From b753c9bc8c5c3ce77e3d82ec913029184758806d Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:17:37 -0700 Subject: [PATCH 01/14] Update .zenodo.json --- .zenodo.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.zenodo.json b/.zenodo.json index 1e901939..f52fd299 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -69,7 +69,7 @@ "license": "BSD-3-Clause", "related_identifiers": [ { - "identifier": "http://tractometry.github.io/pyAFQ", + "identifier": "http://tractometry.org/pyAFQ", "relation": "isPartOf", "scheme": "url" } From ab231ecdf1ef2aa0ce9e3a41615a3d07c69f6f7c Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:18:04 -0700 Subject: [PATCH 02/14] Update AFQ/tasks/viz.py --- AFQ/tasks/viz.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AFQ/tasks/viz.py b/AFQ/tasks/viz.py index 80d32283..c2bfc832 100644 --- a/AFQ/tasks/viz.py +++ b/AFQ/tasks/viz.py @@ -404,7 +404,7 @@ def init_viz_backend(viz_backend_spec="plotly_no_gif", viz_backend_spec : str, optional Which visualization backend to use. See Visualization Backends page in documentation for details: - https://tractometry.github.io/pyAFQ/usage/viz_backend.html + https://tractometry.org/pyAFQ/usage/viz_backend.html One of {"fury", "plotly", "plotly_no_gif"}. Default: "plotly_no_gif" """ From 4c9e26e2893c733060fef8d763fed0b1b8c2ad64 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:18:22 -0700 Subject: [PATCH 03/14] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 55430f70..f62634d1 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # pyAFQ Automated Fiber Quantification ... in Python. -For details, see [Documentation](https://tractometry.github.io/pyAFQ) +For details, see [Documentation](https://tractometry.org/pyAFQ) For further analysis of results, see [AFQ-Insight](https://github.com/richford/AFQ-Insight) From 526be1d51fc5176c66ec559df2ef1490fd720da1 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:23:06 -0700 Subject: [PATCH 04/14] Update bin/pyAFQ --- bin/pyAFQ | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/pyAFQ b/bin/pyAFQ index 9704cf57..b1865e28 100755 --- a/bin/pyAFQ +++ b/bin/pyAFQ @@ -23,7 +23,7 @@ usage = \ Runs full AFQ processing as specified in the configuration file. For details about configuration, see instructions in: -https://tractometry.github.io/pyAFQ/usage/config.html +https://tractometry.org/pyAFQ/usage/config.html The default configuration file looks like: From 4380be0519927401312fc6b34506fc021d2ddc8b Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:23:13 -0700 Subject: [PATCH 05/14] Update bin/pyAFQ --- bin/pyAFQ | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/pyAFQ b/bin/pyAFQ index b1865e28..0fbafb8a 100755 --- a/bin/pyAFQ +++ b/bin/pyAFQ @@ -104,7 +104,7 @@ def parse_cli(arg_dict): logger.info( "Your use of pyAFQ is being recorded using Google Analytics. " "For more information, please refer to the pyAFQ documentation: " - "https://tractometry.github.io/pyAFQ/usage.html#usage-tracking-with-google-analytics. " # noqa + "https://tractometry.org/pyAFQ/usage.html#usage-tracking-with-google-analytics. " # noqa "To turn this off, use the `--notrack` " "flag when using the pyAFQ CLI") import popylar From 88b55c0ce228b9289abe1b7dd8dcaa7ab0bd32ca Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:23:20 -0700 Subject: [PATCH 06/14] Update docs/source/explanations/modeling.rst --- docs/source/explanations/modeling.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/explanations/modeling.rst b/docs/source/explanations/modeling.rst index 6bac424e..e8599df7 100644 --- a/docs/source/explanations/modeling.rst +++ b/docs/source/explanations/modeling.rst @@ -11,7 +11,7 @@ For an interesting perspective on modeling of tissue properties from diffusion MRI data, please refer to a recent paper by Novikov and colleagues [Novikov2018]_. -`This page ` includes +`This page ` includes a list of the model parameters that are accessible through the :class:`AFQ.api.group.GroupAFQ` and :class:`AFQ.api.participant.ParticipantAFQ` objects. From 94ac5c3418f2f0ce36df41e89d9ef37a6ab102ad Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:23:31 -0700 Subject: [PATCH 07/14] Update docs/source/howto/developing/index.rst --- docs/source/howto/developing/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/howto/developing/index.rst b/docs/source/howto/developing/index.rst index df33a1f7..2eec46b1 100644 --- a/docs/source/howto/developing/index.rst +++ b/docs/source/howto/developing/index.rst @@ -20,7 +20,7 @@ As an overview, the pyAFQ code can roughly be divided into 5 sections. 3 - Code which describes tasks within the tractometry workflow. **For most contributors, this is a good place to start**. The user-facing API/CLI use a workflow automatically constructed from these discrete tasks, - as described in `tasks `_ . + as described in `tasks `_ . For shorter tasks, one may only need to edit the relevant task file. For longer tasks, one can add to the files containing low-level functionality. From 9fc15368a39255d481844fb5404a423134d28770 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:23:38 -0700 Subject: [PATCH 08/14] Update docs/source/howto/developing/index.rst --- docs/source/howto/developing/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/howto/developing/index.rst b/docs/source/howto/developing/index.rst index 2eec46b1..f45210d5 100644 --- a/docs/source/howto/developing/index.rst +++ b/docs/source/howto/developing/index.rst @@ -27,7 +27,7 @@ As an overview, the pyAFQ code can roughly be divided into 5 sections. 