Merge pull request #67 from AdaptiveParticles/develop

update paper link, revert workflow checkouts

Author: joeljonsson

.github/workflows/build-deploy.yml

@@ -67,33 +67,6 @@ jobs:
       - name: Submodule recursive
         run: git submodule update --init --recursive
 
-      # PR/push to develop should use the develop branch of LibAPR
-      # for pull requests, we set the LibAPR branch based on the target (base) branch
-      - name: Get branch name (pull request)
-        if: ${{ github.event_name == 'pull_request' }}
-        shell: bash
-        run: echo "BRANCH_NAME=$(echo ${GITHUB_BASE_REF} | tr / -)" >> $GITHUB_ENV
-
-      - name: Get branch name (push)
-        if: ${{ (github.event_name == 'push') && !contains(github.ref, 'tags') }}
-        shell: bash
-        run: echo "BRANCH_NAME=$(echo ${GITHUB_REF#refs/heads/} | tr / -)" >> $GITHUB_ENV
-      
-      - name: Get branch name (tag push)
-        if: ${{ (github.event_name == 'push') && contains(github.ref, 'tags') }}
-        shell: bash
-        run: |
-          raw=$(git branch -r --contains ${{ github.ref }})
-          branch=${raw/origin\/}
-          echo "BRANCH_NAME=$(echo $branch)" >> $GITHUB_ENV
-
-      - name: Checkout LibAPR develop/master branch
-        shell: bash
-        run: |
-          echo "checking out branch ${{ env.BRANCH_NAME }} of submodule external/LibAPR"
-          cd external/LibAPR
-          git checkout ${{ env.BRANCH_NAME }}
-
       # Setup the build machine with the most recent versions of CMake and Ninja. Both are cached if not already: on subsequent runs both will be quickly restored from GitHub cache service.
       - uses: lukka/get-cmake@latest
       # Restore both vcpkg and its artifacts from the GitHub cache service.

.github/workflows/deploy-docs.yml

@@ -39,20 +39,6 @@ jobs:
 
       - name: Submodule recursive
         run: git submodule update --init --recursive
-      
-      - name: Get branch name
-        shell: bash
-        run: |
-          raw=$(git branch -r --contains ${{ github.ref }})
-          branch=${raw/origin\/}
-          echo "BRANCH_NAME=$(echo $branch)" >> $GITHUB_ENV
-
-      - name: Checkout master/develop branch of LibAPR
-        shell: bash
-        run: |
-          echo "checking out branch ${{ env.BRANCH_NAME }} of submodule external/LibAPR"
-          cd external/LibAPR
-          git checkout ${{ env.BRANCH_NAME }}
 
       # Setup the build machine with the most recent versions of CMake and Ninja. Both are cached if not already: on subsequent runs both will be quickly restored from GitHub cache service.
       - uses: lukka/get-cmake@latest

.github/workflows/quick-test.yml

@@ -45,12 +45,6 @@ jobs:
       - name: Submodule recursive
         run: git submodule update --init --recursive
 
-      - name: Checkout develop branch of LibAPR
-        shell: bash
-        run: |
-          cd external/LibAPR
-          git checkout develop
-
       # Setup the build machine with the most recent versions of CMake and Ninja. Both are cached if not already: on subsequent runs both will be quickly restored from GitHub cache service.
       - uses: lukka/get-cmake@latest
       # Restore both vcpkg and its artifacts from the GitHub cache service.

README.md

@@ -21,7 +21,7 @@ can be used directly in a wide range of processing tasks - even on the GPU!
 
 For more detailed information about the APR and its use, see:
 - [Adaptive particle representation of fluorescence microscopy images](https://www.nature.com/articles/s41467-018-07390-9) (nature communications)
-- [Parallel Discrete Convolutions on Adaptive Particle Representations of Images](https://arxiv.org/abs/2112.03592) (arXiv preprint)
+- [Parallel Discrete Convolutions on Adaptive Particle Representations of Images](https://ieeexplore.ieee.org/abstract/document/9796006) (IEEE Transactions on Image Processing)
 
 **pyapr** is built on top of the C++ library [LibAPR] using [pybind11].