Add initial files from init-repo-code

Add files from `examples` directory.

Add previous `example_config.yaml` and modify that it works with new pydantic validation.

Add Python gitignore template from GitHub.

First version to make `to_core_*` methods work

Starting from the pydantic config representations. Ideally, I think one
should rather have `from_config_*` methods in `core.py`, rather than
`to_core_*` methods in `_yaml_data_models.py`, but chose this route as
it's simpler to adapt for now.

Acctually add fixed `example_config.yaml`

clean up

.gitignore

@@ -0,0 +1,163 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+

examples/README.rst

@@ -0,0 +1,12 @@
+Running examples
+================
+
+.. marker-example-text
+
+To run the example you can use the command
+
+.. code-block:: bash
+
+    wcflow files/configs/example_config.yaml
+
+It is important to execute it from the examples folder as the relative paths are hardcoded.

examples/files/configs/example_config.yaml

@@ -0,0 +1,182 @@
+---
+start_date: "2026-01-01T00:00"
+end_date: "2027-01-01T00:00"
+cycles:
+  - init:
+      tasks:
+        - extpar:
+            inputs:
+              - obs_data:
+                  arg_option: "--input"
+            outputs:
+              - extpar_file
+  - icon_bimonthly:
+      period: "P2M"
+      tasks:
+        - preproc:
+            inputs:
+              - grid_file:
+                  arg_option: "-g"
+              - extpar_file:
+                  date: "2026-01-01T00:00"
+                  arg_option: "-p"
+              - ERA5:
+                  arg_option: "-e"
+            outputs:
+              - icon_input
+            depends:
+              - icon:
+                  lag: "-P4M"
+        - icon:
+            inputs:
+              - grid_file:
+                  arg_option: "-g"
+              - icon_input:
+                  arg_option: "--input"
+              #- icon_restart:
+              #    lag: '-P2M'
+            outputs:
+              - stream_1
+              - stream_2
+              #- icon_restart
+        - postproc_1:
+            inputs:
+              - stream_1:
+                  arg_option: "--input"
+            outputs:
+              - postout_1
+        - store_and_clean_1:
+            inputs:
+              - postout_1:
+                  arg_option: "--input"
+              - stream_1:
+                  arg_option: "--stream"
+              - icon_input:
+                  arg_option: "--icon_input"
+            outputs:
+              - stored_data_1
+  - yearly:
+      period: "P1Y"
+      tasks:
+        - postproc_2:
+            inputs:
+              - stream_2:
+                  lag:
+                    - "P0M"
+                  arg_option: "--input"
+            outputs:
+              - postout_2
+        - store_and_clean_2:
+            inputs:
+              - postout_2:
+                  arg_option: "--input"
+              - stream_2:
+                  lag:
+                    - "P0M"
+            outputs:
+              - stored_data_2
+# Each task and piece of data (input and output of tasks) used to
+# define the graph is described in that section
+tasks:
+  - ROOT:
+      # All tasks inherit the root task properties
+      host: santis
+      account: g110
+  - extpar:
+      plugin: extpar
+      command: $PWD/files/scripts/extpar
+      command_option: "--verbose" # todo implement support
+      config: path/to/namelists/dir
+      uenv:
+        squashfs: path/to/squashfs
+        mount_point: runtime/mount/point
+      nodes: 1
+      walltime: "00:02:00"
+  - preproc:
+      plugin: AiiDA Shell
+      command: $PWD/files/scripts/cleanup.sh
+      nodes: 4
+      walltime: "00:02:00"
+      config: path/to/config/dir
+      uenv:
+        squashfs: path/to/squashfs
+        mount_point: runtime/mount/point
+  - icon:
+      plugin: icon
+      command: $PWD/files/scripts/icon
+      nodes: 40
+      walltime: "23:59:59"
+      config: path/to/namelists/dir
+      uenv:
+        squashfs: path/to/squashfs
+        mount_point: runtime/mount/point
+  - postproc_1:
+      plugin: AiiDA Shell
+      command: $PWD/files/scripts/main_script_ocn.sh
+      nodes: 2
+      walltime: "00:05:00"
+      conda_env: path/to/yaml/env/file
+      uenv:
+        squashfs: path/to/squashfs
+        mount_point: runtime/mount/point
+  - postproc_2:
+      plugin: AiiDA Shell
+      command: $PWD/files/scripts/main_script_atm.sh
+      nodes: 2
+      walltime: "00:05:00"
+      src: path/to/src/dir
+      conda_env: path/to/yaml/env/file
+      uenv:
+        squashfs: path/to/squashfs
+        mount_point: runtime/mount/point
+  - store_and_clean_1:
+      plugin: AiiDA Shell
+      command: $PWD/files/scripts/post_clean.sh
+      nodes: 1
+      walltime: "00:01:00"
+  - store_and_clean_2:
+      plugin: AiiDA Shell
+      command: $PWD/files/scripts/post_clean.sh
+      nodes: 1
+      walltime: "00:01:00"
+data:
+  - preproc_output:
+      type: file
+      src: $PWD/files/data/file.ncdf
+  - grid_file:
+      type: file
+      src: $PWD/files/data/grid
+  - obs_data:
+      type: file
+      src: $PWD/files/data/obs_data
+  - ERA5:
+      type: file
+      src: $PWD/files/data/era5
+  - extpar_file:
+      type: file
+      src: output
+  - icon_input:
+      type: file
+      src: output
+  - icon_restart:
+      type: file
+      format: ncdf
+      src: restart
+  - stream_1:
+      type: file
+      src: output_1
+  - stream_2:
+      type: file
+      src: output_2
+  - postout_1:
+      type: file
+      src: postout
+  - postout_2:
+      type: file
+      src: postout
+  - stored_data_1:
+      type: file
+      src: stored_data
+  - stored_data_2:
+      type: file
+      src: stored_data

examples/files/scripts/cleanup.py

@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+
+def main():
+    # Main script execution continues here
+    print("Cleaning")
+
+
+if __name__ == '__main__':
+    main()

examples/files/scripts/cleanup.sh

@@ -0,0 +1 @@
+echo "cleanup" > output

examples/files/scripts/extpar

@@ -0,0 +1 @@
+echo "extpar" > output

examples/files/scripts/icon

@@ -0,0 +1,4 @@
+echo "icon" > restart
+echo "icon" > output
+echo "icon" > output_1
+echo "icon" > output_2