bob.bio.base tagshttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags2023-06-16T12:43:46Zhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v8.0.0v8.0.0<ul data-sourcepos="1:1-83:53" dir="auto">
<li data-sourcepos="1:1-4:0">
<p data-sourcepos="1:3-1:67"><a href="/bob/bob.bio.base/-/merge_requests/307" data-reference-type="merge_request" data-original="bob/bob.bio.base!307" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7783" data-project-path="bob/bob.bio.base" data-iid="307" data-container="body" data-placement="top" title='Resolve "Switch to new CI/CD configuration"' class="gfm gfm-merge_request">!307</a>: Resolve "Switch to new CI/CD configuration"</p>
<p data-sourcepos="3:3-3:28">Fixes <a href="/bob/bob.bio.base/-/issues/188" data-reference-type="issue" data-original="bob/bob.bio.base#188" data-link="false" data-link-reference="false" data-project="1379" data-issue="5631" data-project-path="bob/bob.bio.base" data-iid="188" data-issue-type="issue" data-container="body" data-placement="top" title="Switch to new CI/CD configuration" class="gfm gfm-issue">#188</a></p>
</li>
<li data-sourcepos="5:1-8:0">
<p data-sourcepos="5:3-5:58"><a href="/bob/bob.bio.base/-/merge_requests/308" data-reference-type="merge_request" data-original="bob/bob.bio.base!308" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7799" data-project-path="bob/bob.bio.base" data-iid="308" data-container="body" data-placement="top" title="Move the dummy config files to src" class="gfm gfm-merge_request">!308</a>: Move the dummy config files to src</p>
<p data-sourcepos="7:3-7:71">Doing so makes them available to other packages, like <code>bob.bio.face</code>.</p>
</li>
<li data-sourcepos="9:1-14:0">
<p data-sourcepos="9:3-9:76"><a href="/bob/bob.bio.base/-/merge_requests/306" data-reference-type="merge_request" data-original="bob/bob.bio.base!306" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7730" data-project-path="bob/bob.bio.base" data-iid="306" data-container="body" data-placement="top" title="Fix the ScoreWriter and sparse db scoring all vs all" class="gfm gfm-merge_request">!306</a>: Fix the ScoreWriter and sparse db scoring all vs all</p>
<p data-sourcepos="11:3-11:64">Fixed the <code>ScoreWriter</code> classes looking for a <code>key</code> attribute.</p>
<p data-sourcepos="13:3-13:48">Fixed the name of the <code>for_matching.csv</code> file.</p>
</li>
<li data-sourcepos="15:1-16:0">
<p data-sourcepos="15:3-15:67"><a href="/bob/bob.bio.base/-/merge_requests/309" data-reference-type="merge_request" data-original="bob/bob.bio.base!309" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7804" data-project-path="bob/bob.bio.base" data-iid="309" data-container="body" data-placement="top" title="Allow uninstantiated class to get protocols" class="gfm gfm-merge_request">!309</a>: Allow uninstantiated class to get protocols</p>
</li>
<li data-sourcepos="17:1-20:0">
<p data-sourcepos="17:3-17:64"><a href="/bob/bob.bio.base/-/merge_requests/310" data-reference-type="merge_request" data-original="bob/bob.bio.base!310" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7946" data-project-path="bob/bob.bio.base" data-iid="310" data-container="body" data-placement="top" title="Bob Documentation in intersphinx catalog" class="gfm gfm-merge_request">!310</a>: Bob Documentation in intersphinx catalog</p>
<p data-sourcepos="19:3-19:221">Auto-intershpinx doesn't seem to find itself the correct meta-data for bob packages if they are not included as a dependency in the <code>pyproject.toml</code>, so the links of those packages' documentation are put in the catalog.</p>
</li>
<li data-sourcepos="21:1-22:0">
<p data-sourcepos="21:3-21:76"><a href="/bob/bob.bio.base/-/merge_requests/313" data-reference-type="merge_request" data-original="bob/bob.bio.base!313" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8110" data-project-path="bob/bob.bio.base" data-iid="313" data-container="body" data-placement="top" title="Fix database classes to follow bob.pipelines changes" class="gfm gfm-merge_request">!313</a>: Fix database classes to follow bob.pipelines changes</p>
</li>
<li data-sourcepos="23:1-26:0">
<p data-sourcepos="23:3-23:80"><a href="/bob/bob.bio.base/-/merge_requests/312" data-reference-type="merge_request" data-original="bob/bob.bio.base!312" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8088" data-project-path="bob/bob.bio.base" data-iid="312" data-container="body" data-placement="top" title="Fix the vuln commands to use subject_id, not template_id" class="gfm gfm-merge_request">!312</a>: Fix the vuln commands to use subject_id, not template_id</p>
<p data-sourcepos="25:3-25:29">Fixes <a href="/bob/bob.bio.base/-/issues/189" data-reference-type="issue" data-original="bob/bob.bio.base#189" data-link="false" data-link-reference="false" data-project="1379" data-issue="5759" data-project-path="bob/bob.bio.base" data-iid="189" data-issue-type="issue" data-container="body" data-placement="top" title="Vulnerability analysis compares `template_id` instead of `subject_id`" class="gfm gfm-issue">#189</a>.</p>
</li>
<li data-sourcepos="27:1-28:0">
<p data-sourcepos="27:3-27:50"><a href="/bob/bob.bio.base/-/merge_requests/314" data-reference-type="merge_request" data-original="bob/bob.bio.base!314" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8126" data-project-path="bob/bob.bio.base" data-iid="314" data-container="body" data-placement="top" title="Fix the annotations loader" class="gfm gfm-merge_request">!314</a>: Fix the annotations loader</p>
</li>
<li data-sourcepos="29:1-40:0">
<p data-sourcepos="29:3-29:56"><a href="/bob/bob.bio.base/-/merge_requests/300" data-reference-type="merge_request" data-original="bob/bob.bio.base!300" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7385" data-project-path="bob/bob.bio.base" data-iid="300" data-container="body" data-placement="top" title="Refactor the CSV-based databases" class="gfm gfm-merge_request">!300</a>: Refactor the CSV-based databases</p>
<p data-sourcepos="31:3-31:82">This new format of CSV databases fixes the following issues with the old format:</p>
<ul data-sourcepos="33:3-40:0">
<li data-sourcepos="33:3-34:0">
<p data-sourcepos="33:5-33:216">There is a clear distinction between subject_id (which is the identity of the person behind a Sample) and template_id (which is the unique identifier of a biometric template, for both enroll and probe SampleSets)</p>
</li>
<li data-sourcepos="35:3-36:0">
<p data-sourcepos="35:5-35:132">Implements sparse scoring through a separate <code>for_matching.csv</code> file. In the old format, this was possible through hacks only.</p>
</li>
<li data-sourcepos="37:3-38:0">
<p data-sourcepos="37:5-37:29">Removes the SampleLoaders</p>
</li>
<li data-sourcepos="39:3-40:0">
<p data-sourcepos="39:5-39:59">The implementation is based on the one in bob.pipelines</p>
</li>
</ul>
</li>
<li data-sourcepos="41:1-46:0">
<p data-sourcepos="41:3-41:101"><a href="/bob/bob.bio.base/-/merge_requests/311" data-reference-type="merge_request" data-original="bob/bob.bio.base!311" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8048" data-project-path="bob/bob.bio.base" data-iid="311" data-container="body" data-placement="top" title="Do not wrap a pipeline's transformer with checkpoint if it is already wrapped" class="gfm gfm-merge_request">!311</a>: Do not wrap a pipeline's transformer with checkpoint if it is already wrapped</p>
<p data-sourcepos="43:3-43:88">Tests each step of a pipeline transformer before wrapping it with <code>CheckpointWrapper</code>.</p>
<p data-sourcepos="45:3-45:25">Fixes <a href="/bob/bob.pipelines/-/issues/45" data-reference-type="issue" data-original="bob.pipelines#45" data-link="false" data-link-reference="false" data-project="3609" data-issue="5753" data-project-path="bob/bob.pipelines" data-iid="45" data-issue-type="issue" data-container="body" data-placement="top" title="CheckpointWrapper on annotator, saving the original dataset images as well as the annotations - waste of sapce!" class="gfm gfm-issue">bob.pipelines#45</a>.</p>
</li>
<li data-sourcepos="47:1-50:0">
<p data-sourcepos="47:3-47:69"><a href="/bob/bob.bio.base/-/merge_requests/316" data-reference-type="merge_request" data-original="bob/bob.bio.base!316" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8134" data-project-path="bob/bob.bio.base" data-iid="316" data-container="body" data-placement="top" title="Fix checkpoint wrapper saving in the same dir" class="gfm gfm-merge_request">!316</a>: Fix checkpoint wrapper saving in the same dir</p>
<p data-sourcepos="49:3-49:81">Fixes collisions of samples checkpoint filenames when checkpointing a pipeline.</p>
</li>
<li data-sourcepos="51:1-52:0">
<p data-sourcepos="51:3-51:90"><a href="/bob/bob.bio.base/-/merge_requests/317" data-reference-type="merge_request" data-original="bob/bob.bio.base!317" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8146" data-project-path="bob/bob.bio.base" data-iid="317" data-container="body" data-placement="top" title="[pyproject.toml] Changing documentation link back to master/sphinx" class="gfm gfm-merge_request">!317</a>: [pyproject.toml] Changing documentation link back to master/sphinx</p>
</li>
<li data-sourcepos="53:1-56:0">
<p data-sourcepos="53:3-53:43"><a href="/bob/bob.bio.base/-/merge_requests/315" data-reference-type="merge_request" data-original="bob/bob.bio.base!315" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8129" data-project-path="bob/bob.bio.base" data-iid="315" data-container="body" data-placement="top" title="Rc file name change" class="gfm gfm-merge_request">!315</a>: Rc file name change</p>
<p data-sourcepos="55:3-55:105">change the rc file name to <code>bobrc.toml</code> and remove from the catalog the migrated packages documentation</p>
</li>
<li data-sourcepos="57:1-58:0">
<p data-sourcepos="57:3-57:49"><a href="/bob/bob.bio.base/-/merge_requests/318" data-reference-type="merge_request" data-original="bob/bob.bio.base!318" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8204" data-project-path="bob/bob.bio.base" data-iid="318" data-container="body" data-placement="top" title="Replace clapp by clapper." class="gfm gfm-merge_request">!318</a>: Replace clapp by clapper.</p>
</li>
<li data-sourcepos="59:1-64:0">
<p data-sourcepos="59:3-59:91"><a href="/bob/bob.bio.base/-/merge_requests/319" data-reference-type="merge_request" data-original="bob/bob.bio.base!319" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8219" data-project-path="bob/bob.bio.base" data-iid="319" data-container="body" data-placement="top" title="Use the SampleSet key or the first Sample key in checkpoint wrapper" class="gfm gfm-merge_request">!319</a>: Use the SampleSet key or the first Sample key in checkpoint wrapper</p>
<p data-sourcepos="61:3-61:70">Uses a sample's key if <code>key</code> is not an attribute of the <code>SampleSet</code>.</p>
<p data-sourcepos="63:3-63:29">Fixes <a href="/bob/bob.bio.base/-/issues/190" data-reference-type="issue" data-original="bob/bob.bio.base#190" data-link="false" data-link-reference="false" data-project="1379" data-issue="5775" data-project-path="bob/bob.bio.base" data-iid="190" data-issue-type="issue" data-container="body" data-placement="top" title="SampleSet missing attributes 'key'" class="gfm gfm-issue">#190</a>.</p>
</li>
<li data-sourcepos="65:1-74:0">
<p data-sourcepos="65:3-65:71"><a href="/bob/bob.bio.base/-/merge_requests/320" data-reference-type="merge_request" data-original="bob/bob.bio.base!320" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8334" data-project-path="bob/bob.bio.base" data-iid="320" data-container="body" data-placement="top" title="fix [CSVDatabase]: defining templates metadata." class="gfm gfm-merge_request">!320</a>: fix [CSVDatabase]: defining templates metadata.</p>
<p data-sourcepos="67:3-67:122">Adds a parameter to <code>CSVDatabase</code> to indicate which <code>Sample</code>'s attributes must be present in their template <code>SampleSet</code>.</p>
<p data-sourcepos="69:3-69:60">Adds a unique <code>key</code> attribute to the template <code>SampleSet</code>.</p>
<p data-sourcepos="71:3-71:79">Adds tests to verify the correct loading of template metadata in <code>SampleSet</code>.</p>
<p data-sourcepos="73:3-73:29">fixes <a href="/bob/bob.bio.base/-/issues/191" data-reference-type="issue" data-original="bob/bob.bio.base#191" data-link="false" data-link-reference="false" data-project="1379" data-issue="5799" data-project-path="bob/bob.bio.base" data-iid="191" data-issue-type="issue" data-container="body" data-placement="top" title="Samples lose their metadata when going through PipelineSimple" class="gfm gfm-issue">#191</a>.</p>
</li>
<li data-sourcepos="75:1-78:0">
<p data-sourcepos="75:3-75:72"><a href="/bob/bob.bio.base/-/merge_requests/321" data-reference-type="merge_request" data-original="bob/bob.bio.base!321" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8449" data-project-path="bob/bob.bio.base" data-iid="321" data-container="body" data-placement="top" title="meta [readme]: Switch the readme.rst to markdown" class="gfm gfm-merge_request">!321</a>: meta [readme]: Switch the readme.rst to markdown</p>
<p data-sourcepos="77:3-77:72">Renames README.rst to README.md to be supported by the release script.</p>
</li>
<li data-sourcepos="79:1-83:53">
<p data-sourcepos="79:3-79:74"><a href="/bob/bob.bio.base/-/merge_requests/322" data-reference-type="merge_request" data-original="bob/bob.bio.base!322" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="8592" data-project-path="bob/bob.bio.base" data-iid="322" data-container="body" data-placement="top" title="meta(deps): add bob as dependency in new structure" class="gfm gfm-merge_request">!322</a>: meta(deps): add bob as dependency in new structure</p>
<p data-sourcepos="81:3-81:58">Adapt to the new structure of bob with <code>bob/bob</code> on top.</p>
<p data-sourcepos="83:3-83:53">Moved the <code>resources.py</code> script to a click command.</p>
</li>
</ul>2023-06-16T12:43:46ZYannick DAYERhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v7.1.0v7.1.0<ul data-sourcepos="1:1-1:212" dir="auto">
<li data-sourcepos="1:1-1:212">
<a href="/bob/bob.bio.base/-/merge_requests/304" data-reference-type="merge_request" data-original="bob/bob.bio.base!304" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7526" data-project-path="bob/bob.bio.base" data-iid="304" data-container="body" data-placement="top" title="Add a command to train a pipeline" class="gfm gfm-merge_request">!304</a> Add a command to train a pipeline: Executes only the training part of a <code>PipelineSimple</code>, or fits a <code>sklearn.pipeline</code>. Adds the possibility to split the training with multiple data chunks.</li>
</ul>2022-10-04T13:46:05ZFlavio TARSETTIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v7.0.4v7.0.4<ul data-sourcepos="1:1-2:69" dir="auto">
<li data-sourcepos="1:1-1:139">
<a href="/bob/bob.bio.base/-/merge_requests/303" data-reference-type="merge_request" data-original="bob/bob.bio.base!303" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7454" data-project-path="bob/bob.bio.base" data-iid="303" data-container="body" data-placement="top" title="train group no longer mandatory in CSVDataset" class="gfm gfm-merge_request">!303</a> train group no longer mandatory in CSVDataset: <code>all_samples</code> no longer assumes that all datasets have a <code>train</code> set.</li>
<li data-sourcepos="2:1-2:69">
<a href="/bob/bob.bio.base/-/merge_requests/305" data-reference-type="merge_request" data-original="bob/bob.bio.base!305" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7539" data-project-path="bob/bob.bio.base" data-iid="305" data-container="body" data-placement="top" title="Fix the compare-samples command and add tests" class="gfm gfm-merge_request">!305</a> Fix the compare-samples command and add tests.</li>
</ul>2022-08-23T07:48:29ZYannick DAYERhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v7.0.3v7.0.3<ul data-sourcepos="1:1-2:153" dir="auto">
<li data-sourcepos="1:1-1:81">
<a href="/bob/bob.bio.base/-/merge_requests/301" data-reference-type="merge_request" data-original="bob/bob.bio.base!301" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7442" data-project-path="bob/bob.bio.base" data-iid="301" data-container="body" data-placement="top" title="Fixed issue with score normalization with dev/eval groups" class="gfm gfm-merge_request">!301</a> Fixed issue with score normalization with dev/eval groups.</li>
<li data-sourcepos="2:1-2:153">
