Replace setup.py with pyproject toml (#617)

This MR is on top of #615 and #616 so those should be reviewed and merged first. Currently `run build_python_package` will be in a broken state. Authors: - Gregory Lee (https://github.com/grlee77) Approvers: - Gigon Bae (https://github.com/gigony) - Ray Douglass (https://github.com/raydouglass) - https://github.com/jakirkham URL: #617
rapidsai · Oct 27, 2023 · 1589a0d · 1589a0d
1 parent d489bb3
commit 1589a0d
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,23 +15,22 @@ repos:
     hooks:
       - id: isort
         files: ^python/cucim/src/.*
-        args: ["--settings-path=python/cucim/pyproject_.toml"]
+        args: ["--settings-path=python/cucim/pyproject.toml"]
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:
       - id: black
         files: (python|legate)/.*
-        args: ["--config", "python/cucim/pyproject_.toml"]
+        args: ["--config", "python/cucim/pyproject.toml"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.0.278
     hooks:
       - id: ruff
         files: python/.*$
-        args: ["--exclude", "__init__.py"]
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.4
     hooks:
       - id: codespell
-        args: ["--toml", "python/cucim/pyproject_.toml"]
+        args: ["--toml", "python/cucim/pyproject.toml"]
         additional_dependencies:
           - tomli
diff --git a/ci/release/update-version.sh b/ci/release/update-version.sh
@@ -34,6 +34,7 @@ function sed_runner() {
 sed_runner 's/version = .*/version = '"'${NEXT_SHORT_TAG}'"'/g' docs/source/conf.py
 sed_runner 's/release = .*/release = '"'${NEXT_FULL_TAG}'"'/g' docs/source/conf.py
 
+sed_runner "s/^version = .*/version = \"${NEXT_FULL_TAG}\"/g" python/cucim/pyproject.toml
 sed_runner "s/${CURRENT_LONG_TAG}/${NEXT_FULL_TAG}/g" VERSION
 sed_runner "s/${CURRENT_LONG_TAG}/${NEXT_FULL_TAG}/g" python/cucim/VERSION
 sed_runner "s/__version__ = .*/__version__ = \"${NEXT_FULL_TAG}\"/g" python/cucim/src/cucim/__init__.pyi

diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml
@@ -12,21 +12,21 @@ dependencies:
 - cmake>=3.23.1,!=3.25.0
 - cuda-version=11.8
 - cudatoolkit
-- cupy >=12.0.0
+- cupy>=12.0.0
 - cxx-compiler
 - gcc_linux-64=11.*
 - imagecodecs>=2021.6.8
 - ipython
 - jbig
-- lazy_loader >=0.1
+- lazy_loader>=0.1
 - libcufile-dev=1.4.0.31
 - libcufile=1.4.0.31
 - libnvjpeg-dev=11.6.0.55
 - libnvjpeg=11.6.0.55
 - libwebp-base
 - nbsphinx
 - ninja
-- numpy >=1.21.3
+- numpy>=1.21.3
 - numpydoc
 - nvcc_linux-64=11.8
 - openslide-python>=1.1.2
@@ -40,7 +40,7 @@ dependencies:
 - pytest>=6.2.4
 - python>=3.8,<3.11
 - recommonmark
-- scikit-image >=0.19.0,<0.22.0a0
+- scikit-image>=0.19.0,<0.22.0a0
 - scipy
 - sphinx<6
 - sysroot_linux-64==2.17

diff --git a/conda/environments/all_cuda-120_arch-x86_64.yaml b/conda/environments/all_cuda-120_arch-x86_64.yaml
@@ -13,20 +13,20 @@ dependencies:
 - cuda-cudart-dev
 - cuda-nvcc
 - cuda-version=12.0
-- cupy >=12.0.0
+- cupy>=12.0.0
 - cxx-compiler
 - gcc_linux-64=11.*
 - imagecodecs>=2021.6.8
 - ipython
 - jbig
-- lazy_loader >=0.1
+- lazy_loader>=0.1
 - libcufile-dev
 - libnvjpeg-dev
 - libnvjpeg-static
 - libwebp-base
 - nbsphinx
 - ninja
-- numpy >=1.21.3
+- numpy>=1.21.3
 - numpydoc
 - openslide-python>=1.1.2
 - pip
@@ -39,7 +39,7 @@ dependencies:
 - pytest>=6.2.4
 - python>=3.8,<3.11
 - recommonmark
-- scikit-image >=0.19.0,<0.22.0a0
+- scikit-image>=0.19.0,<0.22.0a0
 - scipy
 - sphinx<6
 - sysroot_linux-64==2.17

