bump version, merge pull request #32 from NiftyPET/devel

NiftyPET · Sep 30, 2021 · b1c3799 · b1c3799
2 parents 4f0121d + e7d9cfd
commit b1c3799
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diff --git a/.github/workflows/comment-bot.yml b/.github/workflows/comment-bot.yml
@@ -29,6 +29,7 @@ jobs:
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "eyes"})
+        github-token: ${{ secrets.GH_TOKEN }}
     - name: Tag Commit
       run: |
         git clone https://${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY} repo
@@ -48,3 +49,4 @@ jobs:
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "rocket"})
+        github-token: ${{ secrets.GH_TOKEN }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,44 +1,58 @@
 name: Test
-on:
-- push
+on: [push, pull_request]
 jobs:
   check:
+    if: github.event_name != 'pull_request' || github.repository_owner != 'NiftyPET'
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: [3.6, 3.9]
-    name: Check py${{ matrix.python }}
+    name: Check
     steps:
     - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
     - uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python }}
     - name: set PYSHA
       run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
     - uses: actions/cache@v1
       with:
         path: ~/.cache/pre-commit
         key: pre-commit|${{ env.PYSHA }}|${{ hashFiles('.pre-commit-config.yaml') }}
-    - run: pip install -U pre-commit twine setuptools wheel setuptools_scm[toml] ninst scikit-build
-    - run: HMUDIR=$HOME python setup.py sdist
-    - run: twine check dist/*
+    - name: dependencies
+      run: |
+        pip install -U pre-commit
+        sudo apt-get install -yqq clang-format
+    - uses: reviewdog/action-setup@v1
+    - if: github.event_name == 'push' || github.event_name == 'pull_request'
+      name: comment
+      run: |
+        if [[ $EVENT == pull_request ]]; then
+          REPORTER=github-pr-review
+        else
+          REPORTER=github-check
+        fi
+        pre-commit run -a todo | reviewdog -efm="%f:%l: %m" -name=TODO -tee -reporter=$REPORTER -filter-mode nofilter
+        pre-commit run -a flake8 | reviewdog -f=pep8 -name=flake8 -tee -reporter=$REPORTER -filter-mode nofilter
+      env:
+        REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        EVENT: ${{ github.event_name }}
     - run: pre-commit run -a --show-diff-on-failure
   test:
-    runs-on: [self-hosted, cuda]
-    name: Test
+    if: github.event_name != 'pull_request' || github.repository_owner != 'NiftyPET'
+    name: Test py${{ matrix.python }}
+    runs-on: [self-hosted, python, cuda, matlab]
+    strategy:
+      matrix:
+        python: [3.6, 3.9]
     steps:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
-    - run: pip install -U -e .[dev]
+    - name: Run setup-python
+      run: setup-python -p${{ matrix.python }}
+    - run: pip install -U --no-binary nimpa -e .[dev]
     - run: pytest
-    - run: codecov
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+    - uses: codecov/codecov-action@v1
+    - name: Post Run setup-python
+      run: setup-python -p${{ matrix.python }} -Dr
+      if: ${{ always() }}
   deploy:
-    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     needs: [check, test]
     name: PyPI Deploy
     runs-on: ubuntu-latest
@@ -47,35 +61,30 @@ jobs:
       with:
         fetch-depth: 0
     - uses: actions/setup-python@v2
+    - id: dist
+      uses: casperdcl/deploy-pypi@v2
       with:
-        python-version: '3.x'
-    - run: pip install -U twine setuptools wheel setuptools_scm[toml] ninst scikit-build
-    - run: HMUDIR=$HOME python setup.py sdist
-    - run: twine upload dist/*
+        requirements: twine setuptools wheel setuptools_scm[toml] ninst scikit-build
+        build: sdist
+        gpg_key: ${{ secrets.GPG_KEY }}
+        password: ${{ secrets.PYPI_TOKEN }}
+        upload: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags') }}
