From 6bad0bfd9487095b930eb563a4e1aa3de65ecbfc Mon Sep 17 00:00:00 2001 From: niksirbi Date: Thu, 2 Jul 2026 11:31:51 +0100 Subject: [PATCH 1/6] completely linkcheck ignore all GIN links --- docs/source/conf.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index ce9c7a54..cdec6c98 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -85,6 +85,7 @@ linkcheck_ignore = [ "https://neuromorpho.org/", "https://liveuclac.sharepoint.com/", # ignore everything on the internal wiki + "https://gin.g-node.org/", # GIN is often slow/unreachable and times out "https://linux.die.net/man/1/rsync", "https://www.uclb.com/", "https://support.zadarastorage.com", @@ -95,10 +96,7 @@ ] # The linkcheck builder will skip verifying that anchors exist when checking # these URLs (e.g. because they are generated by JavaScript). -linkcheck_anchors_ignore_for_url = [ - "https://gin.g-node.org/G-Node/Info/wiki", - "https://gin.g-node.org/G-Node/info/wiki", # ignore both spellings -] +linkcheck_anchors_ignore_for_url = [] linkcheck_retries = 2 # -- Options for HTML output ------------------------------------------------- From 61c970427b3fbb2891a254318fcf0d94134a9ede Mon Sep 17 00:00:00 2001 From: niksirbi Date: Thu, 2 Jul 2026 11:34:46 +0100 Subject: [PATCH 2/6] replace broken paper links with dois, and linkcheck ignore all doi links --- docs/source/conf.py | 1 + .../example_pipelines/examples/README.rst | 2 +- docs/source/electrophysiology/resources.md | 8 ++++---- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index cdec6c98..09c09f63 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -86,6 +86,7 @@ "https://neuromorpho.org/", "https://liveuclac.sharepoint.com/", # ignore everything on the internal wiki "https://gin.g-node.org/", # GIN is often slow/unreachable and times out + "https://doi.org/", # DOIs are stable but publishers often block link checkers "https://linux.die.net/man/1/rsync", "https://www.uclb.com/", "https://support.zadarastorage.com", diff --git a/docs/source/electrophysiology/example_pipelines/examples/README.rst b/docs/source/electrophysiology/example_pipelines/examples/README.rst index 6181b007..d085f18f 100644 --- a/docs/source/electrophysiology/example_pipelines/examples/README.rst +++ b/docs/source/electrophysiology/example_pipelines/examples/README.rst @@ -23,7 +23,7 @@ is a member of the `International Brain Laboratory (IBL) `_ running the -`IBL's standardised behavioural task `_ +`IBL's standardised behavioural task `_ with acute Neuropixels 1.0 recordings. Details of the `analysis pipeline code `__ on the IBL data management system can be found diff --git a/docs/source/electrophysiology/resources.md b/docs/source/electrophysiology/resources.md index 4488848c..99bca335 100644 --- a/docs/source/electrophysiology/resources.md +++ b/docs/source/electrophysiology/resources.md @@ -21,13 +21,13 @@ documentation is a good starting point. Below are a selection of papers that give a history and overview of the extracellular electrophysiology landscape: -[Steinmetz NA et al. (2018). Challenges and opportunities for large-scale electrophysiology with Neuropixels probes. *Current Opinion in Neurobiology*.](https://pubmed.ncbi.nlm.nih.gov/29444488/) +[Steinmetz NA et al. (2018). Challenges and opportunities for large-scale electrophysiology with Neuropixels probes. *Current Opinion in Neurobiology*.](https://doi.org/10.1016/j.conb.2018.01.009) [Buccino AP et al. (2022). Spike sorting: new trends and challenges of the era of high-density probes. *Progress in Biomedical Engineering*.](https://iopscience.iop.org/article/10.1088/2516-1091/ac6b96/meta) [Rey HG et al. (2015). Past, present and future of spike sorting techniques. *Brain Research Bulletin*.