Include benchmark in docs

gdmnl · Jun 13, 2024 · 3c92769 · 3c92769
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diff --git a/README.md b/README.md
@@ -1,6 +1,9 @@
 # Benchmarking Spectral Graph Neural Networks
 
-[![Docs](https://github.com/gdmnl/Spectral-GNN-Benchmark/workflows/Docs/badge.svg)](https://pages.github.com/gdmnl/Spectral-GNN-Benchmark/)
+[![Docs](https://github.com/gdmnl/Spectral-GNN-Benchmark/actions/workflows/docs.yaml/badge.svg)](https://gdmnl.github.io/Spectral-GNN-Benchmark/)
+[![LICENSE](https://img.shields.io/github/license/gdmnl/Spectral-GNN-Benchmark)](LICENSE)
+[![Release](https://img.shields.io/github/v/release/gdmnl/Spectral-GNN-Benchmark?include_prereleases)](https://github.com/gdmnl/Spectral-GNN-Benchmark/releases)
+[![Python](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fgdmnl%2FSpectral-GNN-Benchmark%2Fmain%2Fpyproject.toml)]()
 
 `pyg_spectral` is a [PyTorch Geometric](https://pyg.org)-based framework for analyzing, implementing, and benchmarking spectral GNNs with effectiveness and efficiency evaluations.
 
@@ -13,6 +16,8 @@
 
 ---
 
+[**Documentation**](https://gdmnl.github.io/Spectral-GNN-Benchmark/) | [**GitHub**](https://github.com/gdmnl/Spectral-GNN-Benchmark/)
+
 - [Installation](#installation)
 - [Reproduce Experiments](#reproduce-experiments)
   - [Main Experiments](#main-experiments)

diff --git a/benchmark/dataset_process/__init__.py b/benchmark/dataset_process/__init__.py
@@ -7,4 +7,10 @@
     split_random,
     even_quantile_labels,
     get_iso_nodes_mapping
-)
+)
+
+__all__ = [
+    'Yandex', 'LINKX', 'FB100',
+    'Filter',
+    'idx2mask', 'split_random', 'even_quantile_labels', 'get_iso_nodes_mapping'
+]
diff --git a/benchmark/dataset_process/linkx.py b/benchmark/dataset_process/linkx.py
@@ -22,7 +22,7 @@ class LINKX(InMemoryDataset):
     paper: Large Scale Learning on Non-Homophilous Graphs: New Benchmarks and Strong Simple Methods
     ref: https://github.com/CUAI/Non-Homophily-Large-Scale/
     """
-    dataset_drive_url = {
+    _dataset_drive_url = {
         'snap-patents.mat' : '1ldh23TSY1PwXia6dU0MYcpyEgX-w3Hia',
         'pokec.mat' : '1dNs5E7BrWJbgcHeQ_zuy5Ozp2tRCWG0y',
         'yelp-chi.mat': '1fAXtTVQS4CfEk4asqrFw9EPmlUPGbGtJ',
@@ -32,7 +32,7 @@ class LINKX(InMemoryDataset):
         'wiki_edges.pt': '14X7FlkjrlUgmnsYtPwdh-gGuFla4yb5u', # Wiki 1.9M
         'wiki_features.pt': '1ySNspxbK-snNoAZM7oxiWGvOnTRdSyEK' # Wiki 1.9M
     }
-    splits_drive_url = {
+    _splits_drive_url = {
         'snap-patents_splits.npy' : '12xbBRqd8mtG_XkNLH8dRRNZJvVM4Pw-N',
         'pokec_splits.npy' : '1ZhpAiyTNc0cE_hhgyiqxnkKREHK7MK-_',
     }
@@ -76,12 +76,12 @@ def download(self) -> None:
             download_url(f'{url}/{self.name}.mat', self.raw_dir)
             return
 
-        for fname in self.dataset_drive_url:
+        for fname in self._dataset_drive_url:
             if fname.startswith(self.name):
-                download_google_url(self.dataset_drive_url[fname], self.raw_dir, filename=fname)
-        for fname in self.splits_drive_url:
+                download_google_url(self._dataset_drive_url[fname], self.raw_dir, filename=fname)
+        for fname in self._splits_drive_url:
             if fname.startswith(self.name):
-                download_google_url(self.splits_drive_url[fname], self.raw_dir, filename=fname)
+                download_google_url(self._splits_drive_url[fname], self.raw_dir, filename=fname)
 
     def process(self) -> None:
         if self.name in ['twitch-gamer']:
@@ -118,7 +118,7 @@ def process(self) -> None:
             edge_index = coalesce(edge_index, num_nodes=n)
         kwargs = {'x': x, 'edge_index': edge_index, 'y': y}
 
