Add section to reports that show system info, tedana call and version

.circleci/config.yml

@@ -6,7 +6,6 @@ version: 2.1
 orbs:
   codecov: codecov/[email protected]
 jobs:
-
   makeenv_38:
     docker:
       - image: continuumio/miniconda3
@@ -26,7 +25,7 @@ jobs:
       - save_cache:
           key: conda-py38-v2-{{ checksum "pyproject.toml" }}
           paths:
-              - /opt/conda/envs/tedana_py38
+            - /opt/conda/envs/tedana_py38
 
   unittest_38:
     docker:
@@ -48,7 +47,7 @@ jobs:
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/coverage/.coverage.py38
+            - src/coverage/.coverage.py38
 
   unittest_39:
     docker:
@@ -78,11 +77,11 @@ jobs:
       - save_cache:
           key: conda-py39-v2-{{ checksum "pyproject.toml" }}
           paths:
-              - /opt/conda/envs/tedana_py39
+            - /opt/conda/envs/tedana_py39
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/coverage/.coverage.py39
+            - src/coverage/.coverage.py39
 
   unittest_310:
     docker:
@@ -112,11 +111,11 @@ jobs:
       - save_cache:
           key: conda-py310-v1-{{ checksum "pyproject.toml" }}
           paths:
-              - /opt/conda/envs/tedana_py310
+            - /opt/conda/envs/tedana_py310
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/coverage/.coverage.py310
+            - src/coverage/.coverage.py310
 
   style_check:
     docker:
@@ -153,11 +152,11 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.three-echo
       - store_artifacts:
-          path: /tmp/data
+          path: /tmp/src/tedana/.testing_data_cache/outputs
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/coverage/.coverage.three-echo
+            - src/coverage/.coverage.three-echo
 
   four-echo:
     docker:
@@ -178,11 +177,11 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.four-echo
       - store_artifacts:
-          path: /tmp/data
+          path: /tmp/src/tedana/.testing_data_cache/outputs
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/coverage/.coverage.four-echo
+            - src/coverage/.coverage.four-echo
 
   five-echo:
     docker:
@@ -203,11 +202,11 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.five-echo
       - store_artifacts:
-          path: /tmp/data
+          path: /tmp/src/tedana/.testing_data_cache/outputs
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/coverage/.coverage.five-echo
+            - src/coverage/.coverage.five-echo
 
   reclassify:
     docker:
@@ -228,12 +227,11 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.reclassify
       - store_artifacts:
-          path: /tmp/data
+          path: /tmp/src/tedana/.testing_data_cache/outputs
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/coverage/.coverage.reclassify
-
+            - src/coverage/.coverage.reclassify
 
   t2smap:
     docker:
@@ -254,11 +252,11 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.t2smap
       - store_artifacts:
-          path: /tmp/data
+          path: /tmp/src/tedana/.testing_data_cache/outputs
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/coverage/.coverage.t2smap
+            - src/coverage/.coverage.t2smap
 
   merge_coverage:
     working_directory: /tmp/src/tedana

tedana/reporting/data/html/report_body_template.html

@@ -1,4 +1,9 @@
 <style type="text/css">
+  .report {
+    display: flex;
+    flex-direction: column;
+  }
+
   .content {
     margin-left: 5%;
     margin-right: 5%;
@@ -42,6 +47,14 @@
     margin-top: 20px;
   }
 
+  .info {
+    margin-left: 5%;
+    margin-right: 5%;
+    margin-bottom: 150px;
+    height: auto;
+    float: left;
+  }
+
   button {
     margin-right: 15px;
     width: auto;
@@ -126,6 +139,24 @@
     border-left: #c5a13e 1px solid;
     border-right: #c5a13e 1px solid;
   }
+
+  td {
+    padding: 0.3rem 1.5rem;
+  }
+
+  pre {
+    width: 60%;
+    white-space: pre-wrap; /* Since CSS 2.1 */
+    white-space: -moz-pre-wrap; /* Mozilla, since 1999 */
+    white-space: -pre-wrap; /* Opera 4-6 */
+    white-space: -o-pre-wrap; /* Opera 7 */
+    word-wrap: break-word; /* Internet Explorer 5.5+ */
+  }
+
+  .code_block {
+    padding: 2em !important;
+    border-radius: 5px;
+  }
 </style>
 <script language="javascript">
   function updateCarpetPlot(name) {
@@ -153,27 +184,31 @@
     }
   }
 </script>
-<div class="content">
-  <h1>ICA components</h1>
-  $content
-</div>
-<div class="carpet-plots">
-  <h1>Carpet plots</h1>
-  <div class="carpet-wrapper">
-    <div class="carpet-buttons">
-      $buttons
-    </div>
-    <div class="carpet-plots-image">
-      <img id="imgCarpetPlot" src="./figures/carpet_optcom.svg" />
+<div class="report">
+  <div class="content">
+    <h1>ICA components</h1>
+    $content
+  </div>
+  <div class="carpet-plots">
+    <h1>Carpet plots</h1>
+    <div class="carpet-wrapper">
+      <div class="carpet-buttons">$buttons</div>
+      <div class="carpet-plots-image">
+        <img id="imgCarpetPlot" src="./figures/carpet_optcom.svg" />
+      </div>
     </div>
   </div>
-</div>
-<div class="about">
-  <h1>About tedana</h1>
-  $about
+  <div class="info">
+    <h1>Info</h1>
+    $info
+  </div>
+  <div class="about">
+    <h1>About tedana</h1>
+    $about
 
