refactor plugin structure (#69)

* refactored structure * updated toml file and relaunched ruff linting * further lintage activities * fixed ruff formatting and test files * reverted nomad-lab version in toml * added aliases and updated README * extended conductivity-type quantity * added carrier density deviation quantity * harmonized type=float everywhere * remove unused import * filled default values in special Geometry shapes * Bump up nomad-lab to 1.3.4dev * fixed reference to substrate holder * InsertReduction class refinements * fixed InsertReduction reference * refined recipe classes * refined recipe classes * added starting and ending T in annealing step * Update src/nomad_material_processing/solution/__init__.py Co-authored-by: Sarthak Kapoor <[email protected]> * reformatting * check if aliases work * reverted m_def to old paths in test files * reverted solution m_def * reverted nomad_material_processing.vapor_deposition.pvd.general.PhysicalVaporDeposition * added print statement in tests * added print statement in tests * Explicitely load metainfo before tests. (#72) Co-authored-by: Hampus Näsström <[email protected]> * remove unused import * formatting --------- Co-authored-by: Sarthak Kapoor <[email protected]> Co-authored-by: Sarthak Kapoor <[email protected]> Co-authored-by: Markus Scheidgen <[email protected]> Co-authored-by: Hampus Näsström <[email protected]>
FAIRmat-NFDI · Sep 10, 2024 · 48a0f82 · 48a0f82
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diff --git a/README.md b/README.md
@@ -13,6 +13,25 @@ material processing.
 pip install nomad-material-processing
 ```
 
+### Setting up your OASIS
+Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/plugins/plugins.html#add-a-plugin-to-your-nomad) for all details on how to deploy the plugin on your NOMAD instance.
+
+You don't need to modify the ```nomad.yaml``` configuration file of your NOMAD instance, beacuse the package is pip installed and all the available modules (entry points) are loaded.
+To include, instead, only some of the entry points, you need to specify them in the ```include``` section of the ```nomad.yaml```. In the following lines, a list of all the available entry points:
+
+```yaml
+plugins:
+  include:
+    - "nomad_material_processing:schema"
+    - "nomad_material_processing.solution:schema"
+    - "nomad_material_processing.vapor_deposition.cvd:schema"
+    - "nomad_material_processing.vapor_deposition.pvd:schema"
+    - "nomad_material_processing.vapor_deposition.pvd:mbe_schema"
+    - "nomad_material_processing.vapor_deposition.pvd:pld_schema"
+    - "nomad_material_processing.vapor_deposition.pvd:sputtering_schema"
+    - "nomad_material_processing.vapor_deposition.pvd:thermal_schema"
+ ```
+
 ### Development
 This code is currently under development and for installing and contributing you should clone the repository:
 ```sh

diff --git a/nomad.yaml b/nomad.yaml
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,74 +6,101 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [project]
+classifiers = [
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: MIT License",
+]
 name = "nomad-material-processing"
 dynamic = ["version"]
 description = "A plugin for NOMAD containing base sections for material processing."
 readme = "README.md"
 authors = [
+    { name = "Sarthak Kapoor", email = '[email protected]' },
     { name = "Hampus Näsström", email = '[email protected]' },
     { name = "Andrea Albino", email = '[email protected]' },
     { name = "Sebastian Brückner", email = '[email protected]' },
 ]
-requires-python = ">=3.9"
-classifiers = [
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.9",
-    "License :: OSI Approved :: Apache Software License",
-]
+license = { file = "LICENSE" }
 dependencies = [
-    "nomad-lab>=1.3.3.dev86",
-]
-[project.optional-dependencies]
-dev = [
-    "pytest",
-    "ruff",
-    "structlog>=22.3.0",
+    "nomad-lab>=1.3.4dev",
 ]
 
-[project.license]
-file = "LICENSE"
-
 [project.urls]
 "Homepage" = "https://github.com/FAIRmat-NFDI/nomad-material-processing"
 "Bug Tracker" = "https://github.com/FAIRmat-NFDI/nomad-material-processing/issues"
 
 [tool.uv]
 index-url = "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple"
 
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "ruff",
+    "structlog",
+]
+
 [tool.ruff]
 include = ["src/*.py", "tests/*.py"]
-
-exclude = ["dependencies"]
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+]
 
 # Same as Black.
 line-length = 88
 indent-width = 4
 
 [tool.ruff.lint]
 select = [
-    "E", # pycodestyle
-    "W", # pycodestyle
-    "PL", # pylint
+    # pycodestyle
+    "E",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # isort
+    "I",
+    # pylint
+    "PL",
 ]
+
 ignore = [
-    "E501", # Line too long ({width} > {limit} characters)
-    "E701", # Multiple statements on one line (colon)
-    "E731", # Do not assign a lambda expression, use a def
-    "E402",  # Module level import not at top of file
-    "PLR0911", # Too many return statements
-    "PLR0912", # Too many branches
-    "PLR0913", # Too many arguments in function definition
-    "PLR0915", # Too many statements
-    "PLR2004", # Magic value used instead of constant
-    "PLW0603", # Using the global statement
-    "PLW2901", # redefined-loop-name
-    "PLR1714", # consider-using-in
-    "PLR5501", # else-if-used
+    "F403", # 'from module import *' used; unable to detect undefined names
 ]
+
 fixable = ["ALL"]
 
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+# this is entirely optional, you can remove this if you wish to
 [tool.ruff.format]
 # use single quotes for strings.
 quote-style = "single"
@@ -87,9 +114,22 @@ skip-magic-trailing-comma = false
 # Like Black, automatically detect the appropriate line ending.
 line-ending = "auto"
 
+[tool.setuptools]
+package-dir = { "" = "src" }
+
 [tool.setuptools.packages.find]
-where = [
-    "src",
-]
+where = ["src"]
+
+[project.entry-points.'nomad.plugin']
+
+general_schema = "nomad_material_processing:schema"
+solution_schema = "nomad_material_processing.solution:schema"
+vd_schema = "nomad_material_processing.vapor_deposition:schema"
+cvd_schema = "nomad_material_processing.vapor_deposition.cvd:schema"
+pvd_schema = "nomad_material_processing.vapor_deposition.pvd:schema"
+mbe_schema = "nomad_material_processing.vapor_deposition.pvd:mbe_schema"
+pld_schema = "nomad_material_processing.vapor_deposition.pvd:pld_schema"
+sputtering_schema = "nomad_material_processing.vapor_deposition.pvd:sputtering_schema"
+thermal_schema = "nomad_material_processing.vapor_deposition.pvd:thermal_schema"
 
 [tool.setuptools_scm]