Update dependencies (#1443)

* Bump mkdocs-material from 8.5.10 to 8.5.11 (#1413)

Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 8.5.10 to 8.5.11.
- [Release notes](https://github.com/squidfunk/mkdocs-material/releases)
- [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG)
- [Commits](squidfunk/mkdocs-material@8.5.10...8.5.11)

---
updated-dependencies:
- dependency-name: mkdocs-material
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump black from 22.10.0 to 22.12.0 (#1430)

Bumps [black](https://github.com/psf/black) from 22.10.0 to 22.12.0.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@22.10.0...22.12.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump lark from 1.1.4 to 1.1.5 (#1432)

Bumps [lark](https://github.com/lark-parser/lark) from 1.1.4 to 1.1.5.
- [Release notes](https://github.com/lark-parser/lark/releases)
- [Changelog](https://github.com/lark-parser/lark/blob/master/CHANGELOG.md)
- [Commits](lark-parser/lark@1.1.4...1.1.5)

---
updated-dependencies:
- dependency-name: lark
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump pylint from 2.15.6 to 2.15.8 (#1431)

Bumps [pylint](https://github.com/PyCQA/pylint) from 2.15.6 to 2.15.8.
- [Release notes](https://github.com/PyCQA/pylint/releases)
- [Commits](pylint-dev/pylint@v2.15.6...v2.15.8)

---
updated-dependencies:
- dependency-name: pylint
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump pylint from 2.15.8 to 2.15.9 (#1436)

Bumps [pylint](https://github.com/PyCQA/pylint) from 2.15.8 to 2.15.9.
- [Release notes](https://github.com/PyCQA/pylint/releases)
- [Commits](pylint-dev/pylint@v2.15.8...v2.15.9)

---
updated-dependencies:
- dependency-name: pylint
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump mkdocstrings[python-legacy] from 0.19.0 to 0.19.1 (#1437)

Bumps [mkdocstrings[python-legacy]](https://github.com/mkdocstrings/mkdocstrings) from 0.19.0 to 0.19.1.
- [Release notes](https://github.com/mkdocstrings/mkdocstrings/releases)
- [Changelog](https://github.com/mkdocstrings/mkdocstrings/blob/master/CHANGELOG.md)
- [Commits](mkdocstrings/mkdocstrings@0.19.0...0.19.1)

---
updated-dependencies:
- dependency-name: mkdocstrings[python-legacy]
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump isort from 5.10.1 to 5.11.3 (#1438)

Bumps [isort](https://github.com/pycqa/isort) from 5.10.1 to 5.11.3.
- [Release notes](https://github.com/pycqa/isort/releases)
- [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md)
- [Commits](PyCQA/isort@5.10.1...5.11.3)

---
updated-dependencies:
- dependency-name: isort
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump numpy from 1.23.5 to 1.24.0 (#1439)

Bumps [numpy](https://github.com/numpy/numpy) from 1.23.5 to 1.24.0.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.23.5...v1.24.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump jarvis-tools from 2022.9.16 to 2022.12.11 (#1440)

* Bump jarvis-tools from 2022.9.16 to 2022.12.11

Bumps [jarvis-tools](https://github.com/usnistgov/jarvis) from 2022.9.16 to 2022.12.11.
- [Release notes](https://github.com/usnistgov/jarvis/releases)
- [Commits](usnistgov/jarvis@v2022.09.16...v2022.12.11)

---
updated-dependencies:
- dependency-name: jarvis-tools
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Fix  typo

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Matthew Evans <[email protected]>

* Bump aiida-core from 2.1.2 to 2.2.0

Bumps [aiida-core](https://github.com/aiidateam/aiida-core) from 2.1.2 to 2.2.0.
- [Release notes](https://github.com/aiidateam/aiida-core/releases)
- [Changelog](https://github.com/aiidateam/aiida-core/blob/main/CHANGELOG.md)
- [Commits](aiidateam/aiida-core@v2.1.2...v2.2.0)

---
updated-dependencies:
- dependency-name: aiida-core
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Also bump pyyaml

* Update `pre-commit` hooks

* Update setup.py

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Matthew Evans <[email protected]>
Co-authored-by: Matthew Evans <[email protected]>

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/ambv/black
-    rev: 22.10.0
+    rev: 22.12.0
     hooks:
     - id: black
       name: Blacken
@@ -52,7 +52,7 @@ repos:
         additional_dependencies: ["types-all", "pydantic~=1.10"]
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: v5.11.3
     hooks:
       - id: isort
         name: "isort"

requirements-client.txt

@@ -1,5 +1,5 @@
-aiida-core==2.1.2
+aiida-core==2.2.0
 ase==3.22.1
-jarvis-tools==2022.9.16
-numpy==1.23.5
+jarvis-tools==2022.12.11
+numpy==1.24.0
 pymatgen==2022.7.25

requirements-dev.txt

@@ -1,13 +1,13 @@
-black==22.10.0
+black==22.12.0
 build==0.9.0
 codecov==2.1.12
 flake8==6.0.0
 invoke==1.7.3
-isort==5.10.1
+isort==5.11.3
 jsondiff==2.0.0
 mypy==0.991
 pre-commit==2.20.0
-pylint==2.15.6
+pylint==2.15.9
 pytest==7.2.0
 pytest-cov==4.0.0
 pytest-httpx==0.21.2

requirements-docs.txt

@@ -1,5 +1,5 @@
 mike==1.1.2
 mkdocs==1.4.2
 mkdocs-awesome-pages-plugin==2.8.0
-mkdocs-material==8.5.10
-mkdocstrings[python-legacy]==0.19.0
+mkdocs-material==8.5.11
+mkdocstrings[python-legacy]==0.19.1

requirements.txt

@@ -1,6 +1,6 @@
 email_validator==1.3.0
-lark==1.1.4
+lark==1.1.5
 pydantic==1.10.2
-pyyaml==5.4
+pyyaml==6.0
 requests==2.28.1
 uvicorn==0.20.0

setup.py

@@ -20,11 +20,7 @@
 # Server minded
 elastic_deps = ["elasticsearch-dsl~=7.4,<8.0", "elasticsearch~=7.17"]
 mongo_deps = ["pymongo>=3.12.1,<5", "mongomock~=4.1"]
-server_deps = [
-    "uvicorn~=0.19",
-    "fastapi~=0.86",
-    "pyyaml>=5.4,<7",  # Keep at pyyaml 5.4 for aiida-core support
-] + mongo_deps
+server_deps = ["uvicorn~=0.19", "fastapi~=0.86", "pyyaml~=6.0"] + mongo_deps
 
 
 # Client minded
@@ -39,7 +35,7 @@
 cif_deps = ["numpy~=1.23"]
 pdb_deps = cif_deps
 pymatgen_deps = ["pymatgen~=2022.7"]
-jarvis_deps = ["jarvis-tools==2022.8.27"]
+jarvis_deps = ["jarvis-tools==2022.12.11"]
 client_deps = cif_deps
 
 # General