       env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-        skip_existing: true
-    - id: collect_assets
-      name: Collect assets
+        PATHTOOLS: ${{ github.workspace }}/NiftyPET_tools
+        HMUDIR: ${{ github.workspace }}
+    - id: meta
+      name: Changelog
       run: |
-        echo "::set-output name=asset_path::$(ls dist/*.tar.gz)"
-        echo "::set-output name=asset_name::$(basename dist/*.tar.gz)"
+        echo ::set-output name=tag::${GITHUB_REF#refs/tags/}
         git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
-    - id: create_release
-      uses: actions/create-release@v1
+    - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      uses: softprops/action-gh-release@v1
       env:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
-        tag_name: ${{ github.ref }}
-        release_name: ninst ${{ github.ref }} beta
+        name: nipet ${{ steps.meta.outputs.tag }} stable
         body_path: _CHANGES.md
         draft: true
-    - uses: actions/upload-release-asset@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
-      with:
-        upload_url: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: ${{ steps.collect_assets.outputs.asset_path }}
-        asset_name: ${{ steps.collect_assets.outputs.asset_name }}
-        asset_content_type: application/gzip
+        files: |
+          dist/${{ steps.dist.outputs.targz }}
+          dist/${{ steps.dist.outputs.targz_asc }}
diff --git a/.gitignore b/.gitignore
@@ -1,17 +1,14 @@
 *.py[co]
-__pycache__/
-
-# build
-MANIFEST
 *.so
+__pycache__/
+/_skbuild/
+/_cmake_test_compile/
 /niftypet/nipet/cmake/
 /niftypet/nipet/_dist_ver.py
+MANIFEST
+/*.egg*/
 /build/
 /dist/
-/_skbuild/
-/_cmake_test_compile/
-/*.egg*/
-/.eggs/
-
-/.coverage
+/.coverage*
 /coverage.xml
+/.pytest_cache/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,18 +2,51 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.3.0
+  rev: v4.0.1
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
   - id: check-docstring-first
   - id: check-executables-have-shebangs
   - id: check-toml
+  - id: check-merge-conflict
   - id: check-yaml
+  - id: debug-statements
   - id: end-of-file-fixer
   - id: mixed-line-ending
+  - id: sort-simple-yaml
   - id: trailing-whitespace
-- hooks:
+- repo: local
+  hooks:
+  - id: todo
+    name: Check TODO
+    language: pygrep
+    args: [-i]
+    entry: TODO
+    types: [text]
+    exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$
+- repo: https://gitlab.com/pycqa/flake8
+  rev: 3.9.2
+  hooks:
+  - id: flake8
+    args: [-j8]
+    additional_dependencies:
+    - flake8-bugbear
+    - flake8-comprehensions
+    - flake8-debugger
+    - flake8-string-format
+- repo: https://github.com/google/yapf
+  rev: v0.31.0
+  hooks:
+  - id: yapf
+    args: [-i]
+- repo: https://github.com/PyCQA/isort
+  rev: 5.9.3
+  hooks:
   - id: isort
-  repo: https://github.com/timothycrosley/isort
-  rev: 5.6.4
+- repo: https://github.com/doublify/pre-commit-clang-format
+  rev: '6230247'
+  hooks:
+  - id: clang-format
+    files: \.(cc?|cuh?|cxx|cpp|h|hpp|hxx|java|js)$
+    args: ['-fallback-style=none', '-style={BasedOnStyle: LLVM, ColumnLimit: 99, AllowShortBlocksOnASingleLine: true, AllowShortIfStatementsOnASingleLine: true, AllowShortLoopsOnASingleLine: true}']
diff --git a/examples/demo.ipynb b/examples/demo.ipynb
@@ -234,9 +234,9 @@
     "## Scatter\n",
     "\n",
     "# One OSEM iteration estimate (implicitly using voxel-driven scatter model)\n",
-    "eim = nipet.mmrchain(datain, mMRpars, mu_h=mu_h, mu_o=mu_o, itr=1, outpath=opth)['im']\n",
+    "eim = nipet.mmrchain(datain, mMRpars, mu_h=mu_h, mu_o=mu_o, itr=1, histo=m, outpath=opth)['im']\n",
     "# Recalculate scatter\n",
-    "s = nipet.vsm(datain, (mu_h['im'], mu_o['im']), eim, m, r, mMRpars)\n",
+    "s = nipet.vsm(datain, (mu_h['im'], mu_o['im']), eim, mMRpars, histo=m, rsino=r)\n",
     "print(\"Scatter: %.3g%%\" % (s.sum() / m['psino'].sum() * 100))\n",
     "\n",
     "## Attenuation, Normalisation & Sensitivity\n",

