Merge branch 'master' into ml-evs/list_queries

.github/workflows/deps_lint.yml

@@ -32,6 +32,7 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
+
   pre-commit:
     runs-on: ubuntu-latest
 
@@ -53,6 +54,7 @@ jobs:
       run: |
         pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
 
+
   openapi:
     runs-on: ubuntu-latest
 
@@ -87,28 +89,46 @@ jobs:
         .ci/openapi_diff.sh
         .ci/index_openapi_diff.sh
 
+
   docker-image:
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v1
 
-    - name: Build the Docker image
+    - name: Build the Docker images
       run: docker-compose build
 
-    - name: Test server
+    - name: Start Docker image - server
       run: |
         docker-compose up optimade &
         .github/workflows/wait_for_it.sh localhost:3213 -t 120
         sleep 15
-        docker exec optimade-python-tools_optimade_1 optimade_validator http://localhost:5000/optimade/v0
 
-    - name: Test index server
+    - name: Test server
+      run: docker exec optimade-python-tools_optimade_1 optimade_validator http://localhost:5000/optimade/v0
+
+    - name: Test server - OPTIONAL base URL; vMAJOR.MINOR
+      run: docker exec optimade-python-tools_optimade_1 optimade_validator http://localhost:5000/optimade/v0.10
+
+    - name: Test server - OPTIONAL base URL; vMAJOR.MINOR.PATCH
+      run: docker exec optimade-python-tools_optimade_1 optimade_validator http://localhost:5000/optimade/v0.10.1
+
+    - name: Start Docker image - index server
       run: |
         docker-compose up optimade-index &
         .github/workflows/wait_for_it.sh localhost:3214 -t 120
         sleep 15
-        docker exec optimade-python-tools_optimade-index_1 optimade_validator http://localhost:5001/optimade/v0 --index
+
+    - name: Test index server
+      run: docker exec optimade-python-tools_optimade-index_1 optimade_validator http://localhost:5001/optimade/v0 --index
+
+    - name: Test index server - OPTIONAL base URL; vMAJOR.MINOR
+      run: docker exec optimade-python-tools_optimade-index_1 optimade_validator http://localhost:5001/optimade/v0.10 --index
+
+    - name: Test index server - OPTIONAL base URL; vMAJOR.MINOR.PATCH
+      run: docker exec optimade-python-tools_optimade-index_1 optimade_validator http://localhost:5001/optimade/v0.10.1 --index
+
 
   deps_static:
     runs-on: ubuntu-latest

openapi/index_openapi.json

@@ -2,7 +2,7 @@
   "openapi": "3.0.2",
   "info": {
     "title": "OPTiMaDe API - Index meta-database",
-    "description": "The [Open Databases Integration for Materials Design (OPTiMaDe) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\nThis is the \"special\" index meta-database.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.4.0) v0.4.0.",
+    "description": "The [Open Databases Integration for Materials Design (OPTiMaDe) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\nThis is the \"special\" index meta-database.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.5.0) v0.5.0.",
     "version": "0.10.1"
   },
   "paths": {

openapi/openapi.json

@@ -2,7 +2,7 @@
   "openapi": "3.0.2",
   "info": {
     "title": "OPTiMaDe API",
-    "description": "The [Open Databases Integration for Materials Design (OPTiMaDe) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.4.0) v0.4.0.",
+    "description": "The [Open Databases Integration for Materials Design (OPTiMaDe) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.5.0) v0.5.0.",
     "version": "0.10.1"
   },
   "paths": {

optimade/__init__.py

@@ -1,2 +1,2 @@
-__version__ = "0.4.0"
+__version__ = "0.5.0"
 __api_version__ = "0.10.1"

optimade/server/config.ini

@@ -26,3 +26,9 @@ index_base_url = http://localhost:5001/optimade
 [structures]
 band_gap :
 _mp_chemsys :
+
+[structures.aliases]
+id = task_id
+chemical_formula_descriptive = pretty_formula
+chemical_formula_reduced = pretty_formula
+chemical_formula_anonymous = formula_anonymous

optimade/server/config.py

@@ -169,6 +169,12 @@ def load_from_ini(self):
         else:
             self.provider = self._DEFAULTS("provider")
 
+        self.aliases = {}
+        for endpoint in {"links", "references", "structures"}:
+            if f"{endpoint}.aliases" in config:
+                section = config[f"{endpoint}.aliases"]
+                self.aliases[endpoint] = tuple(section.items())
+
         self.provider_fields = {}
         for endpoint in {"links", "references", "structures"}:
             self.provider_fields[endpoint] = (
@@ -233,5 +239,12 @@ def load_from_json(self):
                 set(config.get("provider_fields", {}).get(endpoint, []))
             )
 
