Merge pull request #85 from Remi-Gau/prep_release

[MNT] prepare for pypi release

Author: Remi-Gau

.github/workflows/check_md_links.yml

@@ -0,0 +1,21 @@
+name: Check Markdown links
+
+# checking for any dead links in markdown files
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches: ['*']
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        use-quiet-mode: 'yes'
+        use-verbose-mode: 'yes'
+        # config-file: '.github/workflows/mlc_config.json'

.github/workflows/package.yml

@@ -0,0 +1,59 @@
+name: Packaging
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  package:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+
+    # Build packages and upload
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python-version: "3.9"
+
+    steps:
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install build
+        run: python -m pip install build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Test PyPI upload
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+          skip_existing: true
+
+      - name: Upload to PyPI (on tags)
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test_and_coverage.yml

@@ -6,14 +6,18 @@ on:
   pull_request:
     branches: [ "*" ]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test_and_coverage:
 
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest]
-        python-version: ['3.8', '3.9']
+        os: [ubuntu-latest, macOS-latest] # windows-latest: does not work because antspyx is not available for windows
+        python-version: ["3.8", "3.9", "3.10"] # '3.11' : some dependencies are not yet available for python 3.11
 
     steps:
 

.github/workflows/test_demo.yml

@@ -6,6 +6,10 @@ on:
   pull_request:
     branches: [ "*" ]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test_demo:
 

.pre-commit-config.yaml

@@ -21,7 +21,6 @@ repos:
         -   id: flake8
             exclude: tests_.*.py|version.*.py|setup.py # ignore tests and versioneer related code
 
-
     - repo: https://github.com/ikamensh/flynt/
       rev: "0.77"
       hooks:

.readthedocs.yml

@@ -17,7 +17,7 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
+  version: "3.8"
   install:
     - method: pip
       path: .

.vscode/settings.json

@@ -1,14 +1,15 @@
 {
-    "makefile.extensionOutputFolder": "./.vscode",
-    "cSpell.words": [
-        "bidsmreye",
-        "bidsname",
-        "bidsutils",
-        "coregister",
-        "coregistration",
-        "eyemask",
-        "filefolder"
-    ],
-    "autoDocstring.docstringFormat": "sphinx",
-    "esbonio.sphinx.confDir": ""
+  "makefile.extensionOutputFolder": "./.vscode",
+  "cSpell.words": [
+    "bidsmreye",
+    "bidsname",
+    "bidsutils",
+    "coregister",
+    "coregistration",
+    "eyemask",
+    "filefolder"
+  ],
+  "autoDocstring.docstringFormat": "sphinx",
+  "esbonio.sphinx.confDir": "",
+  "githubPullRequests.ignoredPullRequestBranches": ["main"]
 }

CONTRIBUTING.md

@@ -7,14 +7,11 @@
         - [Submit Feedback](#submit-feedback)
     - [Get Started!](#get-started)
     - [Pull Request Guidelines](#pull-request-guidelines)
-    - [Tips](#tips)
-    - [Deploying](#deploying)
-    - [Docker recipe](#docker-recipe)
 
 # CONTRIBUTING
 
-Contributions are welcome, and they are greatly appreciated!
-Every little bit helps, and credit will always be given.
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
 
 You can contribute in many ways:
 
@@ -26,35 +23,37 @@ Report bugs at https://github.com/cpp-lln-lab/bidsmreye/issues.
 
 If you are reporting a bug, please include:
 
--   Your operating system name and version.
--   Any details about your local setup that might be helpful in troubleshooting.
--   Detailed steps to reproduce the bug.
+- Your operating system name and version.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug.
 
 ### Fix Bugs
 
-Look through the GitHub issues for bugs.
-Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
 
 ### Implement Features
 
-Look through the GitHub issues for features.
-Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
 
 ### Write Documentation
 
-bidsMReye could always use more documentation,
-whether as part of the official bidsMReye docs, in docstrings,
-or even on the web in blog posts, articles, and such.
+bidsMReye could always use more documentation, whether as part of the official
+bidsMReye docs, in docstrings, or even on the web in blog posts, articles, and
+such.
 
 ### Submit Feedback
 
-The best way to send feedback is to file an issue at https://github.com/cpp-lln-lab/bidsmreye/issues.
+The best way to send feedback is to file an issue at
+https://github.com/cpp-lln-lab/bidsmreye/issues.
 
