[DGL-Go] Change name to dglgo (#3778)

* add

* remove

* fix

* rework the readme and some changes

* add png

* update png

* add recipe get
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

enter/README.md → dglgo/README.md

-# DGL-Enter
+# DGL-Go
 
-(What is DGL-Enter? Why design this? What is it for?)
 
-DGL-Enter is a commanline tool for user to quickly bootstrap models with multiple datasets. And provide full capability for user to customize the pipeline into their own takks.
+DGL-Go is a command line tool for users to get started with training, using and
+studying Graph Neural Networks (GNNs). Data scientists can quickly apply GNNs
+to their problems, whereas researchers will find it useful to customize their
+experiments.
 
-## Installation guide
-You can install DGL-enter easily by `pip install dglenter`. Then you should be able to use DGL-Enter in you commandline tool by type in `dgl-enter`
+
+## Installation and get started
+
+DGL-Go requires DGL v0.8+ so please make sure DGL is updated properly.
+Install DGL-Go by `pip install dglgo` and type `dgl` in your console:
 ```
-Usage: dgl-enter [OPTIONS] COMMAND [ARGS]...
+Usage: dgl [OPTIONS] COMMAND [ARGS]...
 
 Options:
   --help  Show this message and exit.
 
 Commands:
-  config  Generate the config files
-  export  Export the python file from config
-  train   Train the model
+  configure  Generate a configuration file
+  export     Export a runnable python script
+  recipe     Get example recipes
+  train      Launch training
+```
+
+![img](./dglgo.png)
+
+Using DGL-Go is as easy as three steps:
+
+1. Use `dgl configure` to pick the task, dataset and model of your interests. It generates
+   a configuration file for later use. You could also use `dgl recipe get` to retrieve
+   a configuration file we provided.
+1. Use `dgl train` to launch training according to the configuration and see the results.
+1. Use `dgl export` to generate a *self-contained, reproducible* Python script for advanced
+   customization, or try the model on custom data stored in CSV format.
+
+Next, we will walk through all these steps one-by-one.
+
+## Training GraphSAGE for node classification on Cora
+
+Let's use one of the most classical setups -- training a GraphSAGE model for node
+classification on the Cora citation graph dataset as an
+example.
+
+### Step one: `dgl configure`
+
+First step, use `dgl configure` to generate a YAML configuration file.
+
 ```
+dgl configure nodepred --data cora --model sage --cfg cora_sage.yaml
+```
+
+Note that `nodepred` is the name of DGL-Go *pipeline*. For now, you can think of
+pipeline as training task: `nodepred` is for node prediction task; other
+options include `linkpred` for link prediction task, etc. The command will
+generate a configurate file `cora_sage.yaml` which includes:
 
+* Options for the selected dataset (i.e., `cora` here).
+* Model hyperparameters (e.g., number of layers, hidden size, etc.).
+* Training hyperparameters (e.g., learning rate, loss function, etc.).
 
-## Train GraphSAGE on Cora from scratch
-Here we'll use one of the most classic model GraphSAGE and Cora citation graph dataset as an example, to show how easy to train a model with DGL-Enter.
-### Step 1: Use `dgl-enter config` to generate a yaml configuration file
-Run `dgl-enter config nodepred --data cora --model sage --cfg cora_sage.yml`. Then you'll get a configuration file `cora_sage.yml` includes all the configuration to be tuned, with the comments
+Different choices of task, model and datasets may give very different options,
+so DGL-Go also adds a comment for what each option does in the file.
+At this point you can also change options to explore optimization potentials. 
 