<a href="/bob/bob.bio.base/-/merge_requests/302" data-reference-type="merge_request" data-original="bob/bob.bio.base!302" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7450" data-project-path="bob/bob.bio.base" data-iid="302" data-container="body" data-placement="top" title='Support a pipeline with "passthrough" or None as estimator' class="gfm gfm-merge_request">!302</a> Support a pipeline with <code>"passthrough"</code> or <code>None</code> as estimator: Setting an estimator as <code>"passthrough"</code> or <code>None</code> no longer fails.</li>
</ul>2022-07-27T12:50:54ZYannick DAYERhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v7.0.2v7.0.2<ul data-sourcepos="1:1-1:21" dir="auto">
<li data-sourcepos="1:1-1:21">update dependencies</li>
</ul>2022-07-11T10:58:15ZFlavio TARSETTIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v7.0.1v7.0.1<ul data-sourcepos="1:1-1:59" dir="auto">
<li data-sourcepos="1:1-1:59">Fix ATNT interface after changes of <a href="/bob/bob.extension/-/merge_requests/145" data-reference-type="merge_request" data-original="bob/bob.extension!145" data-link="false" data-link-reference="false" data-project="1475" data-merge-request="7332" data-project-path="bob/bob.extension" data-iid="145" data-container="body" data-placement="top" title="Improves the search_file function" class="gfm gfm-merge_request">bob.extension!145</a>
</li>
</ul>2022-06-22T16:44:08ZAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v7.0.0v7.0.0<ul data-sourcepos="1:1-30:279" dir="auto">
<li data-sourcepos="1:1-1:253">
<a href="/bob/bob.bio.base/-/merge_requests/268" data-reference-type="merge_request" data-original="bob/bob.bio.base!268" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6692" data-project-path="bob/bob.bio.base" data-iid="268" data-container="body" data-placement="top" title="Implemented the checkpoint_dir feature" class="gfm gfm-merge_request">!268</a> Implemented the checkpoint_dir feature: Closes <a href="/bob/bob.bio.base/-/issues/164" data-reference-type="issue" data-original="bob/bob.bio.base#164" data-link="false" data-link-reference="false" data-project="1379" data-issue="5177" data-project-path="bob/bob.bio.base" data-iid="164" data-issue-type="issue" data-container="body" data-placement="top" title="Temporary files and caches are written into the result directory" class="gfm gfm-issue">#164</a> There you go. Now we have a <code>--checkpoint-dir</code> option. In case <code>--checkpoint</code> is set and <code>--checkpoint-dir</code> is not set, checkpoints will be saved on the <code>output</code>.</li>
<li data-sourcepos="2:1-2:101">
<a href="/bob/bob.bio.base/-/merge_requests/267" data-reference-type="merge_request" data-original="bob/bob.bio.base!267" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6690" data-project-path="bob/bob.bio.base" data-iid="267" data-container="body" data-placement="top" title='Resolve "resources.py does not list dask clients"' class="gfm gfm-merge_request">!267</a> Resolve "resources.py does not list dask clients": Closes <a href="/bob/bob.bio.base/-/issues/168" data-reference-type="issue" data-original="bob/bob.bio.base#168" data-link="false" data-link-reference="false" data-project="1379" data-issue="5184" data-project-path="bob/bob.bio.base" data-iid="168" data-issue-type="issue" data-container="body" data-placement="top" title="resources.py does not list dask clients" class="gfm gfm-issue">#168</a>
</li>
<li data-sourcepos="3:1-3:119">
<a href="/bob/bob.bio.base/-/merge_requests/269" data-reference-type="merge_request" data-original="bob/bob.bio.base!269" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6712" data-project-path="bob/bob.bio.base" data-iid="269" data-container="body" data-placement="top" title="Creating a setter for AlgorithmTransformer that sets projector file" class="gfm gfm-merge_request">!269</a> Creating a setter for AlgorithmTransformer that sets projector file: Closes <a href="/bob/bob.bio.base/-/issues/167" data-reference-type="issue" data-original="bob/bob.bio.base#167" data-link="false" data-link-reference="false" data-project="1379" data-issue="5182" data-project-path="bob/bob.bio.base" data-iid="167" data-issue-type="issue" data-container="body" data-placement="top" title="Algorithms with training that requires split by class don't seem to work" class="gfm gfm-issue">#167</a>
</li>
<li data-sourcepos="4:1-4:175">
<a href="/bob/bob.bio.base/-/merge_requests/271" data-reference-type="merge_request" data-original="bob/bob.bio.base!271" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6724" data-project-path="bob/bob.bio.base" data-iid="271" data-container="body" data-placement="top" title="Create an option --memory in the vanilla-biometrics CLI command and make..." class="gfm gfm-merge_request">!271</a> Create an option --memory in the vanilla-biometrics CLI command and make checkpointing of the pipeline the default behaviour Closes <a href="/bob/bob.bio.base/-/issues/152" data-reference-type="issue" data-original="bob/bob.bio.base#152" data-link="false" data-link-reference="false" data-project="1379" data-issue="4951" data-project-path="bob/bob.bio.base" data-iid="152" data-issue-type="issue" data-container="body" data-placement="top" title="`bob bio pipelines vanilla-biometrics` should have an option `--memory` instead `--checkpoint`" class="gfm gfm-issue">#152</a>
</li>
<li data-sourcepos="5:1-5:588">
<a href="/bob/bob.bio.base/-/merge_requests/272" data-reference-type="merge_request" data-original="bob/bob.bio.base!272" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6737" data-project-path="bob/bob.bio.base" data-iid="272" data-container="body" data-placement="top" title="Score normalization redesign" class="gfm gfm-merge_request">!272</a> Score normalization redesign: This is the initial redesign of the score-normalization pipeline. I basically dropped all the old code and made the score normalization stuff as a <code>post-processor</code> where such a post-processor is a BaseEstimator. In such a way, we can leverage Checkpointing and Dasking wrappers avoiding the implementation of custom features. Furthermore, it will be easier to implement other calibration strategies. ZNorm is already working and giving the same results as before but with way less code. Still a WIP, though. Closes <a href="/bob/bob.bio.base/-/issues/166" data-reference-type="issue" data-original="bob/bob.bio.base#166" data-link="false" data-link-reference="false" data-project="1379" data-issue="5180" data-project-path="bob/bob.bio.base" data-iid="166" data-issue-type="issue" data-container="body" data-placement="top" title="Score normalization pipeline needs some redesign" class="gfm gfm-issue">#166</a>
</li>
<li data-sourcepos="6:1-6:250">
<a href="/bob/bob.bio.base/-/merge_requests/273" data-reference-type="merge_request" data-original="bob/bob.bio.base!273" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6777" data-project-path="bob/bob.bio.base" data-iid="273" data-container="body" data-placement="top" title="Created an option to force the generation of checkpoints" class="gfm gfm-merge_request">!273</a> Created an option to force the generation of checkpoints: Created an option <code>bob bio pipelines vanilla-biometrics [COMMANDS] --force</code> to force the generation of checkpoints even if they already exist. Close <a href="/bob/bob.bio.base/-/issues/173" data-reference-type="issue" data-original="bob/bob.bio.base#173" data-link="false" data-link-reference="false" data-project="1379" data-issue="5199" data-project-path="bob/bob.bio.base" data-iid="173" data-issue-type="issue" data-container="body" data-placement="top" title="Create an option --force in the VanillaBiometrics CLI command...." class="gfm gfm-issue">#173</a>
</li>
<li data-sourcepos="7:1-7:309">
<a href="/bob/bob.bio.base/-/merge_requests/274" data-reference-type="merge_request" data-original="bob/bob.bio.base!274" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6791" data-project-path="bob/bob.bio.base" data-iid="274" data-container="body" data-placement="top" title="Algorithm to average on scores" class="gfm gfm-merge_request">!274</a> Algorithm to average on scores: Hi, This MR is to develop and add a new algorithm to calculate the final scores by calculating the average of scores over different reference samples of each user. The current version does the averaging on the feature values (in the <code>enroll()</code> function).</li>
<li data-sourcepos="8:1-8:67">
<a href="/bob/bob.bio.base/-/merge_requests/275" data-reference-type="merge_request" data-original="bob/bob.bio.base!275" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6909" data-project-path="bob/bob.bio.base" data-iid="275" data-container="body" data-placement="top" title="Cleaning up PLDA" class="gfm gfm-merge_request">!275</a> Cleaning up PLDA: Close <a href="/bob/bob.bio.base/-/issues/174" data-reference-type="issue" data-original="bob/bob.bio.base#174" data-link="false" data-link-reference="false" data-project="1379" data-issue="5325" data-project-path="bob/bob.bio.base" data-iid="174" data-issue-type="issue" data-container="body" data-placement="top" title="Nightlies failing here" class="gfm gfm-issue">#174</a>
</li>
<li data-sourcepos="9:1-9:46">
<a href="/bob/bob.bio.base/-/merge_requests/277" data-reference-type="merge_request" data-original="bob/bob.bio.base!277" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6950" data-project-path="bob/bob.bio.base" data-iid="277" data-container="body" data-placement="top" title="Remove bob learn linear" class="gfm gfm-merge_request">!277</a> Remove bob learn linear</li>
<li data-sourcepos="10:1-10:199">
<a href="/bob/bob.bio.base/-/merge_requests/276" data-reference-type="merge_request" data-original="bob/bob.bio.base!276" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6918" data-project-path="bob/bob.bio.base" data-iid="276" data-container="body" data-placement="top" title="Support bob tags in Vanilla-biometrics' Checkpoint Wrapper" class="gfm gfm-merge_request">!276</a> Support bob tags in Vanilla-biometrics' Checkpoint Wrapper: - Sets the save function with tags (for saving models). - Uses the <code>save()</code> method of the model object if it exists.</li>
<li data-sourcepos="11:1-11:418">
<a href="/bob/bob.bio.base/-/merge_requests/278" data-reference-type="merge_request" data-original="bob/bob.bio.base!278" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7005" data-project-path="bob/bob.bio.base" data-iid="278" data-container="body" data-placement="top" title="Created the CLI command bob bio pipelines transform" class="gfm gfm-merge_request">!278</a> Created the CLI command bob bio pipelines transform: This MR creates the command <code>bob bio pipelines transform</code> that, well, transforms whatever you have in a database. This can be useful for: * Crop all faces from a dataset * Extract features using a particular feature extractor * Preprocess some audio files using a particular pre-processor This addresses and closes issue <a href="/bob/bob.bio.base/-/issues/175" data-reference-type="issue" data-original="bob/bob.bio.base#175" data-link="false" data-link-reference="false" data-project="1379" data-issue="5330" data-project-path="bob/bob.bio.base" data-iid="175" data-issue-type="issue" data-container="body" data-placement="top" title="Script for feature extraction from database" class="gfm gfm-issue">#175</a>.</li>
<li data-sourcepos="12:1-12:185">
<a href="/bob/bob.bio.base/-/merge_requests/279" data-reference-type="merge_request" data-original="bob/bob.bio.base!279" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7018" data-project-path="bob/bob.bio.base" data-iid="279" data-container="body" data-placement="top" title="Fix protocols with the same name ending being mixed up" class="gfm gfm-merge_request">!279</a> Fix protocols with the same name ending being mixed up: CSVDataset protocols with the same ending in their name (e.g. <code>female</code> and <code>male</code>) are no longer mixed up.</li>
<li data-sourcepos="13:1-13:103">
<a href="/bob/bob.bio.base/-/merge_requests/280" data-reference-type="merge_request" data-original="bob/bob.bio.base!280" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7036" data-project-path="bob/bob.bio.base" data-iid="280" data-container="body" data-placement="top" title="Rename bob bio pipelines vanilla-biometrics commands" class="gfm gfm-merge_request">!280</a> Rename bob bio pipelines vanilla-biometrics commands: Fixes <a href="/bob/bob.bio.base/-/issues/177" data-reference-type="issue" data-original="bob/bob.bio.base#177" data-link="false" data-link-reference="false" data-project="1379" data-issue="5398" data-project-path="bob/bob.bio.base" data-iid="177" data-issue-type="issue" data-container="body" data-placement="top" title="bob bio pipelines vanilla-biometrics is a bad name" class="gfm gfm-issue">#177</a>
</li>
<li data-sourcepos="14:1-14:52">
<a href="/bob/bob.bio.base/-/merge_requests/281" data-reference-type="merge_request" data-original="bob/bob.bio.base!281" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7055" data-project-path="bob/bob.bio.base" data-iid="281" data-container="body" data-placement="top" title="Removed last trace of vanilla" class="gfm gfm-merge_request">!281</a> Removed last trace of vanilla</li>
<li data-sourcepos="15:1-15:177">
<a href="/bob/bob.bio.base/-/merge_requests/282" data-reference-type="merge_request" data-original="bob/bob.bio.base!282" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7076" data-project-path="bob/bob.bio.base" data-iid="282" data-container="body" data-placement="top" title="Remove instructions for installation of bob.db.atnt" class="gfm gfm-merge_request">!282</a> Remove instructions for installation of bob.db.atnt: The definition of atnt is now included in bob.bio.face. Fixed the doc telling to install bob.db.atnt.</li>
<li data-sourcepos="16:1-16:105">
<a href="/bob/bob.bio.base/-/merge_requests/283" data-reference-type="merge_request" data-original="bob/bob.bio.base!283" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7089" data-project-path="bob/bob.bio.base" data-iid="283" data-container="body" data-placement="top" title="Deprecating bob.db.base" class="gfm gfm-merge_request">!283</a> Deprecating bob.db.base: Deprecating bob.db.base, bob.math and bob.sp with this MR</li>
<li data-sourcepos="17:1-17:98">
<a href="/bob/bob.bio.base/-/merge_requests/284" data-reference-type="merge_request" data-original="bob/bob.bio.base!284" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7113" data-project-path="bob/bob.bio.base" data-iid="284" data-container="body" data-placement="top" title="[click] add --no-dask option to pipeline simple" class="gfm gfm-merge_request">!284</a> [click] add --no-dask option to pipeline simple: fixes <a href="/bob/bob.bio.base/-/issues/180" data-reference-type="issue" data-original="bob/bob.bio.base#180" data-link="false" data-link-reference="false" data-project="1379" data-issue="5435" data-project-path="bob/bob.bio.base" data-iid="180" data-issue-type="issue" data-container="body" data-placement="top" title="It is not possible to run experiments without dask wrapper" class="gfm gfm-issue">#180</a>
</li>
<li data-sourcepos="18:1-18:57">
<a href="/bob/bob.bio.base/-/merge_requests/285" data-reference-type="merge_request" data-original="bob/bob.bio.base!285" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7117" data-project-path="bob/bob.bio.base" data-iid="285" data-container="body" data-placement="top" title="Drop bob.db.atnt and add atnt here" class="gfm gfm-merge_request">!285</a> Drop bob.db.atnt and add atnt here</li>
<li data-sourcepos="19:1-19:57">
<a href="/bob/bob.bio.base/-/merge_requests/286" data-reference-type="merge_request" data-original="bob/bob.bio.base!286" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7123" data-project-path="bob/bob.bio.base" data-iid="286" data-container="body" data-placement="top" title="Add more support for atnt database" class="gfm gfm-merge_request">!286</a> Add more support for atnt database</li>
<li data-sourcepos="20:1-20:51">
<a href="/bob/bob.bio.base/-/merge_requests/287" data-reference-type="merge_request" data-original="bob/bob.bio.base!287" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7129" data-project-path="bob/bob.bio.base" data-iid="287" data-container="body" data-placement="top" title="Remove bob.core and bob.math" class="gfm gfm-merge_request">!287</a> Remove bob.core and bob.math</li>
<li data-sourcepos="21:1-21:136">
