Merge remote-tracking branch 'upstream/main' into azure

.pre-commit-config.yaml

@@ -1,12 +1,34 @@
+default_stages: [commit]
+
+default_install_hook_types: [pre-commit, commit-msg]
+
 repos:
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.261
+    hooks:
+      - id: ruff
+        args: [--fix, --ignore, "D,E501"]
+
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black-jupyter
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v4.4.0
     hooks:
-    -   id: check-yaml
-    -   id: end-of-file-fixer
-    -   id: trailing-whitespace
-    -   id: flake8
-  - repo: https://github.com/ambv/black
-    rev: stable
+      - id: check-case-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: destroyed-symlinks
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
     hooks:
-    - id: black
+      - id: codespell
+        stages: [commit, commit-msg]
+        exclude_types: [json, bib, svg]
+        args: [--ignore-words-list, "mater,fwe,te"]

docs/CHANGELOG.md

@@ -1,5 +1,29 @@
 # Changelog
 
+## [v0.51.1](https://github.com/materialsproject/maggma/tree/v0.51.1) (2023-05-22)
+
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.51.0...v0.51.1)
+
+**Merged pull requests:**
+
+- Add ruamel-yaml as a dependency [\#789](https://github.com/materialsproject/maggma/pull/789) ([sivonxay](https://github.com/sivonxay))
+
+## [v0.51.0](https://github.com/materialsproject/maggma/tree/v0.51.0) (2023-05-22)
+
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.50.4...v0.51.0)
+
+**Merged pull requests:**
+
+- Create a MultiStore object and a Store-like object to access it [\#787](https://github.com/materialsproject/maggma/pull/787) ([sivonxay](https://github.com/sivonxay))
+
+## [v0.50.4](https://github.com/materialsproject/maggma/tree/v0.50.4) (2023-04-28)
+
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.50.3...v0.50.4)
+
+**Merged pull requests:**
+
+- Update MongoStore `count` method [\#785](https://github.com/materialsproject/maggma/pull/785) ([munrojm](https://github.com/munrojm))
+
 ## [v0.50.3](https://github.com/materialsproject/maggma/tree/v0.50.3) (2023-02-17)
 
 [Full Changelog](https://github.com/materialsproject/maggma/compare/v0.50.2...v0.50.3)
@@ -106,19 +130,19 @@
 
 ## [v0.49.9](https://github.com/materialsproject/maggma/tree/v0.49.9) (2022-11-01)
 
-[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.49.8...v0.49.9)
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.49.7...v0.49.9)
 
 **Merged pull requests:**
 
 - Parse datetime with dateutil [\#741](https://github.com/materialsproject/maggma/pull/741) ([munrojm](https://github.com/munrojm))
 
-## [v0.49.8](https://github.com/materialsproject/maggma/tree/v0.49.8) (2022-10-25)
+## [v0.49.7](https://github.com/materialsproject/maggma/tree/v0.49.7) (2022-10-25)
 
-[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.49.7...v0.49.8)
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.49.8...v0.49.7)
 
-## [v0.49.7](https://github.com/materialsproject/maggma/tree/v0.49.7) (2022-10-25)
+## [v0.49.8](https://github.com/materialsproject/maggma/tree/v0.49.8) (2022-10-25)
 
-[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.49.6...v0.49.7)
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.49.6...v0.49.8)
 
 **Merged pull requests:**
 
@@ -327,23 +351,23 @@
 
 ## [v0.44.1](https://github.com/materialsproject/maggma/tree/v0.44.1) (2022-03-08)
 
-[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.42.0...v0.44.1)
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.44.0...v0.44.1)
 
 **Merged pull requests:**
 
 - added localhost test for MongoURIStore [\#595](https://github.com/materialsproject/maggma/pull/595) ([jmmshn](https://github.com/jmmshn))
 
-## [v0.42.0](https://github.com/materialsproject/maggma/tree/v0.42.0) (2022-03-07)
+## [v0.44.0](https://github.com/materialsproject/maggma/tree/v0.44.0) (2022-03-07)
 
-[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.43.0...v0.42.0)
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.43.0...v0.44.0)
 
 ## [v0.43.0](https://github.com/materialsproject/maggma/tree/v0.43.0) (2022-03-07)
 
-[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.44.0...v0.43.0)
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.42.0...v0.43.0)
 
-## [v0.44.0](https://github.com/materialsproject/maggma/tree/v0.44.0) (2022-03-07)
+## [v0.42.0](https://github.com/materialsproject/maggma/tree/v0.42.0) (2022-03-07)
 
-[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.41.1...v0.44.0)
+[Full Changelog](https://github.com/materialsproject/maggma/compare/v0.41.1...v0.42.0)
 
 **Merged pull requests:**
 

requirements-docs.txt

@@ -3,3 +3,4 @@ mkdocs-material==8.3.9
 mkdocs-minify-plugin==0.5.0
 mkdocstrings==0.18.1
 jinja2<3.2.0
+ruamel-yaml<18.0

requirements.txt

@@ -19,3 +19,4 @@ orjson==3.8.0
 boto3==1.24.42
 python-dateutil==2.8.2
 pydantic
+ruamel.yaml<0.18

src/maggma/stores/gridfs.py

@@ -8,7 +8,7 @@
 import copy
 import json
 import zlib
-import yaml
+from ruamel import yaml
 from datetime import datetime
 from pymongo.errors import ConfigurationError
 from typing import Any, Dict, Iterator, List, Optional, Tuple, Union
@@ -107,7 +107,7 @@ def from_launchpad_file(cls, lp_file, collection_name, **kwargs):
         Returns:
         """
         with open(lp_file, "r") as f:
-            lp_creds = yaml.load(f, Loader=yaml.FullLoader)
+            lp_creds = yaml.safe_load(f.read())
 
         db_creds = lp_creds.copy()
         db_creds["database"] = db_creds["name"]