+        self.aliases = {}
+        if "aliases" in config:
+            for endpoint in {"links", "references", "structures"}:
+                if endpoint in config["aliases"]:
+                    section = config["aliases"][endpoint]
+                    self.aliases[endpoint] = tuple(section.items())
+
 
 CONFIG = ServerConfig()

optimade/server/mappers/entries.py

@@ -19,6 +19,7 @@ def all_aliases(cls) -> Tuple[Tuple[str, str]]:
                 (CONFIG.provider["prefix"] + field, field)
                 for field in CONFIG.provider_fields.get(cls.ENDPOINT, [])
             )
+            + CONFIG.aliases.get(cls.ENDPOINT, ())
             + cls.ALIASES
         )
 

optimade/server/mappers/structures.py

@@ -6,9 +6,3 @@
 class StructureMapper(ResourceMapper):
 
     ENDPOINT = "structures"
-    ALIASES = (
-        ("id", "task_id"),
-        ("chemical_formula_descriptive", "pretty_formula"),
-        ("chemical_formula_reduced", "pretty_formula"),
-        ("chemical_formula_anonymous", "formula_anonymous"),
-    )

optimade/server/routers/utils.py

@@ -29,8 +29,8 @@
 
 BASE_URL_PREFIXES = {
     "major": f"/optimade/v{__api_version__.split('.')[0]}",
-    "minor": f"/optimade/v{__api_version__.split('.')[1]}",
-    "patch": f"/optimade/v{__api_version__.split('.')[2]}",
+    "minor": f"/optimade/v{'.'.join(__api_version__.split('.')[:2])}",
+    "patch": f"/optimade/v{__api_version__}",
 }
 
 

setup.py

@@ -20,7 +20,7 @@
 
 setup(
     name="optimade",
-    version="0.4.0",
+    version="0.5.0",
     url="https://github.com/Materials-Consortia/optimade-python-tools",
     license="MIT",
     author="OPTiMaDe Development Team",

tasks.py

@@ -56,11 +56,12 @@ def update_openapijson(c):
 def set_optimade_ver(_, ver=""):
     if not ver:
         raise Exception("Please specify --ver='Major.Minor.Patch'")
+    if not re.match("[0-9]+.[0-9]+.[0-9]+", ver):
+        raise Exception("ver MUST be expressed as 'Major.Minor.Patch'")
+
     with open("optimade/__init__.py", "r") as f:
         lines = [
-            re.sub(
-                "__api_version__ = .+", '__api_version__ = "{}"'.format(ver), l.rstrip()
-            )
+            re.sub("__api_version__ = .+", f'__api_version__ = "{ver}"', l.rstrip())
             for l in f
         ]
     with open("optimade/__init__.py", "w") as f:
@@ -69,11 +70,25 @@ def set_optimade_ver(_, ver=""):
 
     with open(".ci/optimade-version.json", "r") as f:
         lines = [
-            re.sub('"message": .+', '"message": "v{}",'.format(ver), l.rstrip())
-            for l in f
+            re.sub('"message": .+', f'"message": "v{ver}",', l.rstrip()) for l in f
         ]
     with open(".ci/optimade-version.json", "w") as f:
         f.write("\n".join(lines))
         f.write("\n")
 
-    print("Bumped OPTiMaDe version to {}".format(ver))
+    with open(".github/workflows/deps_lint.yml", "r") as f:
+        lines = f
+        for regex, version in (
+            ("[0-9]+", ver.split(".")[0]),
+            ("[0-9]+.[0-9]+", ".".join(ver.split(".")[:2])),
+            ("[0-9]+.[0-9]+.[0-9]+", ver),
+        ):
+            lines = [
+                re.sub(f"/optimade/v{regex}", f"/optimade/v{version}", l.rstrip())
+                for l in lines
+            ]
+    with open(".github/workflows/deps_lint.yml", "w") as f:
+        f.write("\n".join(lines))
+        f.write("\n")
+
+    print(f"Bumped OPTiMaDe version to {ver}")

tests/server/config_test.ini

@@ -24,3 +24,9 @@ index_base_url = http://localhost:5001/optimade
 [structures]
 band_gap :
 _mp_chemsys :
+
+[structures.aliases]
+id = task_id
+chemical_formula_descriptive = pretty_formula
+chemical_formula_reduced = pretty_formula
+chemical_formula_anonymous = formula_anonymous

tests/server/config_test.json

@@ -23,5 +23,13 @@
             "band_gap",
             "_mp_chemsys"
         ]
+    },
+    "aliases": {
+        "structures": {
+            "id": "task_id",
+            "chemical_formula_descriptive": "pretty_formula",
+            "chemical_formula_reduced": "pretty_formula",
+            "chemical_formula_anonymous": "formula_anonymous"
+        }
     }
 }