From 67cc0e99713f10208eb314594edb7d53942e317d Mon Sep 17 00:00:00 2001
From: "Brett M. Morris" <bmmorris@stsci.edu>
Date: Mon, 18 Nov 2024 10:44:09 -0500
Subject: [PATCH 1/6] adding links to ramp fitting docs for roman and jwst in
 rampviz

---
 docs/rampviz/plugins.rst                        | 17 ++++++++++++++---
 .../plugins/ramp_extraction/ramp_extraction.vue | 11 +++++++++++
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/docs/rampviz/plugins.rst b/docs/rampviz/plugins.rst
index 82301ea32b..7050becb75 100644
--- a/docs/rampviz/plugins.rst
+++ b/docs/rampviz/plugins.rst
@@ -62,6 +62,17 @@ Slice
 Ramp Extraction
 ===============
 
-Coming soon.
-
-
+Extract a ramp from a ramp cube.
+
+Data products from infrared detectors flow through the official
+`JWST <https://jwst-pipeline.readthedocs.io/en/latest/>`_ or
+`Roman <https://roman-pipeline.readthedocs.io/en/latest/>`_ mission pipelines in levels. Infrared detectors use
+an "up-the-ramp" readout pattern, which is summarized in the
+`JWST documentation <https://jwst-docs.stsci.edu/understanding-exposure-times>`_.
+
+The Ramp Extraction plugin is a quick-look tool, and it does not support all of the features of the mission pipelines.
+The mission pipelines produce rate images from ramp cubes by fitting the samples up the ramp while accounting for
+non-linearity, jumps detected during an integration, saturation, and detector defects. These data quality checks and
+corrections are not applied in the Ramp Extraction plugin. For details on how rate images are derived from ramps, see
+the `JWST pipeline's ramp fitting step <https://roman-pipeline.readthedocs.io/en/latest/roman/ramp_fitting/index.html>`_
+or the `Roman pipeline's ramp fitting step <https://jwst-pipeline.readthedocs.io/en/latest/jwst/ramp_fitting/index.html#ramp-fitting-step>`_.
diff --git a/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue b/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue
index da8194b206..96a649fa34 100644
--- a/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue
+++ b/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue
@@ -56,6 +56,17 @@
     <div @mouseover="() => active_step='extract'">
       <j-plugin-section-header :active="active_step==='extract'">Extract</j-plugin-section-header>
 
+      <v-row>
+        <span class="v-messages v-messages__message text--secondary">
+          Note: this plugin does not detecting defects in ramps, fit the ramps, or apply corrections. For details on
+          how rate images are derived from ramps, see the documentation for the
+          <a href='https://roman-pipeline.readthedocs.io/en/latest/roman/ramp_fitting/index.html' target="_blank">
+            Roman calibration pipeline</a> or the
+          <a href='https://jwst-pipeline.readthedocs.io/en/latest/jwst/ramp_fitting/index.html#ramp-fitting-step' target="_blank">
+            JWST calibration pipeline</a>.
+        </span>
+      </v-row>
+
       <v-row v-if="aperture_selected !== 'None' && !aperture_selected_validity.is_aperture">
         <span class="v-messages v-messages__message text--secondary">
             Aperture: '{{aperture_selected}}' does not support subpixel: {{aperture_selected_validity.aperture_message}}.

From e12672e1946a65224f436edcbc586296c3f9ecf8 Mon Sep 17 00:00:00 2001
From: "Brett M. Morris" <bmmorris@stsci.edu>
Date: Mon, 18 Nov 2024 11:19:45 -0500
Subject: [PATCH 2/6] switch to j-external-link rather than direct html links

---
 jdaviz/components/external_link.vue                    | 10 ++++------
 .../plugins/ramp_extraction/ramp_extraction.vue        |  8 ++++----
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/jdaviz/components/external_link.vue b/jdaviz/components/external_link.vue
index f137fda746..6621dacb48 100644
--- a/jdaviz/components/external_link.vue
+++ b/jdaviz/components/external_link.vue
@@ -1,10 +1,8 @@
 <template>
-  <div style="margin-top: 4px">
-    <a :href="link" target="__blank" style="color: #A75000">
-      <b>{{ linktext || "Learn More" }}</b>
-      <v-icon x-small color="#A75000">mdi-open-in-new</v-icon>
-    </a>
-  </div>
+  <a :href="link" target="__blank" style="color: #A75000">
+    <b>{{ linktext || "Learn More" }}</b>
+    <v-icon x-small color="#A75000">mdi-open-in-new</v-icon>
+  </a>
 </template>
 
