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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/snakemake">Debian Med / snakemake</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/754205225f534b1e3e6a3df2fb72b35a59c7e0c3">75420522</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-10-19T13:42:28+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More invocations of "python" in source tree
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<h4>1 changed file:</h4>
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<a href="#c95b49fcdcf94cb632aec008933196e57cb26c3c">
debian/patches/python2to3.patch
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<h4>Changes:</h4>
<li id="c95b49fcdcf94cb632aec008933196e57cb26c3c">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/754205225f534b1e3e6a3df2fb72b35a59c7e0c3#c95b49fcdcf94cb632aec008933196e57cb26c3c"><strong>debian/patches/python2to3.patch</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">@@ -58,3 +58,54 @@ Index: snakemake/tests/test_tibanna/README.md</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> export TIBANNA_DEFAULT_STEP_FUNCTION_NAME=tibanna_unicorn_johannes</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> snakemake --tibanna --use-conda --configfile=config.json --default-remote-prefix=snakemake-tibanna-test/1</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> ```</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: snakemake/snakemake/script.py</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake.orig/snakemake/script.py</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/snakemake/script.py</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -544,7 +544,7 @@</span> class PythonScript(ScriptBase):</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> def _get_python_version(self):</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> out = self._execute_cmd(</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "python -c \"import sys; print('.'.join(map(str, sys.version_info[:2])))\"",</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "python3 -c \"import sys; print('.'.join(map(str, sys.version_info[:2])))\"",</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> read=True,</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> return tuple(map(int, out.strip().split(".")))</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="p">@@ -553,7 +553,7 @@</span> class PythonScript(ScriptBase):</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> py_exec = sys.executable</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> if self.container_img is not None:</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> # use python from image</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- py_exec = "python"</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ py_exec = "python3"</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> elif self.conda_env is not None or self.env_modules is not None:</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> if self._is_python_env():</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> py_version = self._get_python_version()</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -562,7 +562,7 @@</span> class PythonScript(ScriptBase):</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> if py_version >= MIN_PY_VERSION:</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> # Python version is new enough, make use of environment</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> # to execute script</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- py_exec = "python"</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ py_exec = "python3"</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> else:</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> logger.warning(</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> "Environment defines Python "</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: snakemake/snakemake/unit_tests/templates/ruletest.py.jinja2</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake.orig/snakemake/unit_tests/templates/ruletest.py.jinja2</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/snakemake/unit_tests/templates/ruletest.py.jinja2</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span> def test_{{ ruletest.name }}():</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> # Run the test job.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> sp.check_output([</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "python",</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "python3",</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> "-m",</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> "snakemake", </span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> "{{ ruletest.target }}",</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="p">@@ -53,4 +53,4 @@</span> def test_{{ ruletest.name }}():</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> # To modify this behavior, you can inherit from common.OutputChecker in here</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> # and overwrite the method `compare_files(generated_file, expected_file), </span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> # also see common.py.</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- common.OutputChecker(data_path, expected_path, workdir).check()</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ common.OutputChecker(data_path, expected_path, workdir).check()</span></span></pre>
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