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<h3>
Robbi Nespu pushed to branch master
at <a href="https://salsa.debian.org/med-team/scanpy">Debian Med / scanpy</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/scanpy/-/commit/18bfab70bd9becc252aa0c18de9e5a513e1b493b">18bfab70</a></strong>
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<span>by Robbi Nespu</span>
<i>at 2021-03-23T23:24:03+08:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">patch import scanpy python module on R as sc and sce
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<h4>3 changed files:</h4>
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+
debian/patches/import_sc_sce_on_r.patch
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debian/patches/series
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debian/rules
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<h4>Changes:</h4>
<li id="d0758aa56b15c122a24dcbb21112fed53b1e0d57">
<a href="https://salsa.debian.org/med-team/scanpy/-/commit/18bfab70bd9becc252aa0c18de9e5a513e1b493b#d0758aa56b15c122a24dcbb21112fed53b1e0d57"><strong>debian/patches/import_sc_sce_on_r.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/scanpy/tests/_scripts/seurat_extract_hvg_v3.r b/scanpy/tests/_scripts/seurat_extract_hvg_v3.r</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">index 3ac7087..dc1f835 100644</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scanpy/tests/_scripts/seurat_extract_hvg_v3.r</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scanpy/tests/_scripts/seurat_extract_hvg_v3.r</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -2,7 +2,9 @@</span> library(Seurat)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> library(reticulate)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> use_python("/usr/local/bin/python3")</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-sc <- import("scanpy", convert=FALSE)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+sc <- import("scanpy",as=sc, convert=FALSE)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+sce <- import("scanpy.external",as=sce, convert=FALSE)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> ad <- sc$datasets$pbmc3k()</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> ad$X <- ad$X$toarray()</span></pre>
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<a href="https://salsa.debian.org/med-team/scanpy/-/commit/18bfab70bd9becc252aa0c18de9e5a513e1b493b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">import_sc_sce_on_r.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">refactor_pl_py.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">avoid_setuptools_scm.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/scanpy/-/commit/18bfab70bd9becc252aa0c18de9e5a513e1b493b#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,8 @@ export PYBUILD_AFTER_TEST=rm -rf {build_dir}/pyproject.toml {build_dir}/$(PYBUIL</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> ${RM} -rf .pybuild</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"># If you need to rebuild the Sphinx documentation</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># Add sphinxdoc to the dh --with line</span>
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