Add GitHub Actions Workflows. (#471)

This PR adds GitHub Actions workflows to `cucim`.

### Task list

Coverage required for this PR:
- [x] C++ build
- [x] ~C++ tests~ (There are no C++ tests.)
- [x] Python build
- [x] Python tests
  - Some tests have been marked as `xfail` on ARM following discussion with @jakirkham and @grlee77. Those will be addressed in follow-up work.
- [x] Style checks

Authors:
  - Bradley Dice (https://github.com/bdice)
  - AJ Schmidt (https://github.com/ajschmidt8)

Approvers:
  - AJ Schmidt (https://github.com/ajschmidt8)
  - https://github.com/jakirkham

URL: #471

.github/CODEOWNERS

@@ -10,9 +10,10 @@ python/            @rapidsai/cucim-python-codeowners
 **/cmake/          @rapidsai/cucim-cmake-codeowners
 
 #build/ops code owners
-.github/           @rapidsai/ops-codeowners 
+.github/           @rapidsai/ops-codeowners
 ci/                @rapidsai/ops-codeowners
 conda/             @rapidsai/ops-codeowners
 **/Dockerfile      @rapidsai/ops-codeowners
 **/.dockerignore   @rapidsai/ops-codeowners
 docker/            @rapidsai/ops-codeowners
+dependencies.yaml  @rapidsai/ops-codeowners

.github/ops-bot.yaml

@@ -7,3 +7,4 @@ label_checker: true
 release_drafter: true
 external_contributors: false
 copy_prs: true
+recently_updated: true

.github/workflows/build.yaml

@@ -0,0 +1,54 @@
+name: build
+
+on:
+  push:
+    branches:
+      - "branch-*"
+    tags:
+      - v[0-9][0-9].[0-9][0-9].[0-9][0-9]
+  workflow_dispatch:
+    inputs:
+      branch:
+        required: true
+        type: string
+      date:
+        required: true
+        type: string
+      sha:
+        required: true
+        type: string
+      build_type:
+        type: string
+        default: nightly
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  cpp-build:
+    secrets: inherit
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-matrix-build.yaml@main
+    with:
+      build_type: ${{ inputs.build_type || 'branch' }}
+      branch: ${{ inputs.branch }}
+      date: ${{ inputs.date }}
+      sha: ${{ inputs.sha }}
+  python-build:
+    needs: [cpp-build]
+    secrets: inherit
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-matrix-build.yaml@main
+    with:
+      build_type: ${{ inputs.build_type || 'branch' }}
+      branch: ${{ inputs.branch }}
+      date: ${{ inputs.date }}
+      sha: ${{ inputs.sha }}
+  upload-conda:
+    needs: [cpp-build, python-build]
+    secrets: inherit
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-upload-packages.yaml@main
+    with:
+      build_type: ${{ inputs.build_type || 'branch' }}
+      branch: ${{ inputs.branch }}
+      date: ${{ inputs.date }}
+      sha: ${{ inputs.sha }}

.github/workflows/pr.yaml

@@ -0,0 +1,41 @@
+name: pr
+
+on:
+  push:
+    branches:
+      - "pull-request/[0-9]+"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pr-builder:
+    needs:
+      - checks
+      - conda-cpp-build
+      - conda-python-build
+      - conda-python-tests
+    secrets: inherit
+    uses: rapidsai/shared-action-workflows/.github/workflows/pr-builder.yaml@main
+  checks:
+    secrets: inherit
+    uses: rapidsai/shared-action-workflows/.github/workflows/checks.yaml@main
+  conda-cpp-build:
+    needs: checks
+    secrets: inherit
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-matrix-build.yaml@main
+    with:
+      build_type: pull-request
+  conda-python-build:
+    needs: conda-cpp-build
+    secrets: inherit
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-matrix-build.yaml@main
+    with:
+      build_type: pull-request
+  conda-python-tests:
+    needs: conda-python-build
+    secrets: inherit
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@main
+    with:
+      build_type: pull-request