 If you are proposing a feature:
 
--   Explain in detail how it would work.
--   Keep the scope as narrow as possible, to make it easier to implement.
--   Remember that this is a volunteer-driven project, and that contributions are welcome :)
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- Remember that this is a volunteer-driven project, and that contributions are
+  welcome :)
 
 ## Get Started!
 
@@ -67,12 +66,15 @@ Ready to contribute? Here's how to set up `bidsmreye` for local development.
 git clone [email protected]:your_name_here/bidsmreye.git
 ```
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
+3. Install your local copy into a virtualenv. Assuming you have
+   virtualenvwrapper installed, this is how you set up your fork for local
+   development:
 
 ```bash
 mkvirtualenv bidsmreye
 cd bidsmreye/
-python setup.py develop
+pip install -e .[dev]
+```
 ```
 
 1. Create a branch for local development:
@@ -87,9 +89,8 @@ Now you can make your changes locally.
    tests, including testing other Python versions with tox:
 
 ```bash
-flake8 bidsmreye tests
-python setup.py test or pytest
-tox
+make lint
+make test
 ```
 
 To get flake8 and tox, just pip install them into your virtualenv.
@@ -109,65 +110,9 @@ git push origin name-of-your-bugfix-or-feature
 Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests.
-2. If the pull request adds functionality, the docs should be updated. Put
-   your new functionality into a function with a docstring, and add the
-   feature to the list in README.rst.
+2. If the pull request adds functionality, the docs should be updated. Put your
+   new functionality into a function with a docstring, and add the feature to
+   the list in README.rst.
 3. The pull request should work for Python 3.8, and for PyPy. Check
-   https://travis-ci.com/Remi-Gau/bidsmreye/pull_requests
-   and make sure that the tests pass for all supported Python versions.
-
-## Tips
-
-To run a subset of tests:
-
-```bash
-pytest tests.test_bidsmreye
-```
-
-## Deploying
-
-A reminder for the maintainers on how to deploy.
-Make sure all your changes are committed (including an entry in HISTORY.rst).
-
-Then run
-
-```bash
-bump2version patch # possible: major / minor / patch
-git push
-git push --tags
-```
-
-Travis will then deploy to PyPI if tests pass.
-
-## Docker recipe
-
-Made using neurodocker
-
-```bash
-docker run --rm repronim/neurodocker:0.7.0 generate docker \
-    --base debian:bullseye-slim \
-    --pkg-manager apt \
-    --install "git wget" \
-    --miniconda \
-        version="latest" \
-        create_env="deepmreye" \
-        conda_install="python=3.7 pip" \
-        pip_install="git+https://github.com/DeepMReye/DeepMReye.git" \
-        activate="true" \
-    --run "mkdir -p /inputs/models" \
-    --run "wget https://osf.io/cqf74/download -O /inputs/models/dataset1_guided_fixations.h5" \
-    --output Dockerfile
-```
-
-Build image
-
-```bash
-docker build --tag deepmreye:0.1.0 --file Dockerfile .
-```
-
-Run it
-
-```bash
-docker run -it --rm \
-    deepmreye:0.1.0
-```
+   https://github.com/cpp-lln-lab/bidsMReye/actions and make sure that the
+   tests pass for all supported Python versions.

Makefile

@@ -50,10 +50,6 @@ clean-test: ## remove test and coverage artifacts
 
 ## INSTALL
 
-install: clean  ## install the package to the active Python's site-packages
-	pip install .
-	make models
-
 install_dev: clean ## install the package and development dependencies to the active Python's site-packages
 	pip install -e .[dev]
 	make models
@@ -215,7 +211,7 @@ docker/Dockerfile: ## Dockerfile for the bidsmreye docker image
 	--base debian:stretch-slim \
 	--pkg-manager apt \
 	--install "git wget" \
-	--run "mkdir -p /home/neuro/bidsMReye" \
+	--run "mkdir -p /home/neuro/bidsMReye/models" \
 	--workdir /home/neuro/bidsMReye \
  	--run "wget -q https://osf.io/download/cqf74/ -O models/dataset1_guided_fixations.h5" \
 	--run "wget -q https://osf.io/download/4f6m7/ -O models/dataset2_pursuit.h5" \
@@ -236,7 +232,7 @@ docker/Dockerfile: ## Dockerfile for the bidsmreye docker image
 docker_build: docker/Dockerfile
 	docker build --tag cpplab/bidsmreye:latest --file docker/Dockerfile .
 
-docker/Dockerfile_dev: ## Dockerfile for the bidsmreye docker image using local pacakge
+docker/Dockerfile_dev: ## Dockerfile for the bidsmreye docker image using local package
 	docker run --rm repronim/neurodocker:0.7.0 generate docker \
 	--base debian:stretch-slim \
 	--pkg-manager apt \