Merge pull request #23 from YosefLab/destvi_utils_oier

Issues corrected

Author: ori-kron-wis

.github/workflows/test.yml

@@ -5,7 +5,7 @@ name: destvi_utils
 
 on:
   push:
-    branches: [main]
+    branches: [main, "[0-9]+.[0-9]+.x"]
   pull_request:
     branches: [main]
 
@@ -15,21 +15,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: [3.11, 3.12, 3.13]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache pip
-      uses: actions/cache@v2
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
       with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+        python-version: ${{ matrix.python }}
+        cache: "pip"
+        cache-dependency-path: "**/pyproject.toml"
+
     - name: Install dependencies
       run: |
         pip install pytest-cov

.pre-commit-config.yaml

@@ -1,15 +1,69 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/psf/black
-      rev: 22.3.0
-      hooks:
-          - id: black
-    - repo: https://github.com/PyCQA/flake8
-      rev: 4.0.1
-      hooks:
-          - id: flake8
-    - repo: https://github.com/pycqa/isort
-      rev: 5.10.1
-      hooks:
-          - id: isort
-            name: isort (python)
-            additional_dependencies: [toml]
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.20.0
+    hooks:
+      - id: blacken-docs
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types: [yaml]
+
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 1.0.0
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-mkdocs
+          - mdformat-admon
+        exclude: |
+          (?x)^(
+            \.github/.*\.md
+            | docs/.*\.md
+          )$
+
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.46.0
+    hooks:
+      - id: markdownlint-fix
+        exclude: |
+          (?x)^(
+            \.github/.*\.md
+            | docs/.*\.md
+          )$
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.6
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

destvi_utils/__init__.py

@@ -292,7 +292,9 @@ def explore_gamma_space(
             sc_adata.obs[sc_model.registry_["setup_args"]["labels_key"]] == name_ct
         ].copy()
         is_sparse = issparse(sc_adata_slice.X)
-        normalized_counts = sc_adata_slice.X.A if is_sparse else sc_adata_slice.X
+        normalized_counts = (
+            sc_adata_slice.X.toarray() if is_sparse else sc_adata_slice.X
+        )
         indices_ct = np.where(
             sc_adata.obs[sc_model.registry_["setup_args"]["labels_key"]] == name_ct
         )[0]
@@ -328,7 +330,7 @@ def explore_gamma_space(
         # (A) display top 50 genes + AND - (B) for each gene set, get GSEA
         for d in [0, 1]:
             if output_file is not None:
-                html += f"<h4>Genes associated with SpatialPC{d+1}</h4>"
+                html += f"<h4>Genes associated with SpatialPC{d + 1}</h4>"
             else:
                 print("[bold]Genes associated with SpatialPC{}[/bold]".format(d + 1))
             r = _utils._vcorrcoef(normalized_counts.T, sc_projection[:, d])
@@ -339,9 +341,9 @@ def explore_gamma_space(
                 gl = list(st_adata.var.index[ranking[:50]])
                 enr = gseapy.enrichr(
                     gene_list=gl,
-                    description="pathway",
                     gene_sets="BioPlanet_2019",
                     outdir="test",
+                    organism="Human",
                     no_plot=True,
                 )
                 text_signatures = enr.results.head(10)["Term"].values
@@ -449,12 +451,12 @@ def de_genes(
     mask2 = np.logical_and(mask2, st_adata.obsm[key_proportions][ct] > threshold)
 
     avg_library_size = np.mean(np.sum(expression, axis=1).flatten())
-    exp_px_o = st_model.module.px_o.detach().exp().cpu().numpy()
+    exp_px_r = st_model.module.px_r.detach().exp().cpu().numpy()
     imputations = st_model.get_scale_for_ct(ct).values
     mean = avg_library_size * imputations
 
-    concentration = torch.tensor(avg_library_size * imputations / exp_px_o)
-    rate = torch.tensor(1.0 / exp_px_o)
+    concentration = torch.tensor(avg_library_size * imputations / exp_px_r)
+    rate = torch.tensor(1.0 / exp_px_r)
 
     # slice conditions
     N_mask = N_unmask = N_sample

destvi_utils/_destvi_utils.py

@@ -9,11 +9,11 @@ destvi_utils can be installed via PyPI.
 conda prerequisites
 ###################
 
-1. Install Conda. We typically use the Miniconda_ Python distribution. Use Python version >=3.7.
+1. Install Conda. We typically use the Miniconda_ Python distribution. Use Python version >=3.11.
 
