Updates (#16)

* Update README.md * move requirements file and split into testing and tutorials * made extraneous files obsolete * Updated requirements file location * we don't support integration tests * Rename SCHEMAS to CHANGELOG * rename tutorial * format with isort and black * rename attr to attrs * add tutorials * updated tutorials * Update README.md * remove unnecessary files * format with isort * Delete README.md * Update nx.ipynb * Update TUTORIALS.md * Update conftest.py * Delete test_nx.py * slight rename * Fix code snippet * Update README.md
pszufe · Sep 26, 2024 · 7aefda6 · 7aefda6
1 parent 27bea43
commit 7aefda6
Show file tree

Hide file tree

Showing 26 changed files with 191,963 additions and 87 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -22,7 +22,7 @@ jobs:
     - name: Install packages
       run: |
         python -m pip install --upgrade pip wheel setuptools
-        python -m pip install -r requirements.txt
+        python -m pip install -r requirements/tests.txt
         python -m pip list
 
     - name: Test schema

diff --git a/README.md b/README.md
@@ -1,7 +1,17 @@
-## A set of Hypergraph Exchange Format (HIF) specification & validators
+## The Hypergraph Interchange Format (HIF) standard
 (Work-in-progress)
 
-Hypergraph Exchange Format (HIF) is a forthcoming standard for data exchange between the existing hypergaph libraries. 
+Hypergraph Exchange Format (HIF) is a forthcoming standard for higher-order network data to facilitate seamless data exchange between existing higher-order network libraries. 
+
+### Table of contents for this folder
+
+This repository is organized into the following folders:
+* `examples`: This folder contains examples of higher-order datasets in the HIF standard. For details of its contents, see the [README](/examples/EXAMPLES.md).
+* `requirements`: This folder contains a list of all dependencies used in this project.
+* `schemas`: This folder contains all schemas used for specifying the HIF standard. For details of what has changed with each version, see the [CHANGELOG](/schemas/SCHEMAS.md).
+* `src`: This folder contains addition functionality for checking against the HIF specification.
+* `tests`: This folder contains all of the unit tests used for validating that the schema is correct.
+* `tutorials`: This folder contains tutorials detailing how each library uses the HIF standard and how the HIF standard allows seamless integration between libraries. For details of its contents, see the [README](/examples/TUTORIALS.md).
 
 Initial assumptions about the core of the HIF data format:
 ```
@@ -25,13 +35,7 @@ Initial assumptions about the core of the HIF data format:
     - **direction keywords** : head, tail
 - If a hypergraph is, for instance, directed, the edge direction will be contained in the incidences record with keyword "direction".
 - Isolated nodes and empty edges are entries in "nodes" and "edges" which are not present in the incidences.
-
-### Table of contents for this folder
-
-This repository is organized into three folders:
-* `examples`: This folder contains examples of higher-order datasets in the HIF standard. For details of its contents, see the [README](/examples/EXAMPLES.md).
-* `schemas`: This folder contains all schemas used for specifying the HIF standard. For details of its contents, see the [README](/schemas/SCHEMAS.md).
-* `scripts`: This folder contains scripts for checking that datasets match the HIF standard. For details of its contents, see the [README](/scripts/SCRIPTS.md).
+- This schema explicitely describes all items in the schema using json objects and typing. This is a verbose presentation making it faster to instantiate than list-based schemas requiring a parser.
 
 - *validate_hif.py*: This Python command line executable checks whether a JSON file matches the HIF standard. All errors print to the command line. More details on running this are in the [next section](#validate-files-against-the-hif-standard).
 
@@ -47,8 +51,9 @@ The only option is `--silent`, which suppresses all detailed warnings. Regardles
 ```python
 import fastjsonschema
 import json
+import requests
 
