Updating documentation to Release_2.7_20230809-1037-g177bfaac0af

AllenInstitute · Sep 4, 2024 · 5ea4987 · 5ea4987
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diff --git a/CalculateTPLikePropsFromSweep.html b/CalculateTPLikePropsFromSweep.html
diff --git a/IPNWB/doc/nwb1.html b/IPNWB/doc/nwb1.html
diff --git a/IPNWB/doc/nwb2.html b/IPNWB/doc/nwb2.html
diff --git a/IPNWB/index.html b/IPNWB/index.html
diff --git a/SweepFormula.html b/SweepFormula.html
diff --git a/SweepFormula_PSX.html b/SweepFormula_PSX.html
diff --git a/TPAnalysis_algorithm.html b/TPAnalysis_algorithm.html
diff --git a/_downloads/67f59d897c12b62a94a4795fb94a9ccb/0001-WIP-fast-sphinx-rst-update-cycle.patch b/_downloads/67f59d897c12b62a94a4795fb94a9ccb/0001-WIP-fast-sphinx-rst-update-cycle.patch
@@ -0,0 +1,78 @@
+From 442b099da06bd393b5ae53211ae2c8026dcef869 Mon Sep 17 00:00:00 2001
+From: Thomas Braun <[email protected]>
+Date: Wed, 29 Mar 2023 18:18:04 +0200
+Subject: [PATCH 1/1] WIP: fast sphinx compilation without breathe
+
+---
+ Packages/doc/conf.py         |  6 +++---
+ tools/build-documentation.sh | 27 ---------------------------
+ 2 files changed, 3 insertions(+), 30 deletions(-)
+
+diff --git a/Packages/doc/conf.py b/Packages/doc/conf.py
+index ad61b69d90..13385ff369 100644
+--- a/Packages/doc/conf.py
++++ b/Packages/doc/conf.py
+@@ -16,11 +16,11 @@ def get_version():
+     return "({branch}) {version}".format(branch=branchString.decode('ascii'), version=revString.decode('ascii'))
+
+ # sphinx config
+-extensions = ['sphinx.ext.mathjax', 'sphinx.ext.todo', 'breathe', \
++extensions = ['sphinx.ext.mathjax', 'sphinx.ext.todo',            \
+               'sphinxcontrib.fulltoc', 'sphinxcontrib.images',    \
+               'sphinxcontrib.youtube']
+
+-master_doc = "index"
++master_doc = "user"
+ project= "MIES Igor"
+
+ html_static_path = ['_static']
+@@ -28,7 +28,7 @@ html_static_path = ['_static']
+ html_copy_source = False
+ html_show_sourcelink = False
+
+-exclude_patterns = [ 'releasenotes_template.rst', 'IPNWB/specifications']
++exclude_patterns = [ 'releasenotes_template.rst', 'IPNWB/specifications', 'index.rst']
+
+ cpp_id_attributes = [ 'threadsafe' ]
+
+diff --git a/tools/build-documentation.sh b/tools/build-documentation.sh
+index 1375d65a07..f709100c55 100755
+--- a/tools/build-documentation.sh
++++ b/tools/build-documentation.sh
+@@ -91,33 +91,6 @@ trap "rm -rf ${top_level}/Packages/doc/IPNWB" EXIT
+ # workaround https://github.com/sphinx-contrib/images/pull/31
+ mkdir _video_thumbnail
+
+-if hash breathe-apidoc 2>/dev/null; then
+-  echo "Start breathe-apidoc"
+-
+-  breathe-apidoc -f -o . xml
+-
+-else
+-  echo "Errors building the documentation" 1>&2
+-  echo "breathe-apidoc could not be found" 1>&2
+-  exit 1
+-fi
+-
+-# Add labels to each group and each file
+-# can be referenced via :ref:`Group LabnotebookQueryFunctions`
+-# or :ref:`File MIES_Utilities.ipf`
+-
+-for i in `ls group/group_*.rst`
+-do
+-  name=$(sed -e '$!d' -e 's/.*doxygengroup:: \(.*\)$/\1/' $i)
+-  sed -i "1s/^/.. _Group ${name}:\n\n/" $i
+-done
+-
+-for i in `ls file/*.rst`
+-do
+-  name=$(sed -e '$!d' -e 's/.*doxygenfile:: \(.*\)$/\1/' $i)
+-  sed -i "1s/^/.. _File ${name}:\n\n/" $i
+-done
+-
+ # create rst substitutions for up-to-date IP nightly links
+ grep "IgorPro[0-9]Nightly" $top_level/Packages/MIES_Include.ipf \
+   | sed -e "s/^\/\/ //"                                         \
+-- 
+2.42.0.rc0.windows.1
+
diff --git a/_downloads/94e6e1968a7e69c4ef61a5bb51aad2a2/public-key.cer b/_downloads/94e6e1968a7e69c4ef61a5bb51aad2a2/public-key.cer
diff --git a/_images/AnalysisBrowser.png b/_images/AnalysisBrowser.png
diff --git a/_images/Browser-SettingsHistory.png b/_images/Browser-SettingsHistory.png
diff --git a/_images/Browser-SweepControl.png b/_images/Browser-SweepControl.png
diff --git a/_images/Browser-all.png b/_images/Browser-all.png
diff --git a/_images/BrowserSettingsPanel-Artefact-Removal.png b/_images/BrowserSettingsPanel-Artefact-Removal.png
diff --git a/_images/BrowserSettingsPanel-ChannelSelection.png b/_images/BrowserSettingsPanel-ChannelSelection.png
diff --git a/_images/BrowserSettingsPanel-Dashboard.png b/_images/BrowserSettingsPanel-Dashboard.png
diff --git a/_images/BrowserSettingsPanel-Note.png b/_images/BrowserSettingsPanel-Note.png
diff --git a/_images/BrowserSettingsPanel-Overlay-Sweeps.png b/_images/BrowserSettingsPanel-Overlay-Sweeps.png
diff --git a/_images/BrowserSettingsPanel-PA-plot.png b/_images/BrowserSettingsPanel-PA-plot.png
diff --git a/_images/BrowserSettingsPanel-Settings.png b/_images/BrowserSettingsPanel-Settings.png
diff --git a/_images/BrowserSettingsPanel-Sweepformula.png b/_images/BrowserSettingsPanel-Sweepformula.png
diff --git a/_images/CalculateTPLikePropsFromSweep.svg b/_images/CalculateTPLikePropsFromSweep.svg
diff --git a/_images/DAEphys-Data_Acquisition.png b/_images/DAEphys-Data_Acquisition.png
diff --git a/_images/PulseAverage_images.png b/_images/PulseAverage_images.png
diff --git a/_images/PulseAverage_images_colorscales.png b/_images/PulseAverage_images_colorscales.png
diff --git a/_images/PulseAverage_traces.png b/_images/PulseAverage_traces.png
diff --git a/_images/RelevantColors.png b/_images/RelevantColors.png
diff --git a/_images/SweepFormula-PSX-GUI.png b/_images/SweepFormula-PSX-GUI.png