<a href="/bob/bob.bio.base/-/merge_requests/288" data-reference-type="merge_request" data-original="bob/bob.bio.base!288" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7140" data-project-path="bob/bob.bio.base" data-iid="288" data-container="body" data-placement="top" title="Fix of CSVDataset documentation" class="gfm gfm-merge_request">!288</a> Fix of CSVDataset documentation: Fixed the docstring of CSVDataset. Removed whitespaces in examples of CSV files.</li>
<li data-sourcepos="22:1-22:71">
<a href="/bob/bob.bio.base/-/merge_requests/289" data-reference-type="merge_request" data-original="bob/bob.bio.base!289" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7175" data-project-path="bob/bob.bio.base" data-iid="289" data-container="body" data-placement="top" title="Fix circular imports" class="gfm gfm-merge_request">!289</a> Fix circular imports: Fixes <a href="/bob/bob.bio.base/-/issues/182" data-reference-type="issue" data-original="bob/bob.bio.base#182" data-link="false" data-link-reference="false" data-project="1379" data-issue="5476" data-project-path="bob/bob.bio.base" data-iid="182" data-issue-type="issue" data-container="body" data-placement="top" title="Unable to run the pipeline after the last update of bob.bio.base" class="gfm gfm-issue">#182</a>
</li>
<li data-sourcepos="23:1-23:202">
<a href="/bob/bob.bio.base/-/merge_requests/292" data-reference-type="merge_request" data-original="bob/bob.bio.base!292" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7223" data-project-path="bob/bob.bio.base" data-iid="292" data-container="body" data-placement="top" title="replace is_estimator_stateless with estimator_requires_fit" class="gfm gfm-merge_request">!292</a> replace is_estimator_stateless with estimator_requires_fit: The actual code meant to check if an estimator requires fit or not while the function was named is_estimator_stateless.</li>
<li data-sourcepos="24:1-24:268">
<a href="/bob/bob.bio.base/-/merge_requests/290" data-reference-type="merge_request" data-original="bob/bob.bio.base!290" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7194" data-project-path="bob/bob.bio.base" data-iid="290" data-container="body" data-placement="top" title="PipelineSimple partitioning fixes" class="gfm gfm-merge_request">!290</a> PipelineSimple partitioning fixes: Redefined the heuristic for computing the dask partition sizes to prefer splitting the data between all the available workers. Allowed the user to define a number of partitions instead of only a partition size.</li>
<li data-sourcepos="25:1-25:135">
<a href="/bob/bob.bio.base/-/merge_requests/293" data-reference-type="merge_request" data-original="bob/bob.bio.base!293" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7224" data-project-path="bob/bob.bio.base" data-iid="293" data-container="body" data-placement="top" title="Fix partition-size being ignored" class="gfm gfm-merge_request">!293</a> Fix partition-size being ignored: Fixed <code>--partition-size</code> being ignored when dask-client is passed as a string.</li>
<li data-sourcepos="26:1-26:59">
<a href="/bob/bob.bio.base/-/merge_requests/294" data-reference-type="merge_request" data-original="bob/bob.bio.base!294" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7242" data-project-path="bob/bob.bio.base" data-iid="294" data-container="body" data-placement="top" title="Add UBM-GMM, ISV, and JFA algorithms" class="gfm gfm-merge_request">!294</a> Add UBM-GMM, ISV, and JFA algorithms</li>
<li data-sourcepos="27:1-27:145">
<a href="/bob/bob.bio.base/-/merge_requests/295" data-reference-type="merge_request" data-original="bob/bob.bio.base!295" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7263" data-project-path="bob/bob.bio.base" data-iid="295" data-container="body" data-placement="top" title="Fixes for bob.pipelines changes and docs improvements" class="gfm gfm-merge_request">!295</a> Fixes for bob.pipelines changes and docs improvements: Follow the changes of <a href="/bob/bob.pipelines/-/merge_requests/91" data-reference-type="merge_request" data-original="bob.pipelines!91" data-link="false" data-link-reference="false" data-project="3609" data-merge-request="7246" data-project-path="bob/bob.pipelines" data-iid="91" data-container="body" data-placement="top" title="Many API changes" class="gfm gfm-merge_request">bob.pipelines!91</a>. Fixes <a href="/bob/bob.bio.base/-/issues/184" data-reference-type="issue" data-original="bob/bob.bio.base#184" data-link="false" data-link-reference="false" data-project="1379" data-issue="5489" data-project-path="bob/bob.bio.base" data-iid="184" data-issue-type="issue" data-container="body" data-placement="top" title="cannot import 'isinstance_nested' from 'bob.pipelines.utils'" class="gfm gfm-issue">#184</a>.</li>
<li data-sourcepos="28:1-28:75">
<a href="/bob/bob.bio.base/-/merge_requests/297" data-reference-type="merge_request" data-original="bob/bob.bio.base!297" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7272" data-project-path="bob/bob.bio.base" data-iid="297" data-container="body" data-placement="top" title="Fix _data_valid function" class="gfm gfm-merge_request">!297</a> Fix _data_valid function: Fixes <a href="/bob/bob.bio.base/-/issues/185" data-reference-type="issue" data-original="bob/bob.bio.base#185" data-link="false" data-link-reference="false" data-project="1379" data-issue="5491" data-project-path="bob/bob.bio.base" data-iid="185" data-issue-type="issue" data-container="body" data-placement="top" title="Probe template not accepted if not numpy array" class="gfm gfm-issue">#185</a>
</li>
<li data-sourcepos="29:1-29:331">
<a href="/bob/bob.bio.base/-/merge_requests/296" data-reference-type="merge_request" data-original="bob/bob.bio.base!296" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7264" data-project-path="bob/bob.bio.base" data-iid="296" data-container="body" data-placement="top" title="Changed the API of BioAlgorithm and score post processors" class="gfm gfm-merge_request">!296</a> Changed the API of BioAlgorithm and score post processors: Removed the old Algorithm class and its legacy support Renamed allow_scoring_with_all_biometric_references to score_all_vs_all Changed the API of score post_processors, closes <a href="/bob/bob.bio.base/-/issues/179" data-reference-type="issue" data-original="bob/bob.bio.base#179" data-link="false" data-link-reference="false" data-project="1379" data-issue="5428" data-project-path="bob/bob.bio.base" data-iid="179" data-issue-type="issue" data-container="body" data-placement="top" title="Pass post_process_samples, biometric_references, and probe_samples together" class="gfm gfm-issue">#179</a> and <a href="/bob/bob.bio.base/-/merge_requests/291" data-reference-type="merge_request" data-original="bob/bob.bio.base!291" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7200" data-project-path="bob/bob.bio.base" data-iid="291" data-container="body" data-placement="top" title="Remove post processor selection" class="gfm gfm-merge_request">!291</a> Update the docs accordingly</li>
<li data-sourcepos="30:1-30:279">
<a href="/bob/bob.bio.base/-/merge_requests/298" data-reference-type="merge_request" data-original="bob/bob.bio.base!298" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7287" data-project-path="bob/bob.bio.base" data-iid="298" data-container="body" data-placement="top" title="Follow up of !296" class="gfm gfm-merge_request">!298</a> Follow up of <a href="/bob/bob.bio.base/-/merge_requests/296" data-reference-type="merge_request" data-original="bob/bob.bio.base!296" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="7264" data-project-path="bob/bob.bio.base" data-iid="296" data-container="body" data-placement="top" title="Changed the API of BioAlgorithm and score post processors" class="gfm gfm-merge_request">!296</a>: - Update the docs of distance algorithm - Make PipelineScoreNorm behave like PipelineSimple - Remove dask_score_normalization_pipeline as it was not needed and it was confusing - Add test cases for pipeline click commands</li>
</ul>2022-06-15T12:52:18ZYannick DAYERhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v6.0.0v6.0.0<ul data-sourcepos="1:1-21:78" dir="auto">
<li data-sourcepos="1:1-1:111">
<a href="/bob/bob.bio.base/-/merge_requests/249" data-reference-type="merge_request" data-original="bob/bob.bio.base!249" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6213" data-project-path="bob/bob.bio.base" data-iid="249" data-container="body" data-placement="top" title="Allow a CSVDataset to define `fetch_probes`." class="gfm gfm-merge_request">!249</a> Allow a CSVDataset to define <code>fetch_probes</code>.: Needed by replaymobile-img in bob.bio.face</li>
<li data-sourcepos="2:1-2:57">
<a href="/bob/bob.bio.base/-/merge_requests/248" data-reference-type="merge_request" data-original="bob/bob.bio.base!248" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6212" data-project-path="bob/bob.bio.base" data-iid="248" data-container="body" data-placement="top" title="Support invalid samples and scores" class="gfm gfm-merge_request">!248</a> Support invalid samples and scores</li>
<li data-sourcepos="3:1-3:241">
<a href="/bob/bob.bio.base/-/merge_requests/247" data-reference-type="merge_request" data-original="bob/bob.bio.base!247" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6182" data-project-path="bob/bob.bio.base" data-iid="247" data-container="body" data-placement="top" title="Multiple Improvements" class="gfm gfm-merge_request">!247</a> Multiple Improvements: * Improve the documentation * Refactor database interfaces * Some misc fixes Fixes <a href="/bob/bob.bio.base/-/issues/154" data-reference-type="issue" data-original="bob/bob.bio.base#154" data-link="false" data-link-reference="false" data-project="1379" data-issue="4958" data-project-path="bob/bob.bio.base" data-iid="154" data-issue-type="issue" data-container="body" data-placement="top" title="BioAlgorithm.score is never used (?)" class="gfm gfm-issue">#154</a> <a href="/bob/bob.bio.base/-/issues/153" data-reference-type="issue" data-original="bob/bob.bio.base#153" data-link="false" data-link-reference="false" data-project="1379" data-issue="4955" data-project-path="bob/bob.bio.base" data-iid="153" data-issue-type="issue" data-container="body" data-placement="top" title="The docs for creating a custom pipeline are confusing" class="gfm gfm-issue">#153</a> <a href="/bob/bob.bio.base/-/issues/102" data-reference-type="issue" data-original="bob/bob.bio.base#102" data-link="false" data-link-reference="false" data-project="1379" data-issue="2615" data-project-path="bob/bob.bio.base" data-iid="102" data-issue-type="issue" data-container="body" data-placement="top" title="asking users to run the tests after installation confuses the users" class="gfm gfm-issue">#102</a> <a href="/bob/bob.bio.base/-/issues/137" data-reference-type="issue" data-original="bob/bob.bio.base#137" data-link="false" data-link-reference="false" data-project="1379" data-issue="4635" data-project-path="bob/bob.bio.base" data-iid="137" data-issue-type="issue" data-container="body" data-placement="top" title='Follow-up from "Correct the chain loading and click implementation"' class="gfm gfm-issue">#137</a> <a href="/bob/bob.bio.base/-/issues/144" data-reference-type="issue" data-original="bob/bob.bio.base#144" data-link="false" data-link-reference="false" data-project="1379" data-issue="4669" data-project-path="bob/bob.bio.base" data-iid="144" data-issue-type="issue" data-container="body" data-placement="top" title="Installation instructions should point to bob/docs" class="gfm gfm-issue">#144</a>
</li>
<li data-sourcepos="4:1-4:87">
<a href="/bob/bob.bio.base/-/merge_requests/243" data-reference-type="merge_request" data-original="bob/bob.bio.base!243" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6023" data-project-path="bob/bob.bio.base" data-iid="243" data-container="body" data-placement="top" title="Add the vulnerability analysis commands" class="gfm gfm-merge_request">!243</a> Add the vulnerability analysis commands: Moved from bob.pad.base</li>
<li data-sourcepos="5:1-5:96">
<a href="/bob/bob.bio.base/-/merge_requests/244" data-reference-type="merge_request" data-original="bob/bob.bio.base!244" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6025" data-project-path="bob/bob.bio.base" data-iid="244" data-container="body" data-placement="top" title="Update of the vulnerability analysis commands" class="gfm gfm-merge_request">!244</a> Update of the vulnerability analysis commands: Accepting CSV score files.</li>
<li data-sourcepos="6:1-6:128">
<a href="/bob/bob.bio.base/-/merge_requests/246" data-reference-type="merge_request" data-original="bob/bob.bio.base!246" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6165" data-project-path="bob/bob.bio.base" data-iid="246" data-container="body" data-placement="top" title="Vulnerability analysis documentation" class="gfm gfm-merge_request">!246</a> Vulnerability analysis documentation: Adding documentation on how to evaluate a system for vulnerability.</li>
<li data-sourcepos="7:1-7:344">
<a href="/bob/bob.bio.base/-/merge_requests/252" data-reference-type="merge_request" data-original="bob/bob.bio.base!252" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6268" data-project-path="bob/bob.bio.base" data-iid="252" data-container="body" data-placement="top" title="[legacy] Changed the way vanilla-biometric pipelines are checkpoint wrapped by..." class="gfm gfm-merge_request">!252</a> [legacy] Changed the way vanilla-biometric pipelines are checkpoint wrapped by...: [legacy] Changed the way vanilla-biometric pipelines are checkpoint wrapped by using the bob_features_save_fn and bob_features_load_fn tags This would allow us more flexibility with estimators that already handle <code>bob.pipeline.Samples</code>
</li>
<li data-sourcepos="8:1-8:206">
<a href="/bob/bob.bio.base/-/merge_requests/253" data-reference-type="merge_request" data-original="bob/bob.bio.base!253" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6271" data-project-path="bob/bob.bio.base" data-iid="253" data-container="body" data-placement="top" title="Vulnerability: Add a SampleLoader that prevents negative attack scores computation" class="gfm gfm-merge_request">!253</a> Vulnerability: Add a SampleLoader that prevents negative attack scores computation: Adds a <code>references</code> list to the samples to prevent attack probes to be compared to every reference.</li>
<li data-sourcepos="9:1-9:271">
<a href="/bob/bob.bio.base/-/merge_requests/250" data-reference-type="merge_request" data-original="bob/bob.bio.base!250" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6259" data-project-path="bob/bob.bio.base" data-iid="250" data-container="body" data-placement="top" title="Supporting the CSVWriter in our evaluation scripts" class="gfm gfm-merge_request">!250</a> Supporting the CSVWriter in our evaluation scripts: So far <code>bob bio evaluate</code> (and it's siblings) does not have support for scores written with <code>CSVScoreWriter</code> (<code>bob bio pipelines vanilla-biometrics --write-metadata-scores</code>). This MR fixes that</li>
<li data-sourcepos="10:1-10:306">
<a href="/bob/bob.bio.base/-/merge_requests/254" data-reference-type="merge_request" data-original="bob/bob.bio.base!254" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6283" data-project-path="bob/bob.bio.base" data-iid="254" data-container="body" data-placement="top" title="Update the vulnerability dataset loading method" class="gfm gfm-merge_request">!254</a> Update the vulnerability dataset loading method: - Removed <code>SampleLoaderVulnerability</code> -- Use a normal CSVDataset with <code>SampleLoaderBiometric</code> and <code>is_parse</code> flag instead. - Updated the doc to represent this change and how to build the CSV protocol files for using with <code>is_sparse</code>.</li>
<li data-sourcepos="11:1-11:433">
<a href="/bob/bob.bio.base/-/merge_requests/255" data-reference-type="merge_request" data-original="bob/bob.bio.base!255" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6286" data-project-path="bob/bob.bio.base" data-iid="255" data-container="body" data-placement="top" title="Updates" class="gfm gfm-merge_request">!255</a> Updates: Two updates in the MR. - First, I updated the extension of the ZTNorm score files to <code>.csv</code> - Second, we should return delayed objects while reading the scores in <code>get_split_dataframe</code>. This avoids larger than memory problems. Imagine the scenario where 10 score files with 5.5GB each need to be processed; the code will possibly break at this point. Delaying these readings alleviates this issue.</li>
