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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/cwltool">Debian Med / cwltool</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/cwltool/commit/d35059daa6388ad0bf37e86a74804a51c7b4389b">d35059da</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2018-12-27T13:12:36Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Keep python3-prov dependency to minimize our changes, but keep the --provenance feature disabled.
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8326f11eb059fd0b6bb968d04d7628b096739386">
debian/patches/cleanup-tests
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<a href="#fcb92b9accd9db58b837ef9c16090c7d4830a9f9">
debian/patches/disable_prov
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/cwltool/commit/d35059daa6388ad0bf37e86a74804a51c7b4389b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cwltool (1.0.20181217162649+dfsg-4) unstable; urgency=medium</span>
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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"> * Keep python3-prov dependency to minimize our changes, but keep the --</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> provenance feature disabled.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Thu, 27 Dec 2018 05:12:15 -0800</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">cwltool (1.0.20181217162649+dfsg-3) unstable; urgency=medium</span>
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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"> * Fix our patches to the tests, run them in parallel</span>
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<li id="8326f11eb059fd0b6bb968d04d7628b096739386">
<a href="https://salsa.debian.org/med-team/cwltool/commit/d35059daa6388ad0bf37e86a74804a51c7b4389b#8326f11eb059fd0b6bb968d04d7628b096739386"><strong>debian/patches/cleanup-tests</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="120" 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">@@ -120,7 +120,7 @@ Forwarded: https://github.com/common-workflow-language/cwltool/pull/1024</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="diff"> assert "checksum" not in stdout</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cwltool.orig/tests/test_pack.py</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cwltool/tests/test_pack.py</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12<span class="idiff left right">2,7 +122</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12<span class="idiff left right">3,7 +123</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="diff"> @needs_docker</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="diff"> @pytest.mark.parametrize('wf_path,job_path,namespaced', cwl_to_run)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" 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="129" 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">@@ -129,7 +129,7 @@ Forwarded: https://github.com/common-workflow-language/cwltool/pull/1024</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="diff"> load_tool.loaders = {}</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"> document_loader, workflowobj, uri = fetch_document(</span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14<span class="idiff left right">2,8 +142</span>,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14<span class="idiff left right">3,8 +143</span>,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="diff"> normal_output = StringIO()</span>
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134
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="diff"> packed_output = StringIO()</span>
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135
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="diff"> </span>
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<li id="fcb92b9accd9db58b837ef9c16090c7d4830a9f9">
<a href="https://salsa.debian.org/med-team/cwltool/commit/d35059daa6388ad0bf37e86a74804a51c7b4389b#fcb92b9accd9db58b837ef9c16090c7d4830a9f9"><strong>debian/patches/disable_prov</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">@@ -50,12 +50,13 @@ Description: Disable --provance until python3-proc issue is resolved</td>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> help="Print corresponding RDF graph for workflow and exit")</span>
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51
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cwltool.orig/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cwltool/setup.py</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -57,8 +57,<span class="idiff left right">6</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -57,8 +57,<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> 'mypy-extensions',</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> 'six >= 1.9.0', # >= 1.9.0 required by prov</span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> 'psutil',</span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'prov == 1.5.1',</span></span>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'bagit >= 1.6.4',</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'prov >= 1.5.1',</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> 'typing-extensions',</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> ],</span>
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61
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> extras_require={</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="729" 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="730" 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">@@ -729,12 +730,13 @@ Description: Disable --provance until python3-proc issue is resolved</td>
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729
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# For now, we do not ship the --provenance feature in Debian</span></span>
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731
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cwltool.orig/requirements.txt</span></span>
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731
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732
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cwltool/requirements.txt</span></span>
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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5,8 +5,<span class="idiff left right">6</span> @@</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5,8 +5,<span class="idiff left right">7</span> @@</span></span>
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733
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<td class="diff-line-num new_line" data-linenumber="734" 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">
734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="diff"> schema-salad>=3.0,<3.1</span>
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734
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<td class="diff-line-num new_line" data-linenumber="735" 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">
735
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="diff"> typing>=3.5.3; python_version<"3.6"</span>
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735
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736
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="diff"> pathlib2==2.3.2; python_version<"3"</span>
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736
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737
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-prov==1.5.1</span></span>
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737
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bagit==1.6.4</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+prov>=1.5.1</span></span>
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738
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740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="diff"> mypy-extensions</span>
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739
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="diff"> psutil</span>
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740
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742
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="diff"> subprocess32 >= 3.5.0; os.name=="posix" and python_version<"3.5"</span></pre>
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