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674014/) -[Carlson D et al. (2019). Continuing progress of spike sorting in the era of big data. *Current Opinion in Neurobiology*](https://pubmed.ncbi.nlm.nih.gov/30856552/) +[Carlson D et al. (2019). Continuing progress of spike sorting in the era of big data. *Current Opinion in Neurobiology*](https://doi.org/10.1016/j.conb.2019.02.007) ## Technical Introduction @@ -48,7 +48,7 @@ contains a clearly written overview of common preprocessing steps. Similarly, [Bill Karsh's guide](https://billkarsh.github.io/SpikeGLX/help/catgt_tshift/catgt_tshift/) on SpikeGLX preprocessing tools gives a useful overview. -[de Cheveigné & Nelken (2019)](https://pubmed.ncbi.nlm.nih.gov/30998899/) +[de Cheveigné & Nelken (2019)](https://doi.org/10.1016/j.neuron.2019.02.039) provide a technical treatment of digital filtering, a key step in preprocessing and analysis. ### Spike Sorting @@ -73,7 +73,7 @@ Assessing the quality of spike-sorting is a key to producing high-quality data. These two papers provide a nice introduction to quality metrics for assessing spike sorting outputs: -[Hill DN et al. (2011). Quality Metrics to Accompany Spike Sorting of Extracellular Signals. *Journal of Neuroscience*.](https://www.jneurosci.org/content/31/24/8699) +[Hill DN et al. (2011). Quality Metrics to Accompany Spike Sorting of Extracellular Signals. *Journal of Neuroscience*.](https://doi.org/10.1523/JNEUROSCI.0971-11.2011) [Harris KD et al. (2016). Improving data quality in neuronal population recordings. *Nature Neuroscience*.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5244825/) From 157f3f556a75ed8349defa180f083aa21cc4092b Mon Sep 17 00:00:00 2001 From: niksirbi Date: Thu, 2 Jul 2026 11:41:00 +0100 Subject: [PATCH 3/6] Update relocated documentation links (movement, UCL Neuropixels, SpikeInterface, SpikeForest) --- docs/source/electrophysiology/resources.md | 8 ++++---- docs/source/open_science/GIN-repositories.md | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/electrophysiology/resources.md b/docs/source/electrophysiology/resources.md index 99bca335..89201560 100644 --- a/docs/source/electrophysiology/resources.md +++ b/docs/source/electrophysiology/resources.md @@ -35,8 +35,8 @@ This section includes more technical resources on the different stages of extracellular electrophysiology analysis. A particularly useful resource is the -[Neuropixels](https://www.ucl.ac.uk/neuropixels/courses) course, with their videos published online -(e.g. [2023](https://www.ucl.ac.uk/neuropixels/training/2023-neuropixels-course)). +[Neuropixels](https://www.ucl.ac.uk/brain-sciences/neuropixels/training) course, with their videos published online +(e.g. [2023](https://www.ucl.ac.uk/brain-sciences/research/neuropixels/training/2023-neuropixels-course)). While these are targeted towards Neuropixels users, they are valuable resources for any researcher approaching electrophysiology preprocessing and analysis. @@ -86,7 +86,7 @@ More recently, advances in the automating curation has been made in the [Bombcell package](https://github.com/Julie-Fabre/bombcell). SpikeInterface also maintains a set of quality metrics, -[explained in detail](https://spikeinterface.readthedocs.io/en/latest/modules/qualitymetrics.html) +[explained in detail](https://spikeinterface.readthedocs.io/en/stable/modules/metrics.html) in their documentation. ## SpikeInterface @@ -108,7 +108,7 @@ is mainly focused on preprocessing, spike sorting and quality metrics. and [Nemos](https://github.com/flatironinstitute/nemos) all provide useful toolboxes for analysing data post-sorting. -The [SpikeForest](https://spikeforest.flatironinstitute.org/) +The [SpikeForest](https://github.com/flatironinstitute/spikeforest) project is an excellent resource for assessing the