-Optionally, You can change the config as you want to acheive a better performance. Below is a modified sample based on the template generated by the command above.
-The early stop part is removed for simplicity
+Below shows the configuration file generated by the command above.
 
 ```yaml
 version: 0.0.1
@@ -43,6 +82,9 @@ model:
   dropout: 0.5                # Dropout rate.
   aggregator_type: gcn        # Aggregator type to use (``mean``, ``gcn``, ``pool``, ``lstm``).
 general_pipeline:
+  early_stop:
+    patience: 20              # Steps before early stop
+    checkpoint_path: checkpoint.pth # Early stop checkpoint model file path
   num_epochs: 200             # Number of training epochs
   eval_period: 5              # Interval epochs between evaluations
   optimizer:
@@ -50,13 +92,52 @@ general_pipeline:
     lr: 0.01
     weight_decay: 0.0005
   loss: CrossEntropyLoss
+  save_path: model.pth        # Path to save the model
   num_runs: 1                 # Number of experiments to run
+```
+
+Apart from `dgl configure`, you could also get one of DGL-Go's built-in configuration files
+(called *recipe*) using `dgl recipe`. There are two sub-commands:
 
 ```
+dgl recipe list
+```
+
+will list the available recipes:
+
+```
+➜ dgl recipe list     
+===============================================================================
+| Filename                       |  Pipeline           | Dataset              |
+===============================================================================
+| linkpred_citation2_sage.yaml   |  linkpred           | ogbl-citation2       |
+| linkpred_collab_sage.yaml      |  linkpred           | ogbl-collab          |
+| nodepred_citeseer_sage.yaml    |  nodepred           | citeseer             |
+| nodepred_citeseer_gcn.yaml     |  nodepred           | citeseer             |
+| nodepred-ns_arxiv_gcn.yaml     |  nodepred-ns        | ogbn-arxiv           |
+| nodepred_cora_gat.yaml         |  nodepred           | cora                 |
+| nodepred_pubmed_sage.yaml      |  nodepred           | pubmed               |
+| linkpred_cora_sage.yaml        |  linkpred           | cora                 |
+| nodepred_pubmed_gcn.yaml       |  nodepred           | pubmed               |
+| nodepred_pubmed_gat.yaml       |  nodepred           | pubmed               |
+| nodepred_cora_gcn.yaml         |  nodepred           | cora                 |
+| nodepred_cora_sage.yaml        |  nodepred           | cora                 |
+| nodepred_citeseer_gat.yaml     |  nodepred           | citeseer             |
+| nodepred-ns_product_sage.yaml  |  nodepred-ns        | ogbn-products        |
+===============================================================================
+```
+
+Then use
 
-### Step 2: Use `dgl-enter train` to initiate the training process.   
+```
+dgl recipe get nodepred_cora_sage.yaml
+```
 
-Simply run `dgl-enter train --cfg cora_sage.yml` will start the training process
+to copy the YAML configuration file to your local folder.
+
+### Step 2: `dgl train`
+
+Simply run `dgl train --cfg cora_sage.yaml` will start the training process.
 ```log
 ...
 Epoch 00190 | Loss 1.5225 | TrainAcc 0.9500 | ValAcc 0.6840
@@ -74,18 +155,83 @@ Test Accuracy 0.7740
 Accuracy across 1 runs: 0.774 ± 0.0
 ```
 
-That's all! Basically you only need two line of command to train a graph neural network.
-## Debug your model and advanced customization
+That's all! Basically you only need two commands to train a graph neural network.
 
-That's not everything yet. We belive you may want to change more than the configuration files, to change the training pipeline, calculate new metrics, or look into the code for details.
-DGL-Enter can export a self-contained, runnable python script for you to do anything you like. 
+### Step 3: `dgl export` for more advanced customization
 
-Try `dgl-enter export --cfg cora_sage.yml --output script.py`, and you'll get the script used to train the model, like a magic!
+That's not everything yet. You may want to open the hood and and invoke deeper
+customization. DGL-Go can export a **self-contained, reproducible** Python
+script for you to do anything you like. 
+
+Try `dgl export --cfg cora_sage.yaml --output script.py`,
+and you'll get the script used to train the model. Here's the code snippet:
 