 2. Create a new conda environment::
 
-    conda create -n destvi-env python=3.7
+    conda create -n destvi-env python=3.11
 
 3. Activate your environment::
 

destvi_utils/_utils.py

@@ -10,8 +10,9 @@ classifiers = [
   "Development Status :: 5 - Production/Stable",
   "Intended Audience :: Science/Research",
   "Natural Language :: English",
-  "Programming Language :: Python :: 3.6",
-  "Programming Language :: Python :: 3.7",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Operating System :: MacOS :: MacOS X",
   "Operating System :: Microsoft :: Windows",
   "Operating System :: POSIX :: Linux",
@@ -26,7 +27,7 @@ packages = [
   {include = "destvi_utils"},
 ]
 readme = "README.md"
-version = "0.1.0"
+version = "0.2.0"
 
 [tool.poetry.dependencies]
 adjustText = ">=0.7.1"
@@ -35,7 +36,7 @@ black = {version = ">=20.8b1", optional = true}
 cmap2d = {git = "https://github.com/cane11/cmap2d", tag = "v1.0"}
 codecov = {version = ">=2.0.8", optional = true}
 flake8 = {version = ">=3.7.7", optional = true}
-gseapy = {version = "0.10.2"}
+gseapy = {version = ">=0.10.2"}
 hotspot = {git = "https://github.com/YosefLab/Hotspot", tag = "v1.0"}
 importlib-metadata = {version = "^1.0", python = "<3.8"}
 ipython = ">=7.1.1"
@@ -50,11 +51,11 @@ nbsphinx-link = {version = "*", optional = true}
 pre-commit = {version = ">=2.7.1", optional = true}
 pydata-sphinx-theme = {version = ">=0.4.0", optional = true}
 pytest = {version = ">=4.4", optional = true}
-python = ">=3.7.2,<4.0"
+python = ">=3.11.0,<4.0"
 igraph = {version = "*"}
 scanpy = ">=1.6,<2.0"
 scanpydoc = {version = ">=0.5", optional = true}
-scvi-tools = ">=0.15.0"
+scvi-tools  = {git = "https://github.com/scverse/scvi-tools", tag = "Ori-destvi_v2_2"}
 sphinx = {version = ">=4.1,<4.4", optional = true}
 sphinx-autodoc-typehints = {version = "*", optional = true}
 sphinx-rtd-theme = {version = "*", optional = true}

docs/installation.rst

@@ -1,12 +1,13 @@
 version: 2
 build:
-  image: latest
+  os: ubuntu-20.04
+  tools:
+    python: "3.11"
 sphinx:
   configuration: docs/conf.py
 python:
-  version: 3.7
   install:
-  - method: pip
-    path: .
-    extra_requirements:
-    - docs
+    - method: pip
+      path: .
+      extra_requirements:
+        - docsbuild

pyproject.toml

@@ -1,11 +1,27 @@
 import numpy as np
 from scvi.data import synthetic_iid
 from scvi.model import CondSCVI, DestVI
-
+from unittest.mock import patch, MagicMock
+import pandas as pd
 import destvi_utils
 
 
-def test_destvi():
+@patch("gseapy.enrichr")
+def test_destvi(mock_enrichr):
+    # mock enrichr results
+    fake_df = pd.DataFrame(
+        {
+            "Term": ["fake_pathway"],
+            "Overlap": ["5/100"],
+            "Adjusted P-value": [0.05],
+            "Genes": ["gene_1;gene_2"],
+        }
+    )
+
+    mock_instance = MagicMock()
+    mock_instance.results = fake_df
+    mock_enrichr.return_value = mock_instance
+
     # Step1 learn CondSCVI
     n_latent = 2
     n_labels = 5
@@ -14,7 +30,7 @@ def test_destvi():
     dataset.obsm["spatial"] = np.random.randn(dataset.n_obs, 2)
     dataset.obs["overclustering_vamp"] = list(range(dataset.n_obs))
     CondSCVI.setup_anndata(dataset, labels_key="labels")
-    sc_model = CondSCVI(dataset, n_latent=n_latent, n_layers=n_layers)
+    sc_model = CondSCVI(dataset, n_latent=n_latent, n_layers=n_layers, prior="mog")
     sc_model.train(1, train_size=1)
 
     DestVI.setup_anndata(dataset, layer=None)