rel(2.10.0): Update docs of 2.10 series

nipreps · Jul 4, 2024 · 1da5edd · 1da5edd
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diff --git a/2.10/.buildinfo b/2.10/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: d10f1fea4eb11a3e4eee25c94a5c6abf
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/2.10/.nojekyll b/2.10/.nojekyll
diff --git a/2.10/_images/notebooks_SDC_-_Theory_and_physics_11_0.png b/2.10/_images/notebooks_SDC_-_Theory_and_physics_11_0.png
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diff --git a/2.10/_images/sdcflows-workflows-apply-correction-1.png b/2.10/_images/sdcflows-workflows-apply-correction-1.png
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diff --git a/2.10/_images/sdcflows-workflows-fit-fieldmap-1.png b/2.10/_images/sdcflows-workflows-fit-fieldmap-1.png
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diff --git a/2.10/_modules/index.html b/2.10/_modules/index.html
diff --git a/2.10/_modules/sdcflows/cli/main.html b/2.10/_modules/sdcflows/cli/main.html
diff --git a/2.10/_modules/sdcflows/cli/parser.html b/2.10/_modules/sdcflows/cli/parser.html
diff --git a/2.10/_modules/sdcflows/cli/workflow.html b/2.10/_modules/sdcflows/cli/workflow.html
diff --git a/2.10/_modules/sdcflows/config.html b/2.10/_modules/sdcflows/config.html
diff --git a/2.10/_modules/sdcflows/data.html b/2.10/_modules/sdcflows/data.html
diff --git a/2.10/_modules/sdcflows/fieldmaps.html b/2.10/_modules/sdcflows/fieldmaps.html
diff --git a/2.10/_modules/sdcflows/interfaces/brainmask.html b/2.10/_modules/sdcflows/interfaces/brainmask.html
diff --git a/2.10/_modules/sdcflows/interfaces/bspline.html b/2.10/_modules/sdcflows/interfaces/bspline.html
diff --git a/2.10/_modules/sdcflows/interfaces/epi.html b/2.10/_modules/sdcflows/interfaces/epi.html
diff --git a/2.10/_modules/sdcflows/interfaces/fmap.html b/2.10/_modules/sdcflows/interfaces/fmap.html
diff --git a/2.10/_modules/sdcflows/interfaces/reportlets.html b/2.10/_modules/sdcflows/interfaces/reportlets.html
diff --git a/2.10/_modules/sdcflows/interfaces/utils.html b/2.10/_modules/sdcflows/interfaces/utils.html
diff --git a/2.10/_modules/sdcflows/transform.html b/2.10/_modules/sdcflows/transform.html
diff --git a/2.10/_modules/sdcflows/utils/bimap.html b/2.10/_modules/sdcflows/utils/bimap.html
diff --git a/2.10/_modules/sdcflows/utils/epimanip.html b/2.10/_modules/sdcflows/utils/epimanip.html
diff --git a/2.10/_modules/sdcflows/utils/misc.html b/2.10/_modules/sdcflows/utils/misc.html
diff --git a/2.10/_modules/sdcflows/utils/phasemanip.html b/2.10/_modules/sdcflows/utils/phasemanip.html
diff --git a/2.10/_modules/sdcflows/utils/telemetry.html b/2.10/_modules/sdcflows/utils/telemetry.html
diff --git a/2.10/_modules/sdcflows/utils/tools.html b/2.10/_modules/sdcflows/utils/tools.html
diff --git a/2.10/_modules/sdcflows/utils/wrangler.html b/2.10/_modules/sdcflows/utils/wrangler.html
diff --git a/2.10/_modules/sdcflows/viz/utils.html b/2.10/_modules/sdcflows/viz/utils.html
diff --git a/2.10/_modules/sdcflows/workflows/ancillary.html b/2.10/_modules/sdcflows/workflows/ancillary.html
diff --git a/2.10/_modules/sdcflows/workflows/apply/correction.html b/2.10/_modules/sdcflows/workflows/apply/correction.html
diff --git a/2.10/_modules/sdcflows/workflows/apply/registration.html b/2.10/_modules/sdcflows/workflows/apply/registration.html
diff --git a/2.10/_modules/sdcflows/workflows/base.html b/2.10/_modules/sdcflows/workflows/base.html
diff --git a/2.10/_modules/sdcflows/workflows/fit/base.html b/2.10/_modules/sdcflows/workflows/fit/base.html
diff --git a/2.10/_modules/sdcflows/workflows/fit/fieldmap.html b/2.10/_modules/sdcflows/workflows/fit/fieldmap.html
diff --git a/2.10/_modules/sdcflows/workflows/fit/pepolar.html b/2.10/_modules/sdcflows/workflows/fit/pepolar.html
diff --git a/2.10/_modules/sdcflows/workflows/fit/syn.html b/2.10/_modules/sdcflows/workflows/fit/syn.html
diff --git a/2.10/_modules/sdcflows/workflows/outputs.html b/2.10/_modules/sdcflows/workflows/outputs.html
diff --git a/2.10/_sources/api.rst.txt b/2.10/_sources/api.rst.txt
