Merge branch 'netneurolab:master' into fix-deprecation

.codecov.yml

@@ -0,0 +1,11 @@
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
+comment: false
+github_checks:
+    annotations: false

.github/workflows/docker-release.yml

@@ -0,0 +1,47 @@
+name: publish-docker-image
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - 'main'
+    tags:
+      - '*'
+
+jobs:
+  push_to_registry:
+    if: github.repository_owner == 'netneurolab'
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v1.14.1
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_PASSWORD }}
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v1.14.1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v3.8.0
+        with:
+          images: |
+            ${{ secrets.DOCKER_HUB_USERNAME }}/netneurotools
+            ghcr.io/netneurolab/netneurotools
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v2.10.0
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/docs.yml

@@ -0,0 +1,39 @@
+name: netneurotools-docs
+
+on: 
+  workflow_dispatch:
+  push:
+      branches:
+      - main
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  deploy_page:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          pip install -r docs/requirements.txt
+      - name: Install netneurotools
+        run: |
+          pip install .
+      - name: Build the docs
+        run: |
+          cd docs && make clean html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+        with:
+            path: 'docs/_build/html'
+      - name: Deploy to GitHub Pages
+        uses: actions/deploy-pages@v2

.github/workflows/tests.yml

@@ -1,10 +1,10 @@
-name: netneurotools tests
+name: netneurotools-tests
 
 on: 
   workflow_dispatch:
   push:
     branches:
-      - main
+      - master
   pull_request:
 
 jobs:
@@ -22,9 +22,9 @@ jobs:
       - name: Install dependencies
         run: |
             python -m pip install --upgrade pip
-            python -m pip install flake8
+            python -m pip install ruff
       - name: Run style checks
-        run: flake8 netneurotools
+        run: ruff .
 
   run_tests:
     needs: check_style
@@ -50,9 +50,13 @@ jobs:
           python -m pip install pytest pytest-cov
           python -m pip install -r requirements.txt
       - name: Install netneurotools
-        run: python -m pip install -e .
+        run: python -m pip install .
       - name: Print netneurotools version
         run: python -c "import netneurotools; print(netneurotools.__version__)" 
+      - name: Test submodule import
+        run: |
+          cd ..
+          python -c "from netneurotools import metrics; from netneurotools.datasets import fetch_cammoun2012"
       - name: Run tests
         run: pytest --doctest-modules --cov=netneurotools --cov-report=xml --junitxml=junit/test-results.xml --verbose --pyargs netneurotools
       - name: Upload coverage

Dockerfile

@@ -0,0 +1,17 @@
+FROM python:3.9.7-slim
+
+RUN apt-get update \
+    && apt-get install -y \
+        wget \
+        unzip \
+        libgl1-mesa-glx \
+        libglu1-mesa \
+        libgomp1 \
+        libglib2.0-0
+
+COPY . netneurotools
+
+RUN cd netneurotools \
+    && python3 -m pip install '.[numba]'
+
+CMD python3

README.rst

@@ -1,20 +1,35 @@
 netneurotools: Tools for network neuroscience
 =============================================
 
+|
+
+.. .. image:: https://zenodo.org/badge/375755159.svg
+..    :target: https://zenodo.org/badge/latestdoi/375755159
+..    :alt: Zenodo record
+
+.. image:: https://img.shields.io/pypi/v/netneurotools
+   :target: https://pypi.python.org/pypi/netneurotools/
+   :alt: Latest PyPI version
+
+.. image:: https://img.shields.io/badge/docker-netneurolab/netneurotools-brightgreen.svg?logo=docker&style=flat
+  :target: https://hub.docker.com/r/netneurolab/netneurotools/tags/
+  :alt: Latest Docker image
+
+.. image:: https://github.com/netneurolab/netneurotools/actions/workflows/tests.yml/badge.svg
+  :target: https://github.com/netneurolab/netneurotools/actions/workflows/tests.yml
+  :alt: run-tests status
+
+.. image:: https://github.com/netneurolab/netneurotools/actions/workflows/docs.yml/badge.svg
+  :target: https://netneurolab.github.io/netneurotools/
+  :alt: deploy-docs status
+
+|
+
 This toolbox is a collection of functions written in Python that get frequent
 usage in the `Network Neuroscience Lab <netneurolab.github.io/>`_, housed in
 the `Brain Imaging Centre <https://www.mcgill.ca/bic/home>`_ at
 `McGill University <https://www.mcgill.ca/>`_.
 
-.. image:: https://github.com/netneurolab/netneurotools/actions/workflows/tests.yml/badge.svg
-   :target: https://github.com/netneurolab/netneurotools/actions
-.. image:: https://codecov.io/gh/netneurolab/netneurotools/branch/master/graph/badge.svg
-   :target: https://codecov.io/gh/netneurolab/netneurotools
-.. image:: https://readthedocs.org/projects/netneurotools/badge/?version=latest
-   :target: https://netneurotools.readthedocs.io/en/latest
-.. image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
-   :target: https://opensource.org/licenses/BSD-3-Clause
-
 .. _installation:
 
 Installation

docs/conf.py

@@ -15,7 +15,7 @@
 
 # Add project name, copyright holder, and author(s)
 project = 'netneurotools'
-copyright = '2018-2022, netneurotools developers'
+copyright = '2018-2024, netneurotools developers'
 author = 'Network Neuroscience Lab'
 
 # Import project to get version info