deeptools

LOW

maintainer imjiaoyuan 0 votes scanned 2026-08-20 17:11:42.006138

View on AUR

Why flagged

Uploaded within the last 14 days with 2 or fewer community votes — little peer review so far.

Triggered rules

Low Few votes, recently uploaded zero_votes_recent

Uploaded within the last 14 days with 2 or fewer community votes — little peer review so far.

PKGBUILD

      1# Maintainer: imjiaoyuan <imjiaoyuan@gmail.com>
    
      2
    
      3# Hybrid deepTools package (source-built, same strategy as jcvi):
    
      4#   * deepTools itself: built from the pinned PyPI sdist (sha256-verified wheel).
    
      5#   * official-repo deps (numpy/scipy/matplotlib/plotly/numpydoc) -> pacman (depends)
    
      6#   * everything else (pysam/pyBigWig/py2bit/deeptoolsintervals) -> uv fetches them
    
      7# Rule: only deps in the official repos reuse the system; the rest are bundled.
    
      8
    
      9pkgname=deeptools
    
      10pkgver=3.5.6
    
      11pkgrel=3
    
      12pkgdesc="Tools to process and analyze deep sequencing data (ChIP-seq, ATAC-seq, RNA-seq, etc.)"
    
      13arch=('x86_64')
    
      14url="https://github.com/deeptools/deepTools"
    
      15license=('MIT')
    
      16# Only what the OFFICIAL repos provide comes from pacman:
    
      17depends=('python'
    
      18         'python-numpy' 'python-scipy' 'python-matplotlib'
    
      19         'python-plotly' 'python-numpydoc')
    
      20makedepends=('uv' 'python-build' 'python-wheel' 'python-setuptools')
    
      21options=('!strip')
    
      22_site=/opt/$pkgname
    
      23# Pinned PyPI sdist (stable version-templated URL, no hash prefix).
    
      24source=("deeptools-$pkgver.tar.gz::https://pypi.org/packages/source/d/deeptools/deeptools-$pkgver.tar.gz")
    
      25sha256sums=('2daf06abc8cf2df42f7e0ecacb3784ee95de1db4dd887f69f22a29f27e202369')
    
      26
    
      27build() {
    
      28    cd "$pkgname-$pkgver"
    
      29    # Pure-Python wheel; --no-isolation builds against system setuptools.
    
      30    python -m build --wheel --no-isolation
    
      31}
    
      32
    
      33package() {
    
      34    cd "$pkgname-$pkgver"
    
      35
    
      36    # 1) venv on the system interpreter, WITH system site-packages visible so
    
      37    #    the official numpy/scipy/matplotlib/plotly/numpydoc are importable.
    
      38    UV_PYTHON_PREFERENCE=only-system uv venv --system-site-packages "$pkgdir$_site"
    
      39
    
      40    # 2) Install the LOCALLY built deepTools wheel (no PyPI fetch for the main
    
      41    #    package) plus the deps NOT in the official repos.
    
      42    #    --no-deps: never drag numpy/scipy/etc. into the venv; reuse system ones.
    
      43    UV_PYTHON_PREFERENCE=only-system uv pip install \
    
      44        --python "$pkgdir$_site/bin/python" --no-deps \
    
      45        dist/*.whl pysam pyBigWig py2bit deeptoolsintervals
    
      46
    
      47    # 3) Strip the build-time $pkgdir prefix from console-script shebangs.
    
      48    find "$pkgdir$_site/bin" -type f -exec sed -i "s|$pkgdir||g" {} +
    
      49
    
      50    # 4) Expose only deepTools' own console scripts under /usr/bin
    
      51    #    (skip dependency-provided helpers like sphinx-build).
    
      52    install -d "$pkgdir/usr/bin"
    
      53    while IFS= read -r name; do
    
      54        [[ -e "$pkgdir$_site/bin/$name" ]] &&
    
      55            ln -s "$_site/bin/$name" "$pkgdir/usr/bin/$name"
    
      56    done < <("$pkgdir$_site/bin/python" - <<'PY'
    
      57import importlib.metadata as m
    
      58d = m.distribution('deepTools')
    
      59for e in d.entry_points:
    
      60    if e.group == 'console_scripts':
    
      61        print(e.name)
    
      62PY
    
      63)
    
      64
    
      65    # 5) The python call above re-imports the venv's _virtualenv shim and
    
      66    #    regenerates its .pyc (which embeds the build-time $pkgdir path).
    
      67    #    Delete it last so the package stays free of $pkgdir references.
    
      68    find "$pkgdir$_site" -name '_virtualenv*.pyc' -delete 2>/dev/null
    
      69
    
      70    # 6) Drop the build-path metadata leak from the local-wheel install
    
      71    #    (the $srcdir reference makepkg warns about; uv writes direct_url.json
    
      72    #    with the file:// path when installing from dist/*.whl).
    
      73    find "$pkgdir$_site" -path '*/deeptools-*.dist-info/direct_url.json' -delete
    
      74
    
      75    install -Dm644 LICENSE.txt "$pkgdir/usr/share/licenses/$pkgname/LICENSE.txt"
    
      76}
    
      77

Changes since previous scan

--- PKGBUILD @ 2026-08-16 00:03
+++ PKGBUILD @ 2026-08-20 17:11
@@ -8,11 +8,11 @@
 
 pkgname=deeptools
 pkgver=3.5.6
-pkgrel=2
+pkgrel=3
 pkgdesc="Tools to process and analyze deep sequencing data (ChIP-seq, ATAC-seq, RNA-seq, etc.)"
 arch=('x86_64')
 url="https://github.com/deeptools/deepTools"
-license=('GPL3')
+license=('MIT')
 # Only what the OFFICIAL repos provide comes from pacman:
 depends=('python'
          'python-numpy' 'python-scipy' 'python-matplotlib'

Scan history

Scanned at (UTC)	Severity	Rules
2026-08-20 17:11:42	Low	1
2026-08-16 00:03:42	Clean	2
2026-08-15 15:30:38	Low	1
2026-08-15 00:26:13	Clean	2
2026-08-14 03:27:23	Low	1
2026-08-13 00:17:07	Clean	2
2026-08-12 11:23:23	Low	1
2026-08-12 01:22:13	Low	1