performance of different spike-sorting algorithms across probe types and brain regions. diff --git a/docs/source/open_science/GIN-repositories.md b/docs/source/open_science/GIN-repositories.md index 387aecc1..4d914cde 100644 --- a/docs/source/open_science/GIN-repositories.md +++ b/docs/source/open_science/GIN-repositories.md @@ -395,7 +395,7 @@ Indeed, when we `gin download` a repository from the GIN server, we get a local ## References -- https://movement.neuroinformatics.dev/community/contributing.html#adding-new-data +- https://movement.neuroinformatics.dev/latest/community/contributing.html#adding-new-data - https://gin.g-node.org/G-Node/info/wiki#how-do-i-start - https://gin-howto.readthedocs.io/en/latest/gin-repositories.html - On GIN and its relation to `git-annex` (very high-level): https://gin.g-node.org/G-Node/Info/wiki/GIN+Advantages+Structure From 736aa4b3cb2aee4a1e2dec8e7c87c28fd14eb4d5 Mon Sep 17 00:00:00 2001 From: niksirbi Date: Thu, 2 Jul 2026 11:49:04 +0100 Subject: [PATCH 4/6] ignore cambridgeneurotech links (rejects link checker requests) --- docs/source/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/conf.py b/docs/source/conf.py index 09c09f63..adfbde58 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -87,6 +87,7 @@ "https://liveuclac.sharepoint.com/", # ignore everything on the internal wiki "https://gin.g-node.org/", # GIN is often slow/unreachable and times out "https://doi.org/", # DOIs are stable but publishers often block link checkers + "https://www.cambridgeneurotech.com/", # rejects link checker requests (HTTP 415) "https://linux.die.net/man/1/rsync", "https://www.uclb.com/", "https://support.zadarastorage.com", From bc9716d3af1b5e3d0de4a18da44a74d54a0e4354 Mon Sep 17 00:00:00 2001 From: Niko Sirmpilatze Date: Thu, 2 Jul 2026 13:36:14 +0100 Subject: [PATCH 5/6] Refer to the 2025 neuropixels course Co-authored-by: Adam Tyson --- docs/source/electrophysiology/resources.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/electrophysiology/resources.md b/docs/source/electrophysiology/resources.md index 89201560..30159125 100644 --- a/docs/source/electrophysiology/resources.md +++ b/docs/source/electrophysiology/resources.md @@ -36,7 +36,7 @@ extracellular electrophysiology analysis. A particularly useful resource is the [Neuropixels](https://www.ucl.ac.uk/brain-sciences/neuropixels/training) course, with their videos published online -(e.g. [2023](https://www.ucl.ac.uk/brain-sciences/research/neuropixels/training/2023-neuropixels-course)). +(e.g. [2025](https://www.ucl.ac.uk/brain-sciences/research/neuropixels/training/2025-neuropixels-course)). While these are targeted towards Neuropixels users, they are valuable resources for any researcher approaching electrophysiology preprocessing and analysis. From a030e9e88a947c73b02eb05a97d4cdbf3e534e0a Mon Sep 17 00:00:00 2001 From: Niko Sirmpilatze Date: Thu, 2 Jul 2026 13:36:29 +0100 Subject: [PATCH 6/6] Refer to SpikeForest paper Co-authored-by: Adam Tyson --- docs/source/electrophysiology/resources.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/electrophysiology/resources.md b/docs/source/electrophysiology/resources.md index 30159125..3627a6ee 100644 --- a/docs/source/electrophysiology/resources.md +++ b/docs/source/electrophysiology/resources.md @@ -108,7 +108,7 @@ is mainly focused on preprocessing, spike sorting and quality metrics. and [Nemos](https://github.com/flatironinstitute/nemos) all provide useful toolboxes for analysing data post-sorting. -The [SpikeForest](https://github.com/flatironinstitute/spikeforest) +The [SpikeForest](https://doi.org/10.7554/eLife.55167) project is an excellent resource for assessing the performance of different spike-sorting algorithms across probe types and brain regions.