4 - Code which describes 'definitions', classes which help users describe inputs to pyAFQ. These have particular requirements and must be - BIDS compatible, see `here `_ . + BIDS compatible, see `here `_ . 5 - Code which contains tests, such as in the tests folder and utils/tests. It is important when adding new functionality to add a corresponding test. From 969cf4cf0f648d17f532acd914d1835c9c5489b9 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:23:51 -0700 Subject: [PATCH 09/14] Update docs/source/howto/usage/kwargs.rst --- docs/source/howto/usage/kwargs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/howto/usage/kwargs.rst b/docs/source/howto/usage/kwargs.rst index a11e2163..a3cc5372 100644 --- a/docs/source/howto/usage/kwargs.rst +++ b/docs/source/howto/usage/kwargs.rst @@ -108,7 +108,7 @@ brain_mask_definition: instance from `AFQ.definitions.image`, optional bundle_info: strings, dict, or BundleDict, optional List of bundle names to include in segmentation, or a bundle dictionary (see BundleDict for inspiration), - or a BundleDict. See `Defining Custom Bundle Dictionaries `_ + or a BundleDict. See `Defining Custom Bundle Dictionaries `_ in the `usage` section of pyAFQ's documentation for details. If None, will get all appropriate bundles for the chosen segmentation algorithm. From 5d96789e7e71ddccc363ffe967c4ca67a25a4cf6 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:24:00 -0700 Subject: [PATCH 10/14] Update examples/tutorial_examples/plot_002_bids_layout.py --- examples/tutorial_examples/plot_002_bids_layout.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/tutorial_examples/plot_002_bids_layout.py b/examples/tutorial_examples/plot_002_bids_layout.py index 1c5bc576..61a6365e 100644 --- a/examples/tutorial_examples/plot_002_bids_layout.py +++ b/examples/tutorial_examples/plot_002_bids_layout.py @@ -213,7 +213,7 @@ # which we already have clear definitions of the information # needed to segment them (e.g., waypoint ROIs and probability maps). # For an example that includes custom definition of bundle info, see the -# `plot_callosal_tract_profile example `_. +# `plot_callosal_tract_profile example `_. bundle_info = abd.default18_bd()[ "Left Superior Longitudinal", From f5739880b206b05aed9ce4bc9f5ea19590615365 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:24:08 -0700 Subject: [PATCH 11/14] Update examples/howto_examples/cloudknot_hcp_example.py --- examples/howto_examples/cloudknot_hcp_example.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/howto_examples/cloudknot_hcp_example.py b/examples/howto_examples/cloudknot_hcp_example.py index 039f0133..f2ffa26b 100644 --- a/examples/howto_examples/cloudknot_hcp_example.py +++ b/examples/howto_examples/cloudknot_hcp_example.py @@ -147,7 +147,7 @@ def attach_keys(list_of_arg_lists): ########################################################################## # Define the :meth:`Knot` object to run your jobs on. See -# `this example `_ for more +# `this example `_ for more # details about the arguments to the object. knot = ck.Knot( name='afq-hcp-tractography-201110-0', From ff2a920f46f650a5d846a875c9910c244a73f2f3 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:25:15 -0700 Subject: [PATCH 12/14] Update docs/source/reference/kwargs.rst --- docs/source/reference/kwargs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/reference/kwargs.rst b/docs/source/reference/kwargs.rst index eea01f5d..71c81e72 100644 --- a/docs/source/reference/kwargs.rst +++ b/docs/source/reference/kwargs.rst @@ -258,7 +258,7 @@ n_points_indiv: int or None viz_backend_spec: str, optional Which visualization backend to use. See Visualization Backends page in documentation for details: - https://tractometry.github.io/pyAFQ/usage/viz_backend.html + https://tractometry.org/pyAFQ/usage/viz_backend.html One of {"fury", "plotly", "plotly_no_gif"}. Default: "plotly_no_gif" From f9ef051e67d79b2385c789f849eed91dec7a9f12 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:26:01 -0700 Subject: [PATCH 13/14] Update docs/source/howto/usage/kwargs.rst --- docs/source/howto/usage/kwargs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/howto/usage/kwargs.rst b/docs/source/howto/usage/kwargs.rst index a3cc5372..a4239331 100644 --- a/docs/source/howto/usage/kwargs.rst +++ b/docs/source/howto/usage/kwargs.rst @@ -228,7 +228,7 @@ n_points_indiv: int or None viz_backend_spec: str, optional Which visualization backend to use. See Visualization Backends page in documentation for details: - https://tractometry.github.io/pyAFQ/usage/viz_backend.html + https://tractometry.org/pyAFQ/usage/viz_backend.html One of {"fury", "plotly", "plotly_no_gif"}. Default: "plotly_no_gif" From 9e4648ba95aba964b937f5a2c607c43d0274f24b Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 9 Oct 2024 13:26:16 -0700 Subject: [PATCH 14/14] Update examples/howto_examples/cloudknot_hcp_example.py --- examples/howto_examples/cloudknot_hcp_example.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/howto_examples/cloudknot_hcp_example.py b/examples/howto_examples/cloudknot_hcp_example.py index f2ffa26b..1db42e48 100644 --- a/examples/howto_examples/cloudknot_hcp_example.py +++ b/examples/howto_examples/cloudknot_hcp_example.py @@ -8,7 +8,7 @@ `here `_. We will use the ``Cloudknot`` library to run our AFQ analysis in the AWS Batch service (see also -`this example `_). +`this example `_). In the following we will use ``Cloudknot`` to run multiple configurations of pyAFQ on the HCP dataset. Specifically, here we will run pyAFQ with different tractography seeding strategies.