-        splits_keys = [k.split('_')[0] for k in self.splits_drive_url]
+        splits_keys = [k.split('_')[0] for k in self._splits_drive_url]
         if self.name in splits_keys:
             # 50/25/25 train/valid/test split
             splits_lst = np.load(osp.join(self.raw_dir, f'{self.name}_splits.npy'), allow_pickle=True)

diff --git a/benchmark/trainer/__init__.py b/benchmark/trainer/__init__.py
@@ -3,3 +3,11 @@
 from .base import TrnBase_Trial
 from .fullbatch import TrnFullbatch
 from .minibatch import TrnMinibatch, TrnMinibatch_Trial
+
+__all__ = [
+    'SingleGraphLoader', 'SingleGraphLoader_Trial',
+    'ModelLoader', 'ModelLoader_Trial',
+    'TrnBase_Trial',
+    'TrnFullbatch',
+    'TrnMinibatch', 'TrnMinibatch_Trial',
+]
diff --git a/benchmark/utils/__init__.py b/benchmark/utils/__init__.py
@@ -3,3 +3,9 @@
     force_list_str, force_list_int, list_str, list_int, list_float,)
 from .logger import setup_logger, clear_logger, setup_logpath, ResLogger
 from .checkpoint import CkptLogger
+
+__all__ = [
+    'setup_seed', 'setup_argparse', 'setup_args', 'save_args', 'dict_to_json',
+    'setup_logger', 'clear_logger', 'setup_logpath', 'ResLogger',
+    'CkptLogger',
+]
diff --git a/docs/source/_include/benchmark.dataset_process.rst b/docs/source/_include/benchmark.dataset_process.rst
@@ -0,0 +1,8 @@
+benchmark.dataset\_process
+========================
+
+.. automodule:: benchmark.dataset_process
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
diff --git a/docs/source/_include/benchmark.trainer.rst b/docs/source/_include/benchmark.trainer.rst
@@ -0,0 +1,53 @@
+benchmark.trainer
+===============
+
+.. automodule:: benchmark.trainer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
+
+benchmark.trainer.base
+-------------------
+
+.. automodule:: benchmark.trainer.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
+
+benchmark.trainer.filter
+---------------------
+
+.. automodule:: benchmark.trainer.filter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
+
+benchmark.trainer.load\_data
+-------------------------
+
+.. automodule:: benchmark.trainer.load_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
+
+benchmark.trainer.load\_metric
+---------------------------
+
+.. automodule:: benchmark.trainer.load_metric
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
+
+benchmark.trainer.load\_model
+--------------------------
+
+.. automodule:: benchmark.trainer.load_model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
diff --git a/docs/source/_include/benchmark.utils.rst b/docs/source/_include/benchmark.utils.rst
@@ -0,0 +1,21 @@
+benchmark.utils
+=============
+
+.. automodule:: benchmark.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
+
+
+benchmark.utils.config
+-------------------
+
+.. autosummary::
+   :recursive:
+
+   config.force_list_str
+   config.force_list_int
+   config.list_str
+   config.list_int
+   config.list_float
diff --git a/docs/source/_templates/apidoc/module.rst_t b/docs/source/_templates/apidoc/module.rst_t
@@ -0,0 +1,8 @@
+{%- if show_headings %}
+{{- [basename] | join(' ') | e | heading }}
+
+{% endif -%}
+.. automodule:: {{ qualname }}
+{%- for option in automodule_options %}
+   :{{ option }}:
+{%- endfor %}
diff --git a/docs/source/_templates/apidoc/package.rst_t b/docs/source/_templates/apidoc/package.rst_t
@@ -0,0 +1,52 @@
+{%- macro automodule(modname, options) -%}
+.. automodule:: {{ modname }}
+{%- for option in options %}
+   :{{ option }}:
+{%- endfor %}
+{%- endmacro %}
+
+{%- macro toctree(docnames) -%}
+.. toctree::
+{% for docname in docnames %}
+   {{ docname }}
+{%- endfor %}
+{%- endmacro %}
+
+{%- if is_namespace %}
+{{- [pkgname, "namespace"] | join(" ") | e | heading }}
+{% else %}
+{{- [pkgname] | join(" ") | e | heading }}
+{% endif %}
+
+{%- if modulefirst and not is_namespace %}
+{{ automodule(pkgname, automodule_options) }}
+{% endif %}
+
+{%- if subpackages %}
+Subpackages
+-----------
+
+{{ toctree(subpackages) }}
+{% endif %}
+
+{%- if submodules %}
+Submodules
+----------
+{% if separatemodules %}
+{{ toctree(submodules) }}
+{%- else %}
+{%- for submodule in submodules %}
+{% if show_headings %}
+{{- [submodule] | join(" ") | e | heading(2) }}
+{% endif %}
+{{ automodule(submodule, automodule_options) }}
+{% endfor %}
+{%- endif %}
+{% endif %}
+
+{%- if not modulefirst and not is_namespace %}
+Module contents
+---------------
+
+{{ automodule(pkgname, automodule_options) }}
+{% endif %}
diff --git a/docs/source/_templates/apidoc/toc.rst_t b/docs/source/_templates/apidoc/toc.rst_t
@@ -0,0 +1,7 @@
+{{ header | heading }}
+
+.. toctree::
+   :maxdepth: {{ maxdepth }}
+{% for docname in docnames %}
+   {{ docname }}
+{%- endfor %}
diff --git a/docs/source/_templates/autosummary/class.rst b/docs/source/_templates/autosummary/class.rst
@@ -5,27 +5,25 @@
 .. autoclass:: {{ objname }}
 
