Switch to pyproject.toml package setup (#306)

* Switch to pyproject.toml package setup

* Add keywords to pyproject.toml

* Add flake8 exclude paths

* Update dependencies to match new minimum versions

* Fix setuptools_scm problem displaying version number in conda list

* Minimum version constraint for optional cupy dependency

* Link to contributors page on github

* Fix typo, readme file is RST format

* Update pyproject.toml

Co-authored-by: jakirkham <[email protected]>

* Update pyproject.toml

Co-authored-by: jakirkham <[email protected]>

* Update pyproject.toml

Co-authored-by: jakirkham <[email protected]>

* Update pyproject.toml

Co-authored-by: jakirkham <[email protected]>

* Update pyproject.toml

Co-authored-by: jakirkham <[email protected]>

* Update pyproject.toml

Co-authored-by: jakirkham <[email protected]>

* Update pyproject.toml

Co-authored-by: jakirkham <[email protected]>

* Use 'python -m build', instead of 'python setup.py sdist bdist_wheel'

* Add python3.12 classifier for PyPI

* Replace versioneer with setuptools-scm (simpler to maintain, better long term support)

* Install python build tool with pip, conda-forge versions are out-of-date

* Add pytest-timeout dependency to environment files (otherwise pytest timeout mark will not be recognised)

* Update contributing guide, drop setup.py and use pip install instead

* Try to fix readthedocs getting the  dask-image version string

* Update installation guide to use pip, not setup.py

* Update dependency versions in pyproject.toml

* Install dask-image with pip, not setup.py, for GPU CI tests

* Update some parts of the Makefule for GPU CI tests (removing setup.py)

* ReadTheDocs must install dask_image package

* Add twine to dependencies, update Makefile away from setup.py

---------

Co-authored-by: jakirkham <[email protected]>
Co-authored-by: Marvin Albert <[email protected]>

.coveragerc

@@ -22,7 +22,6 @@ omit =
     */eggs/*
     */.eggs/*
     *tests/*
-    */versioneer.py
     */_version.py
     */_vendor/*
     */dispatch/*

.github/workflows/test_and_deploy.yml

@@ -81,11 +81,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build twine
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         twine upload dist/*

.gitignore

@@ -1,3 +1,6 @@
+# setuptools-scm dynamically generated version
+dask_image/_version.py
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

CONTRIBUTING.rst

@@ -84,12 +84,13 @@ Ready to contribute? Here's how to set up `dask-image` for local development.
 2. Clone your fork locally::
 
     $ git clone [email protected]:your_name_here/dask-image.git
+    $ cd dask-image
 
 3. Install your local copy into an environment. Assuming you have conda installed, this is how you set up your fork for local development (on Windows drop `source`). Replace `"<some version>"` with the Python version used for testing.::
 
     $ conda create -n dask-image-env python="<some version>"
     $ source activate dask-image-env
-    $ python setup.py develop
+    $ python -m pip install -e .
 
 4. Create a branch for local development::
 
@@ -100,7 +101,7 @@ Ready to contribute? Here's how to set up `dask-image` for local development.
 5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions::
 
     $ flake8 dask_image tests
-    $ python setup.py test or py.test
+    $ pytest
 
    To get flake8, just conda install it into your environment.
 
@@ -164,7 +165,7 @@ Finally, install the development version of dask-image::
 
 .. code-block:: console
 
-    $ pip install -e .
+    $ pip install -e ".[test]""
 
 For local testing, please run ``pytest`` in the test environment::
 

MANIFEST.in

@@ -10,5 +10,4 @@ recursive-exclude * *.py[co]
 
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
 
-include versioneer.py
 include dask_image/_version.py

Makefile

@@ -51,13 +51,14 @@ lint: ## check style with flake8
 	flake8 dask_image tests
 
 test: ## run tests quickly with the default Python
-	python setup.py test
+	python -m pip install ".[test]"
+	pytest
 
 test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source dask_image setup.py test
+	coverage run -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
@@ -71,13 +72,13 @@ docs: ## generate Sphinx HTML documentation, including API docs
 	$(BROWSER) docs/_build/html/index.html
 
 release: clean ## package and upload a release
-	python setup.py sdist upload
-	python setup.py bdist_wheel upload
+	python -m build
+	ls -l dist
+	twine upload dist/*
 
 dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
+	python -m build
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages
-	python setup.py install
+	python -m pip install .

