Merge pull request #195 from KrishnaswamyLab/dev

MAGIC v3.0
KrishnaswamyLab · Mar 11, 2021 · 136169c · 136169c
2 parents 0a4f0c6 + c72c463
commit 136169c
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diff --git a/.github/ISSUE_TEMPLATE/question.md b/.github/ISSUE_TEMPLATE/question.md
@@ -6,5 +6,3 @@ labels: question
 assignees: ''
 
 ---
-
-
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -0,0 +1,55 @@
+name: Publish Python  distributions  to PyPI
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'test_deploy'
+    tags:
+      - '*'
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python  distributions  to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@master
+
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+
+    - name: Install pypa/build
+      run: >-
+        cd python &&
+        python -m
+        pip install
+        build
+        --user &&
+        cd ..
+
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        cd python &&
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+        . &&
+        cd ..
+
+    - name: Publish distribution  to Test PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        skip_existing: true
+        password: ${{ secrets.test_pypi_password }}
+        repository_url: https://test.pypi.org/legacy/
+
+    - name: Publish distribution  to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.pypi_password }}
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,94 @@
+name: pre-commit
+on:
+  push:
+    branches-ignore:
+      - 'master'
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Set up environment
+        run: |
+          echo "UBUNTU_VERSION=`grep DISTRIB_RELEASE /etc/lsb-release | sed 's/.*=//g'`" >> $GITHUB_ENV
+          mkdir -p .local/R/site-packages
+          echo "R_LIBS_USER=`pwd`/.local/R/site-packages" >> $GITHUB_ENV
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -y libcurl4-openssl-dev
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+          architecture: "x64"
+
+      - name: Cache pre-commit
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}-
+
+      - name: Run pre-commit
+        uses: pre-commit/[email protected]
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        if: startsWith(runner.os, 'Linux')
+        with:
+          path: ${{env.R_LIBS_USER}}
+          key: precommit-${{env.UBUNTU_VERSION}}-renv-${{ hashFiles('Rmagic/.pre-commit.r_requirements.txt') }}-${{ hashFiles('Rmagic/DESCRIPTION') }}-
+          restore-keys: |
+            precommit-${{env.UBUNTU_VERSION}}-renv-${{ hashFiles('Rmagic/.pre-commit.r_requirements.txt') }}-
+            precommit-${{env.UBUNTU_VERSION}}-renv-
+
+      - name: Install R packages
+        run: |
+          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
+          con = file("Rmagic/.pre-commit.r_requirements.txt", "r")
+          while ( length(pkg <- readLines(con, n = 1)) > 0 ) {
+            renv::install(pkg)
+          }
+          close(con)
+          if (!require("devtools")) install.packages("devtools", repos="http://cloud.r-project.org")
+          devtools::install_dev_deps("./Rmagic", upgrade=TRUE)
+          devtools::install("./Rmagic")
+        shell: Rscript {0}
+
+      - name: Run pre-commit for R
+        run: |
+          cd Rmagic
+          git init
+          git add *
+          pre-commit run --all-files
+          rm -rf .git
+          cd ..
+
+      - name: Commit files
+        if: failure()
+        run: |
+          git checkout -- .github/workflows
+          if [[ `git status --porcelain --untracked-files=no` ]]; then
+            git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+            git config --local user.name "github-actions[bot]"
+            git commit -m "pre-commit" -a
+          fi
+
+      - name: Push changes
+        if: failure()
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -0,0 +1,172 @@
+name: Unit Tests
+
+on:
+  push:
+    branches-ignore:
+      - 'test_deploy'
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+
+  test_python:
+    runs-on: ${{ matrix.config.os }}
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {name: '3.9', os: ubuntu-latest, python: '3.9' }
+        - {name: '3.8', os: ubuntu-latest, python: '3.8' }
+        - {name: '3.7', os: ubuntu-latest, python: '3.7' }
+        - {name: '3.6', os: ubuntu-latest, python: '3.6' }
+
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
+    - name: Check Ubuntu version
+      run: |
+        echo "UBUNTU_VERSION=`grep DISTRIB_RELEASE /etc/lsb-release | sed 's/.*=//g'`" >> $GITHUB_ENV
+
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.config.python }}
+
+    - name: Cache Python packages
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.pythonLocation }}
+        key: ${{runner.os}}-pip-${{ env.pythonLocation }}-${{ hashFiles('python/setup.py') }}
+        restore-keys: ${{runner.os}}-pip-${{ env.pythonLocation }}-
+
+    - name: Install package & dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -U wheel setuptools
+        pip install -U ./python[test]
+        python -c "import magic"
+
+    - name: Run Python tests
+      run: |
+        cd python
+        nose2 -vvv
+        cd ..
