updating 10_entropy notebook

.codecov.yaml

@@ -0,0 +1,25 @@
+comment: false
+github_checks:  # too noisy, even though "a" interactively disables them
+  annotations: false
+
+codecov:
+  notify:
+    require_ci_to_pass: false
+
+coverage:
+  status:
+    patch:
+      default:
+        informational: true
+        target: 95%
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: failure
+    project:
+      default: false
+      library:
+        informational: true
+        target: 90%
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: failure

.github/workflows/code-style.yml → .github/workflows/code-style.yaml

@@ -2,7 +2,7 @@ name: style
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
   cancel-in-progress: true
-on:
+on:  # yamllint disable-line rule:truthy
   pull_request:
   push:
     branches: [main]
@@ -14,32 +14,36 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Python 3.9
         uses: actions/setup-python@v4
         with:
           python-version: '3.9'
           architecture: 'x64'
       - name: Install dependencies
         run: |
-          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off .[style]
-      - name: Run Ruff
-        run: ruff check pycrostates
       - name: Run isort
         uses: isort/isort-action@master
       - name: Run black
         uses: psf/black@stable
         with:
           options: "--check --verbose"
+      - name: Run Ruff
+        run: ruff check pycrostates
       - name: Run codespell
         uses: codespell-project/actions-codespell@master
         with:
           check_filenames: true
           check_hidden: true
-          skip: ./.git,./build,./.github,*.bib
+          skip: ./.git,./build,./.github,*.bib,./.mypy_cache,./.pytest_cache
           ignore_words_file: ./.codespellignore
       - name: Run pydocstyle
         run: pydocstyle .
       - name: Run bibclean
         run: bibclean-check docs/references.bib
+      - name: Run toml-sort
+        run: toml-sort pyproject.toml --check
+      - name: Run yamllint
+        run: yamllint . -c .yamllint.yaml --strict

.github/workflows/publish.yml → .github/workflows/publish.yaml

@@ -1,6 +1,6 @@
 name: publish
 
-on:
+on:  # yamllint disable-line rule:truthy
   release:
     types: [published]
   workflow_dispatch:
@@ -11,15 +11,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Python 3.9
         uses: actions/setup-python@v4
         with:
           python-version: '3.9'
           architecture: 'x64'
       - name: Install dependencies
         run: |
-          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off .[build]
       - name: Build and publish
         env:

.github/workflows/pytest.yaml

@@ -0,0 +1,109 @@
+name: pytest
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+  push:
+    branches: [main]
+  workflow_dispatch:
+  schedule:
+    - cron: '0 8 * * 1'
+
+jobs:
+  pytest:
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu, macos, windows]
+        python-version: [3.9, "3.10", "3.11", "3.12"]
+    name: ${{ matrix.os }} - py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: 'x64'
+      - name: Install package
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools
+          python -m pip install --progress-bar off .[test]
+      - name: Display system information
+        run: pycrostates-sys_info --developer
+      - name: Display MNE info
+        run: mne sys_info -pd
+      - name: Get testing dataset version
+        run: |
+          curl https://raw.githubusercontent.com/mne-tools/mne-testing-data/master/version.txt -o mne_testing_data_version.txt
+      - name: Cache testing dataset
+        uses: actions/cache@v3
+        with:
+          key: mne-testing-${{ hashFiles('mne_testing_data_version.txt') }}
+          path: ~/mne_data
+      - name: Download testing dataset
+        run: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
+      - name: Run pytest
+        run: pytest pycrostates --cov=pycrostates --cov-report=xml --cov-config=pyproject.toml
+      - name: Upload to codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+          flags: unittests  # optional
+          name: codecov-umbrella  # optional
+          verbose: true  # optional (default = false)
+
+  pytest-pip-pre:
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11"]
+    name: pip pre-release - py${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools
+          python -m pip install --progress-bar off .[test]
+          python -m pip install --progress-bar off --upgrade git+https://github.com/mne-tools/mne-python
+          python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy scipy scikit-learn matplotlib
+      - name: Display system information
+        run: pycrostates-sys_info --developer
+      - name: Display MNE info
+        run: mne sys_info -pd
+      - name: Get testing dataset version
+        run: |
+          curl https://raw.githubusercontent.com/mne-tools/mne-testing-data/master/version.txt -o mne_testing_data_version.txt
+      - name: Cache testing dataset
+        uses: actions/cache@v3
+        with:
+          key: mne-testing-${{ hashFiles('mne_testing_data_version.txt') }}
+          path: ~/mne_data
+      - name: Download testing dataset
+        run: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
+      - name: Run pytest
+        run: pytest pycrostates --cov=pycrostates --cov-report=xml --cov-config=pyproject.toml
+      - name: Upload to codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+          flags: unittests  # optional
+          name: codecov-umbrella  # optional
+          verbose: true  # optional (default = false)

