77 sparseoptimization pattern discrepancy

.Rbuildignore

@@ -0,0 +1,67 @@
+^\.travis\.yml$
+^appveyor\.yml$
+^\.lintr$
+^\.astylerc$
+^.*\.Rproj$
+^\.Rproj\.user$
+^ChangeLog
+
+^inst/benchmarks/
+^inst/profiling/
+^inst/vignettes/
+
+^.git
+
+^src/Makevars(?!.in$|.win$)
+^src/Cogaps.o
+^src/GapsParameters.o
+^src/GapsResult.o
+^src/GapsRunner.o
+^src/GapsStatistics.o
+^src/RcppExports.o
+^src/test-runner.o
+^src/atomic/AtomicDomain.o
+^src/atomic/ProposalQueue.o
+^src/cpp_tests/testAtomicDomain.o
+^src/cpp_tests/testDenseGibbsSampler.o
+^src/cpp_tests/testFileParsers.o
+^src/cpp_tests/testHashSets.o
+^src/cpp_tests/testHybridMatrix.o
+^src/cpp_tests/testHybridVector.o
+^src/cpp_tests/testMatrix.o
+^src/cpp_tests/testRandom.o
+^src/cpp_tests/testSerialization.o
+^src/cpp_tests/testSparseGibbsSampler.o
+^src/cpp_tests/testSparseIterator.o
+^src/cpp_tests/testSparseMatrix.o
+^src/cpp_tests/testSparseVector.o
+^src/cpp_tests/testVector.o
+^src/data_structures/HashSets.o
+^src/data_structures/HybridMatrix.o
+^src/data_structures/HybridVector.o
+^src/data_structures/Matrix.o
+^src/data_structures/SparseIterator.o
+^src/data_structures/SparseMatrix.o
+^src/data_structures/SparseVector.o
+^src/data_structures/Vector.o
+^src/file_parser/CsvParser.o
+^src/file_parser/GctParser.o
+^src/file_parser/FileParser.o
+^src/file_parser/TsvParser.o
+^src/file_parser/MtxParser.o
+^src/gibbs_sampler/AlphaParameters.o
+^src/gibbs_sampler/DenseStoragePolicy.o
+^src/gibbs_sampler/SparseStoragePolicy.o
+^src/math/Math.o
+^src/math/MatrixMath.o
+^src/math/Random.o
+^src/math/VectorMath.o
+^src/atomic/Atom.o
+^src/atomic/ConcurrentAtom.o
+^src/atomic/ConcurrentAtomicDomain.o
+^src/file_parser/CharacterDelimitedParser.o
+^src/file_parser/MatrixElement.o
+^src/gibbs_sampler/DenseNormalModel.o
+^src/gibbs_sampler/SparseNormalModel.o
+
+^src/math/VectorMath\.o$

.gitattributes

@@ -0,0 +1 @@
+

.github/workflows/build-push-container.yml

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+#
+name: build-push-container
+
+# Configures this workflow to run every time a change is pushed to the branch called `release`.
+on:
+  push:
+    branches: ['master']
+  workflow_dispatch:
+
+# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+      # 
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GHCR_TOKEN }}
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
+      # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
+      # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/r-build-check.yml

@@ -0,0 +1,12 @@
+name: r-build-check
+on:
+    push:
+        branches: ['master']
+    pull_request:
+        branches: ['master']
+    workflow_dispatch:
+jobs:
+    build-check:
+        uses: FertigLab/actions/.github/workflows/[email protected]
+        with:
+            chargs: 'c("--no-manual")'

.gitignore

@@ -0,0 +1,33 @@
+# ignore R created files
+.Rprofile
+.Rhistory
+
+# ignore compiled files
+*.so
+*.o
+*.dll
+
+.git
+
+# ignore OS X files
+*.DS_Store
+.Rproj.user
+
+# ignore Rstudio files
+CoGAPS.Rproj
+
+# Bioconductor files (used for setting up remotes for `git svn`)
+update_remotes.sh
+
+# ignore emacs files
+*~
+
+# ignore temporary files from autoreconf
+config.log
+config.status
+aclocal.m4
+autom4te.cache/
+src/Makevars
+
+# ignore checkpoint files
+*.out

.travis.yml

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+notifications:
+  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
+
+addons:
+  apt:
+    packages: ccache
+
+cache: ccache
+
+jobs:
+  fast_finish: true
+  allow_failures:
+    - name: Linting
+    - name: Code Formatting
+    - name: Bioconductor Devel Testing - Linux
+    - name: Bioconductor Devel Testing - OSX
+  include:
+    - name: "Bioconductor Release Testing - Linux"
+      os: linux
+      if: tag IS NOT present
+      language: r
+      r: bioc-release
+      repos:
+        CRAN: http://cran.rstudio.com/ 
+      before_install:
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
+
+    - name: "Bioconductor Devel Testing - Linux"
+      os: linux
+      if: tag IS NOT present
+      language: r
+      r: bioc-devel
+      repos:
+        CRAN: http://cran.rstudio.com/ 
+      before_install:
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
+
+    - name: "Bioconductor Release Testing - OSX"
+      os: osx
+      if: tag IS NOT present
+      language: r
+      r: bioc-release
+      repos:
+        CRAN: http://cran.rstudio.com/ 
+
+    - name: "Bioconductor Devel Testing - OSX"
+      os: osx
+      if: tag IS NOT present
+      language: r
+      r: bioc-devel
+      repos:
+        CRAN: http://cran.rstudio.com/ 
+
+    - name: "Test Running in Debug Mode"
+      if: tag IS NOT present
+      language: r
+      r: release
+      before_install:
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
+      install:
+        - R -e 'install.packages(c("BiocManager", "desc"), repos="http://cran.rstudio.com/")'
+        - R -e 'BiocManager::install(desc::desc_get_deps()$package, site_repository=c("http://cran.rstudio.com/"))'
+        - R CMD build --no-build-vignettes .
+        - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
+      script: R -f inst/scripts/debugRuns.R
+
+    - name: "Linting"
+      if: tag IS NOT present
+      script: echo "linting not implemented"
+
+    - name: "Code Formatting"
+      if: tag IS NOT present
+      script: echo "formatting not implemented"
+
+#- stage: Valgrind Analysis
+#  before_install:
+#    - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
+#    - sudo apt-get update -qq
+#    - sudo apt-get install -qq valgrind
+#  install:
+#    - R -e 'install.packages(c("BiocManager", "desc"))'
+#    - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
+#    - R CMD build --no-build-vignettes .
+#    - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
+#  script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
+