-Below 
 ```python
 ...
 
+class GraphSAGE(nn.Module):
+    def __init__(self,
+                 data_info: dict,
+                 embed_size: int = -1,
+                 hidden_size: int = 16,
+                 num_layers: int = 1,
+                 activation: str = "relu",
+                 dropout: float = 0.5,
+                 aggregator_type: str = "gcn"):
+        """GraphSAGE model
+
+        Parameters
+        ----------
+        data_info : dict
+            The information about the input dataset.
+        embed_size : int
+            The dimension of created embedding table. -1 means using original node embedding
+        hidden_size : int
+            Hidden size.
+        num_layers : int
+            Number of hidden layers.
+        dropout : float
+            Dropout rate.
+        activation : str
+            Activation function name under torch.nn.functional
+        aggregator_type : str
+            Aggregator type to use (``mean``, ``gcn``, ``pool``, ``lstm``).
+        """
+        super(GraphSAGE, self).__init__()
+        self.data_info = data_info
+        self.embed_size = embed_size
+        if embed_size > 0:
+            self.embed = nn.Embedding(data_info["num_nodes"], embed_size)
+            in_size = embed_size
+        else:
+            in_size = data_info["in_size"]
+        self.layers = nn.ModuleList()
+        self.dropout = nn.Dropout(dropout)
+        self.activation = getattr(nn.functional, activation)
+
+        for i in range(num_layers):
+            in_hidden = hidden_size if i > 0 else in_size
+            out_hidden = hidden_size if i < num_layers - 1 else data_info["out_size"]
+            self.layers.append(dgl.nn.SAGEConv( in_hidden, out_hidden, aggregator_type))
+
+    def forward(self, graph, node_feat, edge_feat=None):
+        if self.embed_size > 0:
+            dgl_warning(
+                "The embedding for node feature is used, and input node_feat is ignored, due to the provided embed_size.",
+                norepeat=True)
+            h = self.embed.weight
+        else:
+            h = node_feat
+        h = self.dropout(h)
+        for l, layer in enumerate(self.layers):
+            h = layer(graph, h, edge_feat)
+            if l != len(self.layers) - 1:
+                h = self.activation(h)
+                h = self.dropout(h)
+        return h
+
+...
+
 def train(cfg, pipeline_cfg, device, data, model, optimizer, loss_fcn):
     g = data[0]  # Only train on the first graph
     g = dgl.remove_self_loop(g)
@@ -98,6 +244,8 @@ def train(cfg, pipeline_cfg, device, data, model, optimizer, loss_fcn):
     train_mask, val_mask, test_mask = g.ndata['train_mask'].bool(
     ), g.ndata['val_mask'].bool(), g.ndata['test_mask'].bool()
 
+    stopper = EarlyStopping(**pipeline_cfg['early_stop'])
+
     val_acc = 0.
     for epoch in range(pipeline_cfg['num_epochs']):
         model.train()
@@ -112,9 +260,14 @@ def train(cfg, pipeline_cfg, device, data, model, optimizer, loss_fcn):
         if epoch != 0 and epoch % pipeline_cfg['eval_period'] == 0:
             val_acc = accuracy(logits[val_mask], label[val_mask])
 
+            if stopper.step(val_acc, model):
+                break
+
         print("Epoch {:05d} | Loss {:.4f} | TrainAcc {:.4f} | ValAcc {:.4f}".
               format(epoch, loss.item(), train_acc, val_acc))
 
+    stopper.load_checkpoint(model)
+
     model.eval()
     with torch.no_grad():
         logits = model(g, node_feat, edge_feat)
@@ -125,24 +278,26 @@ def train(cfg, pipeline_cfg, device, data, model, optimizer, loss_fcn):
 def main():
     cfg = {
         'version': '0.0.1',
-        'device': 'cpu',
-        'data': {
-            'split_ratio': None},
+        'device': 'cuda:0',
         'model': {
             'embed_size': -1,
             'hidden_size': 16,
-            'num_layers': 1,
+            'num_layers': 2,
             'activation': 'relu',
             'dropout': 0.5,
             'aggregator_type': 'gcn'},
         'general_pipeline': {
+            'early_stop': {
+                'patience': 100,
+                'checkpoint_path': 'checkpoint.pth'},
             'num_epochs': 200,
             'eval_period': 5,
             'optimizer': {
                 'lr': 0.01,
                 'weight_decay': 0.0005},
             'loss': 'CrossEntropyLoss',
-            'num_runs': 1}}
+            'save_path': 'model.pth',
+            'num_runs': 10}}
     device = cfg['device']
     pipeline_cfg = cfg['general_pipeline']
     # load data
@@ -162,109 +317,81 @@ def main():
         **pipeline_cfg["optimizer"])
     # train
     test_acc = train(cfg, pipeline_cfg, device, data, model, optimizer, loss)
+    torch.save(model, pipeline_cfg["save_path"])
     return test_acc
 
 ...
-
 ```
 