+
+    - name: Build docs
+      run: |
+        cd python
+        pip install .[doc]
+        cd doc
+        make html
+        cd ../..
+
+    - name: Coveralls
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_SERVICE_NAME: github
+      run: |
+        coveralls
+
+    - name: Upload check results on fail
+      if: failure()
+      uses: actions/upload-artifact@master
+      with:
+        name: ${{ matrix.config.name }}_results
+        path: check
+
+  test_r:
+    runs-on: ${{ matrix.config.os }}
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {name: 'devel', os: ubuntu-latest, r: 'devel' }
+        - {name: 'release', os: ubuntu-latest, r: 'release' }
+
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
+    - name: Set up environment
+      run: |
+        echo "UBUNTU_VERSION=`grep DISTRIB_RELEASE /etc/lsb-release | sed 's/.*=//g'`" >> $GITHUB_ENV
+        mkdir -p .local/R/site-packages
+        echo "R_LIBS_USER=`pwd`/.local/R/site-packages" >> $GITHUB_ENV
+
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.8"
+
+    - name: Install system dependencies
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt-get update -qq
+        sudo apt-get install -y libcurl4-openssl-dev pandoc
+
+    - name: Cache Python packages
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.pythonLocation }}
+        key: ${{runner.os}}-pip-${{ env.pythonLocation }}-${{ hashFiles('python/setup.py') }}
+        restore-keys: ${{runner.os}}-pip-${{ env.pythonLocation }}-
+
+    - name: Install package & dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -U wheel setuptools
+        pip install -U ./python
+        python -c "import magic"
+
+    - name: Set up R
+      id: setup-r
+      uses: r-lib/actions/setup-r@v1
+      with:
+        r-version: ${{ matrix.config.r }}
+
+    - name: Cache R packages
+      uses: actions/cache@v2
+      if: startsWith(runner.os, 'Linux')
+      with:
+        path: ${{env.R_LIBS_USER}}
+        key: test-${{env.UBUNTU_VERSION}}-renv-${{ steps.setup-r.outputs.installed-r-version }}-${{ hashFiles('Rmagic/DESCRIPTION') }}-
+        restore-keys: |
+          test-${{env.UBUNTU_VERSION}}-renv-${{ steps.setup-r.outputs.installed-r-version }}-
+
+    - name: Install R packages
+      run: |
+        if (!require("devtools")) install.packages("devtools", repos="http://cloud.r-project.org")
+        devtools::install_dev_deps("./Rmagic", upgrade=TRUE)
+        devtools::install("./Rmagic")
+      shell: Rscript {0}
+
+    - name: Install tinytex
+      uses: r-lib/actions/setup-tinytex@v1
+
+    - name: Run R tests
+      run: |
+        cd Rmagic
+        R CMD build .
+        R CMD check --as-cran *.tar.gz
+        cd ..
+
+    - name: Upload check results on fail
+      if: failure()
+      uses: actions/upload-artifact@master
+      with:
+        name: ${{ matrix.config.name }}_results
+        path: check
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,26 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: \.(ai|gz)$
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.6.4
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+      - id: black
+        args: ['--target-version', 'py36']
+  - repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: v1.5.4
+    hooks:
+      - id: autopep8
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.4
+    hooks:
+      - id: flake8
+        additional_dependencies: ['hacking']