.github/workflows/test.yaml

@@ -0,0 +1,24 @@
+name: test
+
+on:
+  workflow_dispatch:
+    inputs:
+      branch:
+        required: true
+        type: string
+      date:
+        required: true
+        type: string
+      sha:
+        required: true
+        type: string
+
+jobs:
+  conda-python-tests:
+    secrets: inherit
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@main
+    with:
+      build_type: nightly
+      branch: ${{ inputs.branch }}
+      date: ${{ inputs.date }}
+      sha: ${{ inputs.sha }}

.pre-commit-config.yaml

@@ -4,20 +4,23 @@
 #   pre-commit install-hooks
 exclude: '^(\.tox|ci/templates|\.bumpversion\.cfg)(/|$)'
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: master
-    hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-      - id: debug-statements
-  - repo: https://github.com/pycqa/isort
-    rev: 5.6.4
+  # TODO: re-enable this after GitHub Actions migration, it currently makes a
+  # large number of changes that shouldn't go in the GitHub Actions PR.
+  #- repo: https://github.com/pre-commit/pre-commit-hooks
+  #  rev: v4.4.0
+  #  hooks:
+  #    - id: trailing-whitespace
+  #    - id: end-of-file-fixer
+  #    - id: debug-statements
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.11.4
     hooks:
       - id: isort
         files: ^python/cucim/src/.*
         args: ["--settings-path=python/cucim/setup.cfg"]
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: master
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
     hooks:
       - id: flake8
+        args: ["--config=python/cucim/setup.cfg"]
         files: ^python/cucim/.*

ci/build_cpp.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+# Copyright (c) 2022, NVIDIA CORPORATION.
+
+set -euo pipefail
+
+source rapids-env-update
+
+export CMAKE_GENERATOR=Ninja
+
+rapids-print-env
+
+rapids-logger "Begin cpp build"
+
+rapids-mamba-retry mambabuild conda/recipes/libcucim
+
+rapids-upload-conda-to-s3 cpp

ci/build_python.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+# Copyright (c) 2022, NVIDIA CORPORATION.
+
+set -euo pipefail
+
+source rapids-env-update
+
+export CMAKE_GENERATOR=Ninja
+
+rapids-print-env
+
+rapids-logger "Begin py build"
+
+CPP_CHANNEL=$(rapids-download-conda-from-s3 cpp)
+
+# TODO: Remove `--no-test` flag once importing on a CPU
+# node works correctly
+rapids-mamba-retry mambabuild \
+  --no-test \
+  --channel "${CPP_CHANNEL}" \
+  conda/recipes/cucim
+
+rapids-upload-conda-to-s3 python

ci/check_style.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+# Copyright (c) 2020-2022, NVIDIA CORPORATION.
+
+set -euo pipefail
+
+rapids-logger "Create checks conda environment"
+. /opt/conda/etc/profile.d/conda.sh
+
+rapids-dependency-file-generator \
+  --output conda \
+  --file_key checks \
+  --matrix "cuda=${RAPIDS_CUDA_VERSION%.*};arch=$(arch);py=${RAPIDS_PY_VERSION}" | tee env.yaml
+
+rapids-mamba-retry env create --force -f env.yaml -n checks
+conda activate checks
+
+# Run pre-commit checks
+pre-commit run --hook-stage manual --all-files --show-diff-on-failure

ci/cpu/build.sh

@@ -36,6 +36,10 @@ echo "PYTHON_VER  : ${PYTHON_VER}"
 export GPUCI_CONDA_RETRY_MAX=1
 export GPUCI_CONDA_RETRY_SLEEP=30
 
+# Workaround to keep Jenkins builds working
+# until we migrate fully to GitHub Actions
+export RAPIDS_CUDA_VERSION="${CUDA}"
+
 export CONDA_BLD_DIR="${WORKSPACE}/.conda-bld"
 
 ################################################################################

ci/gpu/build.sh

@@ -38,6 +38,10 @@ echo "CUDA_VERSION: ${CUDA_VERSION}"
 echo "CUDA_VER    : ${CUDA_VER}"
 echo "PYTHON_VER  : ${PYTHON_VER}"
 