diff --git a/conda/recipes/cucim/build.sh b/conda/recipes/cucim/build.sh
@@ -18,6 +18,6 @@ cp -P python/install/lib/* python/cucim/src/cucim/clara/
 pushd python/cucim
 
 echo "PYTHON: ${PYTHON}"
-$PYTHON setup.py install
+$PYTHON -m pip install . -vv
 
 popd
diff --git a/dependencies.yaml b/dependencies.yaml
@@ -30,6 +30,44 @@ files:
       - cudatoolkit
       - docs
       - py_version
+  py_build:
+    output: pyproject
+    pyproject_dir: python/cucim
+    extras:
+      table: build-system
+    includes:
+      - build
+  py_run:
+    output: pyproject
+    pyproject_dir: python/cucim
+    extras:
+      table: project
+    includes:
+      - run
+  py_optional_test:
+    output: pyproject
+    pyproject_dir: python/cucim
+    extras:
+      table: project.optional-dependencies
+      key: test
+    includes:
+      - test_python
+  py_develop:
+    output: pyproject
+    pyproject_dir: python/cucim
+    extras:
+      table: project.optional-dependencies
+      key: developer
+    includes:
+      - develop
+  py_develop:
+    output: pyproject
+    pyproject_dir: python/cucim
+    extras:
+      table: project.optional-dependencies
+      key: docs
+    includes:
+      - docs
 channels:
   - rapidsai
   - rapidsai-nightly
@@ -38,6 +76,11 @@ channels:
 dependencies:
   build:
     common:
+      # Note:
+      #   Currently omit pyproject output_type from cmake, ninja. The python
+      #   build doesn't use these, but assumes that the C++ libcucim shared
+      #   library had already previously been built and the .so file copied to
+      #   python/cucim/src/cucim/clara/ before calling `pip install .`.
       - output_types: [conda, requirements]
         packages:
           - cmake>=3.23.1,!=3.25.0
@@ -46,6 +89,10 @@ dependencies:
         packages:
           - c-compiler
           - cxx-compiler
+      - output_types: [requirements, pyproject]
+        packages:
+          - setuptools>=24.2.0
+          - wheel
     specific:
       - output_types: conda
         matrices:
@@ -124,9 +171,17 @@ dependencies:
               - cuda-cudart-dev
               - libnvjpeg-dev
               - libcufile-dev
+  develop:
+    common:
+      - output_types: [conda, requirements, pyproject]
+        packages:
+          - pre-commit
+          - black
+          - ruff
+          - isort
   docs:
     common:
-      - output_types: [conda, requirements]
+      - output_types: [conda, requirements, pyproject]
         packages:
           - ipython
           - nbsphinx
@@ -157,25 +212,37 @@ dependencies:
               - python>=3.8,<3.11
   run:
     common:
+      - output_types: [conda, requirements, pyproject]
+        packages:
+          - lazy_loader>=0.1
+          - scikit-image>=0.19.0,<0.22.0a0
+          - scipy
       - output_types: conda
         packages:
+          - cupy>=12.0.0
+          - numpy>=1.21.3
+          # All dependencies below this point are specific to `cucim.clara` and
+          # are not needed for either `cucim.core` or `cucim.skimage`. I did
+          # not include these under a "pyproject" output so that it is still
+          # possible to run `pip install .` from the python/cucim folder
+          # without having build the C++ library at all. This allows, usage of
+          # usage of `cucim.skimage` on Windows, for example.
           - click
-          - cupy >=12.0.0
           - jbig
-          - lazy_loader >=0.1
           - libwebp-base
-          - numpy >=1.21.3
-          - scikit-image >=0.19.0,<0.22.0a0
-          - scipy
           - xz
           - zlib
           - zstd
           # Not sure where these go, if anywhere:
           # - openslide
           # - xorg-libxcb
+      - output_types: [requirements, pyproject]
+        packages:
+          - cupy-cuda11x>=12.0.0
+          - numpy
   test_python:
     common:
-      - output_types: [conda, requirements]
+      - output_types: [conda, requirements, pyproject]
         packages:
           - GPUtil>=1.4.0
           - imagecodecs>=2021.6.8
@@ -191,6 +258,19 @@ dependencies:
           - pip
           - pip:
             - opencv-python-headless>=4.6
-      - output_types: [requirements]
+      - output_types: [requirements, pyproject]
         packages:
           - opencv-python-headless>=4.6
+          # All dependencies below this point are specific to `cucim.clara` and
+          # are not needed for either `cucim.core` or `cucim.skimage`, so are
+          # listed as optional. They are needed in order to run the full test
+          # suite, including the `cucim.clara` package.
+          - click
+          - jbig
+          - libwebp-base
+          - xz
+          - zlib
+          - zstd
+          # Not sure where these go, if anywhere:
+          # - openslide
+          # - xorg-libxcb