Backport PR #2285: Update notebook links in user guides (#2289)

scverse · Oct 11, 2023 · 074ca5d · 074ca5d
1 parent 68f8863
commit 074ca5d
Show file tree

Hide file tree

Showing 13 changed files with 23 additions and 23 deletions.
diff --git a/docs/user_guide/background/transfer_learning.md b/docs/user_guide/background/transfer_learning.md
@@ -12,7 +12,7 @@ The core logic for scArches is implemented in {class}`~scvi.model.base.ArchesMix
 
 :::{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/scarches_scvi_tools`
+-   {doc}`/tutorials/notebooks/scrna/scarches_scvi_tools`
     :::
 
 ### Preliminaries

diff --git a/docs/user_guide/models/amortizedlda.md b/docs/user_guide/models/amortizedlda.md
@@ -20,7 +20,7 @@ The limitations of amortized LDA include:
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/amortized_lda`
+-   {doc}`/tutorials/notebooks/scrna/amortized_lda`
 ```
 
 ## Preliminaries

diff --git a/docs/user_guide/models/autozi.md b/docs/user_guide/models/autozi.md
@@ -5,7 +5,7 @@ is a model for assessing gene-specific levels of zero-inflation in scRNA-seq dat
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/AutoZI_tutorial`
+-   {doc}`/tutorials/notebooks/scrna/AutoZI_tutorial`
 ```
 
 ## Generative process

diff --git a/docs/user_guide/models/cellassign.md b/docs/user_guide/models/cellassign.md
@@ -18,7 +18,7 @@ The limitations of CellAssign include:
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/cellassign_tutorial`
+-   {doc}`/tutorials/notebooks/scrna/cellassign_tutorial`
 ```
 
 ## Preliminaries

diff --git a/docs/user_guide/models/destvi.md b/docs/user_guide/models/destvi.md
@@ -15,7 +15,7 @@ The limitations of DestVI include:
 
 ```{topic} Tutorial:
 
--   {doc}`/tutorials/notebooks/DestVI_tutorial`
+-   {doc}`/tutorials/notebooks/spatial/DestVI_tutorial`
 ```
 
 ## Preliminaries

diff --git a/docs/user_guide/models/linearscvi.md b/docs/user_guide/models/linearscvi.md
@@ -15,7 +15,7 @@ The limitations of LDVAE include:
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/linear_decoder`
+-   {doc}`/tutorials/notebooks/scrna/linear_decoder`
 ```
 
 ## Contrasting with scVI

diff --git a/docs/user_guide/models/multivi.md b/docs/user_guide/models/multivi.md
@@ -16,8 +16,8 @@ The limitations of MultiVI include:
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/api_overview`
--   {doc}`/tutorials/notebooks/MultiVI_tutorial`
+-   {doc}`/tutorials/notebooks/quick_start/api_overview`
+-   {doc}`/tutorials/notebooks/multimodal/MultiVI_tutorial`
 ```
 
 ## Preliminaries

diff --git a/docs/user_guide/models/peakvi.md b/docs/user_guide/models/peakvi.md
@@ -15,10 +15,10 @@ The limitations of peakVI include:
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/api_overview`
--   {doc}`/tutorials/notebooks/PeakVI`
--   {doc}`/tutorials/notebooks/peakvi_in_R`
--   {doc}`/tutorials/notebooks/scarches_scvi_tools`
+-   {doc}`/tutorials/notebooks/quick_start/api_overview`
+-   {doc}`/tutorials/notebooks/atac/PeakVI`
+-   {doc}`/tutorials/notebooks/atac/peakvi_in_R`
+-   {doc}`/tutorials/notebooks/scrna/scarches_scvi_tools`
 ```
 
 ## Preliminaries

diff --git a/docs/user_guide/models/scanvi.md b/docs/user_guide/models/scanvi.md
@@ -17,8 +17,8 @@ The limitations of scANVI include:
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/harmonization`
--   {doc}`/tutorials/notebooks/scarches_scvi_tools`
+-   {doc}`/tutorials/notebooks/scrna/harmonization`
+-   {doc}`/tutorials/notebooks/scrna/scarches_scvi_tools`
 ```
 
 ## Preliminaries

diff --git a/docs/user_guide/models/scvi.md b/docs/user_guide/models/scvi.md
@@ -15,10 +15,10 @@ The limitations of scVI include:
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/api_overview`
--   {doc}`/tutorials/notebooks/harmonization`
--   {doc}`/tutorials/notebooks/scarches_scvi_tools`
--   {doc}`/tutorials/notebooks/scvi_in_R`
+-   {doc}`/tutorials/notebooks/quick_start/api_overview`
+-   {doc}`/tutorials/notebooks/scrna/harmonization`
+-   {doc}`/tutorials/notebooks/scrna/scarches_scvi_tools`
+-   {doc}`/tutorials/notebooks/scrna/scvi_in_R`
 ```
 
 ## Preliminaries

diff --git a/docs/user_guide/models/stereoscope.md b/docs/user_guide/models/stereoscope.md
@@ -14,7 +14,7 @@ The limitations of Stereoscope include:
 
 ```{topic} Tutorial:
 
--   {doc}`/tutorials/notebooks/stereoscope_heart_LV_tutorial`
+-   {doc}`/tutorials/notebooks/spatial/stereoscope_heart_LV_tutorial`
 ```
 
 ## Preliminaries

diff --git a/docs/user_guide/models/tangram.md b/docs/user_guide/models/tangram.md
@@ -10,5 +10,5 @@ Tangram learns a matrix $M$ with shape ($n_{sc} \times n_{sp}$), in which each r
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/tangram_scvi_tools`
+-   {doc}`/tutorials/notebooks/spatial/tangram_scvi_tools`
 ```
diff --git a/docs/user_guide/models/totalvi.md b/docs/user_guide/models/totalvi.md
@@ -15,9 +15,9 @@ The limitations of totalVI include:
 
 ```{topic} Tutorials:
 
--   {doc}`/tutorials/notebooks/totalVI`
--   {doc}`/tutorials/notebooks/cite_scrna_integration_w_totalVI`
--   {doc}`/tutorials/notebooks/scarches_scvi_tools`
+-   {doc}`/tutorials/notebooks/multimodal/totalVI`
+-   {doc}`/tutorials/notebooks/multimodal/cite_scrna_integration_w_totalVI`
+-   {doc}`/tutorials/notebooks/scrna/scarches_scvi_tools`
 ```
 
 ## Preliminaries