Refactor fragments

.github/workflows/pythonpackage.yml

@@ -34,4 +34,5 @@ jobs:
     - name: Test with pytest
       run: |
         pip install pytest
+        pip install pysam
         pytest

docs/source/notebooks/quickstart_mudata.ipynb

@@ -67,12 +67,13 @@
    ],
    "source": [
     "import numpy as np\n",
+    "\n",
     "np.random.seed(1)\n",
     "\n",
     "n, d, k = 1000, 100, 10\n",
     "\n",
-    "z = np.random.normal(loc=np.arange(k), scale=np.arange(k)*2, size=(n,k))\n",
-    "w = np.random.normal(size=(d,k))\n",
+    "z = np.random.normal(loc=np.arange(k), scale=np.arange(k) * 2, size=(n, k))\n",
+    "w = np.random.normal(size=(d, k))\n",
     "y = np.dot(z, w.T)\n",
     "y.shape"
    ]
@@ -134,7 +135,7 @@
    ],
    "source": [
     "d2 = 50\n",
-    "w2 = np.random.normal(size=(d2,k))\n",
+    "w2 = np.random.normal(size=(d2, k))\n",
     "y2 = np.dot(z, w2.T)\n",
     "\n",
     "adata2 = AnnData(y2)\n",
@@ -265,7 +266,7 @@
     }
    ],
    "source": [
-    "mdata.varm['A']"
+    "mdata.varm[\"A\"]"
    ]
   },
   {
@@ -301,7 +302,7 @@
    "source": [
     "# Only keep variables with value > 1 in obs_1\n",
     "# with in-place filtering for the variables\n",
-    "mu.pp.filter_var(adata, adata[\"obs_1\",:].X.flatten() > 1)\n",
+    "mu.pp.filter_var(adata, adata[\"obs_1\", :].X.flatten() > 1)\n",
     "adata"
    ]
   },
@@ -375,7 +376,7 @@
    "source": [
     "# Throw away the last sample in the modality 'B'\n",
     "# with in-place filtering for the observations\n",
-    "mu.pp.filter_obs(mdata.mod[\"B\"], [True for _ in range(n-1)] + [False])"
+    "mu.pp.filter_obs(mdata.mod[\"B\"], [True for _ in range(n - 1)] + [False])"
    ]
   },
   {
@@ -568,7 +569,7 @@
     }
    ],
    "source": [
-    "with mu.set_options(display_style = \"html\", display_html_expand = 0b000):\n",
+    "with mu.set_options(display_style=\"html\", display_html_expand=0b000):\n",
     "    display(mdata)"
    ]
   },
@@ -771,7 +772,7 @@
     }
    ],
    "source": [
-    "with mu.set_options(display_style = \"html\", display_html_expand = 0b000):\n",
+    "with mu.set_options(display_style=\"html\", display_html_expand=0b000):\n",
     "    display(mdata_r)"
    ]
   },
@@ -825,7 +826,7 @@
    "source": [
     "def simple_pca(mdata):\n",
     "    from sklearn import decomposition\n",
-    "    \n",
+    "\n",
     "    x = np.hstack([m.X for m in mdata.mod.values()])\n",
     "\n",
     "    pca = decomposition.PCA(n_components=2)\n",
@@ -834,8 +835,8 @@
     "    # By default, methods operate in-place\n",
     "    # and embeddings are stored in the .obsm slot\n",
     "    mdata.obsm[\"X_pca\"] = components\n",
-    "    \n",
-    "    return "
+    "\n",
+    "    return"
    ]
   },
   {

muon/_atac/__init__.py

@@ -1,4 +1,5 @@
 from . import preproc as pp
 from . import tools as tl
 from . import plot as pl
+from . import fragments as fr
 from .io import *