add pyproject sections to dependencies.yaml and regenerate pyproject.…

…toml
rapidsai · Oct 25, 2023 · 727010a · 727010a
1 parent b9f343d
commit 727010a
Show file tree

Hide file tree

Showing 4 changed files with 127 additions and 55 deletions.
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/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
diff --git a/python/cucim/pyproject.toml b/python/cucim/pyproject.toml
@@ -3,11 +3,10 @@
 
 [build-system]
 build-backend = "setuptools.build_meta"
-# TODO: generate this list with `rapids-dependency-file-generator`
 requires = [
     "setuptools>=24.2.0",
     "wheel",
-] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../dependencies.yaml and run `rapids-dependency-file-generator`.
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 
 [project]
 name = "cucim"
@@ -24,12 +23,13 @@ authors = [
 ]
 license = { text = "Apache 2.0" }
 requires-python = ">=3.8"
-#TODO: add dependencies.yaml and generate this by `rapids-dependency-file-generator` instead
 dependencies = [
-    "click",
-    "numpy",
+    "cupy-cuda11x>=12.0.0",
     "lazy_loader>=0.1",
-] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../dependencies.yaml and run `rapids-dependency-file-generator`.
+    "numpy",
+    "scikit-image>=0.19.0,<0.22.0a0",
+    "scipy",
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
@@ -60,45 +60,37 @@ Tracker = "https://github.com/rapidsai/cucim/issues"
 
 [project.optional-dependencies]
 test = [
-    "cupy-cuda11x>=12.0.0",
-    "scipy",
-    "scikit-image>=0.19",
-    "pytest",
-    "pytest-lazy-fixture",
-    "gputil",
-    "openslide-python",
-] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../dependencies.yaml and run `rapids-dependency-file-generator`.
+    "GPUtil>=1.4.0",
+    "click",
+    "imagecodecs>=2021.6.8",
+    "jbig",
+    "libwebp-base",
+    "opencv-python-headless>=4.6",
+    "openslide-python>=1.1.2",
+    "psutil>=5.8.0",
+    "pytest-cov>=2.12.1",
+    "pytest-lazy-fixture>=0.6.3",
+    "pytest-xdist",
+    "pytest>=6.2.4",
+    "tifffile>=2022.7.28",
+    "xz",
+    "zlib",
+    "zstd",
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 developer = [
     "black",
     "isort",
     "pre-commit",
     "ruff",
-]
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 docs = [
-    "Sphinx==4.5.0",
-    "sphinx-autobuild",
-    "sphinx-book-theme",
-    "sphinxcontrib-bibtex<2.0.0",  # https://github.com/executablebooks/jupyter-book/issues/1137
-    "sphinx-copybutton",
-    "sphinx-panels",
-    "sphinx-thebe",
-    "sphinx-togglebutton",
-    "sphinxemoji",
-    "ablog",
-    "docutils==0.16", # 0.17 causes error. https://github.com/executablebooks/MyST-Parser/issues/343
-    "pydata_sphinx_theme",
-    "myst-parser",
-    "myst-nb",
-    "ipywidgets",
-    "nbclient",
-    "plotly<5",
-    "pandas",
-    "matplotlib",
-    "cupy-cuda110",
-    "numpy",
-    "scipy",
-    "scikit-image",
-]
+    "ipython",
+    "nbsphinx",
+    "numpydoc",
+    "pydata-sphinx-theme",
+    "recommonmark",
+    "sphinx<6",
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 
 [project.entry-points."console_scripts"]
 cucim = "cucim.clara.cli:main"