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<h3>
Rebecca N. Palmer 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/da1a9e8d190789ce423c6fe93532625d1f688c3f">da1a9e8d</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2022-02-20T14:41:54+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tests: skip peppy tests (not in Debian).
</pre>
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<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/1d9c1c81932b2b0a48a08aba2581c86ca3b0db4c">1d9c1c81</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2022-02-20T14:53:22+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tests: use Python 3 subprocesses.
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
debian/patches/python3.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/3e2242a4166b3e2a9b5b490e61bff0c2d7b5ea80...1d9c1c81932b2b0a48a08aba2581c86ca3b0db4c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -2,8 +2,9 @@ snakemake (6.15.5-1) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Upstream bugfix release.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Remove drmaa Recommends, as that package is broken (see #951704).</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Tests: skip peppy tests (not in Debian), use Python 3 subprocesses.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> Sun, 20 Feb 2022 1<span class="idiff left">3:39</span>:0<span class="idiff right">0</span> +0000</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> Sun, 20 Feb 2022 1<span class="idiff left">4:53</span>:0<span class="idiff right">5</span> +0000</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">snakemake (6.15.1-2) unstable; urgency=medium</span>
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<li id="e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/3e2242a4166b3e2a9b5b490e61bff0c2d7b5ea80...1d9c1c81932b2b0a48a08aba2581c86ca3b0db4c#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.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">@@ -58,6 +58,17 @@ Forwarded: no</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> # make sure the output can be interpreted by dot</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> with open(dot_path, "rb") as dot_file, open(pdf_path, "wb") as pdf_file:</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="p">@@ -1426,8 +1426,8 @@</span> def test_github_issue1384():</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> shell(</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> cd {tmpdir}</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python -m snakemake --generate-unit-tests</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pytest -v .tests/unit</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 -m snakemake --generate-unit-tests</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 -m pytest -v .tests/unit</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> finally:</span>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_profile/Snakefile</span></span>
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62
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_profile/Snakefile</span></span>
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63
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"><span class="p">@@ -1,3 +1,3 @@</span></span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/3e2242a4166b3e2a9b5b490e61bff0c2d7b5ea80...1d9c1c81932b2b0a48a08aba2581c86ca3b0db4c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ export PYBUILD_DESTDIR_python3=debian/snakemake</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># copy the tests and run them from there to avoid having to clean up after them</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v {build_dir}/tests/test*.py -k 'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_deploy_hashing and not test_ancient and not test_github_issue1062 and not test_symlink_time_handling and not test_env_modules'</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v {build_dir}/tests/test*.py -k 'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_deploy_hashing and not <span class="idiff left right">test_peppy and not test_modules_peppy and not </span>test_ancient and not test_github_issue1062 and not test_symlink_time_handling and not test_env_modules'</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># Skipped because they download executables (which is forbidden in Debian buildd and debci)</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># Snakefile/snakemake-wrapper/CWL scripts: test_cwl, test_cwl_singularity, test_url_include, test_wrapper, test_module_with_script, test_module_report, test_module_complex(2), test_modules_meta_wrapper</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +19,7 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -v {build_dir}/tests/test*.py</td>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># Skipped due to not-in-Debian dependencies</span>
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21
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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"># python3-moto (RFP #777089): test_default_resources, test_default_remote, test_remote, test_output_file_cache_remote</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># python3-peppy: test_peppy, test_modules_peppy</span>
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22
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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># python3-tibanna: test_tibanna (possibly also specific to one cloud provider?)</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"># python3-tes: test_tes</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/3e2242a4166b3e2a9b5b490e61bff0c2d7b5ea80...1d9c1c81932b2b0a48a08aba2581c86ca3b0db4c#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -25,4 +25,4 @@ export HOME="${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">faulthandler_timeeout</span><span class="o" style="font-weight: 600;">=</span>60 <span class="nt" style="color: #000080;">-v</span> tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'test_pipes_fail'</span> <span class="o" style="font-weight: 600;">||</span> python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">faulthandler_timeeout</span><span class="o" style="font-weight: 600;">=</span>60 <span class="nt" style="color: #000080;">-v</span> tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'test_pipes_fail'</span> <span class="o" style="font-weight: 600;">||</span> python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">faulthandler_timeeout</span><span class="o" style="font-weight: 600;">=</span>60 <span class="nt" style="color: #000080;">-v</span> tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'test_pipes_fail'</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#See debian/rules for why these are excluded</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_deploy_hashing and not test_env_modules and not test_github_issue1062 and not test_pipes_fail'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_deploy_hashing and not <span class="idiff left right">test_peppy and not test_modules_peppy and not </span>test_env_modules and not test_github_issue1062 and not test_pipes_fail'</span></span></pre>
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