Skip to content

Commit

Permalink
docs(master): Update docs of development line
Browse files Browse the repository at this point in the history
  • Loading branch information
nipreps-bot committed Jan 22, 2024
1 parent 67cede1 commit e0a3cb8
Show file tree
Hide file tree
Showing 15 changed files with 110 additions and 92 deletions.
Binary file modified master/api/sdcflows-workflows-apply-correction-1.pdf
Binary file not shown.
Binary file modified master/api/sdcflows-workflows-apply-registration-1.pdf
Binary file not shown.
Binary file modified master/api/sdcflows-workflows-fit-fieldmap-1.pdf
Binary file not shown.
Binary file modified master/api/sdcflows-workflows-fit-fieldmap-2.pdf
Binary file not shown.
Binary file modified master/api/sdcflows-workflows-fit-fieldmap-3.pdf
Binary file not shown.
Binary file modified master/api/sdcflows-workflows-fit-pepolar-1.pdf
Binary file not shown.
Binary file modified master/api/sdcflows-workflows-fit-pepolar-2.pdf
Binary file not shown.
Binary file modified master/api/sdcflows-workflows-fit-syn-1.pdf
Binary file not shown.
Binary file modified master/api/sdcflows-workflows-fit-syn-2.pdf
Binary file not shown.
4 changes: 2 additions & 2 deletions master/api/sdcflows.config.html
Original file line number Diff line number Diff line change
Expand Up @@ -445,7 +445,7 @@ <h2>Other responsibilities<a class="headerlink" href="#other-responsibilities" t

<dl class="py attribute">
<dt class="sig sig-object py" id="sdcflows.config.environment.free_mem">
<span class="sig-name descname"><span class="pre">free_mem</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">11.2</span></em><a class="headerlink" href="#sdcflows.config.environment.free_mem" title="Link to this definition">#</a></dt>
<span class="sig-name descname"><span class="pre">free_mem</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">11.1</span></em><a class="headerlink" href="#sdcflows.config.environment.free_mem" title="Link to this definition">#</a></dt>
<dd><p>Free memory at start.</p>
</dd></dl>

Expand Down Expand Up @@ -596,7 +596,7 @@ <h2>Other responsibilities<a class="headerlink" href="#other-responsibilities" t

<dl class="py attribute">
<dt class="sig sig-object py" id="sdcflows.config.execution.run_uuid">
<span class="sig-name descname"><span class="pre">run_uuid</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'20240118-185229_02199de2-6912-4ed6-88e9-3b25bb0e798a'</span></em><a class="headerlink" href="#sdcflows.config.execution.run_uuid" title="Link to this definition">#</a></dt>
<span class="sig-name descname"><span class="pre">run_uuid</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'20240122-153021_cf3ad91e-ac01-4dfe-ba85-496648586853'</span></em><a class="headerlink" href="#sdcflows.config.execution.run_uuid" title="Link to this definition">#</a></dt>
<dd><p>Unique identifier of this particular run.</p>
</dd></dl>