    {% block methods %}
-   {% block attributes %}
-   {% if attributes %}
-   .. HACK -- the point here is that we don't want this to appear in the output, but the autosummary should still generate the pages.
-      .. autosummary::
-         :toctree:
-      {% for item in all_attributes %}
-         {%- if not item.startswith('_') %}
-         {{ name }}.{{ item }}
-         {%- endif -%}
-      {%- endfor %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: Methods
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
    {% endif %}
    {% endblock %}
 
-   {% if methods %}
-   .. HACK -- the point here is that we don't want this to appear in the output, but the autosummary should still generate the pages.
-      .. autosummary::
-         :toctree:
-      {% for item in all_methods %}
-         {%- if not item.startswith('_') or item in ['__call__'] %}
-         {{ name }}.{{ item }}
-         {%- endif -%}
-      {%- endfor %}
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Attributes
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
    {% endif %}
    {% endblock %}
diff --git a/docs/source/_templates/autosummary/module.rst b/docs/source/_templates/autosummary/module.rst
@@ -1,29 +1,36 @@
-{{ fullname | escape | underline }}
-
-.. rubric:: Description
+{{ fullname | escape | underline}}
 
 .. automodule:: {{ fullname }}
 
-.. currentmodule:: {{ fullname }}
-
-{% if classes %}
-.. rubric:: Classes
-
-.. autosummary::
-    :toctree: .
-    {% for class in classes %}
-    {{ class }}
-    {% endfor %}
-
-{% endif %}
-
-{% if functions %}
-.. rubric:: Functions
-
-.. autosummary::
-    :toctree: .
-    {% for function in functions %}
-    {{ function }}
-    {% endfor %}
-
-{% endif %}
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: Functions
+
+   .. autosummary::
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: Classes
+
+   .. autosummary::
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: Exceptions
+
+   .. autosummary::
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
diff --git a/docs/source/arrangement.md b/docs/source/arrangement.md
@@ -2,6 +2,8 @@
 
 ## Covered Models
 
+Refer to {py:class}`benchmark.trainer.ModelLoader`.
+
 | **Category** | **Model** |
 |:------------:|:----------|
 | Fixed Filter | [GCN](https://arxiv.org/abs/1609.02907), [SGC](https://arxiv.org/pdf/1902.07153), [gfNN](https://arxiv.org/pdf/1905.09550), [GZoom](https://arxiv.org/pdf/1910.02370), [S$^2$GC](https://openreview.net/pdf?id=CYO5T-YjWZV),[GLP](https://arxiv.org/pdf/1901.09993), [APPNP](https://arxiv.org/pdf/1810.05997), [GCNII](https://arxiv.org/pdf/2007.02133), [GDC](https://proceedings.neurips.cc/paper_files/paper/2019/file/23c894276a2c5a16470e6a31f4618d73-Paper.pdf), [DGC](https://arxiv.org/pdf/2102.10739), [AGP](https://arxiv.org/pdf/2106.03058), [GRAND+](https://arxiv.org/pdf/2203.06389)|
@@ -11,6 +13,8 @@
 
 ## Covered Datasets
 
+Refer to {py:class}`benchmark.trainer.SingleGraphLoader`.
+
 | **Source** | **Graph** |
 |:------------:|:----------|
 | [PyG](https://pytorch-geometric.readthedocs.io/en/stable/modules/datasets.html) | cora, citeseer, pubmed, flickr, actor |