-## Recipes
-
-We've prepared a set of finetuned config under `enter/recipes`, that you can try easily to get a reproducable result.
+You can see that everything is collected into one Python script which includes the
+entire `GraphSAGE` model definition, data processing and training loop. Simply running
+`python script.py` will give you the *exact same* result as you've seen by `dgl train`.
+At this point, you can change any part as you wish such as plugging your own GNN module,
+changing the loss function and so on.
 
-For example, using GCN with pubmet dataset, you can use `enter/recipes/nodepred_pubmed_gcn.yml`. 
+## Use DGL-Go on your own dataset
 
-To try it, type in `dgl-enter train --cfg recipes/nodepred_pubmed_gcn.yml` to train the model, or `dgl-enter export --cfg recipes/nodepred_pubmed_gcn.yml` to get the full training script.
+DGL-Go supports training a model on custom dataset by DGL's `CSVDataset`.
 
-## Use DGL-Enter on your own dataset
-You can modify the generated script in anyway you want. However, we also provided an end2end way to use your own dataset, by using our `CSVDataset`. 
+### Step 1: Prepare your CSV and metadata file.
 
-Step 1: Prepare your csv and metadata file.
+Follow the tutorial at [Loading data from CSV
+files](https://docs.dgl.ai/en/latest/guide/data-loadcsv.html#guide-data-pipeline-loadcsv`)
+to prepare your dataset. Generally, the dataset folder should include:
+* At least one CSV file for node data.
+* At least one CSV file for edge data.
+* A metadata file called `meta.yaml`.
 
-Following the tutorial at [Loading data from CSV files](https://docs.dgl.ai/en/latest/guide/data-loadcsv.html#guide-data-pipeline-loadcsv`), Prepare your own CSV dataset includes three files minimally, node data csv, edge data csv and the meta data file (meta.yml).
+### Step 2: `dgl configure` with `--data csv` option
+Run
 
-```yml
-dataset_name: my_csv_dataset
-edge_data:
-- file_name: edges.csv
-node_data:
-- file_name: nodes.csv
+```
+dgl configure nodepred --data csv --model sage --cfg csv_sage.yaml
 ```
 
-Step 2: Choose to csv dataset in the `dgl-enter config` stage
-Try `dgl-enter config nodepred --data csv --model sage --cfg csv_sage.yml`, to use SAGE model for your dataset. You'll see the data part is now the configuration related to CSV dataset. `data_path` is used to specify the data folder, and `./` means the current folder. 
-
-If your dataset doesn't have the builtin split on the nodes for train/val/test, you need to manually set the split ratio in the config yml file, DGL will random generate the split for you.
+to generate the configuration file. You will see that the file includes a section like
+the followings:
 
-```yml
+```yaml
+...
 data:
   name: csv
   split_ratio:                # Ratio to generate split masks, for example set to [0.8, 0.1, 0.1] for 80% train/10% val/10% test. Leave blank to use builtin split in original dataset
   data_path: ./               # metadata.yaml, nodes.csv, edges.csv should in this folder
+...
 ```
 
+Fill in the `data_path` option with the path to your dataset folder.
 