Expand Down
19 changes: 18 additions & 1 deletion master/changes.html
Original file line number Diff line number Diff line change
Expand Up @@ -263,9 +263,25 @@
<article role="main">
<section id="what-s-new">
<h1>What’s new?<a class="headerlink" href="#what-s-new" title="Link to this heading">#</a></h1>
<section id="january-22-2024">
<h2>2.8.1 (January 22, 2024)<a class="headerlink" href="#january-22-2024" title="Link to this heading">#</a></h2>
<p>Bug-fix release in the 2.8.x series.</p>
<p>Fixes doc builds and CLI support for fieldmapless workflows.
Introduces support for BIDS-URIs.</p>
<ul class="simple">
<li><p>FIX: Enable fieldmapless by default in CLI (#426)</p></li>
<li><p>FIX: Pandoc requires Texlive to render LaTeX in notebook (#427)</p></li>
<li><p>FIX: New test <code class="docutils literal notranslate"><span class="pre">test_wrangler_URIs</span></code> had the wrong oracle (#425)</p></li>
<li><p>ENH: Resolve BIDS-URIs (#349)</p></li>
<li><p>TEST: Use less confusing function name for testing CLI with –dry-run (#424)</p></li>
<li><p>MNT: Bump actions/download-artifact from 3 to 4 (#418)</p></li>
<li><p>MNT: Bump actions/upload-artifact from 3 to 4 (#417)</p></li>
<li><p>CI: Move PR doc build into main doc build, add texlive to build dependencies (#428)</p></li>
</ul>
</section>
<section id="january-10-2024">
<h2>2.8.0 (January 10, 2024)<a class="headerlink" href="#january-10-2024" title="Link to this heading">#</a></h2>
<p>New feature release in the 2.8.0 series.</p>
<p>New feature release in the 2.8.x series.</p>
<p>This release fixes a bug in converting SyN-SDC displacements to fieldmaps,
resulting in exaggerated corrections. As this makes changes to the structure
of a workflow and the expected inputs of a workflow node, this release is
Expand Down Expand Up @@ -951,6 +967,7 @@ <h3>0.1.0 (July 22, 2019)<a class="headerlink" href="#july-22-2019" title="Link
<div class="toc-tree">
<ul>
<li><a class="reference internal" href="#">What’s new?</a><ul>
<li><a class="reference internal" href="#january-22-2024">2.8.1 (January 22, 2024)</a></li>
<li><a class="reference internal" href="#january-10-2024">2.8.0 (January 10, 2024)</a></li>
<li><a class="reference internal" href="#december-18-2023">2.7.0 (December 18, 2023)</a></li>
<li><a class="reference internal" href="#november-10-2023">2.6.0 (November 10, 2023)</a></li>
Expand Down
1 change: 1 addition & 0 deletions master/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -389,6 +389,7 @@ <h1>Contents<a class="headerlink" href="#contents" title="Link to this heading">
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="changes.html">What’s new?</a><ul>
<li class="toctree-l2"><a class="reference internal" href="changes.html#january-22-2024">2.8.1 (January 22, 2024)</a></li>
<li class="toctree-l2"><a class="reference internal" href="changes.html#january-10-2024">2.8.0 (January 10, 2024)</a></li>
<li class="toctree-l2"><a class="reference internal" href="changes.html#december-18-2023">2.7.0 (December 18, 2023)</a></li>
<li class="toctree-l2"><a class="reference internal" href="changes.html#november-10-2023">2.6.0 (November 10, 2023)</a></li>
Expand Down
176 changes: 88 additions & 88 deletions master/notebooks/SDC - Theory and physics.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,10 @@
"id": "031f06b5",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:48.080947Z",
"iopub.status.busy": "2024-01-18T18:52:48.080739Z",
"iopub.status.idle": "2024-01-18T18:52:49.114348Z",
"shell.execute_reply": "2024-01-18T18:52:49.113702Z"
"iopub.execute_input": "2024-01-22T15:30:38.841562Z",
"iopub.status.busy": "2024-01-22T15:30:38.841053Z",
"iopub.status.idle": "2024-01-22T15:30:39.674885Z",
