First commit for atomate2-turbomole.

.pre-commit-config.yaml

@@ -1,7 +1,12 @@
 default_language_version:
   python: python3
-
+exclude: ^(tests/testfiles/)
 repos:
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.256
+  hooks:
+  - id: ruff
+    args: [--fix]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -10,12 +15,8 @@ repos:
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/myint/autoflake
-  rev: v2.0.1
-  hooks:
-  - id: autoflake
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.1.0
   hooks:
   - id: black
 - repo: https://github.com/asottile/blacken-docs
@@ -24,10 +25,6 @@ repos:
   - id: blacken-docs
     additional_dependencies: [black]
     exclude: README.md
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
 - repo: https://github.com/pycqa/flake8
   rev: 6.0.0
   hooks:
@@ -49,7 +46,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.991
+  rev: v1.1.1
   hooks:
   - id: mypy
     files: ^src/
@@ -58,13 +55,9 @@ repos:
     - types-pkg_resources==0.1.2
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
+  rev: v2.2.4
   hooks:
   - id: codespell
     stages: [commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te']
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
-  hooks:
-    - id: pyupgrade
-      args: [--py38-plus]
+    types_or: [python, rst, markdown]

README.md

@@ -1,10 +1,11 @@
-# atomate2-addon-template
+# atomate2-turbomole
 
-This is an example add-on package for [atomate2](https://github.com/materialsproject/atomate2).
+Atomate2-turbomole is an add-on package for [atomate2](https://github.com/materialsproject/atomate2).
 
-It is heavily based on
-the equivalent [add-on template for pymatgen](https://github.com/materialsproject/pymatgen-addon-template).
+Atomate2-turbomole is built to work with Turbomole, and is built on top of open source
+libraries such as [pymatgen], [custodian], [jobflow] and [Turbomoleio]
 
 ## License
 
-This add-on is released under the same license as atomate2, modified BSD, the full text of which can be found in this repository.
+This add-on is released under the same license as atomate2, modified BSD, the full text of which can
+be found in this repository.

pyproject.toml

@@ -2,24 +2,20 @@
 requires = ["setuptools >= 42", "versioningit ~= 1.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
-[tools.setuptools]
-packages = ["atomate2.myaddon"]
-[tools.setuptools.find]
-where = ["src"]
-
 [project]
-name = "atomate2-myaddon"
-description = "atomate2-myaddon is an example of a minimal atomate2 namespace add-on."
+name = "atomate2-turbomole"
+description = "The atomate2-turbomole package is a workflow package for Turbomole"
 readme = "README.md"
+keywords = ["high-throughput", "automated", "workflow", "dft", "ab initio", "turbomole"]
 license = { text = "modified BSD" }
-authors = [{ name = "Matthew Evans", email = "matthew.evans@matgenix.com" }]
+authors = [{ name = "David Waroquiers", email = "david.waroquiers@matgenix.com" }]
 dynamic = ["version"]
 classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
-    "Development Status :: 2 - Pre-Alpha",
+    "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
     "Intended Audience :: System Administrators",
     "Intended Audience :: Information Technology",
@@ -28,27 +24,22 @@ classifiers = [
     "Topic :: Scientific/Engineering",
 ]
 requires-python = ">=3.8"
-dependencies =[
-    "atomate2",
-    "pymatgen"
+dependencies = [
+    "pymatgen>=2022.2.10",
+    "custodian>=2024.3.12",
+    "jobflow>=0.1.11",
+    "emmet-core>=0.80.0",
+    "turbomoleio==1.4.0"
 ]
 
 [project.optional-dependencies]
-dev = ["atomate2[dev]"]
-docs = ["atomate2[docs]"]
-tests = ["atomate2[tests]"]
-strict = ["atomate2[strict]"]
-
-[project.urls]
-repository = "https://github.com/matgenix/atomate2-addon-template"
+dev = ["pre-commit>=2.12.1"]
+tests = ["pytest==7.2.2", "pytest-cov==4.0.0", "pytest-mock==3.6.1", "mongomock==4.1.2"]
 
 [tool.versioningit.vcs]
 method = "git"
 default-tag = "0.0.1"
 
-[tool.isort]
-profile = "black"
-
 [tool.flake8]
 max-line-length = 88
 max-doc-length = 88
@@ -62,6 +53,10 @@ rst-roles = "class, func, ref, obj"
 ignore_missing_imports = true
 no_strict_optional = true
 