-Step 3: `train` the model/`export` the script
-Then you can do the same as the tutorial above, either train the model by `dgl-eneter train --cfg csv_sage.yaml` or use `dgl-enter export --cfg csv_sage.yml --output my_dataset.py` to get the training script.
-
-## API Referencce
-
-DGL enter is a new tool for user to bootstrap datasets and common models.
-
-The entry point of enter is `dgl-enter`, and it has three subcommand `config`, `train` and `export`.
-
-### Config
-The config stage is to generate a configuration file on the specific pipeline.
-
-`dgl-enter` currently provides 3 pipelines:
-- nodepred (Node prediction tasks, suitable for small dataset to prototype)
-- nodepred-ns (Node prediction tasks with sampling method, suitable for medium and large dataset)
-- linkpred (Link prediction tasks, to predict whether edge exists among node pairs based on node features)
-
-You can get the full list by `dgl-enter config --help`
-```
-Usage: dgl-enter config [OPTIONS] COMMAND [ARGS]...
-
-  Generate the config files
-
-Options:
-  --help  Show this message and exit.
-
-Commands:
-  linkpred     Link prediction pipeline
-  nodepred     Node classification pipeline
-  nodepred-ns  Node classification sampling pipeline
-```
-
-For each pipeline it will have diffirent options to specified. For example, for node prediction pipeline, you can do `dgl-enter config nodepred --help`, you'll get:
-```
-Usage: dgl-enter config nodepred [OPTIONS]
-
-  Node classification pipeline
+If your dataset does not have any native split for training, validation and test sets,
+you can set the split ratio in the `split_ratio` option, which will
+generate a random split for you.
 
-Options:
-  --data [cora|citeseer|ogbl-collab|csv|reddit|co-buy-computer]
-                                  input data name  [required]
-  --cfg TEXT                      output configuration path  [default:
-                                  cfg.yml]
-  --model [gcn|gat|sage|sgc|gin]  Model name  [required]
-  --device [cpu|cuda]             Device, cpu or cuda  [default: cpu]
-  --help                          Show this message and exit.
-```
+### Step 3: `train` the model / `export` the script
+Then you can do the same as the tutorial above, either train the model by
+`dgl train --cfg csv_sage.yaml` or use `dgl export --cfg csv_sage.yaml
+--output script.py` to get the training script.
 
-You can always get the detailed help information by adding `--help` to the command line
+## FAQ
 
-### Train
-You can train a model on the dataset based on the configuration file generated by `dgl-enter config`, by `dgl-enter train`.
-```
-Usage: dgl-enter train [OPTIONS]
+**Q: What are the available options for each command?**
+A: You can use `--help` for all commands. For example, use `dgl --help` for general
+help message; use `dgl configure --help` for the configuration options; use
+`dgl configure nodepred --help` for the configuration options of node prediction pipeline.
 
-  Train the model
+**Q: What exactly is nodepred/linkpred? How many are they?**
+A: They are called DGl-Go pipelines. A pipeline represents the training methodology for
+a certain task. Therefore, its naming convention is *<task_name>[-<method_name>]*. For example,
+`nodepred` trains the selected GNN model for node classification using full-graph training method;
+while `nodepred-ns` trains the model for node classifiation but using neighbor sampling.
+The first release included three training pipelines (`nodepred`, `nodepred-ns` and `linkpred`)
+but you can expect more will be coming in the future. Use `dgl configure --help` to see
+all the available pipelines.
 
-Options:
-  --cfg TEXT  yaml file name  [default: cfg.yml]
-  --help      Show this message and exit.
-```
+**Q: How to add my model to the official model recipe zoo?**
+A: Currently not supported. We will enable this feature soon. Please stay tuned!
 
-### Export
-Get the self-contained, runnable python script derived from the configuration file by `dgl-enter export`.
+**Q: After training a model on some dataset, how can I apply it to another one?**
+A: The `save_path` option in the generated configuration file allows you to specify where
+to save the model after training. You can then modify the script generated by `dgl export`
+to load the the model checkpoint and evaluate it on another dataset.