"shell.execute_reply": "2024-01-22T15:30:39.674309Z"
}
},
"outputs": [],
Expand All @@ -33,10 +33,10 @@
"id": "bd6b80c5",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:49.117096Z",
"iopub.status.busy": "2024-01-18T18:52:49.116834Z",
"iopub.status.idle": "2024-01-18T18:52:49.135878Z",
"shell.execute_reply": "2024-01-18T18:52:49.135253Z"
"iopub.execute_input": "2024-01-22T15:30:39.677813Z",
"iopub.status.busy": "2024-01-22T15:30:39.677291Z",
"iopub.status.idle": "2024-01-22T15:30:39.695504Z",
"shell.execute_reply": "2024-01-22T15:30:39.694929Z"
}
},
"outputs": [],
Expand Down Expand Up @@ -65,10 +65,10 @@
"id": "900e432b",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:49.138774Z",
"iopub.status.busy": "2024-01-18T18:52:49.138389Z",
"iopub.status.idle": "2024-01-18T18:52:51.199177Z",
"shell.execute_reply": "2024-01-18T18:52:51.198513Z"
"iopub.execute_input": "2024-01-22T15:30:39.698024Z",
"iopub.status.busy": "2024-01-22T15:30:39.697678Z",
"iopub.status.idle": "2024-01-22T15:30:41.706934Z",
"shell.execute_reply": "2024-01-22T15:30:41.706342Z"
}
},
"outputs": [],
Expand All @@ -86,10 +86,10 @@
"id": "e41f635f",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:51.201834Z",
"iopub.status.busy": "2024-01-18T18:52:51.201652Z",
"iopub.status.idle": "2024-01-18T18:52:51.208928Z",
"shell.execute_reply": "2024-01-18T18:52:51.208437Z"
"iopub.execute_input": "2024-01-22T15:30:41.709825Z",
"iopub.status.busy": "2024-01-22T15:30:41.709299Z",
"iopub.status.idle": "2024-01-22T15:30:41.716985Z",
"shell.execute_reply": "2024-01-22T15:30:41.716513Z"
}
},
"outputs": [],
Expand Down Expand Up @@ -169,10 +169,10 @@
"id": "e5f439e3",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:51.211143Z",
"iopub.status.busy": "2024-01-18T18:52:51.210788Z",
"iopub.status.idle": "2024-01-18T18:52:51.279852Z",
"shell.execute_reply": "2024-01-18T18:52:51.279245Z"
"iopub.execute_input": "2024-01-22T15:30:41.719227Z",
"iopub.status.busy": "2024-01-22T15:30:41.718842Z",
"iopub.status.idle": "2024-01-22T15:30:41.784238Z",
"shell.execute_reply": "2024-01-22T15:30:41.783714Z"
}
},
"outputs": [],
Expand All @@ -186,10 +186,10 @@
"id": "4b65f3fe",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:51.282374Z",
"iopub.status.busy": "2024-01-18T18:52:51.282185Z",
"iopub.status.idle": "2024-01-18T18:52:51.285632Z",
"shell.execute_reply": "2024-01-18T18:52:51.285084Z"
"iopub.execute_input": "2024-01-22T15:30:41.786837Z",
"iopub.status.busy": "2024-01-22T15:30:41.786461Z",
"iopub.status.idle": "2024-01-22T15:30:41.789858Z",
"shell.execute_reply": "2024-01-22T15:30:41.789279Z"
}
},
"outputs": [],
Expand All @@ -205,10 +205,10 @@
"id": "a3e1240b",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:51.287718Z",
"iopub.status.busy": "2024-01-18T18:52:51.287411Z",
"iopub.status.idle": "2024-01-18T18:52:51.583143Z",
"shell.execute_reply": "2024-01-18T18:52:51.582516Z"
"iopub.execute_input": "2024-01-22T15:30:41.792085Z",
"iopub.status.busy": "2024-01-22T15:30:41.791751Z",
"iopub.status.idle": "2024-01-22T15:30:42.063745Z",
"shell.execute_reply": "2024-01-22T15:30:42.063120Z"
}
},
"outputs": [
Expand Down Expand Up @@ -243,10 +243,10 @@
"id": "39451ae7",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:51.585618Z",
"iopub.status.busy": "2024-01-18T18:52:51.585270Z",
"iopub.status.idle": "2024-01-18T18:52:51.996467Z",
"shell.execute_reply": "2024-01-18T18:52:51.995862Z"
"iopub.execute_input": "2024-01-22T15:30:42.066231Z",
"iopub.status.busy": "2024-01-22T15:30:42.065875Z",
"iopub.status.idle": "2024-01-22T15:30:42.442038Z",
"shell.execute_reply": "2024-01-22T15:30:42.441399Z"
}
},
"outputs": [
Expand Down Expand Up @@ -279,10 +279,10 @@