<li data-sourcepos="12:1-12:364">
<a href="/bob/bob.bio.base/-/merge_requests/256" data-reference-type="merge_request" data-original="bob/bob.bio.base!256" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6292" data-project-path="bob/bob.bio.base" data-iid="256" data-container="body" data-placement="top" title="Solving possible race condition issues with certain datasets" class="gfm gfm-merge_request">!256</a> Solving possible race condition issues with certain datasets: In some legacy datasets, the same sample can work as a biometric reference and probe. Running distributed experiments might trigger some racing conditions. Since our file system has no file locking mechanism, we might face some random and bizarre bugs. This MR fixes the issue.</li>
<li data-sourcepos="13:1-13:179">
<a href="/bob/bob.bio.base/-/merge_requests/251" data-reference-type="merge_request" data-original="bob/bob.bio.base!251" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6267" data-project-path="bob/bob.bio.base" data-iid="251" data-container="body" data-placement="top" title="Use the CSV ScoreWriter by default in bob pipelines vanilla-biometrics" class="gfm gfm-merge_request">!251</a> Use the CSV ScoreWriter by default in bob pipelines vanilla-biometrics: Adds a Click option to choose between CSV and four-column scores, defaulting to CSV.</li>
<li data-sourcepos="14:1-14:121">
<a href="/bob/bob.bio.base/-/merge_requests/259" data-reference-type="merge_request" data-original="bob/bob.bio.base!259" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6370" data-project-path="bob/bob.bio.base" data-iid="259" data-container="body" data-placement="top" title='Resolve "score_reduction_algorithm in BioAlgorithm cannot be changed"' class="gfm gfm-merge_request">!259</a> Resolve "score_reduction_algorithm in BioAlgorithm cannot be changed": Closes <a href="/bob/bob.bio.base/-/issues/159" data-reference-type="issue" data-original="bob/bob.bio.base#159" data-link="false" data-link-reference="false" data-project="1379" data-issue="5027" data-project-path="bob/bob.bio.base" data-iid="159" data-issue-type="issue" data-container="body" data-placement="top" title="score_reduction_algorithm in BioAlgorithm cannot be changed" class="gfm gfm-issue">#159</a>
</li>
<li data-sourcepos="15:1-15:259">
<a href="/bob/bob.bio.base/-/merge_requests/261" data-reference-type="merge_request" data-original="bob/bob.bio.base!261" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6382" data-project-path="bob/bob.bio.base" data-iid="261" data-container="body" data-placement="top" title="Implemented the hash_fn mechanism into the biometric algorithm" class="gfm gfm-merge_request">!261</a> Implemented the hash_fn mechanism into the biometric algorithm: This will handle cases where we have thousands of biometric references to be enrolled. Do you mind reviewing this one <a href="/lcolbois" data-reference-type="user" data-user="721" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Laurent COLBOIS">@lcolbois</a> Thanks Closes <a href="/bob/bob.bio.base/-/issues/161" data-reference-type="issue" data-original="bob/bob.bio.base#161" data-link="false" data-link-reference="false" data-project="1379" data-issue="5031" data-project-path="bob/bob.bio.base" data-iid="161" data-issue-type="issue" data-container="body" data-placement="top" title="Implement a hash_fn mechanism implemented on bob.pipelines in the BiometricAlgorithm" class="gfm gfm-issue">#161</a>
</li>
<li data-sourcepos="16:1-16:461">
<a href="/bob/bob.bio.base/-/merge_requests/262" data-reference-type="merge_request" data-original="bob/bob.bio.base!262" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6398" data-project-path="bob/bob.bio.base" data-iid="262" data-container="body" data-placement="top" title="[CSVDataset] Expose option to group the probes in SampleSets by reference id" class="gfm gfm-merge_request">!262</a> [CSVDataset] Expose option to group the probes in SampleSets by reference id: This is necessary for the protocol "2.0.2" of bob.bio.face.database.frgc, in which probe reference templates are formed from a set of 4 probe images, which should be regrouped in a single SampleSet. cf. <a href="https://gitlab.idiap.ch/bob/bob.bio.face/-/merge_requests/139" data-reference-type="merge_request" data-original="https://gitlab.idiap.ch/bob/bob.bio.face/-/merge_requests/139" data-link="false" data-link-reference="true" data-project="1382" data-merge-request="6384" data-project-path="bob/bob.bio.face" data-iid="139" data-container="body" data-placement="top" title="FRGC fixes" class="gfm gfm-merge_request">bob.bio.face!139</a> <a href="/tiago.pereira" data-reference-type="user" data-user="134" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Tiago de Freitas Pereira">@tiago.pereira</a> could you please have a look at it as we discussed it together yesterday ?</li>
<li data-sourcepos="17:1-17:83">
<a href="/bob/bob.bio.base/-/merge_requests/263" data-reference-type="merge_request" data-original="bob/bob.bio.base!263" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6416" data-project-path="bob/bob.bio.base" data-iid="263" data-container="body" data-placement="top" title="Updated legacy checkpoint wrapper to used pickle+gzip format" class="gfm gfm-merge_request">!263</a> Updated legacy checkpoint wrapper to used pickle+gzip format</li>
<li data-sourcepos="18:1-18:281">
<a href="/bob/bob.bio.base/-/merge_requests/264" data-reference-type="merge_request" data-original="bob/bob.bio.base!264" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6443" data-project-path="bob/bob.bio.base" data-iid="264" data-container="body" data-placement="top" title="Making Distance algorithm (enroll and scoring) more robust while different..." class="gfm gfm-merge_request">!264</a> Making Distance algorithm (enroll and scoring) more robust while different...: Making Distance algorithm (enroll and scoring) more robust while different sources of data is provided. Related to <a href="https://gitlab.idiap.ch/bob/bob.bio.video/-/merge_requests/46" data-reference-type="merge_request" data-original="https://gitlab.idiap.ch/bob/bob.bio.video/-/merge_requests/46" data-link="false" data-link-reference="true" data-project="1387" data-merge-request="6439" data-project-path="bob/bob.bio.video" data-iid="46" data-container="body" data-placement="top" title="Video support" class="gfm gfm-merge_request">bob.bio.video!46</a>
</li>
<li data-sourcepos="19:1-19:71">
<a href="/bob/bob.bio.base/-/merge_requests/258" data-reference-type="merge_request" data-original="bob/bob.bio.base!258" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6321" data-project-path="bob/bob.bio.base" data-iid="258" data-container="body" data-placement="top" title="Allow reading a mix of old and new format scores" class="gfm gfm-merge_request">!258</a> Allow reading a mix of old and new format scores</li>
<li data-sourcepos="20:1-20:184">
<a href="/bob/bob.bio.base/-/merge_requests/265" data-reference-type="merge_request" data-original="bob/bob.bio.base!265" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6464" data-project-path="bob/bob.bio.base" data-iid="265" data-container="body" data-placement="top" title="[score][load] Always sort scores when sort=True" class="gfm gfm-merge_request">!265</a> [score][load] Always sort scores when sort=True: Fixes a bug introduced in <a href="/bob/bob.bio.base/-/merge_requests/258" data-reference-type="merge_request" data-original="bob/bob.bio.base!258" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6321" data-project-path="bob/bob.bio.base" data-iid="258" data-container="body" data-placement="top" title="Allow reading a mix of old and new format scores" class="gfm gfm-merge_request">!258</a> where scores were not being sorted when the file was a csv file.</li>
<li data-sourcepos="21:1-21:78">
<a href="/bob/bob.bio.base/-/merge_requests/266" data-reference-type="merge_request" data-original="bob/bob.bio.base!266" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6584" data-project-path="bob/bob.bio.base" data-iid="266" data-container="body" data-placement="top" title="Changed the DIR axis names" class="gfm gfm-merge_request">!266</a> Changed the DIR axis names: closes <a href="/bob/bob.bio.base/-/issues/158" data-reference-type="issue" data-original="bob/bob.bio.base#158" data-link="false" data-link-reference="false" data-project="1379" data-issue="5026" data-project-path="bob/bob.bio.base" data-iid="158" data-issue-type="issue" data-container="body" data-placement="top" title="DIR curve should be updated to PNIR vs. FPIR curve" class="gfm gfm-issue">#158</a>
</li>
</ul>2021-11-03T19:52:58ZAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v5.0.0v5.0.0<ul data-sourcepos="1:1-45:233" dir="auto">
<li data-sourcepos="1:1-1:1488">
<a href="/bob/bob.bio.base/-/merge_requests/200" data-reference-type="merge_request" data-original="bob/bob.bio.base!200" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5515" data-project-path="bob/bob.bio.base" data-iid="200" data-container="body" data-placement="top" title="Database interface" class="gfm gfm-merge_request">!200</a> Database interface: Implemented a simple filelist database interface for the VanillaBiometrics based on CSVFiles. The <code>CSVDatasetDevEval</code> needs to have the following format: <code>text my_dataset/ my_dataset/my_protocol/ my_dataset/my_protocol/train.csv my_dataset/my_protocol/train.csv/dev_enroll.csv my_dataset/my_protocol/train.csv/dev_probe.csv my_dataset/my_protocol/train.csv/eval_enroll.csv my_dataset/my_protocol/train.csv/eval_probe.csv ... </code> where each CSV file needs to have the following format: <code>text PATH,SUBJECT path_1,subject_1 path_2,subject_2 path_i,subject_j </code> This formart allows the usage of metadata by following the pattern below: <code>text PATH,SUBJECT,METADATA_1,METADATA_2,METADATA_k path_1,subject_1,A,B,C path_2,subject_2,A,B,1 path_i,subject_j,2,3,4 </code> We can imagine other implementations of this. For instance, <code>CSVDatasetCrossValidation</code> that given a csv file, it splits "on-the-fly" several data for enrolling, probing and training. Or <code>CSVDatasetWithEyesAnnotation</code>, that handles annotations for Face Rec pipelines. I still need to implement a mechanism that takes <code>zip</code> files as input to <code>CSVDatasetDevEval</code>. That way we can ship databases as simple zip files ping <a href="/ydayer" data-reference-type="user" data-user="609" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Yannick DAYER">@ydayer</a> <a href="/amohammadi" data-reference-type="user" data-user="277" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Amir MOHAMMADI">@amohammadi</a> I'll merge this tomorrow. I need this to support the efforts on <code>bob.bio.vein</code>.</li>
<li data-sourcepos="2:1-2:213">
<a href="/bob/bob.bio.base/-/merge_requests/201" data-reference-type="merge_request" data-original="bob/bob.bio.base!201" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5520" data-project-path="bob/bob.bio.base" data-iid="201" data-container="body" data-placement="top" title="Correct the chain loading and click implementation" class="gfm gfm-merge_request">!201</a> Correct the chain loading and click implementation: The vanilla biometrics script was not using our click API correctly, this fixes that. Please refer to bob.extension's docs for more info.</li>
<li data-sourcepos="3:1-3:145">
<a href="/bob/bob.bio.base/-/merge_requests/194" data-reference-type="merge_request" data-original="bob/bob.bio.base!194" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5376" data-project-path="bob/bob.bio.base" data-iid="194" data-container="body" data-placement="top" title="New documentation bob.bio.base" class="gfm gfm-merge_request">!194</a> New documentation bob.bio.base: Redoing bob.bio.base documentation We might rebrand this package to <code>scikit-biometrics</code>
</li>
<li data-sourcepos="4:1-4:265">
<a href="/bob/bob.bio.base/-/merge_requests/203" data-reference-type="merge_request" data-original="bob/bob.bio.base!203" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5585" data-project-path="bob/bob.bio.base" data-iid="203" data-container="body" data-placement="top" title="Fix Dask shutting down automatically when calling from a script" class="gfm gfm-merge_request">!203</a> Fix Dask shutting down automatically when calling from a script: Defers the shutdown task to the user by putting the execution of Vanilla-Biometrics in its own function. The <code>bob bio pipelines vanilla-biometrics</code> command calls this function.</li>
<li data-sourcepos="5:1-5:1108">
<a href="/bob/bob.bio.base/-/merge_requests/180" data-reference-type="merge_request" data-original="bob/bob.bio.base!180" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="4931" data-project-path="bob/bob.bio.base" data-iid="180" data-container="body" data-placement="top" title="[dask] Preparing bob.bio.base for dask pipelines" class="gfm gfm-merge_request">!180</a> [dask] Preparing bob.bio.base for dask pipelines: <strong>THIS IS A WIP</strong> Working out how <code>bob.bio.base</code> should be with dask pipelines. Some things to be done in the MR is. - [x] Remove all traces of <code>verify.py</code>. Pipelines needs to be defined with dask. This includes the removal of: <code>FileSelector</code>, <code>Grid</code> configurations, <code>./script/grid_search</code>, <code>./script/enroll</code>, <code>./script/extract</code>, <code>./script/preprocess</code>, <code>./baselines</code> - [x] Move the biometrics pipeline from <code>bob.pipelines</code> to here - [ ] Document the package on: 1-) How to use the resources available (databases, algorithms, preprocessors, etc..), 2-) How to create new databases, 3-) How to create new pipelines (this should be in bob.pipelines) - [x] Rethink the file list interface - [ ] Review which dependencies to keep. For instance, <code>bob.learn.linear</code>, <code>bob.learn.em</code>, <code>bob.learn.activation</code>, <code>bob.math</code> (consider use scikit-learn). - [x] Implement missing pipelines (for instance, score normalization/calibration pipeline) - [x] Database paths patched in <code>~/.bobrc</code> - [ ] Redesign the resource.py as CLI commands</li>
<li data-sourcepos="6:1-6:228">
<a href="/bob/bob.bio.base/-/merge_requests/204" data-reference-type="merge_request" data-original="bob/bob.bio.base!204" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5653" data-project-path="bob/bob.bio.base" data-iid="204" data-container="body" data-placement="top" title="Remove stackable preprocessors and extractors" class="gfm gfm-merge_request">!204</a> Remove stackable preprocessors and extractors: Now that we have standardized on scikit-learn transformers, scikit-learn alternatives such as FunctionTransformer, Pipeline, and FeatureUnion should be used</li>
<li data-sourcepos="7:1-7:38">
<a href="/bob/bob.bio.base/-/merge_requests/202" data-reference-type="merge_request" data-original="bob/bob.bio.base!202" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5563" data-project-path="bob/bob.bio.base" data-iid="202" data-container="body" data-placement="top" title="Dask annotators" class="gfm gfm-merge_request">!202</a> Dask annotators</li>
<li data-sourcepos="8:1-8:177">
<a href="/bob/bob.bio.base/-/merge_requests/205" data-reference-type="merge_request" data-original="bob/bob.bio.base!205" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5657" data-project-path="bob/bob.bio.base" data-iid="205" data-container="body" data-placement="top" title="Fix annotators kwargs" class="gfm gfm-merge_request">!205</a> Fix annotators kwargs: The kwargs were not passed correctly in the FailSafe annotator. Removed the shutdown of dask clients in the <code>annotate</code> commands.</li>
<li data-sourcepos="9:1-9:35">
<a href="/bob/bob.bio.base/-/merge_requests/207" data-reference-type="merge_request" data-original="bob/bob.bio.base!207" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5663" data-project-path="bob/bob.bio.base" data-iid="207" data-container="body" data-placement="top" title="Fixed [typo]" class="gfm gfm-merge_request">!207</a> Fixed [typo]</li>
<li data-sourcepos="10:1-10:100">
<a href="/bob/bob.bio.base/-/merge_requests/206" data-reference-type="merge_request" data-original="bob/bob.bio.base!206" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5659" data-project-path="bob/bob.bio.base" data-iid="206" data-container="body" data-placement="top" title="Created decorators" class="gfm gfm-merge_request">!206</a> Created decorators: Added two decorators that checks <code>mxnet</code> and <code>tensorflow</code>
