diff options
| author | Andreas Tille <tille@debian.org> | 2023-01-14 16:32:08 +0100 |
|---|---|---|
| committer | Andreas Tille <tille@debian.org> | 2023-01-14 16:32:08 +0100 |
| commit | 8c15308017eb7ed2916f8f8d6c7a681333970002 (patch) | |
| tree | 4d27a44ce6590b34a5756cd4e665e048a75a3426 | |
| parent | 62b451c51157f6bf73f6e16b5c7226555fbadfba (diff) | |
| parent | b508a3f2bfa489f3496e29926423750d13900f2c (diff) | |
pyranges (0.0.111+ds-4) unstable; urgency=medium
* Team upload.
* Adapt to numpy 1.24
Closes: #1028852
* Standards-Version: 4.6.2 (routine-update)
* No tab in license text (routine-update)
[dgit import unpatched pyranges 0.0.111+ds-4]
| -rw-r--r-- | debian/README.source | 23 | ||||
| -rw-r--r-- | debian/changelog | 57 | ||||
| -rw-r--r-- | debian/control | 37 | ||||
| -rw-r--r-- | debian/copyright | 34 | ||||
| -rw-r--r-- | debian/missing-sources/control.sam | 10028 | ||||
| -rw-r--r-- | debian/missing-sources/test_sorted.sam | 10028 | ||||
| -rw-r--r-- | debian/patches/fix_dtype.patch | 15 | ||||
| -rw-r--r-- | debian/patches/numpy_1.24.patch | 56 | ||||
| -rw-r--r-- | debian/patches/reorder.patch | 10 | ||||
| -rw-r--r-- | debian/patches/series | 3 | ||||
| -rwxr-xr-x | debian/rules | 28 | ||||
| -rw-r--r-- | debian/salsa-ci.yml | 11 | ||||
| -rw-r--r-- | debian/source/format | 1 | ||||
| -rw-r--r-- | debian/source/options | 1 | ||||
| -rw-r--r-- | debian/upstream/metadata | 27 | ||||
| -rw-r--r-- | debian/watch | 4 |
16 files changed, 20363 insertions, 0 deletions
diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 0000000..43916d3 --- /dev/null +++ b/debian/README.source @@ -0,0 +1,23 @@ +Upstream provides binary files without sources for: + +* tests/test_data/test_sorted.bam.bai +* tests/test_data/test_sorted.bam +* pyranges/example_data/control.bam.bai +* pyranges/example_data/control.bam + +These have been converted to corresponding text (.sam) files with the commands: +* samtools view -h -o test_sorted.sam test_sorted.bam +* samtools view -h -o control.sam control.bam + +And the corresponding *.sam files are added to: debian/missing-sources + +They can be generated back with the following commands: + +* cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam +* cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam +* samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai +* samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai + +These commands are also being run in debian/rules since these binaries are needed for testing. + + -- Nilesh Patra <npatra974@gmail.com> Sun, 21 Jun 2020 20:13:10 +0530 diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..81007e2 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,57 @@ +pyranges (0.0.111+ds-4) unstable; urgency=medium + + * Team upload. + * Adapt to numpy 1.24 + Closes: #1028852 + * Standards-Version: 4.6.2 (routine-update) + * No tab in license text (routine-update) + + -- Andreas Tille <tille@debian.org> Sat, 14 Jan 2023 16:32:08 +0100 + +pyranges (0.0.111+ds-3) unstable; urgency=medium + + * Team Upload. + * Add patch to fix FTBFS (Closes: ##1022476) + * Remove myself from uploaders + + -- Nilesh Patra <nilesh@debian.org> Mon, 24 Oct 2022 11:42:28 +0530 + +pyranges (0.0.111+ds-2) unstable; urgency=medium + + * Team upload. + * d/control: tests depend on python3-pytest-xdist. + * d/rules: enable parallel test runs for substantial runtime improvement. + This is made possible by the new test dependency. The objective is to + help investigations related to pytest 7 regression in bug #1013703. + * d/control: declare compliance to standards version 4.6.1. + + -- Étienne Mollier <emollier@debian.org> Mon, 04 Jul 2022 22:36:50 +0200 + +pyranges (0.0.111+ds-1) unstable; urgency=medium + + [ Steffen Möller ] + * Update metadata - yet another fix + + [ Nilesh Patra ] + * New upstream version 0.0.111+ds + * Run cme + * Add patch to fix tests + + -- Nilesh Patra <nilesh@debian.org> Wed, 03 Nov 2021 07:06:31 +0000 + +pyranges (0.0.85+ds-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * Remove trailing whitespace in debian/copyright (routine-update) + * debian/copyright: use spaces rather than tabs to start continuation lines. + * Remove .hypothesis dir in examples + + -- Andreas Tille <tille@debian.org> Mon, 02 Nov 2020 10:56:13 +0100 + +pyranges (0.0.79+ds-1) unstable; urgency=medium + + [ Steffen Moeller, Nilesh Patra ] + * Initial release (Closes: #963015) + + -- Nilesh Patra <npatra974@gmail.com> Sun, 21 Jun 2020 20:13:10 +0530 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..d5b99ea --- /dev/null +++ b/debian/control @@ -0,0 +1,37 @@ +Source: pyranges +Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> +Uploaders: Steffen Moeller <moeller@debian.org> +Section: python +Testsuite: autopkgtest-pkg-python +Priority: optional +Build-Depends: debhelper-compat (= 13), + dh-python, + python3-setuptools, + python3-all, + python3-ncls <!nocheck>, + python3-pyrle <!nocheck>, + python3-pytest <!nocheck>, + python3-pytest-xdist <!nocheck>, + python3-sorted-nearest, + python3-hypothesis, + bedtools, + samtools +Standards-Version: 4.6.2 +Vcs-Browser: https://salsa.debian.org/med-team/pyranges +Vcs-Git: https://salsa.debian.org/med-team/pyranges.git +Homepage: https://github.com/biocore-ntnu/pyranges +Rules-Requires-Root: no + +Package: python3-pyranges +Architecture: all +Depends: ${python3:Depends}, + ${misc:Depends} +Suggests: python-pyranges-doc +Description: 2D representation of genomic intervals and their annotations + A PyRanges object must have the columns Chromosome, Start and + End. These describe the genomic position and function as implicit row + labels. A Strand column is optional and adds strand information to the + intervals. Any other columns are allowed and are considered metadata. + . + The structure can be filled from .bed, .bam or .gff files, also from + tabular or textual representations. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..b5eaf4a --- /dev/null +++ b/debian/copyright @@ -0,0 +1,34 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: PyRanges +Source: https://github.com/biocore-ntnu/pyranges +Files-Excluded: tests/test_data/test_sorted.bam.bai + tests/test_data/test_sorted.bam + pyranges/example_data/control.bam.bai + pyranges/example_data/control.bam + +Files: * +Copyright: 2019 Endre Bakken Stovner +License: Expat + +Files: debian/* +Copyright: 2020 Steffen Moeller <moeller@debian.org> +License: Expat + +License: Expat + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + . + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. diff --git a/debian/missing-sources/control.sam b/debian/missing-sources/control.sam new file mode 100644 index 0000000..948bc5e --- /dev/null +++ b/debian/missing-sources/control.sam @@ -0,0 +1,10028 @@ +@HD VN:1.0 SO:coordinate +@PG ID:BEDTools_bedToBam VN:Vv2.22.1 +@PG ID:samtools PN:samtools PP:BEDTools_bedToBam VN:1.10 CL:samtools view -h -o control.sam control.bam +@SQ SN:chr1 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:249250621 +@SQ SN:chr2 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:243199373 +@SQ SN:chr3 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:198022430 +@SQ SN:chr4 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:191154276 +@SQ SN:chr5 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:180915260 +@SQ SN:chr6 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:171115067 +@SQ SN:chr7 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:159138663 +@SQ SN:chrX AS:../epic/scripts/chromsizes/hg19.chromsizes LN:155270560 +@SQ SN:chr8 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:146364022 +@SQ SN:chr9 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:141213431 +@SQ SN:chr10 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:135534747 +@SQ SN:chr11 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:135006516 +@SQ SN:chr12 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:133851895 +@SQ SN:chr13 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:115169878 +@SQ SN:chr14 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:107349540 +@SQ SN:chr15 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:102531392 +@SQ SN:chr16 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:90354753 +@SQ SN:chr17 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:81195210 +@SQ SN:chr18 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:78077248 +@SQ SN:chr20 