diff --git a/niftypet/CMakeLists.txt b/niftypet/CMakeLists.txt
@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.18 FATAL_ERROR)
 if("${NIPET_BUILD_VERSION}" STREQUAL "")
-set(NIPET_BUILD_VERSION 2 CACHE STRING "version" FORCE)
+  set(NIPET_BUILD_VERSION 2 CACHE STRING "version" FORCE)
 endif()
 project(nipet LANGUAGES C CXX CUDA VERSION "${NIPET_BUILD_VERSION}")
 
@@ -9,17 +9,39 @@ cmake_policy(SET CMP0074 NEW)  # <PackageName>_ROOT hints for find_package
 cmake_policy(SET CMP0104 NEW)  # CMAKE_CUDA_ARCHITECTURES
 find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED)
 find_package(CUDAToolkit REQUIRED)
+execute_process(
+  COMMAND "${Python3_EXECUTABLE}" -c "import cuvec; print(cuvec.include_path)"
+  OUTPUT_VARIABLE CUVEC_INCLUDE_DIRS
+  OUTPUT_STRIP_TRAILING_WHITESPACE)
+if("${CUVEC_INCLUDE_DIRS}" STREQUAL "")
+  message(WARNING "Could not find cuvec includes")
+else()
+  message(STATUS "Found cuvec includes: ${CUVEC_INCLUDE_DIRS}")
+endif()
 if(SKBUILD)
-find_package(PythonExtensions REQUIRED)
+  find_package(PythonExtensions REQUIRED)
+  set(LIB_TYPE "MODULE")
+else()
+  set(LIB_TYPE "SHARED")
 endif()
 cmake_policy(POP)
 
 message(STATUS "CUDA architectures: ${CMAKE_CUDA_ARCHITECTURES}")
 if("${CMAKE_BUILD_TYPE}" STREQUAL "")
-set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
 endif()
 message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
 
+option(CUVEC_DEBUG "Print out CUDA malloc & free operations" OFF)
+if(CUVEC_DEBUG)
+  add_compile_definitions(CUVEC_DEBUG)
+endif(CUVEC_DEBUG)
+message(STATUS "cuvec debugging: ${CUVEC_DEBUG}")
+if("${NIPET_CU_THREADS}" STREQUAL "")
+  set(NIPET_CU_THREADS 1024 CACHE STRING
+    "Maximum number of CUDA threads per block (should be less than cudaDeviceProp::maxThreadsDim)" FORCE)
+endif()
+add_compile_definitions(NIPET_CU_THREADS=${NIPET_CU_THREADS})
 add_subdirectory(nipet)
 
 include(CMakePackageConfigHelpers)

diff --git a/niftypet/nipet/CMakeLists.txt b/niftypet/nipet/CMakeLists.txt
@@ -13,7 +13,7 @@ add_library(NiftyPET::${PROJECT_NAME} ALIAS ${PROJECT_NAME})
 target_include_directories(${PROJECT_NAME} PUBLIC
   "$<BUILD_INTERFACE:${${CMAKE_PROJECT_NAME}_INCLUDE_DIRS}>"
   "$<INSTALL_INTERFACE:niftypet/${CMAKE_PROJECT_NAME}/include>")
-target_link_libraries(${PROJECT_NAME} ${Python3_LIBRARIES} ${CUDA_LIBRARIES})
+target_link_libraries(${PROJECT_NAME} ${Python3_LIBRARIES} CUDA::cudart_static)
 
 if(SKBUILD)
 python_extension_module(${PROJECT_NAME})