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+Library API (application program interface)
+===========================================
+
+Information on specific functions, classes, and methods.
+
+.. toctree::
+   :glob:
+
+   api/sdcflows.cli
+   api/sdcflows.config
+   api/sdcflows.data
+   api/sdcflows.fieldmaps
+   api/sdcflows.interfaces
+   api/sdcflows.transform
+   api/sdcflows.utils
+   api/sdcflows.viz
+   api/sdcflows.workflows
diff --git a/2.10/_sources/api/sdcflows.cli.main.rst.txt b/2.10/_sources/api/sdcflows.cli.main.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.cli.main module
+========================
+
+.. automodule:: sdcflows.cli.main
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.cli.parser.rst.txt b/2.10/_sources/api/sdcflows.cli.parser.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.cli.parser module
+==========================
+
+.. automodule:: sdcflows.cli.parser
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.cli.rst.txt b/2.10/_sources/api/sdcflows.cli.rst.txt
@@ -0,0 +1,16 @@
+sdcflows.cli package
+====================
+
+.. automodule:: sdcflows.cli
+   :members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   sdcflows.cli.main
+   sdcflows.cli.parser
+   sdcflows.cli.workflow
diff --git a/2.10/_sources/api/sdcflows.cli.workflow.rst.txt b/2.10/_sources/api/sdcflows.cli.workflow.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.cli.workflow module
+============================
+
+.. automodule:: sdcflows.cli.workflow
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.config.rst.txt b/2.10/_sources/api/sdcflows.config.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.config module
+======================
+
+.. automodule:: sdcflows.config
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.data.rst.txt b/2.10/_sources/api/sdcflows.data.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.data package
+=====================
+
+.. automodule:: sdcflows.data
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.fieldmaps.rst.txt b/2.10/_sources/api/sdcflows.fieldmaps.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.fieldmaps module
+=========================
+
+.. automodule:: sdcflows.fieldmaps
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.interfaces.brainmask.rst.txt b/2.10/_sources/api/sdcflows.interfaces.brainmask.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.interfaces.brainmask module
+====================================
+
+.. automodule:: sdcflows.interfaces.brainmask
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.interfaces.bspline.rst.txt b/2.10/_sources/api/sdcflows.interfaces.bspline.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.interfaces.bspline module
+==================================
+
+.. automodule:: sdcflows.interfaces.bspline
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.interfaces.epi.rst.txt b/2.10/_sources/api/sdcflows.interfaces.epi.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.interfaces.epi module
+==============================
+
+.. automodule:: sdcflows.interfaces.epi
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.interfaces.fmap.rst.txt b/2.10/_sources/api/sdcflows.interfaces.fmap.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.interfaces.fmap module
+===============================
+
+.. automodule:: sdcflows.interfaces.fmap
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.interfaces.reportlets.rst.txt b/2.10/_sources/api/sdcflows.interfaces.reportlets.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.interfaces.reportlets module
+=====================================
+
+.. automodule:: sdcflows.interfaces.reportlets
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.interfaces.rst.txt b/2.10/_sources/api/sdcflows.interfaces.rst.txt
@@ -0,0 +1,19 @@
+sdcflows.interfaces package
+===========================
+
+.. automodule:: sdcflows.interfaces
+   :members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   sdcflows.interfaces.brainmask
+   sdcflows.interfaces.bspline
+   sdcflows.interfaces.epi
