From 41e1945be7b1e1b96e66144f92272db1e02d1a91 Mon Sep 17 00:00:00 2001 From: Michelle Wang Date: Wed, 8 May 2024 10:04:56 -0400 Subject: [PATCH 1/2] [ENH] Add top-level note in Nipoppy pages about new Read the Docs website (#193) * try to add note to Overview page * try to fix path * add same note to every other Nipoppy doc page * accept suggestion for custom note title Co-authored-by: Sebastian Urchs --------- Co-authored-by: Sebastian Urchs --- docs/nipoppy/cli_note.md | 9 +++++++++ docs/nipoppy/code_org.md | 4 ++++ docs/nipoppy/configs.md | 4 ++++ docs/nipoppy/data_org.md | 4 ++++ docs/nipoppy/glossary.md | 4 ++++ docs/nipoppy/installation.md | 4 ++++ docs/nipoppy/overview.md | 4 ++++ docs/nipoppy/trackers.md | 4 ++++ docs/nipoppy/workflow/bids_conv.md | 4 ++++ docs/nipoppy/workflow/dicom_org.md | 4 ++++ docs/nipoppy/workflow/proc_pipe/fmriprep.md | 4 ++++ docs/nipoppy/workflow/proc_pipe/mriqc.md | 4 ++++ 12 files changed, 53 insertions(+) create mode 100644 docs/nipoppy/cli_note.md diff --git a/docs/nipoppy/cli_note.md b/docs/nipoppy/cli_note.md new file mode 100644 index 00000000..dc2f1872 --- /dev/null +++ b/docs/nipoppy/cli_note.md @@ -0,0 +1,9 @@ +!!! note "Nipoppy docs are moving" + + Nipoppy is undergoing a major refactor to move from scripts to a + command-line interface (CLI) and Python API. The new documentation website + (work in progress) can be found at [nipoppy.readthedocs.io](nipoppy.readthedocs.io). + + If you are using the (soon-to-be legacy) scripts from Nipoppy 0.1.0, this is + still the correct place to be. But we encourage you to check out the new + website! diff --git a/docs/nipoppy/code_org.md b/docs/nipoppy/code_org.md index 765acbd0..7963589d 100644 --- a/docs/nipoppy/code_org.md +++ b/docs/nipoppy/code_org.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## Code organization --- diff --git a/docs/nipoppy/configs.md b/docs/nipoppy/configs.md index f71c7b86..504a6987 100644 --- a/docs/nipoppy/configs.md +++ b/docs/nipoppy/configs.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## Global files --- diff --git a/docs/nipoppy/data_org.md b/docs/nipoppy/data_org.md index 61f87a6e..b3fec387 100644 --- a/docs/nipoppy/data_org.md +++ b/docs/nipoppy/data_org.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## Data organization --- diff --git a/docs/nipoppy/glossary.md b/docs/nipoppy/glossary.md index cc3a3e9d..6a72274c 100644 --- a/docs/nipoppy/glossary.md +++ b/docs/nipoppy/glossary.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## Glossary This page lists some definitions for important/recurring terms used in the Nipoppy framework. diff --git a/docs/nipoppy/installation.md b/docs/nipoppy/installation.md index f93d746c..c343829a 100644 --- a/docs/nipoppy/installation.md +++ b/docs/nipoppy/installation.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## Code installation and dataset setup --- diff --git a/docs/nipoppy/overview.md b/docs/nipoppy/overview.md index f7804f14..38ce1ff6 100644 --- a/docs/nipoppy/overview.md +++ b/docs/nipoppy/overview.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## What is Nipoppy? [Nipoppy](https://github.com/neurodatascience/nipoppy) is a lightweight framework for analyzing (neuro)imaging and clinical data. It is designed to help users do the following: diff --git a/docs/nipoppy/trackers.md b/docs/nipoppy/trackers.md index 1eba3cb7..059fa7fc 100644 --- a/docs/nipoppy/trackers.md +++ b/docs/nipoppy/trackers.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## Track data availability status --- diff --git a/docs/nipoppy/workflow/bids_conv.md b/docs/nipoppy/workflow/bids_conv.md index 1e959bca..8c4aa187 100644 --- a/docs/nipoppy/workflow/bids_conv.md +++ b/docs/nipoppy/workflow/bids_conv.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## Objective --- diff --git a/docs/nipoppy/workflow/dicom_org.md b/docs/nipoppy/workflow/dicom_org.md index b3f6d0e6..ba72e2dd 100644 --- a/docs/nipoppy/workflow/dicom_org.md +++ b/docs/nipoppy/workflow/dicom_org.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## Objective --- diff --git a/docs/nipoppy/workflow/proc_pipe/fmriprep.md b/docs/nipoppy/workflow/proc_pipe/fmriprep.md index f8cd07a5..fbe3b97c 100644 --- a/docs/nipoppy/workflow/proc_pipe/fmriprep.md +++ b/docs/nipoppy/workflow/proc_pipe/fmriprep.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## Objective --- diff --git a/docs/nipoppy/workflow/proc_pipe/mriqc.md b/docs/nipoppy/workflow/proc_pipe/mriqc.md index e394a9e6..1259f2fb 100644 --- a/docs/nipoppy/workflow/proc_pipe/mriqc.md +++ b/docs/nipoppy/workflow/proc_pipe/mriqc.md @@ -1,3 +1,7 @@ +{% + include-markdown "nipoppy/cli_note.md" +%} + ## MRIQC image processing pipeline --- From 62ba5937ecd5baf10b0ad5ab8d396f5b9495ee44 Mon Sep 17 00:00:00 2001 From: Michelle Wang Date: Wed, 8 May 2024 11:31:49 -0400 Subject: [PATCH 2/2] Fix broken link to Nipoppy docs! (#195) * fix broken link... --- docs/nipoppy/cli_note.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/nipoppy/cli_note.md b/docs/nipoppy/cli_note.md index dc2f1872..30a7b939 100644 --- a/docs/nipoppy/cli_note.md +++ b/docs/nipoppy/cli_note.md @@ -2,7 +2,8 @@ Nipoppy is undergoing a major refactor to move from scripts to a command-line interface (CLI) and Python API. The new documentation website - (work in progress) can be found at [nipoppy.readthedocs.io](nipoppy.readthedocs.io). + (work in progress) can be found at + [https://nipoppy.readthedocs.io/](https://nipoppy.readthedocs.io/). If you are using the (soon-to-be legacy) scripts from Nipoppy 0.1.0, this is still the correct place to be. But we encourage you to check out the new