 <script>
diff --git a/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue b/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue
index 96a649fa34..f793f9531b 100644
--- a/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue
+++ b/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue
@@ -60,10 +60,10 @@
         <span class="v-messages v-messages__message text--secondary">
           Note: this plugin does not detecting defects in ramps, fit the ramps, or apply corrections. For details on
           how rate images are derived from ramps, see the documentation for the
-          <a href='https://roman-pipeline.readthedocs.io/en/latest/roman/ramp_fitting/index.html' target="_blank">
-            Roman calibration pipeline</a> or the
-          <a href='https://jwst-pipeline.readthedocs.io/en/latest/jwst/ramp_fitting/index.html#ramp-fitting-step' target="_blank">
-            JWST calibration pipeline</a>.
+          <j-external-link link='https://roman-pipeline.readthedocs.io/en/latest/roman/ramp_fitting/index.html' linktext='Roman pipeline'>
+          </j-external-link> or the
+          <j-external-link link='https://jwst-pipeline.readthedocs.io/en/latest/jwst/ramp_fitting/index.html#ramp-fitting-step' linktext='JWST pipeline'>
+          </j-external-link>.
         </span>
       </v-row>
 

From 7c3d1c3067fea170482c8d3e5be5cd65ebe4edd6 Mon Sep 17 00:00:00 2001
From: "Brett M. Morris" <bmmorris@stsci.edu>
Date: Mon, 18 Nov 2024 13:08:02 -0500
Subject: [PATCH 3/6] link to stable rather than latest, use intersphinx

---
 docs/conf.py                                                 | 5 ++++-
 docs/rampviz/plugins.rst                                     | 4 ++--
 .../rampviz/plugins/ramp_extraction/ramp_extraction.vue      | 4 ++--
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index ef97c8a0c9..14d5788526 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -289,7 +289,10 @@
     'specreduce': ('https://specreduce.readthedocs.io/en/stable/', None),
     'specutils': ('https://specutils.readthedocs.io/en/stable/', None),
     'stdatamodels': ('https://stdatamodels.readthedocs.io/en/latest/', None),
-    'traitlets': ('https://traitlets.readthedocs.io/en/stable/', None)})
+    'traitlets': ('https://traitlets.readthedocs.io/en/stable/', None),
+    'jwst': ('https://jwst-pipeline.readthedocs.io/en/stable/', None),
+    'romancal': ('https://roman-pipeline.readthedocs.io/en/stable/', None),
+})
 
 # Options for linkcheck
 linkcheck_ignore = ['https://github.com/spacetelescope/jdaviz/settings/branches']
diff --git a/docs/rampviz/plugins.rst b/docs/rampviz/plugins.rst
index 7050becb75..e977130ac7 100644
--- a/docs/rampviz/plugins.rst
+++ b/docs/rampviz/plugins.rst
@@ -74,5 +74,5 @@ The Ramp Extraction plugin is a quick-look tool, and it does not support all of
 The mission pipelines produce rate images from ramp cubes by fitting the samples up the ramp while accounting for
 non-linearity, jumps detected during an integration, saturation, and detector defects. These data quality checks and
 corrections are not applied in the Ramp Extraction plugin. For details on how rate images are derived from ramps, see
-the `JWST pipeline's ramp fitting step <https://roman-pipeline.readthedocs.io/en/latest/roman/ramp_fitting/index.html>`_
-or the `Roman pipeline's ramp fitting step <https://jwst-pipeline.readthedocs.io/en/latest/jwst/ramp_fitting/index.html#ramp-fitting-step>`_.
+the JWST pipeline's :doc:`jwst:jwst/ramp_fitting/index` step or the Roman pipeline's
+:doc:`romancal:roman/ramp_fitting/index` step.
diff --git a/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue b/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue
index f793f9531b..826c3145fe 100644
--- a/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue
+++ b/jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.vue
@@ -60,9 +60,9 @@
         <span class="v-messages v-messages__message text--secondary">
           Note: this plugin does not detecting defects in ramps, fit the ramps, or apply corrections. For details on
           how rate images are derived from ramps, see the documentation for the
-          <j-external-link link='https://roman-pipeline.readthedocs.io/en/latest/roman/ramp_fitting/index.html' linktext='Roman pipeline'>
+          <j-external-link link='https://roman-pipeline.readthedocs.io/en/stable/roman/ramp_fitting/index.html' linktext='Roman pipeline'>
           </j-external-link> or the
-          <j-external-link link='https://jwst-pipeline.readthedocs.io/en/latest/jwst/ramp_fitting/index.html#ramp-fitting-step' linktext='JWST pipeline'>
+          <j-external-link link='https://jwst-pipeline.readthedocs.io/en/stable/jwst/ramp_fitting/index.html#ramp-fitting-step' linktext='JWST pipeline'>
           </j-external-link>.
         </span>
       </v-row>