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:63025520 +@SQ SN:chrY AS:../epic/scripts/chromsizes/hg19.chromsizes LN:59373566 +@SQ SN:chr19 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:59128983 +@SQ SN:chr22 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:51304566 +@SQ SN:chr21 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:48129895 +@SQ SN:chrM AS:../epic/scripts/chromsizes/hg19.chromsizes LN:16571 +U0 16 chr1 887772 255 25M * 0 0 * * +U0 16 chr1 994661 255 25M * 0 0 * * +U0 0 chr1 1041103 255 25M * 0 0 * * +U0 16 chr1 1770384 255 25M * 0 0 * * +U0 16 chr1 1995142 255 25M * 0 0 * * +U0 16 chr1 2063985 255 25M * 0 0 * * +U0 0 chr1 2129360 255 25M * 0 0 * * +U0 0 chr1 2239109 255 25M * 0 0 * * +U0 0 chr1 2318806 255 25M * 0 0 * * +U0 16 chr1 3006133 255 25M * 0 0 * * +U0 16 chr1 3089341 255 25M * 0 0 * * +U0 0 chr1 3093886 255 25M * 0 0 * * +U0 0 chr1 3096509 255 25M * 0 0 * * +U0 0 chr1 3102896 255 25M * 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AS:../epic/scripts/chromsizes/hg19.chromsizes LN:249250621 +@SQ SN:chr2 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:243199373 +@SQ SN:chr3 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:198022430 +@SQ SN:chr4 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:191154276 +@SQ SN:chr5 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:180915260 +@SQ SN:chr6 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:171115067 +@SQ SN:chr7 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:159138663 +@SQ SN:chrX AS:../epic/scripts/chromsizes/hg19.chromsizes LN:155270560 +@SQ SN:chr8 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:146364022 +@SQ SN:chr9 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:141213431 +@SQ SN:chr10 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:135534747 +@SQ SN:chr11 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:135006516 +@SQ SN:chr12 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:133851895 +@SQ SN:chr13 AS:../epic/scripts/chromsizes/hg19.chromsizes LN:115169878 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2021-11-03 +--- a/pyranges/methods/concat.py ++++ b/pyranges/methods/concat.py +@@ -43,7 +43,8 @@ + if any(strand_info) and not all(strand_info): + new_res = {} + for k, v in res.items(): +- v.loc[:, "Strand"] = v.Strand.cat.add_categories(["."]) ++ type_v = v.Strand.astype('category') ++ v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) + new_res[k] = v.assign(Strand=v.Strand.fillna(".")) + res = pr.PyRanges(new_res) + res.Strand = res.Strand diff --git a/debian/patches/numpy_1.24.patch b/debian/patches/numpy_1.24.patch new file mode 100644 index 0000000..6182909 --- /dev/null +++ b/debian/patches/numpy_1.24.patch @@ -0,0 +1,56 @@ +Description: Adapt to numpy 1.24 +Bug-Debian: https://bugs.debian.org/1028852 +Author: Andreas Tille <tille@debian.org> +Last-Update: Sat, 14 Jan 2023 16:30:10 +0100 + +--- a/tests/test_binary.py ++++ b/tests/test_binary.py +@@ -232,7 +232,7 @@ def test_coverage(gr, gr2, strandedness) + names= + "Chromosome Start End Name Score Strand NumberOverlaps FractionOverlaps" + .split(), +- dtype={"FractionOverlap": np.float}, ++ dtype={"FractionOverlap": float}, + sep="\t") + + result = gr.coverage(gr2, strandedness=strandedness) +--- a/pyranges/pyranges.py ++++ b/pyranges/pyranges.py +@@ -1705,7 +1705,7 @@ class PyRanges(): + For printing, the PyRanges was sorted on Chromosome and Strand. + """ + +- subsetter = np.zeros(len(self), dtype=np.bool) ++ subsetter = np.zeros(len(self), dtype=bool) + subsetter[:n] = True + return self[subsetter] + +@@ -3571,7 +3571,7 @@ class PyRanges(): + ValueError: Cannot take a larger sample than population when 'replace=False' + """ + sample = np.random.choice(len(self), size=n, replace=False) +- subsetter = np.zeros(len(self), dtype=np.bool) ++ subsetter = np.zeros(len(self), dtype=bool) + subsetter[sample] = True + return self[subsetter] + +@@ -4533,7 +4533,7 @@ class PyRanges(): + For printing, the PyRanges was sorted on Chromosome and Strand. + """ + +- subsetter = np.zeros(len(self), dtype=np.bool) ++ subsetter = np.zeros(len(self), dtype=bool) + subsetter[(len(self) - n):] = True + return self[subsetter] + +--- a/tests/hypothesis_helper.py ++++ b/tests/hypothesis_helper.py +@@ -269,7 +269,7 @@ def genomicfeature(draw): + dataset = getattr(pr.data, dataset_name)() + dataset = dataset[dataset.Feature.isin(["gene", "transcript", "exon"])] + +- # subsetter = draw(arrays(np.bool, shape=len(dataset))) ++ # subsetter = draw(arrays(bool, shape=len(dataset))) + gene_ids = list(dataset.gene_id.drop_duplicates()) + genes = draw( + st.lists(st.sampled_from(gene_ids), unique="True", min_size=1)) diff --git a/debian/patches/reorder.patch b/debian/patches/reorder.patch new file mode 100644 index 0000000..c3033b7 --- /dev/null +++ b/debian/patches/reorder.patch @@ -0,0 +1,10 @@ +--- a/setup.py ++++ b/setup.py +@@ -1,6 +1,6 @@ + import os +-from distutils.core import setup + from setuptools import find_packages ++from distutils.core import setup + + __version__ = open("pyranges/version.py").readline().split(" = ")[1].replace( + '"', '').strip() diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..b9467fc --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,3 @@ +fix_dtype.patch +reorder.patch +numpy_1.24.patch diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..50fbe09 --- /dev/null +++ b/debian/rules @@ -0,0 +1,28 @@ +#!/usr/bin/make -f +# See debhelper(7) (uncomment to enable) +# output every command that modifies files on the build system. +#export DH_VERBOSE = 1 + +export PYBUILD_NAME=pyranges +export PYBUILD_BEFORE_TEST=cp -av {dir}/tests/*.bed {build_dir}/tests && \ + cp -av {dir}/tests/test_data {build_dir}/tests && \ + cp -av {dir}/tests/data {build_dir}/tests && \ + cp -av {dir}/pyranges/example_data {build_dir}/pyranges +export PYBUILD_TEST_ARGS=-n $(shell nproc) + +%: + dh $@ --with python3 --buildsystem=pybuild + +override_dh_auto_build: + dh_auto_build + echo 'Generating corresponding files ...' + cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam + cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam + samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai + samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai + +override_dh_install: + dh_install + find debian/ -name *.bam* | xargs rm -rf + find debian/ -name 'hi' | xargs rm -rf + find debian/ -name '.hypothesis' | xargs rm -rf diff --git a/debian/salsa-ci.yml b/debian/salsa-ci.yml new file mode 100644 index 0000000..260ebbe --- /dev/null +++ b/debian/salsa-ci.yml @@ -0,0 +1,11 @@ +# For more information on what jobs are run see: +# https://salsa.debian.org/salsa-ci-team/pipeline +# +# To enable the jobs, go to your repository (at salsa.debian.org) +# and click over Settings > CI/CD > Expand (in General pipelines). +# In "Custom CI config path" write debian/salsa-ci.yml and click +# in "Save Changes". The CI tests will run after the next commit. +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/source/options b/debian/source/options new file mode 100644 index 0000000..cb61fa5 --- /dev/null +++ b/debian/source/options @@ -0,0 +1 @@ +extend-diff-ignore = "^[^/]*[.]egg-info/" diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..0463544 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,27 @@ +--- +Archive: GitHub +Bug-Database: https://github.com/biocore-ntnu/pyranges/issues +Bug-Submit: https://github.com/biocore-ntnu/pyranges/issues/new +Changelog: https://github.com/biocore-ntnu/pyranges/tags +Reference: + - Author: Endre Bakken Stovner and Pål Sætrom + Title: > + PyRanges: efficient comparison of genomic intervals in Python + Journal: Bioinformatics + Volume: 36 + Number: 3 + Day: 1 + Month: 2 + Year: 2020 + Pages: 918–919 + URL: https://doi.org/10.1093/bioinformatics/btz615 + DOI: 10.1093/bioinformatics/btz615 +Registry: + - Name: OMICtools + Entry: OMICS_34860 + - Name: bio.tools + Entry: PyRanges + - Name: conda:bioconda + Entry: pyranges +Repository: https://github.com/biocore-ntnu/pyranges.git +Repository-Browse: https://github.com/biocore-ntnu/pyranges diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..e287673 --- /dev/null +++ b/debian/watch @@ -0,0 +1,4 @@ +version=4 +opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%pyranges-$1.tar.gz%,repacksuffix=+ds,dversionmangle=auto" \ + https://github.com/biocore-ntnu/pyranges/tags \ + (?:.*?/)?v?(\d[\d.]*)\.tar\.gz |