+# Workaround to keep Jenkins builds working
+# until we migrate fully to GitHub Actions
+export RAPIDS_CUDA_VERSION="${CUDA}"
+
 ################################################################################
 # SETUP - Check environment
 ################################################################################

ci/test_python.sh

@@ -0,0 +1,66 @@
+#!/bin/bash
+# Copyright (c) 2022, NVIDIA CORPORATION.
+
+# Common setup steps shared by Python test jobs
+
+set -euo pipefail
+
+. /opt/conda/etc/profile.d/conda.sh
+
+rapids-logger "Generate Python testing dependencies"
+rapids-dependency-file-generator \
+  --output conda \
+  --file_key test_python \
+  --matrix "cuda=${RAPIDS_CUDA_VERSION%.*};arch=$(arch);py=${RAPIDS_PY_VERSION}" | tee env.yaml
+
+rapids-mamba-retry env create --force -f env.yaml -n test
+
+# Temporarily allow unbound variables for conda activation.
+set +u
+conda activate test
+set -u
+
+rapids-logger "Downloading artifacts from previous jobs"
+CPP_CHANNEL=$(rapids-download-conda-from-s3 cpp)
+PYTHON_CHANNEL=$(rapids-download-conda-from-s3 python)
+
+RAPIDS_TESTS_DIR=${RAPIDS_TESTS_DIR:-"${PWD}/test-results"}
+RAPIDS_COVERAGE_DIR=${RAPIDS_COVERAGE_DIR:-"${PWD}/coverage-results"}
+mkdir -p "${RAPIDS_TESTS_DIR}" "${RAPIDS_COVERAGE_DIR}"
+SUITEERROR=0
+
+rapids-print-env
+
+rapids-mamba-retry install \
+  --channel "${CPP_CHANNEL}" \
+  --channel "${PYTHON_CHANNEL}" \
+  libcucim cucim
+
+rapids-logger "Check GPU usage"
+nvidia-smi
+
+set +e
+
+rapids-logger "pytest cucim"
+pushd python/cucim
+pytest \
+  --cache-clear \
+  --junitxml="${RAPIDS_TESTS_DIR}/junit-cucim.xml" \
+  --numprocesses=8 \
+  --dist=loadscope \
+  --cov-config=.coveragerc \
+  --cov=cucim \
+  --cov-report=xml:"${RAPIDS_COVERAGE_DIR}/cucim-coverage.xml" \
+  --cov-report=term \
+  src \
+  tests/unit \
+  tests/performance
+exitcode=$?
+
+if (( ${exitcode} != 0 )); then
+    SUITEERROR=${exitcode}
+    echo "FAILED: 1 or more tests in cucim"
+fi
+popd
+
+exit ${SUITEERROR}

conda/environments/all_cuda-115_arch-x86_64.yaml

@@ -0,0 +1,49 @@
+# This file is generated by `rapids-dependency-file-generator`.
+# To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
+channels:
+- rapidsai
+- rapidsai-nightly
+- conda-forge
+- nvidia
+dependencies:
+- GPUtil>=1.4.0
+- c-compiler
+- click
+- cmake>=3.23.1,!=3.25.0
+- cudatoolkit=11.5
+- cupy >=10,<12.0.0a0
+- cxx-compiler
+- gcc_linux-64=9.*
+- imagecodecs>=2021.6.8
+- ipython
+- jbig
+- jpeg
+- libwebp-base
+- nbsphinx
+- ninja
+- numpy
+- numpydoc
+- nvcc_linux-64=11.5
+- openslide-python>=1.1.2
+- pip
+- pre-commit
+- psutil>=5.8.0
+- pydata-sphinx-theme
+- pytest-cov>=2.12.1
+- pytest-lazy-fixture>=0.6.3
+- pytest-xdist
+- pytest>=6.2.4
+- python>=3.8,<3.10
+- recommonmark
+- scikit-image >=0.19.0,<0.20.0a0
+- scipy
+- sphinx
+- sysroot_linux-64==2.17
+- tifffile>=2022.7.28
+- xz
+- yasm
+- zlib
+- zstd
+- pip:
+  - opencv-python-headless>=4.6
+name: all_cuda-115_arch-x86_64