</li>
<li data-sourcepos="11:1-11:128">
<a href="/bob/bob.bio.base/-/merge_requests/208" data-reference-type="merge_request" data-original="bob/bob.bio.base!208" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5700" data-project-path="bob/bob.bio.base" data-iid="208" data-container="body" data-placement="top" title="Fixing sphinx warnings" class="gfm gfm-merge_request">!208</a> Fixing sphinx warnings: It's a WIP. I have 34 warnings to be fixed so far. ping <a href="/ydayer" data-reference-type="user" data-user="609" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Yannick DAYER">@ydayer</a> <a href="/amohammadi" data-reference-type="user" data-user="277" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Amir MOHAMMADI">@amohammadi</a>
</li>
<li data-sourcepos="12:1-12:66">
<a href="/bob/bob.bio.base/-/merge_requests/209" data-reference-type="merge_request" data-original="bob/bob.bio.base!209" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5704" data-project-path="bob/bob.bio.base" data-iid="209" data-container="body" data-placement="top" title="Putting annotator back to the documentation" class="gfm gfm-merge_request">!209</a> Putting annotator back to the documentation</li>
<li data-sourcepos="13:1-13:58">
<a href="/bob/bob.bio.base/-/merge_requests/210" data-reference-type="merge_request" data-original="bob/bob.bio.base!210" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5714" data-project-path="bob/bob.bio.base" data-iid="210" data-container="body" data-placement="top" title="[annotators][FailSafe] improvements" class="gfm gfm-merge_request">!210</a> [annotators][FailSafe] improvements</li>
<li data-sourcepos="14:1-14:130">
<a href="/bob/bob.bio.base/-/merge_requests/212" data-reference-type="merge_request" data-original="bob/bob.bio.base!212" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5720" data-project-path="bob/bob.bio.base" data-iid="212" data-container="body" data-placement="top" title="Improvements on CheckpointWrapper" class="gfm gfm-merge_request">!212</a> Improvements on CheckpointWrapper: Related to <a href="https://gitlab.idiap.ch/bob/bob.pipelines/-/merge_requests/48" data-reference-type="merge_request" data-original="https://gitlab.idiap.ch/bob/bob.pipelines/-/merge_requests/48" data-link="false" data-link-reference="true" data-project="3609" data-merge-request="5718" data-project-path="bob/bob.pipelines" data-iid="48" data-container="body" data-placement="top" title="Improvements on CheckpointWrapper" class="gfm gfm-merge_request">bob.pipelines!48</a>
</li>
<li data-sourcepos="15:1-15:165">
<a href="/bob/bob.bio.base/-/merge_requests/214" data-reference-type="merge_request" data-original="bob/bob.bio.base!214" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5722" data-project-path="bob/bob.bio.base" data-iid="214" data-container="body" data-placement="top" title="Optimize scoring if `allow_scoring_with_all_biometric_references == False`" class="gfm gfm-merge_request">!214</a> Optimize scoring if <code>allow_scoring_with_all_biometric_references == False</code>: ..by caching biometric references. This speeds things up by a lot</li>
<li data-sourcepos="16:1-16:99">
<a href="/bob/bob.bio.base/-/merge_requests/211" data-reference-type="merge_request" data-original="bob/bob.bio.base!211" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5716" data-project-path="bob/bob.bio.base" data-iid="211" data-container="body" data-placement="top" title="[legacy databases] delay loading of annotations" class="gfm gfm-merge_request">!211</a> [legacy databases] delay loading of annotations: Depends on <a href="/bob/bob.pipelines/-/merge_requests/47" data-reference-type="merge_request" data-original="bob.pipelines!47" data-link="false" data-link-reference="false" data-project="3609" data-merge-request="5715" data-project-path="bob/bob.pipelines" data-iid="47" data-container="body" data-placement="top" title="Multiple changes" class="gfm gfm-merge_request">bob.pipelines!47</a>
</li>
<li data-sourcepos="17:1-17:514">
<a href="/bob/bob.bio.base/-/merge_requests/213" data-reference-type="merge_request" data-original="bob/bob.bio.base!213" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5721" data-project-path="bob/bob.bio.base" data-iid="213" data-container="body" data-placement="top" title="[VanillaBiometrics] Make some dask arguments visible in the CLI commands" class="gfm gfm-merge_request">!213</a> [VanillaBiometrics] Make some dask arguments visible in the CLI commands: Sometimes our heuristics that defines <code>dask.bag.partition_size</code> and <code>n_workers</code> is not enough to cover all range of problems. In this MR I'm adding the options <code>--dask-partition-size</code> and <code>--dask-n-workers</code> in the <code>vanilla-biometrics</code> CLI command, so that users can explicitly set, respectively, the dask bag partition size and the number of workers to start an experiment without having to play around with the API.</li>
<li data-sourcepos="18:1-18:98">
<a href="/bob/bob.bio.base/-/merge_requests/216" data-reference-type="merge_request" data-original="bob/bob.bio.base!216" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5724" data-project-path="bob/bob.bio.base" data-iid="216" data-container="body" data-placement="top" title="[click][VanillaBiometrics] Fixed click options" class="gfm gfm-merge_request">!216</a> [click][VanillaBiometrics] Fixed click options: Closes <a href="/bob/bob.bio.base/-/issues/148" data-reference-type="issue" data-original="bob/bob.bio.base#148" data-link="false" data-link-reference="false" data-project="1379" data-issue="4708" data-project-path="bob/bob.bio.base" data-iid="148" data-issue-type="issue" data-container="body" data-placement="top" title='Follow-up from "[VanillaBiometrics] Make some dask arguments visible in the CLI commands"' class="gfm gfm-issue">#148</a>
</li>
<li data-sourcepos="19:1-19:153">
<a href="/bob/bob.bio.base/-/merge_requests/218" data-reference-type="merge_request" data-original="bob/bob.bio.base!218" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5726" data-project-path="bob/bob.bio.base" data-iid="218" data-container="body" data-placement="top" title="[test_utils] Do not re-download ATNT database" class="gfm gfm-merge_request">!218</a> [test_utils] Do not re-download ATNT database: if the data is already inside the low-level db package. Fixes <a href="/bob/bob.bio.base/-/issues/127" data-reference-type="issue" data-original="bob/bob.bio.base#127" data-link="false" data-link-reference="false" data-project="1379" data-issue="3208" data-project-path="bob/bob.bio.base" data-iid="127" data-issue-type="issue" data-container="body" data-placement="top" title="WARNING: Downloading the AT&T database" class="gfm gfm-issue">#127</a>
</li>
<li data-sourcepos="20:1-20:77">
<a href="/bob/bob.bio.base/-/merge_requests/219" data-reference-type="merge_request" data-original="bob/bob.bio.base!219" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5735" data-project-path="bob/bob.bio.base" data-iid="219" data-container="body" data-placement="top" title="Remove fiddling with bob.pipelines.Samples's internals" class="gfm gfm-merge_request">!219</a> Remove fiddling with bob.pipelines.Samples's internals</li>
<li data-sourcepos="21:1-21:217">
<a href="/bob/bob.bio.base/-/merge_requests/217" data-reference-type="merge_request" data-original="bob/bob.bio.base!217" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5725" data-project-path="bob/bob.bio.base" data-iid="217" data-container="body" data-placement="top" title="Add a method to retrieve all the samples of a dataset" class="gfm gfm-merge_request">!217</a> Add a method to retrieve all the samples of a dataset: Added a functionality to get all the samples at once. For legacy databases, it uses the all_files method. Closes <a href="/bob/bob.bio.base/-/issues/146" data-reference-type="issue" data-original="bob/bob.bio.base#146" data-link="false" data-link-reference="false" data-project="1379" data-issue="4701" data-project-path="bob/bob.bio.base" data-iid="146" data-issue-type="issue" data-container="body" data-placement="top" title="[API] Database interface - retrieve all samples" class="gfm gfm-issue">#146</a>
</li>
<li data-sourcepos="22:1-22:218">
<a href="/bob/bob.bio.base/-/merge_requests/220" data-reference-type="merge_request" data-original="bob/bob.bio.base!220" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5744" data-project-path="bob/bob.bio.base" data-iid="220" data-container="body" data-placement="top" title="[scripts][pipelines] allow dask-clients as strings" class="gfm gfm-merge_request">!220</a> [scripts][pipelines] allow dask-clients as strings: Some strings like single-threaded, processes, ... are now allowed as options for the dask-client click option. Depends on <a href="/bob/bob.extension/-/merge_requests/122" data-reference-type="merge_request" data-original="bob.extension!122" data-link="false" data-link-reference="false" data-project="1475" data-merge-request="5743" data-project-path="bob/bob.extension" data-iid="122" data-container="body" data-placement="top" title="[click_helper][ResourceOption] Allow exceptions when loading entry points" class="gfm gfm-merge_request">bob.extension!122</a>
</li>
<li data-sourcepos="23:1-23:85">
<a href="/bob/bob.bio.base/-/merge_requests/221" data-reference-type="merge_request" data-original="bob/bob.bio.base!221" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5745" data-project-path="bob/bob.bio.base" data-iid="221" data-container="body" data-placement="top" title="Added the memory_demanding attribute as part of the legacy APi" class="gfm gfm-merge_request">!221</a> Added the memory_demanding attribute as part of the legacy APi</li>
<li data-sourcepos="24:1-24:478">
<a href="/bob/bob.bio.base/-/merge_requests/222" data-reference-type="merge_request" data-original="bob/bob.bio.base!222" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5747" data-project-path="bob/bob.bio.base" data-iid="222" data-container="body" data-placement="top" title='Follow-up to "Add a method to retrieve all the samples of a dataset"' class="gfm gfm-merge_request">!222</a> Follow-up to "Add a method to retrieve all the samples of a dataset": Closes <a href="/bob/bob.bio.base/-/issues/149" data-reference-type="issue" data-original="bob/bob.bio.base#149" data-link="false" data-link-reference="false" data-project="1379" data-issue="4712" data-project-path="bob/bob.bio.base" data-iid="149" data-issue-type="issue" data-container="body" data-placement="top" title='Follow-up from "Add a method to retrieve all the samples of a dataset"' class="gfm gfm-issue">#149</a> The <code>all_samples</code> methods now correctly handles the 'train' group, returning only the samples of a group if that group is given as parameter. The 'groups' parameters contents are now verified with <code>bob.db.base.check_parameters_for_validity</code>. Groups of 'legacy database interfaces' different from 'train', 'dev', or 'eval' are now handled correctly.</li>
<li data-sourcepos="25:1-25:165">
<a href="/bob/bob.bio.base/-/merge_requests/223" data-reference-type="merge_request" data-original="bob/bob.bio.base!223" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5751" data-project-path="bob/bob.bio.base" data-iid="223" data-container="body" data-placement="top" title="Used the DelayedSampleSetCached in the BioAlgorithmCheckpointWrapper" class="gfm gfm-merge_request">!223</a> Used the DelayedSampleSetCached in the BioAlgorithmCheckpointWrapper: Depends on <a href="https://gitlab.idiap.ch/bob/bob.pipelines/-/merge_requests/53" data-reference-type="merge_request" data-original="https://gitlab.idiap.ch/bob/bob.pipelines/-/merge_requests/53" data-link="false" data-link-reference="true" data-project="3609" data-merge-request="5750" data-project-path="bob/bob.pipelines" data-iid="53" data-container="body" data-placement="top" title="Updates" class="gfm gfm-merge_request">bob.pipelines!53</a>
</li>
<li data-sourcepos="26:1-26:96">
<a href="/bob/bob.bio.base/-/merge_requests/225" data-reference-type="merge_request" data-original="bob/bob.bio.base!225" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5760" data-project-path="bob/bob.bio.base" data-iid="225" data-container="body" data-placement="top" title="[test.utils] Handle ModuleNotFoundError when bob.db.atnt is not available" class="gfm gfm-merge_request">!225</a> [test.utils] Handle ModuleNotFoundError when bob.db.atnt is not available</li>
<li data-sourcepos="27:1-27:90">
<a href="/bob/bob.bio.base/-/merge_requests/226" data-reference-type="merge_request" data-original="bob/bob.bio.base!226" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5774" data-project-path="bob/bob.bio.base" data-iid="226" data-container="body" data-placement="top" title="[legacy] Updated subject to reference_id in the lecacy DB interface" class="gfm gfm-merge_request">!226</a> [legacy] Updated subject to reference_id in the lecacy DB interface</li>
<li data-sourcepos="28:1-28:125">
<a href="/bob/bob.bio.base/-/merge_requests/227" data-reference-type="merge_request" data-original="bob/bob.bio.base!227" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5777" data-project-path="bob/bob.bio.base" data-iid="227" data-container="body" data-placement="top" title="Make compare samples work with DelayedSample instead of Sample" class="gfm gfm-merge_request">!227</a> Make compare samples work with DelayedSample instead of Sample: this allow us to use <code>bob.bio.rankone</code>
</li>
<li data-sourcepos="29:1-29:94">
<a href="/bob/bob.bio.base/-/merge_requests/230" data-reference-type="merge_request" data-original="bob/bob.bio.base!230" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5784" data-project-path="bob/bob.bio.base" data-iid="230" data-container="body" data-placement="top" title="[dask] Moved dask_get_partition_size from bob.bio.base to bob.pipelines" class="gfm gfm-merge_request">!230</a> [dask] Moved dask_get_partition_size from bob.bio.base to bob.pipelines</li>
<li data-sourcepos="30:1-30:419">
<a href="/bob/bob.bio.base/-/merge_requests/229" data-reference-type="merge_request" data-original="bob/bob.bio.base!229" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5780" data-project-path="bob/bob.bio.base" data-iid="229" data-container="body" data-placement="top" title="Check stateless" class="gfm gfm-merge_request">!229</a> Check stateless: Small change where background model samples are not loaded if the main pipeline is stateless. The world set typically is much larger than the dev and eval set, so it is a bit of a waste to load. NB. The make_pipeline utility from scikit-learn generates pipelines that are never stateless, even if all transformers in the sequence are stateless, which makes this change useful.</li>
<li data-sourcepos="31:1-31:71">
<a href="/bob/bob.bio.base/-/merge_requests/228" data-reference-type="merge_request" data-original="bob/bob.bio.base!228" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5779" data-project-path="bob/bob.bio.base" data-iid="228" data-container="body" data-placement="top" title="moved VALID_DASK_CLIENT_STRINGS to bob.pipelines" class="gfm gfm-merge_request">!228</a> moved VALID_DASK_CLIENT_STRINGS to bob.pipelines</li>
<li data-sourcepos="32:1-32:582">
<a href="/bob/bob.bio.base/-/merge_requests/224" data-reference-type="merge_request" data-original="bob/bob.bio.base!224" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5759" data-project-path="bob/bob.bio.base" data-iid="224" data-container="body" data-placement="top" title="Adapting CSVDevEval to work with our current FileList Structure" class="gfm gfm-merge_request">!224</a> Adapting CSVDevEval to work with our current FileList Structure: This is a WIP, which means Work in Progress. In this MR I structured the files from the proposed CSV interface to be the same as in the current FileList we have. Furthermore, the current <code>.lst</code> files can be used in the <code>CSVDatasetDevEval</code> with some of the bells and whistles the current LST files has (e.g usage of external annotations). The goal is of the MR is to: 1. Be able to use the current file lists we have 2. Allow the extra functionalities we currently have with the CSVs.</li>
<li data-sourcepos="33:1-33:80">