From 82f1168eabc0ce828adbc9709eedca139f18e298 Mon Sep 17 00:00:00 2001
From: "Brett M. Morris" <morrisbrettm@gmail.com>
Date: Tue, 19 Nov 2024 09:44:35 -0500
Subject: [PATCH 4/6] Update docs/rampviz/plugins.rst

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>
---
 docs/rampviz/plugins.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/rampviz/plugins.rst b/docs/rampviz/plugins.rst
index e977130ac7..ea3ae63e82 100644
--- a/docs/rampviz/plugins.rst
+++ b/docs/rampviz/plugins.rst
@@ -65,7 +65,7 @@ Ramp Extraction
 Extract a ramp from a ramp cube.
 
 Data products from infrared detectors flow through the official
-`JWST <https://jwst-pipeline.readthedocs.io/en/latest/>`_ or
+:ref:`JWST <jwst:user-docs>` or
 `Roman <https://roman-pipeline.readthedocs.io/en/latest/>`_ mission pipelines in levels. Infrared detectors use
 an "up-the-ramp" readout pattern, which is summarized in the
 `JWST documentation <https://jwst-docs.stsci.edu/understanding-exposure-times>`_.

From 44d0552250916b56ebdf0857fa54e10c58018866 Mon Sep 17 00:00:00 2001
From: "Brett M. Morris" <morrisbrettm@gmail.com>
Date: Tue, 19 Nov 2024 09:46:51 -0500
Subject: [PATCH 5/6] Update docs/rampviz/plugins.rst

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>
---
 docs/rampviz/plugins.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/rampviz/plugins.rst b/docs/rampviz/plugins.rst
index ea3ae63e82..196819d4ac 100644
--- a/docs/rampviz/plugins.rst
+++ b/docs/rampviz/plugins.rst
@@ -75,4 +75,4 @@ The mission pipelines produce rate images from ramp cubes by fitting the samples
 non-linearity, jumps detected during an integration, saturation, and detector defects. These data quality checks and
 corrections are not applied in the Ramp Extraction plugin. For details on how rate images are derived from ramps, see
 the JWST pipeline's :doc:`jwst:jwst/ramp_fitting/index` step or the Roman pipeline's
-:doc:`romancal:roman/ramp_fitting/index` step.
+:ref:`romancal:ramp_fitting_step` step.

From ae970a59394ecac457c01ef6f2bb2d2698f78883 Mon Sep 17 00:00:00 2001
From: "Brett M. Morris" <morrisbrettm@gmail.com>
Date: Tue, 19 Nov 2024 09:56:35 -0500
Subject: [PATCH 6/6] Update docs/rampviz/plugins.rst

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>
---
 docs/rampviz/plugins.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/rampviz/plugins.rst b/docs/rampviz/plugins.rst
index 196819d4ac..d911f9a5f2 100644
--- a/docs/rampviz/plugins.rst
+++ b/docs/rampviz/plugins.rst
@@ -74,5 +74,5 @@ The Ramp Extraction plugin is a quick-look tool, and it does not support all of
 The mission pipelines produce rate images from ramp cubes by fitting the samples up the ramp while accounting for
 non-linearity, jumps detected during an integration, saturation, and detector defects. These data quality checks and
 corrections are not applied in the Ramp Extraction plugin. For details on how rate images are derived from ramps, see
-the JWST pipeline's :doc:`jwst:jwst/ramp_fitting/index` step or the Roman pipeline's
+the JWST pipeline's :ref:`jwst:ramp_fitting_step` step or the Roman pipeline's
 :ref:`romancal:ramp_fitting_step` step.