[WIP] New Release v2

.travis.yml → ._to_be_removed_travis.yml

@@ -39,6 +39,7 @@ before_install:
   - conda update --yes conda
 
 install:
+  - git submodule update --init  --recursive 
   - export PATH=/home/travis/miniconda3/bin:$PATH
   - conda create --yes -n env_kprocessor python=$MB_PYTHON_VERSION
   - source activate env_kprocessor

.github/workflows/cibuildwheel.yml

@@ -0,0 +1,94 @@
+name: cibuildwheel
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest ] # , windows-2019, macos-10.15 ]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Build wheels
+        uses: joerick/[email protected]
+
+        env:
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.6"
+          CIBW_SKIP: pp* cp27-manylinux* *-manylinux_{aarch64,ppc64le,s390x}
+          CIBW_ARCHS_LINUX: x86_64
+          CIBW_MANYLINUX_X86_64_IMAGE: quay.io/pypa/manylinux2014_x86_64:latest
+          CIBW_BEFORE_BUILD: |
+            yum install bzip2 -y
+            pip install --upgrade pip
+            pip install cmake
+            yum install zlib-devel -y
+            yum install centos-release-scl-rh -y
+            yum install doxygen -y
+            yum install devtoolset-7-toolchain -y
+            yum groupinstall -y "development tools"
+            yum install boost-devel -y
+            yum install -y zlib-devel bzip2-devel openssl-devel ncurses-devel sqlite-devel readline-devel tk-devel gdbm-devel db4-devel libpcap-devel xz-devel expat-devel
+            cmake -BKP_BUILD
+            cmake --build KP_BUILD -j4
+
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: ./wheelhouse/*.whl
+
+  upload_pypi:
+    needs: build_wheels
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/download-artifact@v2
+        id: fetch_artifacts
+        with:
+          path: 'wheels/'
+
+      - name: Publish package to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_KPROCESSOR_API_KEY }} #PYPI_KPROCESSOR_API_KEY
+          repository_url: https://test.pypi.org/legacy/
+          packages_dir: ${{steps.fetch_artifacts.outputs.download-path}}/artifact/
+          skip_existing: true
+          verbose: true
+
+  upload_bintray:
+    needs: build_wheels
+    runs-on: ubuntu-latest
+    env:
+      kProcessor_version: 2.0
+
+    steps:
+      - uses: actions/checkout@v1
+      - name: Fetch wheels from artifacts
+        id: fetch_artifacts
+        uses: actions/download-artifact@v2
+        with:
+          path: 'wheels/'
+
+
+      - name: Bintray
+        run: |
+          for whl_file in ${{steps.fetch_artifacts.outputs.download-path}}/artifact/*whl;
+          do
+            curl -T $whl_file -umr-eyes:${{ secrets.BINTRAY_API_KEY }} -H "X-Bintray-Override:1" -H "X-Bintray-Version:${{env.kProcessor_version}}" -H "X-Bintray-Package:kProcessor" https://api.bintray.com/content/mr-eyes/wheels/
+          done
+          curl -X POST -umr-eyes:${{ secrets.BINTRAY_API_KEY }} https://api.bintray.com/content/mr-eyes/wheels/kProcessor/${{env.kProcessor_version}}/publish

.github/workflows/ubuntu.yml

@@ -0,0 +1,52 @@
+name: Ubuntu
+
+on: [push, pull_request]
+
+env:
+  CTEST_OUTPUT_ON_FAILURE: 1
+  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  CPM_SOURCE_CACHE: ${{ github.workspace }}/cpm_modules
+
+jobs:
+  build:
+    runs-on: ubuntu-18.04
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Set up GCC
+        uses: egor-tensin/setup-gcc@v1
+        with:
+          version: 9
+          platform: x64
+      - name: Setup cmake
+        uses: jwlawson/[email protected]
+        with:   
+         cmake-version: 'latest'
+      - name: Use cmake
+        run: cmake --version
+      - name: Use g++
+        run: g++ --version  && git status
+      - name: install dependecies
+        run: sudo apt-get install  swig cmake python3-dev zlib1g-dev libghc-bzlib-dev python3-distutils libboost-all-dev
+
+      # - name: configure
+      #   run: cmake -Stest -Bbuild -DENABLE_TEST_COVERAGE=1 -DCMAKE_BUILD_TYPE=Debug
+
+      - name: configure
+        run: cmake -Bbuild -DBUILD_ALL=1
+
+      - name: build
+        run: cmake --build build -j1
+
+      - name: test
+        run: cd build/tests/kProcessorLibTests/ && ./testKprocessorLib
+
+      # - name: test
+      #   run: |
+      #     cd build
+      #     ctest --build-config Debug
+      - name: collect code coverage
+        run: bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"

.gitignore

@@ -36,3 +36,14 @@ Kprocessor
 docs/doxygen/*
 
 cmake-build-debug/tests/gtest/src/gtest2/googletest/scripts/test/Makefile
+.idea/*
+cmake-build-debug/*
+cmake-build-release/*
+profile/*
+.vscode/launch.json
+.vscode/settings.json
+.vscode/tasks.json
+out/build/*
+.vs/*
+CMakeSettings.json
+/cmake-build-release-wsl/

.gitmodules

@@ -7,6 +7,18 @@
 [submodule "ThirdParty/cereal"]
 	path = ThirdParty/cereal
 	url = https://github.com/USCiLab/cereal.git
+[submodule "ThirdParty/mum-hash"]
+	path = ThirdParty/mum-hash
+	url = https://github.com/vnmakarov/mum-hash.git
+[submodule "ThirdParty/KMC"]
+	path = ThirdParty/KMC
+	url = https://github.com/refresh-bio/KMC.git
 [submodule "ThirdParty/MQF"]
 	path = ThirdParty/MQF
-	url = https://github.com/dib-lab/MQF
+	url = https://github.com/dib-lab/MQF.git
+[submodule "ThirdParty/caches"]
+	path = ThirdParty/caches
+	url = https://github.com/vpetrigo/caches.git
+[submodule "ThirdParty/sshash"]
+	path = ThirdParty/sshash
+	url = https://github.com/jermp/sshash.git