Merge branch 'dev' into 'main'

Dev

See merge request iek-3/shared-code/ethos_penalps!28

.vscode/extensions.json

@@ -0,0 +1,10 @@
+{
+    "recommendations": [
+        "ms-python.flake8",
+        "ms-python.black-formatter",
+        "ms-python.isort",
+        "njpwerner.autodocstring",
+        "ms-python.pylint",
+        "ms-python.mypy-type-checker"
+    ]
+}

.vscode/settings.json

@@ -3,15 +3,32 @@
         "editor.defaultFormatter": "ms-python.black-formatter"
     },
     "cSpell.words": [
+        "autoapi",
+        "autodoc",
+        "autosummary",
+        "bibtex",
         "figwidth",
+        "Ginter",
         "jsonpickle",
+        "Korzeniowska",
+        "maxdepth",
         "penalps",
-        "pydantic"
+        "pydantic",
+        "targetname",
+        "timedelta"
     ],
     "python.testing.pytestArgs": [
         "."
     ],
     "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
     "python.testing.pytestPath": "C:\\Users\\Julian\\mambaforge",
+    "pylint.args": [
+        "--disable=W0611, W0719, C0114, C0115, W0105, C0116, C0123,C0301",
+        "--max-line-length=120"
+    ],
+    "flake8.args": [
+        "--max-line-length=120    ",
+        "--ignore=F401, W503,E501"
+    ],
 }

README.md

@@ -18,8 +18,8 @@ objects. After the material flow simulation is completed, a set of production or
 ![Main Component Overview](paper/main_component_overview.png)
 *Depiction of the main components and workflow of ETHOS.PeNALPS*
 
-A further description of the model definition can be found [here](ethos_penalps_articles/model_description.md). 
-Also two examples for a [toffee production process](examples/toffee_example.md) and a [b-pillar production process](examples/b_pillar_example.md) are available.
+A further description of the model definition can be found [here]([ethos_penalps_articles/model_description.md](https://ethospenalps.readthedocs.io/en/latest/ethos_penalps_articles/model_description.html)). 
+Also two examples for a [toffee production process](https://ethospenalps.readthedocs.io/en/latest/examples/toffee_example.html) and a [b-pillar production process](https://ethospenalps.readthedocs.io/en/latest/examples/b_pillar_example.html) are available.
 
 
 # Installation

documentation/_config.yml

@@ -1,7 +1,7 @@
 # Book settings
 # Learn more at https://jupyterbook.org/customize/config.html
 
-title: ETHOS.PeNALPS 
+title: ETHOS.PeNALPS
 author: Julian Belina
 logo: ./visualizations/logos/fzj_logo.svg
 
@@ -19,12 +19,11 @@ latex:
 # bibtex_bibfiles:
 #   - references.bib
 
-
 # Information about where the book exists on the web
 repository:
-  url: https://github.com/FZJ-IEK3-VSA/ETHOS_PeNALPS  # Online location of your book
-  path_to_book: documentation  # Optional path to your book, relative to the repository root
-  branch: main  # Which branch of the repository should be used when creating links (optional)
+  url: https://github.com/FZJ-IEK3-VSA/ETHOS_PeNALPS # Online location of your book
+  path_to_book: documentation # Optional path to your book, relative to the repository root
+  branch: main # Which branch of the repository should be used when creating links (optional)
 
 # Add GitHub buttons to your book
 # See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
@@ -39,22 +38,18 @@ sphinx:
     - sphinx.ext.autosummary
     - sphinx.ext.inheritance_diagram
 
-
-
   config:
-    autoapi_dirs : ['../src/ethos_penalps']
+    autoapi_dirs: ["../src/ethos_penalps"]
     autoapi_add_toctree_entry: false
-    autoapi_file_patterns : ['*.py']
+    autoapi_file_patterns: ["*.py"]
     autosummary_generate: false
     autoapi_keep_files: true
     autoapi_generate_api_docs: true
     suppress_warnings: ["etoc.toctree"]
-
-    # exclude_patterns : ['_build', '_templates','ethos_elpsi_articles','autoapi','visualizations','knowledge_articles','documentation']
 
-  autoapi_options: 
+    # exclude_patterns : ['_build', '_templates','autoapi','visualizations','knowledge_articles','documentation']
+
+  autoapi_options:
     show-module-summary: true
 bibtex_bibfiles:
   - references.bib
-
-

documentation/_toc.yml

@@ -4,31 +4,31 @@
 format: jb-book
 root: contents
 
-
-options:  # The options key will be applied to all chapters, but not sub-sections
+options: # The options key will be applied to all chapters, but not sub-sections
   numbered: True
-
-
 
 parts:
-- caption: Basic Articles
-  maxdepth: 3
-  chapters:
-    - file: ethos_penalps_articles/simulation_workflow.md
-    - file: ethos_penalps_articles/model_description.md
-    - file: ethos_penalps_articles/bibliography.md
-- caption: API 
-  chapters:
-  - file: autoapi/ethos_penalps/index.rst
-- caption: Examples
-  chapters:
-  - file: examples/b_pillar_example.md
-  - file: examples/toffee_example.md
-
-
-
-
-
-
-
-
+  - caption: Tutorial
+    maxdepth: 3
+    chapters:
+      - file: ethos_penalps_tutorial/overview.md
+      - file: ethos_penalps_tutorial/single_cooker_process_chain.md
+      - file: ethos_penalps_tutorial/add_more_states.md
+      - file: ethos_penalps_tutorial/add_more_chains.md
+      - file: ethos_penalps_tutorial/connect_two_process_steps_exclusively.md
+      - file: ethos_penalps_tutorial/connect_three_or_more_process_steps.md
+  - caption: Basic Articles
+    maxdepth: 3
+    chapters:
+      - file: ethos_penalps_articles/simulation_workflow.md
+      - file: ethos_penalps_articles/model_description.md
+  - caption: API
+    chapters:
+      - file: autoapi/ethos_penalps/index.rst
+  - caption: Examples
+    chapters:
+      - file: examples/b_pillar_example.md
+      - file: examples/toffee_example.md
+  - caption: Bibliography
+    chapters:
+      - file: ethos_penalps_articles/bibliography.md