<a href="/bob/bob.bio.base/-/merge_requests/231" data-reference-type="merge_request" data-original="bob/bob.bio.base!231" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5789" data-project-path="bob/bob.bio.base" data-iid="231" data-container="body" data-placement="top" title="Renamed CSVDatasetDevEval to CSVDataset" class="gfm gfm-merge_request">!231</a> Renamed CSVDatasetDevEval to CSVDataset: .... it's easier</li>
<li data-sourcepos="34:1-34:32">
<a href="/bob/bob.bio.base/-/merge_requests/232" data-reference-type="merge_request" data-original="bob/bob.bio.base!232" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5793" data-project-path="bob/bob.bio.base" data-iid="232" data-container="body" data-placement="top" title="Move code" class="gfm gfm-merge_request">!232</a> Move code</li>
<li data-sourcepos="35:1-35:157">
<a href="/bob/bob.bio.base/-/merge_requests/233" data-reference-type="merge_request" data-original="bob/bob.bio.base!233" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5803" data-project-path="bob/bob.bio.base" data-iid="233" data-container="body" data-placement="top" title="CSVSampleLoaders as transformers" class="gfm gfm-merge_request">!233</a> CSVSampleLoaders as transformers: Depends on <a href="https://gitlab.idiap.ch/bob/bob.pipelines/-/merge_requests/60" data-reference-type="merge_request" data-original="https://gitlab.idiap.ch/bob/bob.pipelines/-/merge_requests/60" data-link="false" data-link-reference="true" data-project="3609" data-merge-request="5802" data-project-path="bob/bob.pipelines" data-iid="60" data-container="body" data-placement="top" title="CSVSampleLoaders as transformers" class="gfm gfm-merge_request">bob.pipelines!60</a> ping <a href="/amohammadi" data-reference-type="user" data-user="277" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Amir MOHAMMADI">@amohammadi</a> <a href="/ydayer" data-reference-type="user" data-user="609" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Yannick DAYER">@ydayer</a>
</li>
<li data-sourcepos="36:1-36:54">
<a href="/bob/bob.bio.base/-/merge_requests/234" data-reference-type="merge_request" data-original="bob/bob.bio.base!234" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5811" data-project-path="bob/bob.bio.base" data-iid="234" data-container="body" data-placement="top" title="Fixed issues in the ScoreWriter" class="gfm gfm-merge_request">!234</a> Fixed issues in the ScoreWriter</li>
<li data-sourcepos="37:1-37:148">
<a href="/bob/bob.bio.base/-/merge_requests/235" data-reference-type="merge_request" data-original="bob/bob.bio.base!235" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5815" data-project-path="bob/bob.bio.base" data-iid="235" data-container="body" data-placement="top" title="[ztnorm][scorewriter] Updates" class="gfm gfm-merge_request">!235</a> [ztnorm][scorewriter] Updates: - Used DelayedSampleSetCached in the ZTNormCheckpointWrapper - Cleaning up the CSVScoreWriter</li>
<li data-sourcepos="38:1-38:344">
<a href="/bob/bob.bio.base/-/merge_requests/236" data-reference-type="merge_request" data-original="bob/bob.bio.base!236" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5826" data-project-path="bob/bob.bio.base" data-iid="236" data-container="body" data-placement="top" title="[Fix] Correction of scores path" class="gfm gfm-merge_request">!236</a> [Fix] Correction of scores path: This fixes an issue introduced in <a href="https://gitlab.idiap.ch/bob/bob.bio.base/-/commit/cb83794da843358b822b8d75abfdecc1db7f770c#ffca3ee0885ed8d9ceff5bb4100ee9f6413bc6a5" data-reference-type="commit" data-original="this commit" data-link="true" data-link-reference="true" data-project="1379" data-commit="cb83794da843358b822b8d75abfdecc1db7f770c" data-container="body" data-placement="top" title="Fixed partition size isse with the ZT-Norm pipeline" class="gfm gfm-commit has-tooltip">this commit</a> where the path to the output scores file was wrong for non <code>.csv</code> score file format. ping <a href="/tiago.pereira" data-reference-type="user" data-user="134" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Tiago de Freitas Pereira">@tiago.pereira</a>
</li>
<li data-sourcepos="39:1-39:173">
<a href="/bob/bob.bio.base/-/merge_requests/238" data-reference-type="merge_request" data-original="bob/bob.bio.base!238" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5830" data-project-path="bob/bob.bio.base" data-iid="238" data-container="body" data-placement="top" title="Created the function `get_temp_directory`" class="gfm gfm-merge_request">!238</a> Created the function <code>get_temp_directory</code>: ... this is useful for legacy algorithms Related to <a href="https://gitlab.idiap.ch/bob/bob.bio.face/-/issues/39" data-reference-type="issue" data-original="https://gitlab.idiap.ch/bob/bob.bio.face/-/issues/39" data-link="false" data-link-reference="true" data-project="1382" data-issue="4751" data-project-path="bob/bob.bio.face" data-iid="39" data-issue-type="issue" data-container="body" data-placement="top" title="[LGBPHS] wrong tempfiles path when running on the grid" class="gfm gfm-issue">bob.bio.face#39</a>
</li>
<li data-sourcepos="40:1-40:96">
<a href="/bob/bob.bio.base/-/merge_requests/239" data-reference-type="merge_request" data-original="bob/bob.bio.base!239" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5908" data-project-path="bob/bob.bio.base" data-iid="239" data-container="body" data-placement="top" title="Raised a warning when data is not available to process vanilla-biometrics" class="gfm gfm-merge_request">!239</a> Raised a warning when data is not available to process vanilla-biometrics</li>
<li data-sourcepos="41:1-41:84">
<a href="/bob/bob.bio.base/-/merge_requests/240" data-reference-type="merge_request" data-original="bob/bob.bio.base!240" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5952" data-project-path="bob/bob.bio.base" data-iid="240" data-container="body" data-placement="top" title="Doc cleanup" class="gfm gfm-merge_request">!240</a> Doc cleanup: Did a pass in Grammaly and corrected the errors.</li>
<li data-sourcepos="42:1-42:412">
<a href="/bob/bob.bio.base/-/merge_requests/241" data-reference-type="merge_request" data-original="bob/bob.bio.base!241" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5956" data-project-path="bob/bob.bio.base" data-iid="241" data-container="body" data-placement="top" title="Legacy database wrapper was not supporting this properly supporting the use case where `model_id<>client_id`" class="gfm gfm-merge_request">!241</a> Legacy database wrapper was not supporting this properly supporting the use case where <code>model_id<>client_id</code>: Making the bob.bio.base database interface support samplesets where the <strong>reference_id</strong> is different from <strong>subject_id</strong>. There are some databases protocols that needs such support. Furthermore the legacy database interface was not supporting this properly ping <a href="/mguenther" data-reference-type="user" data-user="320" data-container="body" data-placement="top" class="gfm gfm-project_member js-user-link" title="Manuel Günther">@mguenther</a>
</li>
<li data-sourcepos="43:1-43:109">
<a href="/bob/bob.bio.base/-/merge_requests/242" data-reference-type="merge_request" data-original="bob/bob.bio.base!242" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6001" data-project-path="bob/bob.bio.base" data-iid="242" data-container="body" data-placement="top" title="[bob.piplines] sample loaders have moved in bob.pipelines" class="gfm gfm-merge_request">!242</a> [bob.piplines] sample loaders have moved in bob.pipelines: Depends on <a href="/bob/bob.pipelines/-/merge_requests/62" data-reference-type="merge_request" data-original="bob.pipelines!62" data-link="false" data-link-reference="false" data-project="3609" data-merge-request="5986" data-project-path="bob/bob.pipelines" data-iid="62" data-container="body" data-placement="top" title="Implement a new simple generic csv-based database interface" class="gfm gfm-merge_request">bob.pipelines!62</a>
</li>
<li data-sourcepos="44:1-44:87">
<a href="/bob/bob.bio.base/-/merge_requests/243" data-reference-type="merge_request" data-original="bob/bob.bio.base!243" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6023" data-project-path="bob/bob.bio.base" data-iid="243" data-container="body" data-placement="top" title="Add the vulnerability analysis commands" class="gfm gfm-merge_request">!243</a> Add the vulnerability analysis commands: Moved from bob.pad.base</li>
<li data-sourcepos="45:1-45:233">
<a href="/bob/bob.bio.base/-/merge_requests/245" data-reference-type="merge_request" data-original="bob/bob.bio.base!245" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="6050" data-project-path="bob/bob.bio.base" data-iid="245" data-container="body" data-placement="top" title="Score checkpoint are more robust" class="gfm gfm-merge_request">!245</a> Score checkpoint are more robust: In this MR I'm changing the way we checkpoint scores. I moved from the joblib pickling to pickle and compress with gzip myself. This seems more robust with our file system.</li>
</ul>2021-04-13T17:08:31ZAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v4.1.2b0v4.1.2b0First beta [skip-ci]Tiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v4.1.1v4.1.1<ul data-sourcepos="1:1-4:580" dir="auto">
<li data-sourcepos="1:1-1:91">
<a href="/bob/bob.bio.base/-/merge_requests/183" data-reference-type="merge_request" data-original="bob/bob.bio.base!183" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="4993" data-project-path="bob/bob.bio.base" data-iid="183" data-container="body" data-placement="top" title="Remove usage of numpy.testing.decorators" class="gfm gfm-merge_request">!183</a> Remove usage of numpy.testing.decorators: Fixes <a href="/bob/bob.bio.base/-/issues/132" data-reference-type="issue" data-original="bob/bob.bio.base#132" data-link="false" data-link-reference="false" data-project="1379" data-issue="4177" data-project-path="bob/bob.bio.base" data-iid="132" data-issue-type="issue" data-container="body" data-placement="top" title="`numpy.testing.decorators.setastest` is no longer available in the latest `numpy 1.18`" class="gfm gfm-issue">#132</a>
</li>
<li data-sourcepos="2:1-2:104">
<a href="/bob/bob.bio.base/-/merge_requests/170" data-reference-type="merge_request" data-original="bob/bob.bio.base!170" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3572" data-project-path="bob/bob.bio.base" data-iid="170" data-container="body" data-placement="top" title="Explain how new databases are configured" class="gfm gfm-merge_request">!170</a> Explain how new databases are configured: using bob's global configuration system</li>
<li data-sourcepos="3:1-3:130">
<a href="/bob/bob.bio.base/-/merge_requests/191" data-reference-type="merge_request" data-original="bob/bob.bio.base!191" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5236" data-project-path="bob/bob.bio.base" data-iid="191" data-container="body" data-placement="top" title='Resolve "`check_existence` flag incorrectly handled in filelistdatabase query"' class="gfm gfm-merge_request">!191</a> Resolve "<code>check_existence</code> flag incorrectly handled in filelistdatabase query": Closes <a href="/bob/bob.bio.base/-/issues/134" data-reference-type="issue" data-original="bob/bob.bio.base#134" data-link="false" data-link-reference="false" data-project="1379" data-issue="4342" data-project-path="bob/bob.bio.base" data-iid="134" data-issue-type="issue" data-container="body" data-placement="top" title="`check_existence` flag incorrectly handled in filelistdatabase query" class="gfm gfm-issue">#134</a>
</li>
<li data-sourcepos="4:1-4:580">
<a href="/bob/bob.bio.base/-/merge_requests/198" data-reference-type="merge_request" data-original="bob/bob.bio.base!198" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="5444" data-project-path="bob/bob.bio.base" data-iid="198" data-container="body" data-placement="top" title="Fixing and adding features to the scores generation script" class="gfm gfm-merge_request">!198</a> Fixing and adding features to the scores generation script: I was using the score 'gen' script, but needed some features. Added: - A way of specifying how the number of scores is defined (number of subjects and probes, or manually specified); - A way to generate different scores for dev and eval; - Tests for the gen script. Changed: - The way the scores are generated (each probe against each reference model, instead of randomly). Fixed: - Duplicate click options (-p); - 'positive scores' were generated with a 'negative scores' variable.</li>
</ul>2020-10-02T19:32:22ZTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v4.1.0v4.1.0<ul data-sourcepos="1:1-3:229" dir="auto">
<li data-sourcepos="1:1-1:65">
<a href="/bob/bob.bio.base/-/merge_requests/178" data-reference-type="merge_request" data-original="bob/bob.bio.base!178" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="4602" data-project-path="bob/bob.bio.base" data-iid="178" data-container="body" data-placement="top" title="Fixed issue with numpy.ndarray.resize py37" class="gfm gfm-merge_request">!178</a> Fixed issue with numpy.ndarray.resize py37</li>
<li data-sourcepos="2:1-2:139">
<a href="/bob/bob.bio.base/-/merge_requests/179" data-reference-type="merge_request" data-original="bob/bob.bio.base!179" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="4757" data-project-path="bob/bob.bio.base" data-iid="179" data-container="body" data-placement="top" title="Separate semilogx and TPR options in ROC plots" class="gfm gfm-merge_request">!179</a> Separate semilogx and TPR options in ROC plots: Depends on <a href="https://gitlab.idiap.ch/bob/bob.measure/merge_requests/98" data-reference-type="merge_request" data-original="https://gitlab.idiap.ch/bob/bob.measure/merge_requests/98" data-link="false" data-link-reference="true" data-project="1521" data-merge-request="4756" data-project-path="bob/bob.measure" data-iid="98" data-container="body" data-placement="top" title="Separate semilogx and TPR options in ROC plots" class="gfm gfm-merge_request">bob.measure!98</a>
</li>
<li data-sourcepos="3:1-3:229">
<a href="/bob/bob.bio.base/-/merge_requests/176" data-reference-type="merge_request" data-original="bob/bob.bio.base!176" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="4411" data-project-path="bob/bob.bio.base" data-iid="176" data-container="body" data-placement="top" title="Add bob bio annotate-samples command" class="gfm gfm-merge_request">!176</a> Add bob bio annotate-samples command: This command works very similar to bob bio annotate except that works without a db interface. Instead, it requires a list of samples and two functions to do the job.</li>
</ul>2020-02-17T19:02:53ZAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v4.0.2v4.0.2<ul data-sourcepos="1:1-2:20" dir="auto">
<li data-sourcepos="1:1-1:65">
<a href="/bob/bob.bio.base/-/merge_requests/178" data-reference-type="merge_request" data-original="bob/bob.bio.base!178" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="4602" data-project-path="bob/bob.bio.base" data-iid="178" data-container="body" data-placement="top" title="Fixed issue with numpy.ndarray.resize py37" class="gfm gfm-merge_request">!178</a> Fixed issue with numpy.ndarray.resize py37</li>
<li data-sourcepos="2:1-2:20">Python 3.7 support</li>
</ul>2019-10-29T20:00:31ZTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v4.0.1v4.0.1<ul data-sourcepos="1:1-4:58" dir="auto">
<li data-sourcepos="1:1-1:103">
<a href="/bob/bob.bio.base/-/merge_requests/171" data-reference-type="merge_request" data-original="bob/bob.bio.base!171" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3621" data-project-path="bob/bob.bio.base" data-iid="171" data-container="body" data-placement="top" title="Implemented multiple subjects score generation, unknown probes and fixed issues" class="gfm gfm-merge_request">!171</a> Implemented multiple subjects score generation, unknown probes and fixed issues:</li>
<li data-sourcepos="2:1-2:85">
<a href="/bob/bob.bio.base/-/merge_requests/172" data-reference-type="merge_request" data-original="bob/bob.bio.base!172" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3624" data-project-path="bob/bob.bio.base" data-iid="172" data-container="body" data-placement="top" title="Fix the tests after legend loc option change in bob.measure!89" class="gfm gfm-merge_request">!172</a> Fix the tests after legend loc option change in <a href="/bob/bob.measure/-/merge_requests/89" data-reference-type="merge_request" data-original="bob.measure!89" data-link="false" data-link-reference="false" data-project="1521" data-merge-request="3623" data-project-path="bob/bob.measure" data-iid="89" data-container="body" data-placement="top" title="Add a base class for subplot-based plots" class="gfm gfm-merge_request">bob.measure!89</a>
