Merge pull request #91 from saezlab/dev

v1.0.5
saezlab · Feb 25, 2024 · 0882c9c · 0882c9c
2 parents 1543d16 + 3766e0c
commit 0882c9c
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,49 @@
+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - commit
+    - push
+minimum_pre_commit_version: 2.9.3
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.5.0
+      hooks:
+          - id: check-merge-conflict
+          - id: check-ast
+          - id: check-symlinks
+          - id: check-added-large-files
+            args: ['--maxkb=5000']
+          - id: fix-encoding-pragma
+            args: [--remove]
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: trailing-whitespace
+            exclude: ^.bumpversion.cfg$
+          - id: name-tests-test
+            args: [--django]
+          - id: check-case-conflict
+          - id: check-docstring-first
+          - id: check-yaml
+          - id: check-toml
+          - id: requirements-txt-fixer
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.16.0
+      hooks:
+          - id: blacken-docs
+    - repo: https://github.com/pre-commit/pygrep-hooks
+      rev: v1.10.0
+      hooks:
+          - id: python-no-eval
+          - id: python-use-type-annotations
+          - id: python-check-blanket-noqa
+          - id: rst-backticks
+          - id: rst-directive-colons
+          - id: rst-inline-touching-normal
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      # Ruff version.
+      rev: v0.1.3
+      hooks:
+        - id: ruff
+          args: [--fix, --exit-non-zero-on-fix, --exclude, __init__.py]
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -110,6 +110,9 @@ Prior knowledge
    liana.resource.show_resources
    liana.resource.generate_lr_geneset
    liana.resource.explode_complexes
+   liana.resource.get_metalinks
+   liana.resource.describe_metalinks
+   liana.resource.get_metalinks_values
 
 Intracellular
 ----------------------------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -42,6 +42,8 @@ spatially-resolved, and multi-modal omics data.
 
    notebooks/basic_usage
 
+   notebooks/prior_knowledge
+
    notebooks/liana_c2c
 
    notebooks/mofacellular
@@ -59,3 +61,5 @@ spatially-resolved, and multi-modal omics data.
    notebooks/misty
 
    notebooks/bivariate
+
+   notebooks/sma
diff --git a/docs/source/notebooks/basic_usage.ipynb b/docs/source/notebooks/basic_usage.ipynb
diff --git a/docs/source/notebooks/bivariate.ipynb b/docs/source/notebooks/bivariate.ipynb
diff --git a/docs/source/notebooks/liana_c2c.ipynb b/docs/source/notebooks/liana_c2c.ipynb
diff --git a/docs/source/notebooks/misty.ipynb b/docs/source/notebooks/misty.ipynb
diff --git a/docs/source/notebooks/mofacellular.ipynb b/docs/source/notebooks/mofacellular.ipynb
@@ -275,7 +275,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 8/8 [00:03<00:00,  2.52it/s]\n"
+      "100%|██████████| 8/8 [00:03<00:00,  2.38it/s]\n"
      ]
     }
    ],
@@ -650,7 +650,13 @@
       "        ######################################################### \n",
       "       \n",
       " \n",
-      "        \n",
+      "        \n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
       "Loaded view='CD14' group='group1' with N=16 samples and D=4061 features...\n",
       "Loaded view='CD4T' group='group1' with N=16 samples and D=5457 features...\n",
       "Loaded view='DCs' group='group1' with N=16 samples and D=1389 features...\n",

diff --git a/docs/source/notebooks/mofatalk.ipynb b/docs/source/notebooks/mofatalk.ipynb