0.1.1: add scikit-misc and louvain dependencies, force numpy < 2

cantinilab · Jul 13, 2024 · a0778e6 · a0778e6
1 parent 87ac516
commit a0778e6
Show file tree

Hide file tree

Showing 6 changed files with 187 additions and 29 deletions.
diff --git a/docs/source/faq.rst b/docs/source/faq.rst
@@ -5,7 +5,7 @@ If you encounter an issue or have a question that is not addressed in this FAQ,
 please open an issue on the `github repository <https://github.com/cantinilab/scconfluence>`_.
 
 What should I do if the inferred latent embeddings from different modalities are completely separated?
-""""""""""""""""""""
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 There are two parameters that can be adjusted to avoid this issue. The first one is the
 `sinkhorn_loss_weight` parameter, which controls the weight of the Sinkhorn loss in the
 overall loss function. Increasing it should lead to a more mixed latent space but this
@@ -15,7 +15,7 @@ Increasing it will lead to a more less mass being discarded from the sinkhorn
 regularization's transport plan and therefore to a more mixed latent space.
 
 What should I do if the inferred cell embeddings from one (or more) modality don't seem to preserve their structure?
-""""""""""""""""""""
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 If you have access to cell labels for one modality, you
 might want to plot those information on top of the UMAP of the inferred embeddings to

diff --git a/docs/source/tutorials/RNA_ATAC_pbmc_tutorial.ipynb b/docs/source/tutorials/RNA_ATAC_pbmc_tutorial.ipynb
@@ -40,14 +40,6 @@
     "## Imports"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "7b119996",
-   "metadata": {},
-   "source": [
-    "Of note, `scikit-misc` as well as `louvain` should be installed (can be done with pip) for this notebook to be executed."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 1,

diff --git a/docs/source/tutorials/RNA_FISH_tutorial.ipynb b/docs/source/tutorials/RNA_FISH_tutorial.ipynb
@@ -24,14 +24,6 @@
     "## Imports"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "7b119996",
-   "metadata": {},
-   "source": [
-    "Of note, `scikit-misc` should be installed (can be done with pip) for this notebook to be executed."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 1,

diff --git a/docs/source/tutorials/RNA_PROT_tutorial.ipynb b/docs/source/tutorials/RNA_PROT_tutorial.ipynb
@@ -40,14 +40,6 @@
     "## Imports"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "7b119996",
-   "metadata": {},
-   "source": [
-    "Of note, `scikit-misc` as well as `louvain` should be installed (can be done with pip) for this notebook to be executed."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -70,7 +62,6 @@
     "from scipy.spatial.distance import cdist\n",
     "import muon as mu\n",
     "import numpy as np\n",
-    "import anndata as ad\n",
     "import scanpy as sc\n",
     "import torch\n",
     "torch.manual_seed(1792)\n",