continuous_integration/environment-3.10.yml

@@ -6,16 +6,19 @@ channels:
 dependencies:
   - python=3.10.*
   - pip==23.0.1
-  - wheel==0.38.4
   - coverage==7.2.1
   - flake8==6.0.0
   - pytest==7.2.2
   - pytest-cov==4.0.0
   - pytest-flake8==1.1.1
+  - pytest-timeout >=2.3.1
   - dask==2024.4.1
   - numpy==1.24.2
   - scipy==1.10.1
   - scikit-image==0.19.3
   - pims==0.6.1
   - slicerator==1.1.0
   - pandas==2.0.0
+  - twine==5.0.0
+  - pip:
+    - build==1.2.1

continuous_integration/environment-3.11.yml

@@ -6,16 +6,19 @@ channels:
 dependencies:
   - python=3.11.*
   - pip==23.0.1
-  - wheel==0.38.4
   - coverage==7.2.1
   - flake8==6.0.0
   - pytest==7.2.2
   - pytest-cov==4.0.0
   - pytest-flake8==1.1.1
+  - pytest-timeout >=2.3.1
   - dask==2024.4.1
   - numpy==1.24.2
   - scipy==1.10.1
   - scikit-image==0.19.3
   - pims==0.6.1
   - slicerator==1.1.0
   - pandas==2.0.0
+  - twine==5.0.0
+  - pip:
+    - build==1.2.1

continuous_integration/environment-3.12.yml

@@ -6,16 +6,19 @@ channels:
 dependencies:
   - python=3.12.*
   - pip==24.0
-  - wheel==0.43.0
   - coverage==7.5.1
   - flake8==7.0.0
   - pytest==8.2.0
   - pytest-cov==5.0.0
   - pytest-flake8==1.1.1
+  - pytest-timeout >=2.3.1
   - dask==2024.4.1
   - numpy==1.26.4
   - scipy==1.13.0
   - scikit-image==0.22.0
   - pims==0.6.1
   - slicerator==1.1.0
   - pandas==2.2.2
+  - twine==5.0.0
+  - pip:
+    - build==1.2.1

continuous_integration/environment-3.9.yml

@@ -6,16 +6,19 @@ channels:
 dependencies:
   - python=3.9.*
   - pip==24.0
-  - wheel==0.43.0
   - coverage==7.5.1
   - flake8==7.0.0
   - pytest==8.2.0
   - pytest-cov==5.0.0
   - pytest-flake8==1.1.1
+  - pytest-timeout >=2.3.1
   - dask==2024.4.1
   - numpy==1.26.4
   - scipy==1.13.0
   - scikit-image==0.22.0
   - pims==0.6.1
   - slicerator==1.1.0
   - pandas==2.2.2
+  - twine==5.0.0
+  - pip:
+    - build==1.2.1

continuous_integration/environment-doc.yml

@@ -6,7 +6,6 @@ channels:
 dependencies:
   - python=3.9.*
   - pip==22.3
-  - wheel==0.37.1
   - jinja2<3.1
   - dask==2024.4.1
   - numpy==1.23.4
@@ -16,6 +15,8 @@ dependencies:
   - slicerator==1.1.0
   - pandas==2.0.0
   - pip:
+    - build==1.2.1
+    - ..  # install dask_image from this repository source
     # FIXME: This workaround is required until we have sphinx>=5, as enabled by
     #        dask-sphinx-theme no longer pinning sphinx-book-theme==0.2.0. This is
     #        tracked in https://github.com/dask/dask-sphinx-theme/issues/68.

continuous_integration/gpuci/build.sh

@@ -44,7 +44,7 @@ rapids-logger "Install cupy"
 python -m pip install cupy-cuda112 -f https://pip.cupy.dev/pre
 
 rapids-logger "Install dask-image"
-python setup.py install
+python -m pip install .
 
 rapids-logger "Check Python versions"
 python --version

dask_image/__init__.py

@@ -1,8 +0,0 @@
-# -*- coding: utf-8 -*-
-from ._version import get_versions
-
-__version__ = get_versions()['version']
-del get_versions
-
-from . import _version
-__version__ = _version.get_versions()['version']