</li>
<li data-sourcepos="3:1-3:48">
<a href="/bob/bob.bio.base/-/merge_requests/175" data-reference-type="merge_request" data-original="bob/bob.bio.base!175" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="4386" data-project-path="bob/bob.bio.base" data-iid="175" data-container="body" data-placement="top" title="small fix in help message" class="gfm gfm-merge_request">!175</a> small fix in help message</li>
<li data-sourcepos="4:1-4:58">
<a href="/bob/bob.bio.base/-/merge_requests/174" data-reference-type="merge_request" data-original="bob/bob.bio.base!174" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="4369" data-project-path="bob/bob.bio.base" data-iid="174" data-container="body" data-placement="top" title="Adds a sort command and small fixes" class="gfm gfm-merge_request">!174</a> Adds a sort command and small fixes</li>
</ul>2019-06-21T05:15:16ZTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v4.0.0v4.0.0<ul data-sourcepos="1:1-58:62" dir="auto">
<li data-sourcepos="1:1-1:34">Breaking and significant changes</li>
<li data-sourcepos="2:1-2:41">Removed the old <code>evaluate.py</code> script.</li>
<li data-sourcepos="3:1-3:74">Functionality to load biometric scores are now in <code>bob.bio.base.score</code>
</li>
<li data-sourcepos="4:1-4:64">Added new scripts for plotting and evaluations. Refer to docs.</li>
<li data-sourcepos="5:1-5:47">Added a new baselines concept. Refer to docs.</li>
<li data-sourcepos="6:1-6:18">Detailed changes</li>
<li data-sourcepos="7:1-8:12">
<a href="/bob/bob.bio.base/-/merge_requests/147" data-reference-type="merge_request" data-original="bob.bio.base!147" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3269" data-project-path="bob/bob.bio.base" data-iid="147" data-container="body" data-placement="top" title="Update installation instructions since conda's usage has changed." class="gfm gfm-merge_request">!147</a> Update installation instructions since conda's usage
has changed.</li>
<li data-sourcepos="9:1-9:55">
<a href="/bob/bob.bio.base/-/merge_requests/148" data-reference-type="merge_request" data-original="bob.bio.base!148" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3284" data-project-path="bob/bob.bio.base" data-iid="148" data-container="body" data-placement="top" title="Archive CSU issue #109" class="gfm gfm-merge_request">!148</a> Archive CSU: closes <a href="/bob/bob.bio.base/-/issues/109" data-reference-type="issue" data-original="bob.bio.base#109" data-link="false" data-link-reference="false" data-project="1379" data-issue="2975" data-project-path="bob/bob.bio.base" data-iid="109" data-issue-type="issue" data-container="body" data-placement="top" title="Archiving bob.bio.csu" class="gfm gfm-issue">#109</a>
</li>
<li data-sourcepos="10:1-19:34">
<a href="/bob/bob.bio.base/-/merge_requests/146" data-reference-type="merge_request" data-original="bob.bio.base!146" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3233" data-project-path="bob/bob.bio.base" data-iid="146" data-container="body" data-placement="top" title="Add 4-5-col files related functionalities and add click commands" class="gfm gfm-merge_request">!146</a> Add 4-5-col files related functionalities and add
click commands: In this merge: * Add loading functionalities from
<code>bob.measure</code> * Add the following click commands (as substitutes for
old script evaluate.py) using 4- or 5 - scores input files: * <code>bob bio metrics</code> * <code>bob bio roc</code> * <code>bob bio det</code> * <code>bob bio epc</code> * <code>bob bio hist</code> * <code>bob bio evaluate</code> : calls all the
above commands at once * <code>bob bio cmc</code> * <code>bob bio dic</code> *
<code>bob bio gen</code> Plots follow ISO standards. The underlying
implementation of the mentioned commands uses <code>bob.measure</code> base
classes. Fixes <a href="/bob/bob.bio.base/-/issues/108" data-reference-type="issue" data-original="bob.bio.base#108" data-link="false" data-link-reference="false" data-project="1379" data-issue="2950" data-project-path="bob/bob.bio.base" data-iid="108" data-issue-type="issue" data-container="body" data-placement="top" title="Nightlies are failing because of tests in this package" class="gfm gfm-issue">#108</a>
</li>
<li data-sourcepos="20:1-21:71">
<a href="/bob/bob.bio.base/-/merge_requests/149" data-reference-type="merge_request" data-original="bob.bio.base!149" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3301" data-project-path="bob/bob.bio.base" data-iid="149" data-container="body" data-placement="top" title="Set io-big flag for the demanding grid config" class="gfm gfm-merge_request">!149</a> Set io-big flag for the demanding grid config: Closes
bob.bio.base#110 Anyone cares to review this one? It's harmless.</li>
<li data-sourcepos="22:1-23:67">
<a href="/bob/bob.bio.base/-/merge_requests/143" data-reference-type="merge_request" data-original="bob.bio.base!143" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3158" data-project-path="bob/bob.bio.base" data-iid="143" data-container="body" data-placement="top" title="Set of click commands for bio base" class="gfm gfm-merge_request">!143</a> Set of click commands for bio base: From
<a href="/bob/bob.bio.base/-/issues/65" data-reference-type="issue" data-original="bob.bio.base#65" data-link="false" data-link-reference="false" data-project="1379" data-issue="2032" data-project-path="bob/bob.bio.base" data-iid="65" data-issue-type="issue" data-container="body" data-placement="top" title="evaluation script is too complicated and does not make use of the internal structure" class="gfm gfm-issue">#65</a> Provide commands in bio base: - bob bio metrics</li>
<li data-sourcepos="24:1-24:62">bob bio roc - bob bio evaluate (Very similar to evalute.py)</li>
<li data-sourcepos="25:1-26:22">
<a href="/bob/bob.bio.base/-/merge_requests/152" data-reference-type="merge_request" data-original="bob.bio.base!152" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3357" data-project-path="bob/bob.bio.base" data-iid="152" data-container="body" data-placement="top" title="Removed unused import imp and solving #83" class="gfm gfm-merge_request">!152</a> Removed unused import imp and solving <a href="/bob/bob.bio.base/-/issues/83" data-reference-type="issue" data-original="bob.bio.base#83" data-link="false" data-link-reference="false" data-project="1379" data-issue="2381" data-project-path="bob/bob.bio.base" data-iid="83" data-issue-type="issue" data-container="body" data-placement="top" title="The of module `imp` is deprecated" class="gfm gfm-issue">#83</a>:
Closes <a href="/bob/bob.bio.base/-/issues/83" data-reference-type="issue" data-original="bob.bio.base#83" data-link="false" data-link-reference="false" data-project="1379" data-issue="2381" data-project-path="bob/bob.bio.base" data-iid="83" data-issue-type="issue" data-container="body" data-placement="top" title="The of module `imp` is deprecated" class="gfm gfm-issue">#83</a>
</li>
<li data-sourcepos="27:1-28:23">
<a href="/bob/bob.bio.base/-/merge_requests/153" data-reference-type="merge_request" data-original="bob.bio.base!153" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3359" data-project-path="bob/bob.bio.base" data-iid="153" data-container="body" data-placement="top" title="Added the protocol argument issue #111" class="gfm gfm-merge_request">!153</a> Added the protocol argument issue <a href="/bob/bob.bio.base/-/issues/111" data-reference-type="issue" data-original="bob.bio.base#111" data-link="false" data-link-reference="false" data-project="1379" data-issue="3029" data-project-path="bob/bob.bio.base" data-iid="111" data-issue-type="issue" data-container="body" data-placement="top" title='Follow-up from "Exposing the method groups in our FileDatabase API"' class="gfm gfm-issue">#111</a>:
Closes <a href="/bob/bob.bio.base/-/issues/111" data-reference-type="issue" data-original="bob.bio.base#111" data-link="false" data-link-reference="false" data-project="1379" data-issue="3029" data-project-path="bob/bob.bio.base" data-iid="111" data-issue-type="issue" data-container="body" data-placement="top" title='Follow-up from "Exposing the method groups in our FileDatabase API"' class="gfm gfm-issue">#111</a>
</li>
<li data-sourcepos="29:1-29:46">
<a href="/bob/bob.bio.base/-/merge_requests/154" data-reference-type="merge_request" data-original="bob.bio.base!154" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3361" data-project-path="bob/bob.bio.base" data-iid="154" data-container="body" data-placement="top" title="Fixes in ROC and DET labels" class="gfm gfm-merge_request">!154</a> Fixes in ROC and DET labels</li>
<li data-sourcepos="30:1-31:28">
<a href="/bob/bob.bio.base/-/merge_requests/157" data-reference-type="merge_request" data-original="bob.bio.base!157" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3378" data-project-path="bob/bob.bio.base" data-iid="157" data-container="body" data-placement="top" title="Fixed bob bio dir x_labels and y_labels" class="gfm gfm-merge_request">!157</a> Fixed bob bio dir x_labels and y_labels: The labels of
the DIR plot were incorrect.</li>
<li data-sourcepos="32:1-33:37">
<a href="/bob/bob.bio.base/-/merge_requests/155" data-reference-type="merge_request" data-original="bob.bio.base!155" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3368" data-project-path="bob/bob.bio.base" data-iid="155" data-container="body" data-placement="top" title="Write parameters in a temporary config file to enable chain loading" class="gfm gfm-merge_request">!155</a> Write parameters in a temporary config file to enable
chain loading: Fixes <a href="/bob/bob.bio.base/-/issues/116" data-reference-type="issue" data-original="bob.bio.base#116" data-link="false" data-link-reference="false" data-project="1379" data-issue="3040" data-project-path="bob/bob.bio.base" data-iid="116" data-issue-type="issue" data-container="body" data-placement="top" title="Baseline subdirectory should not contain the name of the database" class="gfm gfm-issue">#116</a>
</li>
<li data-sourcepos="34:1-34:69">
<a href="/bob/bob.bio.base/-/merge_requests/150" data-reference-type="merge_request" data-original="bob.bio.base!150" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3329" data-project-path="bob/bob.bio.base" data-iid="150" data-container="body" data-placement="top" title="Exposing the method groups in our FileDatabase API" class="gfm gfm-merge_request">!150</a> Exposing the method groups in our FileDatabase API</li>
<li data-sourcepos="35:1-35:57">
<a href="/bob/bob.bio.base/-/merge_requests/158" data-reference-type="merge_request" data-original="bob.bio.base!158" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3418" data-project-path="bob/bob.bio.base" data-iid="158" data-container="body" data-placement="top" title="Add prefix aliasing for Click commands" class="gfm gfm-merge_request">!158</a> Add prefix aliasing for Click commands</li>
<li data-sourcepos="36:1-37:44">
<a href="/bob/bob.bio.base/-/merge_requests/160" data-reference-type="merge_request" data-original="bob.bio.base!160" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3445" data-project-path="bob/bob.bio.base" data-iid="160" data-container="body" data-placement="top" title="Titltes" class="gfm gfm-merge_request">!160</a> Titltes: Allows a list of titles Fixes
<a href="/bob/bob.bio.base/-/issues/121" data-reference-type="issue" data-original="bob.bio.base#121" data-link="false" data-link-reference="false" data-project="1379" data-issue="3089" data-project-path="bob/bob.bio.base" data-iid="121" data-issue-type="issue" data-container="body" data-placement="top" title="Titles for ROC plots" class="gfm gfm-issue">#121</a>. Requires <a href="/bob/bob.measure/-/merge_requests/67" data-reference-type="merge_request" data-original="bob.measure!67" data-link="false" data-link-reference="false" data-project="1521" data-merge-request="3444" data-project-path="bob/bob.measure" data-iid="67" data-container="body" data-placement="top" title="Titles" class="gfm gfm-merge_request">bob.measure!67</a>
</li>
<li data-sourcepos="38:1-39:57">
<a href="/bob/bob.bio.base/-/merge_requests/159" data-reference-type="merge_request" data-original="bob.bio.base!159" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3441" data-project-path="bob/bob.bio.base" data-iid="159" data-container="body" data-placement="top" title='Resolve "Documentation does not include a link to the recordings of the IJCB tutorial"' class="gfm gfm-merge_request">!159</a> Resolve "Documentation does not include a link to the
recordings of the IJCB tutorial": Closes <a href="/bob/bob.bio.base/-/issues/122" data-reference-type="issue" data-original="bob.bio.base#122" data-link="false" data-link-reference="false" data-project="1379" data-issue="3092" data-project-path="bob/bob.bio.base" data-iid="122" data-issue-type="issue" data-container="body" data-placement="top" title="Documentation does not include a link to the recordings of the IJCB tutorial" class="gfm gfm-issue">#122</a>
</li>
<li data-sourcepos="40:1-42:49">
<a href="/bob/bob.bio.base/-/merge_requests/161" data-reference-type="merge_request" data-original="bob.bio.base!161" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3453" data-project-path="bob/bob.bio.base" data-iid="161" data-container="body" data-placement="top" title="Change --eval option default and Various fixes" class="gfm gfm-merge_request">!161</a> Change --eval option default and Various fixes: fixes
<a href="/bob/bob.bio.base/-/issues/112" data-reference-type="issue" data-original="bob.bio.base#112" data-link="false" data-link-reference="false" data-project="1379" data-issue="3031" data-project-path="bob/bob.bio.base" data-iid="112" data-issue-type="issue" data-container="body" data-placement="top" title="Severe Issue `bob bio metric`" class="gfm gfm-issue">#112</a>. Add and clean histo options. See
<a href="/bob/bob.measure/-/merge_requests/67" data-reference-type="merge_request" data-original="bob.measure!67" data-link="false" data-link-reference="false" data-project="1521" data-merge-request="3444" data-project-path="bob/bob.measure" data-iid="67" data-container="body" data-placement="top" title="Titles" class="gfm gfm-merge_request">bob.measure!67</a>#note_30951 Requires <a href="/bob/bob.measure/-/merge_requests/68" data-reference-type="merge_request" data-original="bob.measure!68" data-link="false" data-link-reference="false" data-project="1521" data-merge-request="3452" data-project-path="bob/bob.measure" data-iid="68" data-container="body" data-placement="top" title="Change --eval option default and Various fixes" class="gfm gfm-merge_request">bob.measure!68</a>
</li>
<li data-sourcepos="43:1-44:14">
<a href="/bob/bob.bio.base/-/merge_requests/163" data-reference-type="merge_request" data-original="bob.bio.base!163" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3484" data-project-path="bob/bob.bio.base" data-iid="163" data-container="body" data-placement="top" title="Reduce repition between commands" class="gfm gfm-merge_request">!163</a> Reduce repition between commands: Depends on
<a href="/bob/bob.measure/-/merge_requests/70" data-reference-type="merge_request" data-original="bob.measure!70" data-link="false" data-link-reference="false" data-project="1521" data-merge-request="3479" data-project-path="bob/bob.measure" data-iid="70" data-container="body" data-placement="top" title="Improvements to new metrics codes" class="gfm gfm-merge_request">bob.measure!70</a>
</li>
<li data-sourcepos="45:1-45:69">
<a href="/bob/bob.bio.base/-/merge_requests/162" data-reference-type="merge_request" data-original="bob.bio.base!162" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3482" data-project-path="bob/bob.bio.base" data-iid="162" data-container="body" data-placement="top" title="Removed traces of evaluate.py in the documentation" class="gfm gfm-merge_request">!162</a> Removed traces of evaluate.py in the documentation</li>
<li data-sourcepos="46:1-46:64">
<a href="/bob/bob.bio.base/-/merge_requests/164" data-reference-type="merge_request" data-original="bob.bio.base!164" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3489" data-project-path="bob/bob.bio.base" data-iid="164" data-container="body" data-placement="top" title="Fix test according to changes in nbins option" class="gfm gfm-merge_request">!164</a> Fix test according to changes in nbins option</li>