-schema = json.load(open("hif_schema_v0.1.0.json","r"))
+schema = requests.get("https://raw.githubusercontent.com/pszufe/HIF_validators/main/schemas/hif_schema_v0.1.0.json").json()
 validator = fastjsonschema.compile(schema)
 hiftext = json.load(open(filename,'r'))
 validator(hiftext)
@@ -66,10 +71,8 @@ The authors, co-authors or contributors of the following software libraries are
 This project is an ongoing colaborative work of the following people (alphabetical order):
 - [Audun Myers](https://www.audunmyers.com/) (Pacific Northwest National Laboratory) 
 - [Brenda Praggastis](https://www.pnnl.gov/people/brenda-praggastis)  (Pacific Northwest National Laboratory)
-- [Caterina Debacco](https://www.cdebacco.com/) (Max Planck Institute for Intelligent Systems)
 - [Cliff Joslyn](https://www.pnnl.gov/people/cliff-joslyn) (Pacific Northwest National Laboratory)
 - [Francesco Lotito](https://scholar.google.it/citations?user=_r_zQAwAAAAJ&hl=en) (University of Trento)
 - [Martín Coll](https://about.me/mcoll)  (University of Buenos Aires)
 - [Nicholas Landry](https://nwlandry.com/) (University of Virginia) 
-- [Przemyslaw Szufel](https://szufel.pl/) (SGH Warsaw School of Economics)
-
+- [Przemyslaw Szufel](https://szufel.pl/) (SGH Warsaw School of Economics)
diff --git a/schemas/performance_testing.py → _OBS/performance_testing.py b/schemas/performance_testing.py → _OBS/performance_testing.py
diff --git a/schemas/performance_testing_output.txt → _OBS/performance_testing_output.txt b/schemas/performance_testing_output.txt → _OBS/performance_testing_output.txt
diff --git a/requirements.txt b/requirements.txt
diff --git a/requirements/tests.txt b/requirements/tests.txt
@@ -0,0 +1,2 @@
+fastjsonschema
+pytest
diff --git a/requirements/tutorials.txt b/requirements/tutorials.txt
@@ -0,0 +1,5 @@
+hypergraphx
+hypernetx
+networkx
+xgi
+requests
diff --git a/schemas/CHANGELOG.md b/schemas/CHANGELOG.md
@@ -0,0 +1,4 @@
+# Changelog
+
+## v0.1.0  
+Initial schema for the Hypergraph Interchange Format (HIF) standard.
diff --git a/schemas/SCHEMAS.md b/schemas/SCHEMAS.md
diff --git a/schemas/hif_schema_v0.1.0.json b/schemas/hif_schema_v0.1.0.json
@@ -1,11 +1,11 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
     "$id": "https://raw.githubusercontent.com/pszufe/HIF_validators/main/schemas/hif_schema_v0.1.0.json",
-    "title": "Schema for Hypergraph Interchange Format - HIF",
+    "title": "Hypergraph Interchange Format v0.1.0",
     "type": "object",
     "properties":{
         "network-type": {
-            "enum": ["undirected","directed","asc"]           
+            "enum": ["undirected","directed","asc"]
         },
         "metadata": {
             "type":"object"
@@ -27,7 +27,7 @@
                         "direction": {
                             "enum": ["head","tail"]
                         },
-                        "attr": {
+                        "attrs": {
                             "type": "object"
                         },
                         "unevaluatedProperties": false
@@ -46,7 +46,7 @@
                     "weight": {
                         "type":"number"
                     },
-                    "attr": {
+                    "attrs": {
                         "type": "object"
                     } ,                    
                     "unevaluatedProperties": false              
@@ -65,7 +65,7 @@
                     "weight": {
                         "type":"number"
                     },
-                    "attr": {
+                    "attrs": {
                         "type": "object"
                     } ,                    
                     "unevaluatedProperties": false              

diff --git a/scripts/SCRIPTS.md b/scripts/SCRIPTS.md
diff --git a/scripts/__init__.py b/scripts/__init__.py
diff --git a/scripts/nx.py b/scripts/nx.py
diff --git a/scripts/hif.py → src/hif.py b/scripts/hif.py → src/hif.py
@@ -19,7 +19,11 @@ def validate_network_type(data, verbose):
                     )
 
     # in the case of simplicial complexes, make sure that the edges are maximal
-    if "network-type" in data and data["network-type"] == "asc" and "incidences" in data:
+    if (
+        "network-type" in data
+        and data["network-type"] == "asc"
+        and "incidences" in data
+    ):
         edgedict = defaultdict(set)
         for record in data["incidences"]:
             e = record[0]
@@ -31,4 +35,4 @@ def validate_network_type(data, verbose):
                     if verbose:
                         print(
                             f"Only maximal faces should be stored for simplicial complexes."
-                    )
+                        )
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,8 +1,7 @@
 import json
 
-import pytest
-import requests
 import fastjsonschema
+import pytest
 
 schema = "schemas/hif_schema_v0.1.0.json"
 json_dir = "tests/test_files"
@@ -12,22 +11,27 @@
 def validator():
     return fastjsonschema.compile(json.load(open(schema)))
 
+
 @pytest.fixture
 def empty():
     return json.load(open(f"{json_dir}/empty.json", "r"))
 
+
 @pytest.fixture
 def single_node():
     return json.load(open(f"{json_dir}/single_node.json", "r"))
 
+
 @pytest.fixture
 def single_edge():
     return json.load(open(f"{json_dir}/single_edge.json", "r"))
 
+
 @pytest.fixture
 def single_incidence():
     return json.load(open(f"{json_dir}/single_incidence.json", "r"))
 
+
 @pytest.fixture
 def bad_top_level_field():
     return json.load(open(f"{json_dir}/bad_top_level_field.json", "r"))

diff --git a/tests/test_nx.py b/tests/test_nx.py
diff --git a/tutorials/TUTORIALS.md b/tutorials/TUTORIALS.md
@@ -0,0 +1,7 @@
+# List of tutorials
+
+* `integration.ipynb`: This tutorial demonstrates how to use the HIF standard to facilitate data exchange between different libraries.
+* `hgx.ipynb`:
+* `hnx.ipynb`:
+* `nx.ipynb`:
+* `xgi.ipynb`: This tutorial demonstrates how to use the HIF functionality available in XGI