Reorganize package

.ci/index_openapi_diff.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 # Note: This returns exit code 0, if the two specs agree, otherwise exit code 1
-docker run -t -v $(pwd):/specs:ro quen2404/openapi-diff /specs/index_openapi.json /specs/local_index_openapi.json
+docker run -t -v $(pwd):/specs:ro quen2404/openapi-diff /specs/openapi/index_openapi.json /specs/openapi/local_index_openapi.json

.ci/json_diff.sh

@@ -2,8 +2,8 @@
 python -c "from optimade.server.main import app, update_schema; update_schema(app)"
 python -c "from optimade.server.main_index import app, update_schema; update_schema(app)"
 
-diff=$(jsondiff openapi.json local_openapi.json);
-index_diff=$(jsondiff index_openapi.json local_index_openapi.json);
+diff=$(jsondiff ./openapi/openapi.json ./openapi/local_openapi.json);
+index_diff=$(jsondiff ./openapi/index_openapi.json ./openapi/local_index_openapi.json);
 
 if [ ! "$diff" = "{}" ]; then
     echo -e "Generated OpenAPI spec for test server did not match committed version.\nRun 'invoke update_openapijson' and re-commit.\nDiff:\n$diff";

.ci/openapi_diff.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 # Note: This returns exit code 0, if the two specs agree, otherwise exit code 1
-docker run -t -v $(pwd):/specs:ro quen2404/openapi-diff /specs/openapi.json /specs/local_openapi.json
+docker run -t -v $(pwd):/specs:ro quen2404/openapi-diff /specs/openapi/openapi.json /specs/openapi/local_openapi.json

.github/workflows/deps_lint.yml

@@ -73,13 +73,19 @@ jobs:
         docker pull quen2404/openapi-diff
 
     - name: Validate OpenAPI specifications
-      run: openapi-spec-validator openapi.json
+      run: |
+        openapi-spec-validator openapi/openapi.json
+        openapi-spec-validator openapi/index_openapi.json
 
-    - name: Update OpenAPI schema
-      run: python -c "from optimade.server.main import app, update_schema; update_schema(app)"
+    - name: Update OpenAPI schemes
+      run: |
+        python -c "from optimade.server.main import app, update_schema; update_schema(app)"
+        python -c "from optimade.server.main_index import app, update_schema; update_schema(app)"
 
     - name: Check if OpenAPI schemes match
-      run: .ci/openapi_diff.sh
+      run: |
+        .ci/openapi_diff.sh
+        .ci/index_openapi_diff.sh
 
   deps_static:
     runs-on: ubuntu-latest
@@ -116,7 +122,7 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         flags: unittests
-        yml: ./codecov.yml
+        yml: ./.codecov.yml
 
   deps_eager:
     runs-on: ubuntu-latest

README.md

@@ -113,9 +113,9 @@ start
 # Assumes graphviz installed on system (e.g. `conda install -c anaconda graphviz`) and `pip install pydot`
 from lark.tree import pydot__tree_to_png
 
-pydot__tree_to_png(tree, "exampletree.png")
+pydot__tree_to_png(tree, "images/exampletree.png")
 ```
-![example tree](exampletree.png)
+![example tree](images/exampletree.png)
 
 #### Flow for Parsing User-Supplied Filter and Converting to Backend Query
 

optimade/server/main.py

@@ -29,13 +29,9 @@
 
 
 test_paths = {
-    "structures": Path(__file__)
-    .resolve()
-    .parent.joinpath("tests/test_structures.json"),
-    "references": Path(__file__)
-    .resolve()
-    .parent.joinpath("tests/test_references.json"),
-    "links": Path(__file__).resolve().parent.joinpath("tests/test_links.json"),
+    "structures": Path(__file__).resolve().parent.joinpath("data/test_structures.json"),
+    "references": Path(__file__).resolve().parent.joinpath("data/test_references.json"),
+    "links": Path(__file__).resolve().parent.joinpath("data/test_links.json"),
 }
 if not CONFIG.use_real_mongo and (path.exists() for path in test_paths.values()):
     import bson.json_util
@@ -93,7 +89,7 @@ def load_entries(endpoint_name: str, endpoint_collection: MongoCollection):
 
 def update_schema(app):
     """Update OpenAPI schema in file 'local_openapi.json'"""
-    with open("local_openapi.json", "w") as f:
+    with open("openapi/local_openapi.json", "w") as f:
         json.dump(app.openapi(), f, indent=2)
 
 

optimade/server/main_index.py

@@ -69,7 +69,7 @@
 
 def update_schema(app):
     """Update OpenAPI schema in file 'local_index_openapi.json'"""
-    with open("local_index_openapi.json", "w") as f:
+    with open("openapi/local_index_openapi.json", "w") as f:
         json.dump(app.openapi(), f, indent=2)
 
 

tasks.py

@@ -37,5 +37,5 @@ def setver(_, patch=False, new_ver=""):
 
 @task
 def update_openapijson(c):
-    c.run("cp local_openapi.json openapi.json")
-    c.run("cp local_index_openapi.json index_openapi.json")
+    c.run("cp openapi/local_openapi.json openapi/openapi.json")
+    c.run("cp openapi/local_index_openapi.json openapi/index_openapi.json")

optimade/models/tests/test_models.py → tests/models/test_models.py

@@ -15,7 +15,7 @@ def test_good_structures(self):
         test_structures_path = (
             Path(__file__)
             .resolve()
-            .parent.joinpath("../../server/tests/test_structures.json")
+            .parent.joinpath("../../optimade/server/data/test_structures.json")
         )
         with open(test_structures_path, "r") as f:
             good_structures = json.load(f)
@@ -65,7 +65,7 @@ def test_good_references(self):
         test_refs_path = (
             Path(__file__)
             .resolve()
-            .parent.joinpath("../../server/tests/test_references.json")
+            .parent.joinpath("../../optimade/server/data/test_references.json")
         )
         with open(test_refs_path, "r") as f:
             good_refs = json.load(f)