refactor the repo and add a CLI

Author: gilrrei

.gitignore

@@ -0,0 +1,160 @@
+# 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/#use-with-ide
+.pdm.toml
+
+# 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/

README.md

@@ -13,23 +13,27 @@ This is already rather nice because we only have acceptable dependencies, i.e. o
 ```
 conda create --name <name-of-environment> python=3.10
 conda activate <name-of-environment>
+```
 
-pip install lnmmeshio
-
-pip install trame
-pip install trame-vuetify trame-vtk
-pip install trame-components
-pip install --upgrade trame-plotly
+## How to install the 4C-webviewer
 
-pip install plotly
-pip install pandas
-pip install vtk
+Go to the source directory and in the activated environment run
+```
+pip install -e .
 ```
 
 ## How to run the 4C-Webviewer
 
-Change to the directory of the repo. Activate the created conda environment and run
+To start the webviewer, in the conda environment run:
+```
+fourc_webviewer
+```
+To directly open a dat file use
+```
+fourc_webviewer --dat_file <path-to-file>
+```
 
+Alternatively change to the directory of the repo. Activate the created conda environment and run
 ```
 python main.py
 ```

fourc_webviewer/__init__.py

@@ -0,0 +1,18 @@
+import argparse
+
+import fourc_webviewer.run_webserver as webserver
+
+
+def main():
+    arguments = get_arguments()
+    webserver.run_webviewer(**arguments)
+
+
+def get_arguments():
+    parser = argparse.ArgumentParser(description="4C Webviewer")
+    parser.add_argument("--dat_file", type=str, help="input file path to visualize")
+
+    args = parser.parse_args()
+
+    # return arguments as dict
+    return vars(args)

fourc_webviewer/cli_utils.py

@@ -1,4 +1,4 @@
-from input_file_utils.dat_file_visualization import function_plot_figure
+from fourc_webviewer.input_file_utils.dat_file_visualization import function_plot_figure
 
 import plotly
 

gui_utils.py fourc_webviewer/gui_utils.pygui_utils.py renamed to fourc_webviewer/gui_utils.py

@@ -4,7 +4,7 @@
 import plotly.express as px
 import re
 
-from input_file_utils.read_dat_file import (
+from fourc_webviewer.input_file_utils.read_dat_file import (
     add_dat_file_data_to_dis,
     validate_dat_file_path,
 )

fourc_webviewer/input_file_utils/__init__.py

@@ -4,7 +4,7 @@
 import os
 import re
 
-from python_utils import list_is_iterable
+from fourc_webviewer.python_utils import list_is_iterable
 
 
 def add_dat_file_data_to_dis(dis):