Improvements

mioflow/__init__.py

@@ -0,0 +1,12 @@
+from mioflow.mioflow import MIOFlow, train_mioflow
+from mioflow.gaga import (
+    Autoencoder,
+    fit_gaga,
+    train_gaga,
+    train_gaga_two_phase,
+    PointCloudDataset,
+    RowStochasticDataset,
+    dataloader_from_pc,
+    train_valid_loader_from_pc,
+)
+from mioflow.core.datasets import TimeSeriesDataset

mioflow/mioflow.py

@@ -12,16 +12,10 @@
 import torchsde
 from tqdm import tqdm
 
-try:
-    from mioflow.core.models.ode_model import ODEFunc
-    from mioflow.core.models.sde_model import SDEFunc
-    from mioflow.core.losses import ot_loss, density_loss, energy_loss
-    from mioflow.core.datasets import TimeSeriesDataset
-except ImportError:
-    from core.models.ode_model import ODEFunc
-    from core.models.sde_model import SDEFunc
-    from core.losses import ot_loss, density_loss, energy_loss
-    from core.datasets import TimeSeriesDataset
+from mioflow.core.models.ode_model import ODEFunc
+from mioflow.core.models.sde_model import SDEFunc
+from mioflow.core.losses import ot_loss, density_loss, energy_loss
+from mioflow.core.datasets import TimeSeriesDataset
 
 
 class MIOFlow:

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mioflow"
-version = "0.1.12"
+version = "0.1.13"
 description = "MIOFlow is a Python package for modeling and analyzing single-cell RNA-seq data using optimal flows."
 readme = "README.md"
 requires-python = ">=3.8"
@@ -43,8 +43,9 @@ dependencies = [
     "torch-geometric>=2.6.1",
 ]
 
-[tool.setuptools]
-packages = ["mioflow"]
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["mioflow*"]
 
 [build-system]
 requires = ["setuptools>=61.0", "wheel"]

tutorials/01_mioflow_colab.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -164,7 +164,7 @@
     }
    ],
    "source": [
-    "!pip install pandas==2.2.0 mioflow gdown"
+    "!pip install pandas mioflow gdown"
    ]
   },
   {

tutorials/01_mioflow_vanilla.ipynb

@@ -36,7 +36,6 @@
     "%load_ext autoreload\n",
     "%autoreload 2\n",
     "\n",
-    "import sys\n",
     "import numpy as np\n",
     "import pandas as pd\n",
     "import scanpy as sc\n",
@@ -46,9 +45,8 @@
     "from sklearn.preprocessing import StandardScaler\n",
     "from sklearn.metrics.pairwise import pairwise_distances\n",
     "\n",
-    "sys.path.insert(0, '../MIOFlow')\n",
-    "from gaga import Autoencoder, train_gaga_two_phase, dataloader_from_pc\n",
-    "from mioflow import MIOFlow\n"
+    "from mioflow.gaga import Autoencoder, train_gaga_two_phase, dataloader_from_pc\n",
+    "from mioflow.mioflow import MIOFlow\n"
    ]
   },
   {
@@ -280,15 +278,7 @@
     }
    ],
    "source": [
-    "import importlib\n",
-    "\n",
-    "sys.path.insert(0, '../MIOFlow')\n",
-    "import mioflow\n",
-    "# After making changes to my_module:\n",
-    "importlib.reload(mioflow)\n",
-    "\n",
-    "\n",
-    "mf = mioflow.MIOFlow(\n",
+    "mf = MIOFlow(\n",
     "    adata,\n",
     "    gaga_model=gaga_model,\n",
     "    gaga_input_scaler=scaler_pca,    # fitted on X_pca — used for encode() and inverse_transform()\n",
@@ -310,7 +300,7 @@
     "    n_trajectories=100,\n",
     "    n_bins=100,\n",
     "    exp_dir='.',\n",
-    ")"
+    ")\n"
    ]
   },
   {
@@ -818,4 +808,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}