.pre-commit-config.yaml

@@ -0,0 +1,56 @@
+ci:
+    skip: [codespell, pydocstyle, yamllint]
+
+repos:
+    - repo: https://github.com/pycqa/isort
+      rev: 5.12.0
+      hooks:
+          - id: isort
+            files: pycrostates
+
+    - repo: https://github.com/psf/black-pre-commit-mirror
+      rev: 23.10.1
+      hooks:
+          - id: black
+            args: [--quiet]
+            files: pycrostates
+
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.1.4
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix]
+            files: pycrostates
+
+    - repo: https://github.com/codespell-project/codespell
+      rev: v2.2.6
+      hooks:
+          - id: codespell
+            args: [--check-filenames, --ignore-words=.codespellignore, --skip=*.bib]
+
+    - repo: https://github.com/pycqa/pydocstyle
+      rev: 6.3.0
+      hooks:
+          - id: pydocstyle
+            files: pycrostates
+            additional_dependencies: [tomli]
+
+    - repo: https://github.com/mscheltienne/bibclean
+      rev: 0.7.1
+      hooks:
+          - id: bibclean-fix
+            files: docs/references.bib
+            args: [--exit-non-zero-on-fix]
+
+    - repo: https://github.com/pappasam/toml-sort
+      rev: v0.23.1
+      hooks:
+          - id: toml-sort-fix
+            files: pyproject.toml
+
+    - repo: https://github.com/adrienverge/yamllint
+      rev: v1.32.0
+      hooks:
+          - id: yamllint
+            args: [--strict, -c, .yamllint.yaml]
+            files: (.github/|.codecov.yaml|.pre-commit-config.yaml|.prospector.yaml|.readthedocs.yaml)

.prospector.yaml

@@ -28,4 +28,4 @@ pep257:
 
 pylint:
   disable:
-    - too-many-arguments
+    - too-many-arguments

.readthedocs.yml → .readthedocs.yaml

@@ -7,22 +7,19 @@ version: 2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
+   builder: html
    configuration: docs/source/conf.py
+   fail_on_warning: true
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
    install:
-   - method: pip
-     path: .
-     extra_requirements:
-       - docs
+      - method: pip
+        path: .
+        extra_requirements:
+           - docs
 
 build:
-  os: ubuntu-20.04
-  tools:
-    python: "3.8"
-
-sphinx:
-  builder: html
-  configuration: docs/source/conf.py
-  fail_on_warning: true
+   os: ubuntu-20.04
+   tools:
+      python: "3.10"

.yamllint.yaml

@@ -0,0 +1,5 @@
+extends: default
+
+rules:
+  line-length: disable
+  document-start: disable

README.md

@@ -2,7 +2,7 @@
 [![PyPI version](https://badge.fury.io/py/pycrostates.svg)](https://badge.fury.io/py/pycrostates)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/pycrostates.svg)](https://anaconda.org/conda-forge/pycrostates)
 [![Documentation Status](https://readthedocs.org/projects/pycrostates/badge/?version=latest)](https://pycrostates.readthedocs.io/en/latest/?badge=latest)
-[![Build Status](https://dev.azure.com/vferat/pycrostates/_apis/build/status/vferat.pycrostates?branchName=main)](https://dev.azure.com/vferat/pycrostates/_build/latest?definitionId=1&branchName=main)
+[![tests](https://github.com/vferat/pycrostates/actions/workflows/pytest.yaml/badge.svg?branch=main)](https://github.com/vferat/pycrostates/actions/workflows/pytest.yaml)
 [![codecov](https://codecov.io/gh/vferat/pycrostates/branch/master/graph/badge.svg?token=47COGGCGX8)](https://codecov.io/gh/vferat/pycrostates)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/029e425f90614943b0a944e03922b637)](https://www.codacy.com/gh/vferat/pycrostates/dashboard?utm_source=github.com&utm_medium=referral&utm_content=vferat/pycrostates&utm_campaign=Badge_Grade)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.04564/status.svg)](https://doi.org/10.21105/joss.04564)
@@ -38,7 +38,7 @@ To cite specific version numbers of the software, you can use the DOIs provided
 by [Zenodo](https://zenodo.org/record/7129852).
 
 ## Contributing
-
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/vferat/pycrostates/main.svg)](https://results.pre-commit.ci/latest/github/vferat/pycrostates/main)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->