+   sdcflows.interfaces.fmap
+   sdcflows.interfaces.reportlets
+   sdcflows.interfaces.utils
diff --git a/2.10/_sources/api/sdcflows.interfaces.utils.rst.txt b/2.10/_sources/api/sdcflows.interfaces.utils.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.interfaces.utils module
+================================
+
+.. automodule:: sdcflows.interfaces.utils
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.transform.rst.txt b/2.10/_sources/api/sdcflows.transform.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.transform module
+=========================
+
+.. automodule:: sdcflows.transform
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.utils.bimap.rst.txt b/2.10/_sources/api/sdcflows.utils.bimap.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.utils.bimap module
+===========================
+
+.. automodule:: sdcflows.utils.bimap
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.utils.epimanip.rst.txt b/2.10/_sources/api/sdcflows.utils.epimanip.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.utils.epimanip module
+==============================
+
+.. automodule:: sdcflows.utils.epimanip
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.utils.misc.rst.txt b/2.10/_sources/api/sdcflows.utils.misc.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.utils.misc module
+==========================
+
+.. automodule:: sdcflows.utils.misc
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.utils.phasemanip.rst.txt b/2.10/_sources/api/sdcflows.utils.phasemanip.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.utils.phasemanip module
+================================
+
+.. automodule:: sdcflows.utils.phasemanip
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.utils.rst.txt b/2.10/_sources/api/sdcflows.utils.rst.txt
@@ -0,0 +1,20 @@
+sdcflows.utils package
+======================
+
+.. automodule:: sdcflows.utils
+   :members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   sdcflows.utils.bimap
+   sdcflows.utils.epimanip
+   sdcflows.utils.misc
+   sdcflows.utils.phasemanip
+   sdcflows.utils.telemetry
+   sdcflows.utils.tools
+   sdcflows.utils.wrangler
diff --git a/2.10/_sources/api/sdcflows.utils.telemetry.rst.txt b/2.10/_sources/api/sdcflows.utils.telemetry.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.utils.telemetry module
+===============================
+
+.. automodule:: sdcflows.utils.telemetry
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.utils.tools.rst.txt b/2.10/_sources/api/sdcflows.utils.tools.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.utils.tools module
+===========================
+
+.. automodule:: sdcflows.utils.tools
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.utils.wrangler.rst.txt b/2.10/_sources/api/sdcflows.utils.wrangler.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.utils.wrangler module
+==============================
+
+.. automodule:: sdcflows.utils.wrangler
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.viz.rst.txt b/2.10/_sources/api/sdcflows.viz.rst.txt
@@ -0,0 +1,14 @@
+sdcflows.viz package
+====================
+
+.. automodule:: sdcflows.viz
+   :members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   sdcflows.viz.utils
diff --git a/2.10/_sources/api/sdcflows.viz.utils.rst.txt b/2.10/_sources/api/sdcflows.viz.utils.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.viz.utils module
+=========================
+
+.. automodule:: sdcflows.viz.utils
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.ancillary.rst.txt b/2.10/_sources/api/sdcflows.workflows.ancillary.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.workflows.ancillary module
+===================================
+
+.. automodule:: sdcflows.workflows.ancillary
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.apply.correction.rst.txt b/2.10/_sources/api/sdcflows.workflows.apply.correction.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.workflows.apply.correction module
+==========================================
+
+.. automodule:: sdcflows.workflows.apply.correction