+[tool.pytest.ini_options]
+addopts = "--strict-markers --cov=atomate2.turbomole --cov-config=pyproject.toml --cov-report=html --cov-report=term"
+filterwarnings = []
+
 [tool.coverage.run]
 include = ["src/*"]
 parallel = true
@@ -77,11 +72,101 @@ exclude_lines = [
     '^\s*assert False(,|$)',
     'if typing.TYPE_CHECKING:',
     '^\s*@overload( |$)',
+    'pragma: no cover',
+    'NotImplementedError',
+]
+partial_branches = [
+    'pragma: no branch',
 ]
+fail_under = 100
+
+[tool.ruff]
+target-version = "py38"
+select = [
+    "B",   # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "D",   # pydocstyle
+    "E",   # pycodestyle
+    "F",   # pyflakes
+    "I",   # isort
+    "PLE", # pylint error
+    "PLW", # pylint warning
+    "Q",   # flake8-quotes
+    "RUF", # Ruff-specific rules
+    "SIM", # flake8-simplify
+    "TID", # tidy imports
+    "UP",  # pyupgrade
+    "W",   # pycodestyle
+    "YTT", # flake8-2020
+]
+pydocstyle.convention = "numpy"
+isort.known-first-party = ["atomate2.turbomole"]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["F401"]
+"**/tests/*" = ["D"]
+
+[tool.setuptools.package-data]
+"atomate2.turbomole.schemas.calc_types" = ["*.yaml"]
 
-[tool.autoflake]
-in-place = true
-remove-all-unused-imports = true
-remove-unused-variables = true
-ignore-init-module-imports = true
-expand-star-imports = true
+#
+#
+#
+#
+#[tool.poetry]
+#name = "turbomole"
+#version = "0.3.1"
+#description = "The turbomole package is a workflow package for Toyota Motor Europe"
+#authors = ["davidwaroquiers <david.waroquiers@matgenix.com>"]
+#packages = [
+#  { include = "turbomole", from = "src" }
+#]
+#
+#[tool.poetry.dependencies]
+#python = "^3.8"
+#custodian = "^2021.2.8"
+#jobflow = "^0.1.2"
+#fireworks = "^2.0.3"
+#
+#[tool.poetry.dev-dependencies]
+#pytest = "^5.2"
+#pytest-cov = "^2.10.1"
+#coverage = {version = "^5.3", extras = ["toml"]}
+#pytest-mock = "^3.3.1"
+#pre-commit = "^2.9.3"
+#isort = "^5.6.4"
+#black = "^20.8b1"
+#flake8 = "^3.8.4"
+#pylint = "^2.6.0"
+#pydocstyle = "^6.1.1"
+#mypy = "^0.790"
+#
+#[build-system]
+#requires = ["poetry-core>=1.0.0"]
+#build-backend = "poetry.core.masonry.api"
+#
+#[tool.isort]
+#profile = "black"
+#
+#[tool.pydocstyle]
+#inherit = false
+#
+#[tool.pytest.ini_options]
+#minversion = "6.1.2"
+#testpaths = "tests"
+##addopts = "--strict-markers --cov=src/turbomole -cov-config=pyproject.toml --cov-report html --cov-report term"
+#
+## Coverage options
+#[tool.coverage.run]
+#source = ["turbomole"]
+#branch = true
+#
+#[tool.coverage.report]
+#exclude_lines = [
+#    "pragma: no cover",
+#    "raise NotImplementedError",
+#]
+#fail_under = 100
+#
+#[tool.coverage.html]
+#directory = "htmlcov"

src/atomate2/turbomole/__init__.py

@@ -0,0 +1,5 @@
+# Part of atomate2-turbomole package.
+
+"""Main module of the atomate2-turbomole package."""
+
+from atomate2.turbomole._version import __version__

src/atomate2/turbomole/_version.py

@@ -0,0 +1,11 @@
+# Part of atomate2-turbomole package.
+
+# Automatically get the version of the package
+# For python versions < 3.8, importlib.metadata module did not exist,
+# had to use importlib_metadata instead.
+try:  # pragma: no cover
+    from importlib.metadata import version
+except ModuleNotFoundError:  # pragma: no cover
+    from importlib_metadata import version  # type: ignore
+
+__version__ = version("atomate2-turbomole")

src/atomate2/turbomole/custodian/__init__.py

@@ -0,0 +1 @@
+"""Custodian jobs in atomate2-turbomole."""