"id": "acb35b9f",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:51.999371Z",
"iopub.status.busy": "2024-01-18T18:52:51.998917Z",
"iopub.status.idle": "2024-01-18T18:52:52.321911Z",
"shell.execute_reply": "2024-01-18T18:52:52.321316Z"
"iopub.execute_input": "2024-01-22T15:30:42.444534Z",
"iopub.status.busy": "2024-01-22T15:30:42.444137Z",
"iopub.status.idle": "2024-01-22T15:30:42.721320Z",
"shell.execute_reply": "2024-01-22T15:30:42.720807Z"
}
},
"outputs": [
Expand Down Expand Up @@ -319,10 +319,10 @@
"id": "668ea6a6",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:52.324560Z",
"iopub.status.busy": "2024-01-18T18:52:52.324085Z",
"iopub.status.idle": "2024-01-18T18:52:52.329767Z",
"shell.execute_reply": "2024-01-18T18:52:52.329325Z"
"iopub.execute_input": "2024-01-22T15:30:42.724424Z",
"iopub.status.busy": "2024-01-22T15:30:42.724017Z",
"iopub.status.idle": "2024-01-22T15:30:42.729487Z",
"shell.execute_reply": "2024-01-22T15:30:42.729003Z"
}
},
"outputs": [],
Expand All @@ -336,10 +336,10 @@
"id": "3cbfad11",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:52.331920Z",
"iopub.status.busy": "2024-01-18T18:52:52.331586Z",
"iopub.status.idle": "2024-01-18T18:52:52.698190Z",
"shell.execute_reply": "2024-01-18T18:52:52.697616Z"
"iopub.execute_input": "2024-01-22T15:30:42.731659Z",
"iopub.status.busy": "2024-01-22T15:30:42.731328Z",
"iopub.status.idle": "2024-01-22T15:30:43.046009Z",
"shell.execute_reply": "2024-01-22T15:30:43.045464Z"
}
},
"outputs": [
Expand Down Expand Up @@ -373,10 +373,10 @@
"id": "1ee31e08",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:52.701150Z",
"iopub.status.busy": "2024-01-18T18:52:52.700763Z",
"iopub.status.idle": "2024-01-18T18:52:52.703968Z",
"shell.execute_reply": "2024-01-18T18:52:52.703490Z"
"iopub.execute_input": "2024-01-22T15:30:43.049023Z",
"iopub.status.busy": "2024-01-22T15:30:43.048613Z",
"iopub.status.idle": "2024-01-22T15:30:43.051752Z",
"shell.execute_reply": "2024-01-22T15:30:43.051205Z"
}
},
"outputs": [],
Expand All @@ -391,10 +391,10 @@
"id": "396081d6",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:52.706254Z",
"iopub.status.busy": "2024-01-18T18:52:52.705907Z",
"iopub.status.idle": "2024-01-18T18:52:53.069651Z",
"shell.execute_reply": "2024-01-18T18:52:53.068988Z"
"iopub.execute_input": "2024-01-22T15:30:43.053818Z",
"iopub.status.busy": "2024-01-22T15:30:43.053503Z",
"iopub.status.idle": "2024-01-22T15:30:43.406248Z",
"shell.execute_reply": "2024-01-22T15:30:43.405608Z"
}
},
"outputs": [
Expand Down Expand Up @@ -428,10 +428,10 @@
"id": "e62a83e0",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:53.072182Z",
"iopub.status.busy": "2024-01-18T18:52:53.071830Z",
"iopub.status.idle": "2024-01-18T18:52:53.398167Z",
"shell.execute_reply": "2024-01-18T18:52:53.397612Z"
"iopub.execute_input": "2024-01-22T15:30:43.408750Z",
"iopub.status.busy": "2024-01-22T15:30:43.408394Z",
"iopub.status.idle": "2024-01-22T15:30:43.729185Z",
"shell.execute_reply": "2024-01-22T15:30:43.728665Z"
}
},
"outputs": [
Expand Down Expand Up @@ -472,10 +472,10 @@
"id": "cc305def",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:53.401434Z",
"iopub.status.busy": "2024-01-18T18:52:53.400934Z",
"iopub.status.idle": "2024-01-18T18:52:53.403766Z",
"shell.execute_reply": "2024-01-18T18:52:53.403269Z"
"iopub.execute_input": "2024-01-22T15:30:43.732153Z",
"iopub.status.busy": "2024-01-22T15:30:43.731768Z",
"iopub.status.idle": "2024-01-22T15:30:43.734467Z",
"shell.execute_reply": "2024-01-22T15:30:43.733969Z"
}
},
"outputs": [],
Expand All @@ -489,10 +489,10 @@
"id": "daf70d82",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:53.405815Z",
