Merge pull request #259 from rsagroup/publishing

Publishing from CI

.github/workflows/publish.yml

@@ -0,0 +1,41 @@
+
+
+name: Publish
+
+on:
+  push:
+    branches:
+      - main
+  release:
+     types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  call-test-build:
+    uses: ./.github/workflows/testbuild.yml
+
+  publish-artifacts:
+    environment: production
+    needs: call-test-build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download all  artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: artifacts
+      - name: List files
+        run: ls -R artifacts
+      - name: Gather artifacts
+        run: |
+          mkdir dist
+          mv artifacts/source/*.tar.gz dist/
+          mv artifacts/wheels-macos-latest/*.whl dist/
+          mv artifacts/wheels-ubuntu-latest/*.whl dist/
+          mv artifacts/wheels-windows-latest/*.whl dist/
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v1.5.1
+        with:
+          verbose: true
+          password: ${{ secrets.API_TOKEN_PYPI }}

.github/workflows/pull_request.yml → .github/workflows/testbuild.yml

@@ -1,15 +1,21 @@
-name: pull_request_builds
+name: Test and Build
 
 on:
   pull_request:
     types: [opened, synchronize, reopened]
+  workflow_call:
+
+permissions:
+  contents: read
 
 jobs:
 
   tests:
     runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
     - uses: actions/setup-python@v4
       with:
         python-version: '3.10'
@@ -35,6 +41,8 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
     - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
@@ -58,6 +66,10 @@ jobs:
       run: pip install -r tests/requirements.txt
     - name: Unit tests
       run: pytest
+    - name: Check package compliance
+      run: |
+        pip install -q twine
+        twine check dist/*
     - name: Store artifact
       uses: actions/upload-artifact@v3
       with:
@@ -74,6 +86,8 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
     - uses: actions/setup-python@v4
       with:
         python-version: '3.10'
@@ -85,8 +99,10 @@ jobs:
       uses: pypa/cibuildwheel@v2.11.1
       with:
         output-dir: dist
-    - name: Install test dependencies
-      run: pip install -r tests/requirements.txt
+    - name: Check package compliance
+      run: |
+        pip install -q twine
+        twine check dist/*
     - name: Store artifact
       uses: actions/upload-artifact@v3
       with:

CONTRIBUTING.md

@@ -8,6 +8,12 @@ Your cycle
 5. When you're done with the feature, ask for reviews from two team members or ask the maintainers for help.
 6. When the reviewers have approved the Pull Request, they will merge it into the master branch. At this point you want to checkout the master branch again and pull so that you have your latest changes, and can open a new branch for a new feature. 
 
+Here is an example shell command to build rsatoolbox, install it in your environment, and run the unit tests on it, in one go:
+
+```sh
+python -m build && sleep 1 && pip install --pre --force-reinstall dist/*.whl && pytest
+```
+
 
 Rules
 =====
@@ -22,6 +28,14 @@ Rules
 or alternatively, ping @ilogue or @HeikoSchuett and we will assign reviewers.
 
 
+Deployment
+==========
+
+
+- when a PR is merged into the branch main, it is build as a pre-release (or "development") package and uploaded to pypi. The latest pre-release version can be installed using `pip install --pre rsatoolbox`
+- when a release tag is added to the branch main, the package is instead marked as a released (or "stable") version.
+
+
 Naming scheme
 =============
 

README.md

@@ -14,12 +14,13 @@ Conceived during the RSA retreat 2019 in Blue Mountains.
 
 #### Getting Started
 
-The easiest way to install rsatoolbox is with pip:
+To install the latest stable version of rsatoolbox with pip:
 
 ```sh
 pip install rsatoolbox
 ```
 
+
 here is a simple code sample:
 
 ```python

docs/source/conf.py

@@ -14,6 +14,7 @@
 #
 import os
 import sys
+from pkg_resources import get_distribution
 sys.path.insert(0, os.path.abspath('.'))
 sys.path.insert(0, os.path.abspath('../'))
 
@@ -23,10 +24,11 @@
 copyright = '2021, rsatoolbox authors'
 author = 'rsatoolbox authors'
 
+# The full version
+release = get_distribution('rsatoolbox').version
+
 # The short X.Y version
-version = '0.0'
-# The full version, including alpha/beta/rc tags
-release = '0.0.5'
+version = '.'.join(release.split('.')[:2])
 
 
 # -- General configuration ---------------------------------------------------

docs/source/getting_started.rst

@@ -3,12 +3,20 @@
 Getting started
 ===============
 
-The easiest way to install rsatoolbox is with pip:
+To install the latest release of rsatoolbox:
 
 .. code-block:: sh
 
     pip install rsatoolbox
 
+
+To get the bleeding edge or "pre-release" version:
+
+.. code-block:: sh
+
+    pip install --pre rsatoolbox
+
+
 To use rsatoolbox:
 
 .. code-block:: python

pyproject.toml

@@ -1,23 +1,23 @@
 [build-system]
 requires = [
     "setuptools~=65.3",
-    "setuptools-scm",
+    "setuptools-scm[toml]~=7.0.0",
     "wheel",
     "numpy>=1.21.2",
     "scipy",
-    "cython~=3.0.0a11"
+    "cython~=3.0.0a11",
+    "twine~=4.0.1"
 ]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "rsatoolbox"
 description = "Representational Similarity Analysis (RSA) in Python"
 requires-python = ">=3.7,<3.11"
-version = "0.0.5"
 authors = [
     {name="rsatoolbox authors"},
 ]
-keywords = ["neuroscience "]
+keywords = ["neuroscience"]
 license = {file = "LICENSE"}
 classifiers = [
       'Programming Language :: Python',
@@ -31,11 +31,17 @@ classifiers = [
       'Programming Language :: Python :: 3.9',
       'Programming Language :: Python :: 3.10',
 ]
-dynamic = ["readme", "dependencies"]
+dynamic = ["readme", "dependencies", "version"]
 
-[tool.setuptools]
-packages = ["rsatoolbox"]
-package-dir = {"" = "src"}
+[project.urls]
+homepage = "https://github.com/rsagroup/rsatoolbox"
+documentation = "https://rsatoolbox.readthedocs.io/"
+
+[tool.setuptools_scm]
+local_scheme = "no-local-version"
+
+[tool.setuptools.packages.find]
+where = ["src"]
 
 [tool.setuptools.dynamic]
 readme = {file = "README.md"}

setup.py

@@ -1,17 +1,14 @@
+"""Setup.py now only remains as a build script for the cython extensions.
+Using setup.py for other things is now deprecated:
+    setup.py test -> pytest
+    setup.py develop -> pip install -e
+"""
 from setuptools import setup, Extension
-from Cython.Build import build_ext ## missing dev time req
-from os.path import isfile
+import setuptools_scm  # noqa # pylint: disable=unused-import
+from Cython.Build import build_ext
 
-test_requires = []
-if isfile('tests/requirements.txt'):
-    with open('tests/requirements.txt') as reqfile:
-        test_requires = reqfile.read().splitlines()
 
 setup(
-    tests_require=test_requires,
-    test_suite='tests',
-    url = "https://github.com/rsagroup/rsatoolbox",
-    zip_safe = False,
     ext_modules = [
         Extension(
             "rsatoolbox.cengine.similarity",