-  <h1>References</h1>
-  $references
+    <h1>References</h1>
+    $references
+  </div>
 </div>
 
 $javascript

tedana/reporting/data/html/report_head_template.html

@@ -1,38 +1,70 @@
 <!DOCTYPE html>
 <html lang="en">
+  <head>
+    <title>tedana report</title>
+    <meta
+      name="viewport"
+      content="width = device-width, initial-scale = 1"
+      charset="UTF-8"
+    />
+    <script
+      src="https://cdn.bokeh.org/bokeh/release/bokeh-$bokehversion.min.js"
+      crossorigin="anonymous"
+    ></script>
+    <script
+      src="https://cdn.bokeh.org/bokeh/release/bokeh-widgets-$bokehversion.min.js"
+      crossorigin="anonymous"
+    ></script>
+    <script
+      src="https://cdn.bokeh.org/bokeh/release/bokeh-tables-$bokehversion.min.js"
+      crossorigin="anonymous"
+    ></script>
+    <link
+      rel="stylesheet"
+      href="https://unpkg.com/[email protected]/build/pure-min.css"
+      integrity="sha384-oAOxQR6DkCoMliIh8yFnu25d7Eq/PHS21PClpwjOTeU2jRSq11vu66rf90/cZr47"
+      crossorigin="anonymous"
+    />
 
-<head>
-<title>tedana report</title>
-<meta name="viewport" content="width = device-width, initial-scale = 1" charset="UTF-8">
-<script src="https://cdn.bokeh.org/bokeh/release/bokeh-$bokehversion.min.js"
-        crossorigin="anonymous"></script>
-<script src="https://cdn.bokeh.org/bokeh/release/bokeh-widgets-$bokehversion.min.js"
-        crossorigin="anonymous"></script>
-<script src="https://cdn.bokeh.org/bokeh/release/bokeh-tables-$bokehversion.min.js"
-        crossorigin="anonymous"></script>
-<link rel="stylesheet" href="https://unpkg.com/[email protected]/build/pure-min.css"
-    integrity="sha384-oAOxQR6DkCoMliIh8yFnu25d7Eq/PHS21PClpwjOTeU2jRSq11vu66rf90/cZr47" crossorigin="anonymous">
-<!-- CSS for the report -->
-<style type="text/css">
-    body {
-        padding: 10px 20px 10px 20px;
-    }
-</style>
+    <link
+      rel="stylesheet"
+      href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/styles/tokyo-night-dark.min.css"
+    />
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/highlight.min.js"></script>
+
+    <!-- and it's easy to individually load additional languages -->
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/languages/go.min.js"></script>
 
-</head>
+    <script>
+      hljs.highlightAll();
+    </script>
+
+    <!-- CSS for the report -->
+    <style type="text/css">
+      body {
+        padding: 10px 20px 10px 20px;
+      }
+    </style>
+  </head>
 
-<nav>
-  <div class="pure-menu pure-menu-horizontal">
-    <a href="https://github.com/ME-ICA/tedana" class="pure-menu-heading pure-menu-link">tedana $version</a>
-    <ul class="pure-menu-list">
+  <nav>
+    <div class="pure-menu pure-menu-horizontal">
+      <a
+        href="https://github.com/ME-ICA/tedana"
+        class="pure-menu-heading pure-menu-link"
+        >tedana $version</a
+      >
+      <ul class="pure-menu-list">
         <li class="pure-menu-item">
-            <a href="https://tedana.readthedocs.io" class="pure-menu-link">Reporting documentation</a>
+          <a href="https://tedana.readthedocs.io" class="pure-menu-link"
+            >Reporting documentation</a
+          >
         </li>
-    </ul>
-  </div>
-</nav>
+      </ul>
+    </div>
+  </nav>
 
-<body>
+  <body>
     $body
-</body>
+  </body>
 </html>

tedana/reporting/data/html/report_info_table_template.html

@@ -0,0 +1,44 @@
+<div>
+  <p>
+    <span class="title">Tedana command used:</span>
+    <pre class="language-python">
+      <code class="code_block">
+        $command
+      </code>
+    </pre>
+  </p>
+  <table>
+    <tr>
+      <td class="title">System:</td>
+      <td>$system</td>
+    </tr>
+    <tr>
+      <td class="title">Node:</td>
+      <td>$node</td>
+    </tr>
+    <tr>
+      <td class="title">Release:</td>
+      <td>$release</td>
+    </tr>
+    <tr>
+      <td class="title">System version:</td>
+      <td>$sysversion</td>
+    </tr>
+    <tr>
+      <td class="title">Machine:</td>
+      <td>$machine</td>
+    </tr>
+    <tr>
+      <td class="title">Processor:</td>
+      <td>$processor</td>
+    </tr>
+    <tr>
+      <td class="title">Python:</td>
+      <td>$python</td>
+    </tr>
+    <tr>
+      <td class="title">Tedana version:</td>
+      <td>$tedana</td>
+    </tr>
+  </table>
+</div>