"iopub.status.busy": "2024-01-18T18:52:53.405635Z",
"iopub.status.idle": "2024-01-18T18:52:53.754050Z",
"shell.execute_reply": "2024-01-18T18:52:53.753487Z"
"iopub.execute_input": "2024-01-22T15:30:43.736586Z",
"iopub.status.busy": "2024-01-22T15:30:43.736243Z",
"iopub.status.idle": "2024-01-22T15:30:44.072721Z",
"shell.execute_reply": "2024-01-22T15:30:44.072150Z"
}
},
"outputs": [
Expand Down Expand Up @@ -548,10 +548,10 @@
"id": "c0daa39a",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:53.757436Z",
"iopub.status.busy": "2024-01-18T18:52:53.757234Z",
"iopub.status.idle": "2024-01-18T18:52:53.761002Z",
"shell.execute_reply": "2024-01-18T18:52:53.760501Z"
"iopub.execute_input": "2024-01-22T15:30:44.075976Z",
"iopub.status.busy": "2024-01-22T15:30:44.075584Z",
"iopub.status.idle": "2024-01-22T15:30:44.079079Z",
"shell.execute_reply": "2024-01-22T15:30:44.078500Z"
}
},
"outputs": [],
Expand All @@ -566,10 +566,10 @@
"id": "48a18834",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:53.762978Z",
"iopub.status.busy": "2024-01-18T18:52:53.762801Z",
"iopub.status.idle": "2024-01-18T18:52:53.765980Z",
"shell.execute_reply": "2024-01-18T18:52:53.765507Z"
"iopub.execute_input": "2024-01-22T15:30:44.081200Z",
"iopub.status.busy": "2024-01-22T15:30:44.080855Z",
"iopub.status.idle": "2024-01-22T15:30:44.083695Z",
"shell.execute_reply": "2024-01-22T15:30:44.083246Z"
}
},
"outputs": [],
Expand All @@ -584,10 +584,10 @@
"id": "a66a77e1",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:53.767914Z",
"iopub.status.busy": "2024-01-18T18:52:53.767739Z",
"iopub.status.idle": "2024-01-18T18:52:53.928598Z",
"shell.execute_reply": "2024-01-18T18:52:53.927927Z"
"iopub.execute_input": "2024-01-22T15:30:44.086101Z",
"iopub.status.busy": "2024-01-22T15:30:44.085664Z",
"iopub.status.idle": "2024-01-22T15:30:44.214674Z",
"shell.execute_reply": "2024-01-22T15:30:44.214041Z"
}
},
"outputs": [
Expand Down Expand Up @@ -624,10 +624,10 @@
"id": "a7006222",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:53.930846Z",
"iopub.status.busy": "2024-01-18T18:52:53.930661Z",
"iopub.status.idle": "2024-01-18T18:52:54.118401Z",
"shell.execute_reply": "2024-01-18T18:52:54.117863Z"
"iopub.execute_input": "2024-01-22T15:30:44.216895Z",
"iopub.status.busy": "2024-01-22T15:30:44.216714Z",
"iopub.status.idle": "2024-01-22T15:30:44.372123Z",
"shell.execute_reply": "2024-01-22T15:30:44.371497Z"
}
},
"outputs": [
Expand Down Expand Up @@ -663,10 +663,10 @@
"id": "62a33f4b",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:54.121103Z",
"iopub.status.busy": "2024-01-18T18:52:54.120729Z",
"iopub.status.idle": "2024-01-18T18:52:54.282212Z",
"shell.execute_reply": "2024-01-18T18:52:54.281637Z"
"iopub.execute_input": "2024-01-22T15:30:44.374382Z",
"iopub.status.busy": "2024-01-22T15:30:44.374203Z",
"iopub.status.idle": "2024-01-22T15:30:44.508042Z",
"shell.execute_reply": "2024-01-22T15:30:44.507445Z"
}
},
"outputs": [
Expand Down Expand Up @@ -698,10 +698,10 @@
"id": "e116767b",
"metadata": {
"execution": {
"iopub.execute_input": "2024-01-18T18:52:54.284731Z",
"iopub.status.busy": "2024-01-18T18:52:54.284353Z",
"iopub.status.idle": "2024-01-18T18:52:54.470747Z",
"shell.execute_reply": "2024-01-18T18:52:54.470228Z"
"iopub.execute_input": "2024-01-22T15:30:44.510493Z",
"iopub.status.busy": "2024-01-22T15:30:44.510160Z",
"iopub.status.idle": "2024-01-22T15:30:44.694909Z",
"shell.execute_reply": "2024-01-22T15:30:44.694301Z"
}
},
"outputs": [
Expand Down
Binary file modified master/objects.inv
Binary file not shown.
2 changes: 1 addition & 1 deletion master/searchindex.js

Large diffs are not rendered by default.

0 comments on commit e0a3cb8

Please sign in to comment.