Feature/automatic replace

wellies/__init__.py

@@ -46,6 +46,7 @@ def wrapper(*args, **kwargs):
 from .data import StaticDataStore
 from .deployment import deploy_suite
 from .hosts import EcflowServer
+from .hosts import DeployHost
 from .hosts import get_host
 from .log_archiving import ArchivedRepeatFamily
 from .tasks import EcfResourcesTask

wellies/deployment.py

@@ -215,3 +215,5 @@ def deploy_suite(
             logger.info(f"Definition file: {target_repo}/{name}.def")
     else:
         logger.info("No deploy option activated. Deployment aborted")
+
+    return f"{target_repo}/{name}.def"

wellies/hosts.py

@@ -16,9 +16,17 @@ class EcflowServer:
     hostname: str
     user: str
     deploy_dir: str
+    port: str = "3141"
     group: str = None  # Optional suites group for the ecflow server
 
 
+@dataclass
+class DeployHost:
+    hostname: str
+    user: str
+    port: str = "22"
+
+
 def get_host(
     hostname: str,
     user: str,

wellies/quickstart.py

@@ -23,7 +23,7 @@
     "user": "{USER}",
     "author": pw_user.pw_gecos,
     "output_root": "{HOME}/output",
-    "deploy_root": "{HOME}/pyflow",
+    "deploy_root": "{HOME}/pyflow"
 }
 
 
@@ -102,6 +102,29 @@ def write_file(fpath: str, content: str) -> None:
         path.join(root_path, "profiles.yaml"),
         renderer.render("profiles.yaml_t", options),
     )
+    write_file(
+        path.join(root_path, "pyproject.toml"),
+        renderer.render("pyproject.toml_t", options),
+    )
+    write_file(
+        path.join(root_path, ".gitignore"),
+        renderer.render(".gitignore_t", options),
+    )
+
+    #create launch.json for VSCode
+    vscode_dir = path.join(root_path, ".vscode")
+    os.makedirs(vscode_dir, exist_ok=True)
+    options['lib_dir'] = options.get('lib_dir', f"{out_root.replace('{name}', project).replace('{HOME}', os.environ['HOME']).replace('{PERM}', os.environ['PERM']).replace('{HPCPERM}', os.environ['HPCPERM'])}/local")
+    options['src_dir'] = options.get('src_dir', f"{out_root.replace('{name}', project).replace('{HOME}', '${env:HOME}').replace('{PERM}', '${env:PERM}').replace('{HPCPERM}', '${env:HPCPERM}')}/src")
+    options['suite_env'] = options.get('suite_env', 'suite_env')
+    write_file(
+        path.join(vscode_dir, "launch.json"),
+        renderer.render("launch.json_t", options),
+    )
+    write_file(
+        path.join(vscode_dir, "tasks.json"),
+        renderer.render("tasks.json_t", options),
+    )
 
     # create suite folder containing config.py and nodes.py
     suite_dir = path.join(root_path, project)
@@ -116,6 +139,38 @@ def write_file(fpath: str, content: str) -> None:
     )
     write_file(path.join(suite_dir, "__init__.py"), "")  # empty __init__.py
 
+    # create snippets folder containing ecf stubs
+    snippets_dir = path.join(root_path, "snippets")
+    os.makedirs(snippets_dir, exist_ok=True)
+    write_file(
+        path.join(snippets_dir, "dummy"),
+        renderer.render("dummy_t", options),
+    )
+    write_file(
+        path.join(snippets_dir, "clean_init"),
+        renderer.render("clean_init_t", options),
+    )
+    write_file(
+        path.join(snippets_dir, "self_destruct"),
+        renderer.render("self_destruct_t", options),
+    )
+
+    # create src folder containing source files called in ecf scritps
+    src_dir = path.join(root_path, "src")
+    os.makedirs(src_dir, exist_ok=True)
+    write_file(
+        path.join(src_dir, "dummy.py"),
+        renderer.render("dummy.py_t", options),
+    )
+
+    # create manuals folder containing the suite manual
+    manuals_dir = path.join(root_path, "manuals")
+    os.makedirs(manuals_dir, exist_ok=True)
+    write_file(
+        path.join(manuals_dir, "generic.man_t"),
+        renderer.render("generic.man_t_t", options),
+    )
+
     # create config folder containing yaml files
     config_dir = path.join(root_path, "configs")
     os.makedirs(config_dir, exist_ok=True)
@@ -135,6 +190,10 @@ def write_file(fpath: str, content: str) -> None:
         path.join(config_dir, "data.yaml"),
         renderer.render("data.yaml_t", options),
     )
+    write_file(
+        path.join(config_dir, "src.yaml"),
+        renderer.render("src.yaml_t", options),
+    )
 
     # write test file
     test_dir = path.join(root_path, "tests")
@@ -271,6 +330,7 @@ def main(argv: List[str] = sys.argv[1:]) -> int:
         r"\W", "_", options["project"]
     )  # can't have special characters in python module names
     options["profiles"] = '"profiles.yaml"'  # default profiles file
+
     try:
         if "interactive" in options:
             ask_user(options)

wellies/templates/.gitignore_t

@@ -0,0 +1,210 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# 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
+.envrc
+.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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# generated man pages
+*.man