<li data-sourcepos="47:1-48:42">
<a href="/bob/bob.bio.base/-/merge_requests/165" data-reference-type="merge_request" data-original="bob.bio.base!165" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3497" data-project-path="bob/bob.bio.base" data-iid="165" data-container="body" data-placement="top" title="Set names for different bio metrics" class="gfm gfm-merge_request">!165</a> Set names for different bio metrics: Bio specific names
for metrics when using bob.measure Metrics</li>
<li data-sourcepos="49:1-50:47">
<a href="/bob/bob.bio.base/-/merge_requests/166" data-reference-type="merge_request" data-original="bob.bio.base!166" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3503" data-project-path="bob/bob.bio.base" data-iid="166" data-container="body" data-placement="top" title="Add a command for multi protocol (N-fold cross validation) analysis" class="gfm gfm-merge_request">!166</a> Add a command for multi protocol (N-fold cross
validation) analysis: Similar to <a href="/bob/bob.measure/-/merge_requests/79" data-reference-type="merge_request" data-original="bob.measure!79" data-link="false" data-link-reference="false" data-project="1521" data-merge-request="3499" data-project-path="bob/bob.measure" data-iid="79" data-container="body" data-placement="top" title="Add a command for multi protocol (N-fold cross validation) analysis" class="gfm gfm-merge_request">bob.measure!79</a>
</li>
<li data-sourcepos="51:1-52:31">
<a href="/bob/bob.bio.base/-/merge_requests/167" data-reference-type="merge_request" data-original="bob.bio.base!167" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3511" data-project-path="bob/bob.bio.base" data-iid="167" data-container="body" data-placement="top" title="Various fixes" class="gfm gfm-merge_request">!167</a> Various fixes: Requires <a href="/bob/bob.measure/-/merge_requests/82" data-reference-type="merge_request" data-original="bob.measure!82" data-link="false" data-link-reference="false" data-project="1521" data-merge-request="3509" data-project-path="bob/bob.measure" data-iid="82" data-container="body" data-placement="top" title="Various fixes" class="gfm gfm-merge_request">bob.measure!82</a> Similar to
<a href="/bob/bob.measure/-/merge_requests/82" data-reference-type="merge_request" data-original="bob.measure!82" data-link="false" data-link-reference="false" data-project="1521" data-merge-request="3509" data-project-path="bob/bob.measure" data-iid="82" data-container="body" data-placement="top" title="Various fixes" class="gfm gfm-merge_request">bob.measure!82</a> for bio commands</li>
<li data-sourcepos="53:1-54:16">
<a href="/bob/bob.bio.base/-/merge_requests/168" data-reference-type="merge_request" data-original="bob.bio.base!168" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3536" data-project-path="bob/bob.bio.base" data-iid="168" data-container="body" data-placement="top" title="Documentation changes in bob bio annotate" class="gfm gfm-merge_request">!168</a> Documentation changes in bob bio annotate: Depends on
<a href="/bob/bob.extension/-/merge_requests/86" data-reference-type="merge_request" data-original="bob.extension!86" data-link="false" data-link-reference="false" data-project="1475" data-merge-request="3522" data-project-path="bob/bob.extension" data-iid="86" data-container="body" data-placement="top" title="Dump config file" class="gfm gfm-merge_request">bob.extension!86</a>
</li>
<li data-sourcepos="55:1-56:23">
<a href="/bob/bob.bio.base/-/merge_requests/156" data-reference-type="merge_request" data-original="bob.bio.base!156" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3376" data-project-path="bob/bob.bio.base" data-iid="156" data-container="body" data-placement="top" title="Using the proper verify script depending on system" class="gfm gfm-merge_request">!156</a> Using the proper verify script depending on system:
Closes <a href="/bob/bob.bio.base/-/issues/119" data-reference-type="issue" data-original="bob.bio.base#119" data-link="false" data-link-reference="false" data-project="1379" data-issue="3049" data-project-path="bob/bob.bio.base" data-iid="119" data-issue-type="issue" data-container="body" data-placement="top" title="bob.bio.baselines always calls verify.py but for some baselines it's better to call verify_{gmm,isv,ivector}.py" class="gfm gfm-issue">#119</a>
</li>
<li data-sourcepos="57:1-57:48">
<a href="/bob/bob.bio.base/-/merge_requests/151" data-reference-type="merge_request" data-original="bob.bio.base!151" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3349" data-project-path="bob/bob.bio.base" data-iid="151" data-container="body" data-placement="top" title="Created the Baselines Concept" class="gfm gfm-merge_request">!151</a> Created the Baselines Concept</li>
<li data-sourcepos="58:1-58:62">
<a href="/bob/bob.bio.base/-/merge_requests/169" data-reference-type="merge_request" data-original="bob.bio.base!169" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="3556" data-project-path="bob/bob.bio.base" data-iid="169" data-container="body" data-placement="top" title="Change assert to assert_click_runner_result" class="gfm gfm-merge_request">!169</a> Change assert to assert_click_runner_result</li>
</ul>2018-07-19T09:06:03ZAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v3.3.0v3.3.0<ul data-sourcepos="1:1-15:29" dir="auto">
<li data-sourcepos="1:1-1:27">Migrate to conda based CI</li>
<li data-sourcepos="2:1-2:24">Updated docs and tests</li>
<li data-sourcepos="3:1-3:50">Added allow_missing_files option and added tests</li>
<li data-sourcepos="4:1-4:73">Removed write_commands function in grid_search (closes <a href="/bob/bob.bio.base/-/issues/71" data-reference-type="issue" data-original="bob.bio.base#71" data-link="false" data-link-reference="false" data-project="1379" data-issue="2220" data-project-path="bob/bob.bio.base" data-iid="71" data-issue-type="issue" data-container="body" data-placement="top" title="line code starts with ./bin/" class="gfm gfm-issue">#71</a>)</li>
<li data-sourcepos="5:1-5:52">Added annotator, updated documentation accordingly</li>
<li data-sourcepos="6:1-6:39">Allow for comment lines in file-lists</li>
<li data-sourcepos="7:1-7:65">Improves verbosity for preprocessing, extraction and enrollment</li>
<li data-sourcepos="8:1-8:37">bob.db.base.Database is deprecated.</li>
<li data-sourcepos="9:1-9:56">Using config file loading mechanism from bob.extension</li>
<li data-sourcepos="10:1-10:45">Fix debug message (closes <a href="/bob/bob.bio.base/-/issues/103" data-reference-type="issue" data-original="bob.bio.base#103" data-link="false" data-link-reference="false" data-project="1379" data-issue="2644" data-project-path="bob/bob.bio.base" data-iid="103" data-issue-type="issue" data-container="body" data-placement="top" title="Small bug in debug message" class="gfm gfm-issue">#103</a>)</li>
<li data-sourcepos="11:1-11:65">Fixed the exception that is raised when score file is not found</li>
<li data-sourcepos="12:1-12:70">Mentions bob.bio.vein on bob.bio.base docs (closes <a href="/bob/bob.bio.base/-/issues/104" data-reference-type="issue" data-original="bob.bio.base#104" data-link="false" data-link-reference="false" data-project="1379" data-issue="2680" data-project-path="bob/bob.bio.base" data-iid="104" data-issue-type="issue" data-container="body" data-placement="top" title="mention bob.bio.vein in the documentation too" class="gfm gfm-issue">#104</a>)</li>
<li data-sourcepos="13:1-13:68">Added metadata in preprocessing, feature extraction, and algorithm</li>
<li data-sourcepos="14:1-14:73">Removed write_commands function in grid_search (closes <a href="/bob/bob.bio.base/-/issues/71" data-reference-type="issue" data-original="bob.bio.base#71" data-link="false" data-link-reference="false" data-project="1379" data-issue="2220" data-project-path="bob/bob.bio.base" data-iid="71" data-issue-type="issue" data-container="body" data-placement="top" title="line code starts with ./bin/" class="gfm gfm-issue">#71</a>)</li>
<li data-sourcepos="15:1-15:29">Improve replace directories</li>
</ul>2018-04-13T13:15:10ZTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v3.2.1v3.2.1<ul data-sourcepos="1:1-1:85" dir="auto">
<li data-sourcepos="1:1-1:85">Changed backend in <code>bob/bio/base/scripts/evaluate.py</code> to <code>'pdf'</code> instead of <code>'agg'</code>
</li>
</ul>2017-09-26T21:06:56ZManuel Gunthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v3.2.0v3.2.0<ul data-sourcepos="1:1-13:65" dir="auto">
<li data-sourcepos="1:1-1:50">
<a href="/bob/bob.bio.base/-/merge_requests/89" data-reference-type="merge_request" data-original="bob.bio.base!89" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2398" data-project-path="bob/bob.bio.base" data-iid="89" data-container="body" data-placement="top" title="Fixed database test to incorporate the no_zt option from !80; closes bob/bob.bio.spear#28" class="gfm gfm-merge_request">!89</a> [ci] Fixed issue with matplotlib</li>
<li data-sourcepos="2:1-2:60">
<a href="/bob/bob.bio.base/-/merge_requests/95" data-reference-type="merge_request" data-original="bob.bio.base!95" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2442" data-project-path="bob/bob.bio.base" data-iid="95" data-container="body" data-placement="top" title='Resolve "There is absolutely no need for having a "Client" class in the FileListDatabase implementation"' class="gfm gfm-merge_request">!95</a> Removed class client from FileListDatabase</li>
<li data-sourcepos="3:1-3:103">
<a href="/bob/bob.bio.base/-/merge_requests/94" data-reference-type="merge_request" data-original="bob.bio.base!94" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2437" data-project-path="bob/bob.bio.base" data-iid="94" data-container="body" data-placement="top" title='Resolve "No way of plotting open-set DIR curves"' class="gfm gfm-merge_request">!94</a> Implemented the plots for the Detection Identification Rate (open-set identification)</li>
<li data-sourcepos="4:1-4:50">
<a href="/bob/bob.bio.base/-/merge_requests/93" data-reference-type="merge_request" data-original="bob.bio.base!93" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2433" data-project-path="bob/bob.bio.base" data-iid="93" data-container="body" data-placement="top" title="Small corrections to the documentation and command line help" class="gfm gfm-merge_request">!93</a> Corrections in the documentation</li>
<li data-sourcepos="5:1-5:84">
<a href="/bob/bob.bio.base/-/merge_requests/92" data-reference-type="merge_request" data-original="bob.bio.base!92" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2425" data-project-path="bob/bob.bio.base" data-iid="92" data-container="body" data-placement="top" title='Resolve "The documentation does not mention usage of single configuration files"' class="gfm gfm-merge_request">!92</a> Documented the configuration file input for the <code>verify.py</code> script</li>
<li data-sourcepos="6:1-6:116">
<a href="/bob/bob.bio.base/-/merge_requests/90" data-reference-type="merge_request" data-original="bob.bio.base!90" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2402" data-project-path="bob/bob.bio.base" data-iid="90" data-container="body" data-placement="top" title='Resolve "In evaluate.py, there is no way of using both 4- and 5-column score files"' class="gfm gfm-merge_request">!90</a> Implemented a way to use, at the same time, 4 and 5 columns score file in the <code>evaluate.py</code> script</li>
<li data-sourcepos="7:1-7:44">
<a href="/bob/bob.bio.base/-/merge_requests/88" data-reference-type="merge_request" data-original="bob.bio.base!88" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2391" data-project-path="bob/bob.bio.base" data-iid="88" data-container="body" data-placement="top" title="Improve the evaluate script plots" class="gfm gfm-merge_request">!88</a> Improved ROC and CMC plots</li>
<li data-sourcepos="8:1-8:85">
<a href="/bob/bob.bio.base/-/merge_requests/87" data-reference-type="merge_request" data-original="bob.bio.base!87" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2363" data-project-path="bob/bob.bio.base" data-iid="87" data-container="body" data-placement="top" title="Corrected INFO log when training enroller" class="gfm gfm-merge_request">!87</a> Fixed * ZT files are processed even when no ZT processing is wanted</li>
<li data-sourcepos="9:1-9:44">
<a href="/bob/bob.bio.base/-/merge_requests/81" data-reference-type="merge_request" data-original="bob.bio.base!81" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2049" data-project-path="bob/bob.bio.base" data-iid="81" data-container="body" data-placement="top" title="Removed TeX dependency" class="gfm gfm-merge_request">!81</a> Droped dependency on Latex</li>
<li data-sourcepos="10:1-10:81">
<a href="/bob/bob.bio.base/-/merge_requests/86" data-reference-type="merge_request" data-original="bob.bio.base!86" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2353" data-project-path="bob/bob.bio.base" data-iid="86" data-container="body" data-placement="top" title="Implemented five-column score file -- only during concatenation" class="gfm gfm-merge_request">!86</a> Implemented five-column score file -* only during concatenation</li>
<li data-sourcepos="11:1-11:93">
<a href="/bob/bob.bio.base/-/merge_requests/83" data-reference-type="merge_request" data-original="bob.bio.base!83" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2120" data-project-path="bob/bob.bio.base" data-iid="83" data-container="body" data-placement="top" title="Improve suggestion on variable naming convention to match python's (closes #81)" class="gfm gfm-merge_request">!83</a> Improve suggestion on variable naming convention to match python's standard</li>
<li data-sourcepos="12:1-12:104">
<a href="/bob/bob.bio.base/-/merge_requests/78" data-reference-type="merge_request" data-original="bob.bio.base!78" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2033" data-project-path="bob/bob.bio.base" data-iid="78" data-container="body" data-placement="top" title='Resolve "`Algorithm.read_probe` should not exist"' class="gfm gfm-merge_request">!78</a> Removed <code>Algorithm.read_probe</code> method, since this is already solved via <code>bob.bio.base</code>
</li>
<li data-sourcepos="13:1-13:65">
<a href="/bob/bob.bio.base/-/merge_requests/82" data-reference-type="merge_request" data-original="bob.bio.base!82" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="2063" data-project-path="bob/bob.bio.base" data-iid="82" data-container="body" data-placement="top" title="Add a function to read features with generators" class="gfm gfm-merge_request">!82</a> Add a function to read features with generators</li>
</ul>2018-03-31T17:54:57ZTiago Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v3.1.2v3.1.2<ul data-sourcepos="1:1-4:45" dir="auto">
<li data-sourcepos="1:1-3:0">
<p data-sourcepos="1:3-2:48"><a href="/bob/bob.bio.base/-/merge_requests/73" data-reference-type="merge_request" data-original="!73" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="1773" data-project-path="bob/bob.bio.base" data-iid="73" data-container="body" data-placement="top" title="Incorporate a general overview of biometric verification and illustrate biometric verification experiment flow in bob.bio.base doc" class="gfm gfm-merge_request">!73</a> : Incorporate a general overview of biometric verification and illustrate
biometric verification experiment flow in docs</p>
</li>
<li data-sourcepos="4:1-4:45">
<p data-sourcepos="4:3-4:45"><a href="/bob/bob.bio.base/-/merge_requests/77" data-reference-type="merge_request" data-original="!77" data-link="false" data-link-reference="false" data-project="1379" data-merge-request="1887" data-project-path="bob/bob.bio.base" data-iid="77" data-container="body" data-placement="top" title="Improve the instllation instructions" class="gfm gfm-merge_request">!77</a> : Improve the instillation instructions</p>
</li>
</ul>2017-06-01T16:31:59ZAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/tags/v3.1.1v3.1.1<ul data-sourcepos="1:1-4:109" dir="auto">
<li data-sourcepos="1:1-1:36">use super() in class constructors</li>
<li data-sourcepos="2:1-2:74">re-arranged command line options and more reusable code of command line</li>
<li data-sourcepos="3:1-3:35">a slightly updated documentation</li>
<li data-sourcepos="4:1-4:109">Updated code to pass original_directory and original_extension to <code>bob.db.base.Database</code>, as now required</li>
</ul>2017-05-23T00:36:01ZPavel Korshunov