Public release

.Rprofile

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+#### -- Packrat Autoloader (version 0.5.0) -- ####
+source("packrat/init.R")
+#### -- End Packrat Autoloader -- ####
+
+options(bitmapType = "cairo")
+
+
+read_h5ad <- function(filename) {
+    builtins <- reticulate::import_builtins()
+    anndata <- reticulate::import("anndata", convert = FALSE)
+
+    Mapping <- reticulate::import("typing")$Mapping
+    DataFrame <- reticulate::import("pandas")$DataFrame
+    isinstance <- builtins$isinstance
+
+    adata <- anndata$read_h5ad(filename)
+
+    .convert <- function(obj) {
+        if (!isinstance(obj, Mapping) || isinstance(obj, DataFrame)) {
+            return(reticulate::py_to_r(obj))
+        }
+        ret <- list()
+        for (item in builtins$list(obj$keys())) {
+            ret[[item]] <- .convert(obj[[item]])
+        }
+        return(ret)
+    }
+
+    X <- .convert(adata$X$tocsc())
+    layers <- .convert(adata$layers)
+    obs <- .convert(adata$obs)
+    var <- .convert(adata$var)
+    obsm <- .convert(adata$obsm)
+    varm <- .convert(adata$varm)
+    obsp <- .convert(adata$obsp)
+    varp <- .convert(adata$varp)
+    uns <- .convert(adata$uns)
+    rownames(X) <- rownames(obs)
+    colnames(X) <- rownames(var)
+
+    return(list(
+        X = X, layers = layers,
+        obs = obs, var = var,
+        obsm = obsm, varm = varm,
+        obsp = obsp, varp = varp,
+        uns = uns
+    ))
+}
+
+
+safe_sd <- function(x) {
+    if (length(x) == 1)
+        return(0.0)
+    return(sd(x))
+}
+
+
+ggplot_theme <- function(...) {
+    return(ggplot2::theme(
+        text = ggplot2::element_text(family = "ArialMT"),
+        plot.background = ggplot2::element_blank(),
+        panel.grid.major = ggplot2::element_line(color = "#EEEEEE", linetype = "longdash"),
+        panel.grid.minor = ggplot2::element_blank(),
+        panel.background = ggplot2::element_rect(fill = "#FFFFFF"),
+        legend.background = ggplot2::element_blank(),
+        legend.box.background = ggplot2::element_blank(),
+        axis.line = ggplot2::element_line(color = "#000000"),
+        ...
+    ))
+}
+
+
+ggplot_save <- function(filename, ...) {
+    ggplot2::ggsave(filename, ..., dpi = 600, bg = "transparent")
+}

.github/workflows/build.yml

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+name: build
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt install -y libxml2-utils pandoc
+        sudo wget -O /usr/bin/bedtools https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
+        sudo chmod +x /usr/bin/bedtools
+        pip install --upgrade pip flit
+        flit install -s
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 scglue --count --select=E9,F63,F7,F82 --show-source --statistics
+    - name: Test with pytest
+      run: |
+        pytest --cov="scglue" --cov-report="xml:cov.xml" tests --cpu-only
+        COVERAGE=$(xmllint --xpath "/coverage/@line-rate" cov.xml | awk -F\" '{cov = sprintf("%.0f%%", $2 * 100); print(cov);}')
+        echo "COVERAGE=${COVERAGE}" >> $GITHUB_ENV
+    - name: Create coverage badge
+      uses: schneegans/[email protected]
+      with:
+        auth: ${{ secrets.GIST_SECRET }}
+        gistID: ${{ secrets.GIST_ID }}
+        filename: coverage.json
+        label: coverage
+        message: ${{ env.COVERAGE }}
+        color: green
+    - name: Build documentation
+      run: |
+        sphinx-build -b html docs docs/_build
+    - name: Get version
+      run: |
+        VERSION=$(python -c "from scglue import __version__; print(__version__)")
+        echo "VERSION=${VERSION}" >> $GITHUB_ENV
+    - name: Create version badge
+      uses: schneegans/[email protected]
+      with:
+        auth: ${{ secrets.GIST_SECRET }}
+        gistID: ${{ secrets.GIST_ID }}
+        filename: version.json
+        label: version
+        message: ${{ env.VERSION }}
+        color: blue

.github/workflows/release.yml

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+name: release
+
+on:
+  release:
+    types: [released]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run:
+        pip install --upgrade pip flit
+    - name: Build package
+      run: |
+        flit build
+        ls -lh dist
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: caozj
+        password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

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+__pycache__
+.coverage*
+.ipynb_checkpoints
+.snakemake
+.snakemake_timestamp
+*.annotated_links
+*.bak
+*.bed*
+*.bigWig
+*.chain*
+*.cprof
+*.csv*
+*.dill
+*.docx
+*.egg-info
+*.err
+*.fa
+*.feather
+*.gaf*
+*.graphml*
+*.gtf*
+*.h5ad
+*.html
+*.ipynb
+*.jpg
+*.json
+*.links
+*.log
+*.loom
+*.meme
+*.mp4
+*.mtx*
+*.obo
+*.old
+*.out
+*.owl
+*.pdf
+*.pkl*
+*.png
+*.pt
+*.pyc
+*.tbl
+*.tfevents.*
+*.tsv*
+*@neomake*
+*Untitled*
+.deprecated
+reports
+conda
+cov.xml
+dask-worker-space
+objectdb
+packrat/lib
+packrat/lib*/
+packrat/src/
+tmp
+tools
+dist

.readthedocs.yml

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+version: 2
+build:
+  image: latest
+sphinx:
+  configuration: docs/conf.py
+python:
+  version: 3.8
+  install:
+  - method: pip
+    path: .
+    extra_requirements:
+    - doc