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.apply.registration.rst.txt b/2.10/_sources/api/sdcflows.workflows.apply.registration.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.workflows.apply.registration module
+============================================
+
+.. automodule:: sdcflows.workflows.apply.registration
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.apply.rst.txt b/2.10/_sources/api/sdcflows.workflows.apply.rst.txt
@@ -0,0 +1,15 @@
+sdcflows.workflows.apply package
+================================
+
+.. automodule:: sdcflows.workflows.apply
+   :members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   sdcflows.workflows.apply.correction
+   sdcflows.workflows.apply.registration
diff --git a/2.10/_sources/api/sdcflows.workflows.base.rst.txt b/2.10/_sources/api/sdcflows.workflows.base.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.workflows.base module
+==============================
+
+.. automodule:: sdcflows.workflows.base
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.fit.base.rst.txt b/2.10/_sources/api/sdcflows.workflows.fit.base.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.workflows.fit.base module
+==================================
+
+.. automodule:: sdcflows.workflows.fit.base
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.fit.fieldmap.rst.txt b/2.10/_sources/api/sdcflows.workflows.fit.fieldmap.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.workflows.fit.fieldmap module
+======================================
+
+.. automodule:: sdcflows.workflows.fit.fieldmap
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.fit.pepolar.rst.txt b/2.10/_sources/api/sdcflows.workflows.fit.pepolar.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.workflows.fit.pepolar module
+=====================================
+
+.. automodule:: sdcflows.workflows.fit.pepolar
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.fit.rst.txt b/2.10/_sources/api/sdcflows.workflows.fit.rst.txt
@@ -0,0 +1,17 @@
+sdcflows.workflows.fit package
+==============================
+
+.. automodule:: sdcflows.workflows.fit
+   :members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   sdcflows.workflows.fit.base
+   sdcflows.workflows.fit.fieldmap
+   sdcflows.workflows.fit.pepolar
+   sdcflows.workflows.fit.syn
diff --git a/2.10/_sources/api/sdcflows.workflows.fit.syn.rst.txt b/2.10/_sources/api/sdcflows.workflows.fit.syn.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.workflows.fit.syn module
+=================================
+
+.. automodule:: sdcflows.workflows.fit.syn
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.outputs.rst.txt b/2.10/_sources/api/sdcflows.workflows.outputs.rst.txt
@@ -0,0 +1,6 @@
+sdcflows.workflows.outputs module
+=================================
+
+.. automodule:: sdcflows.workflows.outputs
+   :members:
+   :show-inheritance:
diff --git a/2.10/_sources/api/sdcflows.workflows.rst.txt b/2.10/_sources/api/sdcflows.workflows.rst.txt
@@ -0,0 +1,25 @@
+sdcflows.workflows package
+==========================
+
+.. automodule:: sdcflows.workflows
+   :members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 1
+
+   sdcflows.workflows.apply
+   sdcflows.workflows.fit
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   sdcflows.workflows.ancillary
+   sdcflows.workflows.base
+   sdcflows.workflows.outputs
diff --git a/2.10/_sources/changes.rst.txt b/2.10/_sources/changes.rst.txt
@@ -0,0 +1,5 @@
+-----------
+What's new?
+-----------
+
+.. include:: ../CHANGES.rst
diff --git a/2.10/_sources/cli.rst.txt b/2.10/_sources/cli.rst.txt
@@ -0,0 +1,8 @@
+Standalone command line usage
+=============================
+*SDCFlows* can execute fieldmap estimation from a BIDS-compliant dataset by using the *standalone command line interface*:
+
+.. argparse::
+   :module: sdcflows.cli.parser
+   :func: _parser
+   :prog: sdcflows
diff --git a/2.10/_sources/examples.rst.txt b/2.10/_sources/examples.rst.txt
@@ -0,0 +1,8 @@
+Examples
+========
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   notebooks/SDC - Theory and physics