enter/dglenter/cli/cli.py → dglgo/dglgo/cli/cli.py

@@ -4,15 +4,17 @@ from ..model import *
 from .config_cli import config_app
 from .train_cli import train
 from .export_cli import export
+from .recipe_cli import recipe_app
 
 no_args_is_help = False
-app = typer.Typer(no_args_is_help=no_args_is_help, add_completion=False)
-app.add_typer(config_app, name="config", no_args_is_help=no_args_is_help)
-app.command(help="Train the model", no_args_is_help=no_args_is_help)(train)
-app.command(help="Export the python file from config", no_args_is_help=no_args_is_help)(export)
+app = typer.Typer(no_args_is_help=True, add_completion=False)
+app.add_typer(config_app, name="configure", no_args_is_help=no_args_is_help)
+app.add_typer(recipe_app, name="recipe", no_args_is_help=True)
+app.command(help="Launch training", no_args_is_help=no_args_is_help)(train)
+app.command(help="Export a runnable python script", no_args_is_help=no_args_is_help)(export)
 
 def main():
     app()
 
 if __name__ == "__main__":
-    app()
+    app()
\ No newline at end of file

enter/dglenter/cli/config_cli.py → dglgo/dglgo/cli/config_cli.py

@@ -6,9 +6,9 @@ import typing
 import yaml
 from pathlib import Path
 
-config_app = typer.Typer(help="Generate the config files")
+config_app = typer.Typer(help="Generate a configuration file")
 for key, pipeline in PipelineFactory.registry.items():
     config_app.command(key, help=pipeline.get_description())(pipeline.get_cfg_func())
 
 if __name__ == "__main__":
-    config_app()
+    config_app()
\ No newline at end of file

enter/dglenter/cli/export_cli.py → dglgo/dglgo/cli/export_cli.py

@@ -10,8 +10,8 @@ import isort
 import autopep8
 
 def export(
-    cfg: str = typer.Option("cfg.yml", help="config yaml file name"),
-    output: str = typer.Option("output.py", help="output python file name")
+    cfg: str = typer.Option("cfg.yaml", help="config yaml file name"),
+    output: str = typer.Option("script.py", help="output python file name")
 ):
     user_cfg = yaml.safe_load(Path(cfg).open("r"))
     pipeline_name = user_cfg["pipeline_name"]

dglgo/dglgo/cli/recipe_cli.py

+from pathlib import Path
+from typing import Optional
+import typer
+import os
+import shutil
+import yaml
+
+def list_recipes():
+    file_current_dir = Path(__file__).resolve().parent
+    recipe_dir = file_current_dir.parent.parent / "recipes"
+    file_list = list(recipe_dir.glob("*.yaml"))
+    header = "| {:<30} |  {:<18} | {:<20} |".format("Filename", "Pipeline", "Dataset")
+    typer.echo("="*len(header))
+    typer.echo(header)
+    typer.echo("="*len(header))
+    for file in file_list:
+        cfg = yaml.safe_load(Path(file).open("r"))
+        typer.echo("| {:<30} |  {:<18} | {:<20} |".format(file.name, cfg["pipeline_name"], cfg["data"]["name"]))
+    typer.echo("="*len(header))
+
+def copy_recipes(dir: str = typer.Option("dglgo_example_recipes", help="directory name for recipes")):
+    file_current_dir = Path(__file__).resolve().parent
+    recipe_dir = file_current_dir.parent.parent / "recipes"
+    current_dir = Path(os.getcwd())
+    new_dir = current_dir / dir
+    new_dir.mkdir(parents=True, exist_ok=True)
+    for file in recipe_dir.glob("*.yaml"):
+        shutil.copy(file, new_dir)
+    print("Example recipes are copied to {}".format(new_dir.absolute()))
+
+def get_recipe(recipe_name: Optional[str] = typer.Argument(None, help="The recipe filename to get, e.q. nodepred_citeseer_gcn.yaml")):
+    if recipe_name is None:
+        typer.echo("Usage: dgl recipe get [RECIPE_NAME] \n")
+        typer.echo(" Copy the recipe to current directory \n")
+        typer.echo(" Arguments:")
+        typer.echo("  [RECIPE_NAME]  The recipe filename to get, e.q. nodepred_citeseer_gcn.yaml\n")
+        typer.echo("Here are all avaliable recipe filename")
+        list_recipes()
+    else:
+        file_current_dir = Path(__file__).resolve().parent
+        recipe_dir = file_current_dir.parent.parent / "recipes"
+        current_dir = Path(os.getcwd())
+        recipe_path = recipe_dir / recipe_name
+        shutil.copy(recipe_path, current_dir)
+        print("Recipe {} is copied to {}".format(recipe_path.absolute(), current_dir.absolute()))
+
+
+recipe_app = typer.Typer(help="Get example recipes")
+recipe_app.command(name="list", help="List all available example recipes")(list_recipes)
+recipe_app.command(name="copy", help="Copy all available example recipes to current directory")(copy_recipes)
+recipe_app.command(name="get", help="Copy the recipe to current directory")(get_recipe)
+
+if __name__ == "__main__":
+    recipe_app()

