Merge branch 'master' into dev1

* master: (23 commits)
  Rm deprecated
  Fixes
  Bump version
  Rm and demote less interesting exc
  Fix mpl issue
  Fix coverage
  Improve format
  Autoformat
  Test up to py312
  Autoformat
  Revise dependencies
  Use "upstream" pathos/dill for MP
  Fix MP
  Autoformat
  Comment, tiny
  Clean pyproject of flake8/autopep
  Sync ipynb
  Format via ruff in pre-commit
  Ruff isort
  amend
  ...

.github/workflows/tests.yml

@@ -8,39 +8,38 @@ on:
       - dev1
       - "!gh-pages"
 env:
-  IS_CI: 'true'
+  IS_CI: "true"
 
 jobs:
-
   bundled:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.9', '3.10', '3.11']
-        jobtype: ['test']
+        os: ["ubuntu-latest"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"] # NB: also see versions for 'conda'
+        jobtype: ["test"]
         include:
-          - os: 'ubuntu-latest'
-            python-version: '3.10'
-            jobtype: 'lint'
-          - os: 'ubuntu-latest'
-            python-version: '3.10'
-            jobtype: 'coverage'
-          - os: 'macos-latest'
-            python-version: '3.10'
-            jobtype: 'test'
+          - os: "ubuntu-latest"
+            python-version: "3.10"
+            jobtype: "lint"
+          - os: "ubuntu-latest"
+            python-version: "3.10"
+            jobtype: "coverage"
+          - os: "macos-latest"
+            python-version: "3.10"
+            jobtype: "test"
     env:
       JOBTYPE: ${{ matrix.jobtype }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'setup.py'
+          cache: "pip"
+          cache-dependency-path: "setup.py"
 
       - name: Install dependencies
         run: |
@@ -69,22 +68,22 @@ jobs:
 
   conda:
     defaults:
-          run:
-            shell: bash -el {0}
+      run:
+        shell: bash -el {0}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.9', '3.10', '3.11']
+        os: ["ubuntu-latest"]
+        python-version: ["3.9", "3.12"]
         include:
-          - os: 'macos-latest'
-            python-version: '3.10'
-          - os: 'windows-latest'
-            python-version: '3.9'
+          - os: "macos-latest"
+            python-version: "3.12"
+          - os: "windows-latest"
+            python-version: "3.12"
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -29,24 +29,8 @@ repos:
     -   id: mixed-line-ending
         args: ['--fix=no']
 
--   repo: https://github.com/flakeheaven/flakeheaven
-    rev: 3.2.1
-    hooks:
-    -   id: flakeheaven
-        additional_dependencies: [
-          flake8-docstrings,
-          flake8-bugbear,
-          flake8-comprehensions,
-          flake8-isort,
-          flake8-builtins,
-          pep8-naming,
-        ]
-
--   repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
-    hooks:
-    -   id: isort
-        exclude: |
-            (?x)^(
-                examples/.*.py
-            )$
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.0
+  hooks:
+    - id: ruff
+    - id: ruff-format

README.md

@@ -98,12 +98,12 @@ open the [Anaconda terminal](https://docs.conda.io/projects/conda/en/latest/user
 and run the following commands:
 
 ```sh
-conda create --yes --name dapper-env python=3.9
+conda create --yes --name dapper-env python=3.12
 conda activate dapper-env
 python --version
 ```
 
-Ensure the printed version is 3.9 or more.  
+Ensure the printed version is as desired.
 *Keep using the same terminal for the commands below.*
 
 ### Install

conftest.py

@@ -1,4 +1,5 @@
 """Configures pytest (beyond the ini file)."""
+
 import matplotlib as mpl
 import numpy
 import pytest

dapper/__init__.py

@@ -4,7 +4,7 @@
 .. include:: ./README.md
 """
 
-__version__ = "1.6.0"
+__version__ = "1.7.0"
 
 # A parsimonious list of imports used in the examples
 from .dpr_config import rc

dapper/da_methods/__init__.py

@@ -2,6 +2,7 @@
 
 .. include:: ./README.md
 """
+
 from pathlib import Path
 
 
@@ -82,7 +83,7 @@ def dataclass_with_defaults(cls):
         def set_field(name, type_, val):
             """Set the inherited (i.e. default, i.e. has value) field."""
             # Ensure annotations
-            cls.__annotations__ = getattr(cls, '__annotations__', {})
+            cls.__annotations__ = getattr(cls, "__annotations__", {})
             # Set annotation
             cls.__annotations__[name] = type_
             # Set value
@@ -102,7 +103,7 @@ def set_field(name, type_, val):
         # Define the new assimilate method (has bells and whistles)
         def assimilate(self, HMM, xx, yy, desc=None, fail_gently=False, **stat_kwargs):
             # Progressbar name
-            pb_name_hook = self.da_method if desc is None else desc # noqa
+            pb_name_hook = self.da_method if desc is None else desc  # noqa
 
             # Init stats
             self.stats = dapper.stats.Stats(self, HMM, xx, yy, **stat_kwargs)
@@ -120,27 +121,30 @@ def assimilate(self, HMM, xx, yy, desc=None, fail_gently=False, **stat_kwargs):
                     # Don't use _print_cropped_traceback here -- It would
                     # crop out errors in the DAPPER infrastructure itself.
                     raise
-            self.stat("duration", time.time()-time0)
+            self.stat("duration", time.time() - time0)
 
         # Overwrite the assimilate method with the new one
         try:
             _assimilate = cls.assimilate
         except AttributeError as error:
             raise AttributeError(
                 "Classes decorated by da_method()"
-                " must define a method called 'assimilate'.") from error
+                " must define a method called 'assimilate'."
+            ) from error
         cls.assimilate = functools.wraps(_assimilate)(assimilate)
 
         # Shortcut for register_stat
         def stat(self, name, value):
             dapper.stats.register_stat(self.stats, name, value)
+
         cls.stat = stat
 
         # Make self.__class__.__name__ an attrib.
         # Used by xpList.table_prep().
         cls.da_method = cls.__name__
 
         return cls
+
     return dataclass_with_defaults
 
 
@@ -155,15 +159,17 @@ def crop_traceback(ERR):
         msg = "Traceback (most recent call last):\n"
         try:
             # If in IPython, use its coloring functionality
-            __IPYTHON__  # type: ignore
+            __IPYTHON__  # type: ignore # noqa: B018
         except (NameError, ImportError):
             msg += "".join(traceback.format_tb(ERR.__traceback__))
         else:
             from IPython.core.debugger import Pdb
+
             pdb_instance = Pdb()
             pdb_instance.curframe = inspect.currentframe()
 
             import dapper.da_methods
+
             keep = False
             for frame in traceback.walk_tb(ERR.__traceback__):
                 if keep:
@@ -175,10 +181,12 @@ def crop_traceback(ERR):
         return msg
 
     msg = crop_traceback(ERR) + "\nError message: " + str(ERR)
-    msg += ("\n\nResuming execution."
-            "\nIf instead you wish to raise the exceptions as usual,"
-            "\nwhich will halt the execution (and enable post-mortem debug),"
-            "\nthen use `fail_gently=False`")
+    msg += (
+        "\n\nResuming execution."
+        "\nIf instead you wish to raise the exceptions as usual,"
+        "\nwhich will halt the execution (and enable post-mortem debug),"
+        "\nthen use `fail_gently=False`"
+    )
     print(msg, file=sys.stderr)