id: check-ast
@@ -10,14 +10,14 @@ repos:
     - id: check-added-large-files
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 3.9.2
+  rev: 7.0.0
   hooks:
     - id: flake8
       args: ["--max-line-length=105", "--select=C,E,F,W,B,B950", "--ignore=E203,E501,W503"]
       exclude: docs/source/conf.py
 
-- repo: https://github.com/pre-commit/mirrors-isort
-  rev: v5.10.1
+- repo: https://github.com/PyCQA/isort
+  rev: 5.13.2
   hooks:
   - id: isort
     additional_dependencies: [toml]
@@ -29,7 +29,7 @@ repos:
     - id: seed-isort-config
 
 - repo: https://github.com/psf/black
-  rev: 22.10.0
+  rev: 24.3.0
   hooks:
   - id: black
     language_version: python3

.readthedocs.yml

@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
@@ -18,7 +24,6 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
     - requirements: docs/requirements.txt
 

docs/conf.py

@@ -26,7 +26,7 @@
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-# needs_sphinx = '1.0'
+needs_sphinx = "1.4"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -74,8 +74,8 @@
 
 # link to github issues
 extlinks = {
-    "issue": ("https://github.com/GliderToolsCommunity/GliderTools/issues/%s", "GH#"),
-    "pull": ("https://github.com/GliderToolsCommunity/GliderTools/issues/%s", "GH#"),
+    "issue": ("https://github.com/GliderToolsCommunity/GliderTools/issues/%s", "GH#%s"),
+    "pull": ("https://github.com/GliderToolsCommunity/GliderTools/issues/%s", "GH#%s"),
 }
 
 # The language for content autogenerated by Sphinx. Refer to documentation

docs/requirements.txt

@@ -1,2 +1,4 @@
 glidertools
-docutils<0.18
+docutils
+recommonmark
+sphinx-rtd-theme

glidertools/cleaning.py

@@ -711,9 +711,7 @@ def savitzky_golay(var, window_size, order, deriv=0, rate=1, interpolate=True):
         y = array(arr)
 
     # precompute coefficients
-    b = mat(
-        [[k**i for i in order_range] for k in range(-half_window, half_window + 1)]
-    )
+    b = mat([[k**i for i in order_range] for k in range(-half_window, half_window + 1)])
     m = linalg.pinv(b).A[deriv] * rate**deriv * factorial(deriv)
     # pad the signal at the extremes with
     # values taken from the signal itself

glidertools/utils.py

@@ -261,9 +261,9 @@ def calc_dive_phase(time, depth, dive_depth_threshold=15):
 
     phase[velocity > 0.5] = 1  # down dive
     phase[velocity < -0.5] = 4  # up dive
-    phase[
-        (depth > dive_depth_threshold) & (velocity >= -0.5) & (velocity <= 0.5)
-    ] = 3  # inflexion
+    phase[(depth > dive_depth_threshold) & (velocity >= -0.5) & (velocity <= 0.5)] = (
+        3  # inflexion
+    )
     phase[depth <= dive_depth_threshold] = 0  # surface drift
     phase[isnan(phase)] = 6
     phase = phase.astype(int)

setup.cfg

@@ -67,6 +67,7 @@ classifiers =
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
 
 ## Add your email here
 author_email = "[email protected]"