enter/dglenter/cli/train_cli.py → dglgo/dglgo/cli/train_cli.py

@@ -5,12 +5,11 @@ from enum import Enum
 import typing
 import yaml
 from pathlib import Path
-
 import isort
 import autopep8
 
 def train(
-    cfg: str = typer.Option("cfg.yml", help="config yaml file name"),
+    cfg: str = typer.Option("cfg.yaml", help="config yaml file name"),
 ):
     user_cfg = yaml.safe_load(Path(cfg).open("r"))
     pipeline_name = user_cfg["pipeline_name"]
@@ -18,8 +17,8 @@ def train(
 
     f_code = autopep8.fix_code(output_file_content, options={'aggressive': 1})
     f_code = isort.code(f_code)
-    exec(f_code,  {'__name__': '__main__'})
-
+    code = compile(f_code, 'dglgo_tmp.py', 'exec')
+    exec(code,  {'__name__': '__main__'})
 
 if __name__ == "__main__":
     train_app = typer.Typer()

enter/dglenter/model/node_encoder/gcn.py → dglgo/dglgo/model/node_encoder/gcn.py

@@ -49,7 +49,7 @@ class GCN(nn.Module):
             in_hidden = hidden_size if i > 0 else in_size
             out_hidden = hidden_size if i < num_layers - 1 else data_info["out_size"]
 
-            self.layers.append(dgl.nn.GraphConv(in_hidden, out_hidden, norm=norm))
+            self.layers.append(dgl.nn.GraphConv(in_hidden, out_hidden, norm=norm, allow_zero_in_degree=True))
 
         self.dropout = nn.Dropout(p=dropout)
         self.act = getattr(torch, activation)

enter/dglenter/model/node_encoder/gin.py → dglgo/dglgo/model/node_encoder/gin.py

@@ -12,6 +12,8 @@ class GIN(nn.Module):
                  aggregator_type='sum'):
         """Graph Isomophism Networks
 
+        Edge feature is ignored in this model.
+
         Parameters
         ----------
         data_info : dict

enter/dglenter/model/node_encoder/sage.py → dglgo/dglgo/model/node_encoder/sage.py

@@ -55,7 +55,7 @@ class GraphSAGE(nn.Module):
             h = node_feat
         h = self.dropout(h)
         for l, layer in enumerate(self.layers):
-            h = layer(graph, h)
+            h = layer(graph, h, edge_feat)
             if l != len(self.layers) - 1:
                 h = self.activation(h)
                 h = self.dropout(h)
@@ -64,7 +64,7 @@ class GraphSAGE(nn.Module):
     def forward_block(self, blocks, node_feat, edge_feat = None):
         h = node_feat
         for l, (layer, block) in enumerate(zip(self.layers, blocks)):
-            h = layer(block, h)
+            h = layer(block, h, edge_feat)
             if l != len(self.layers) - 1:
                 h = self.activation(h)
                 h = self.dropout(h)

enter/dglenter/model/node_encoder/sgc.py → dglgo/dglgo/model/node_encoder/sgc.py

@@ -14,6 +14,8 @@ class SGC(nn.Module):
                  bias=True, k=2):
         """ Simplifying Graph Convolutional Networks
 
+        Edge feature is ignored in this model.
+
         Parameters
         ----------
         data_info : dict