Merge pull request #1 from yossibokorbleile/devel

Update: GUI framework is now Streamlit

.gitignore

@@ -6,3 +6,7 @@ docs
 *.out
 APF*/
 PD*/
+.python-version
+pyproject.toml
+*.lock
+

examples/settings_examples.ini

@@ -26,17 +26,10 @@ IMAGE = FALSE
 COKERNEL = FALSE
 SAVE_PLOTS = TRUE
 
-<<<<<<< HEAD
 [BACTH]
 MODE = BACTH
 STRUCTURE_FILE = examples/
 STRUCTURE_NAME = ZIF
-=======
-[BATCH]
-MODE = BATCH
-PARENT_DIR = /home/ubuntu/structures/TopologicalMaterialAnalysis/examples
-FILE_EXT= xyz
->>>>>>> refs/remotes/origin/main
 SAMPLE_START = 0
 SAMPLE_END = 2
 SAMPLE_STEP = 1

examples/structure-types.ini

@@ -11,5 +11,12 @@ RADII = 0.389, 0.718, 0.635, 1.491
 REPEAT_X = 1
 REPEAT_Y = 1
 REPEAT_Z = 1
+SAMPLE_INDEX = 0
+KERNEL = TRUE
+IMAGE = TRUE
+COKERNEL = TRUE
+SAVE_PLOTS = TRUE
+THICKNESS = 0.1
+N_THREADS = 16
 
 

requirements-dev.lock

@@ -0,0 +1,312 @@
+# generated by rye
+# use `rye lock` or `rye sync` to update this lockfile
+#
+# last locked with the following flags:
+#   pre: false
+#   features: []
+#   all-features: false
+#   with-sources: false
+#   generate-hashes: false
+
+-e file:.
+addict==2.4.0
+    # via justpy
+aiofiles==24.1.0
+    # via justpy
+    # via nicegui
+aiohttp==3.9.5
+    # via nicegui
+    # via python-socketio
+    # via wslink
+aiosignal==1.3.1
+    # via aiohttp
+altair==5.3.0
+    # via streamlit
+annotated-types==0.7.0
+    # via pydantic
+anyio==4.4.0
+    # via httpx
+    # via starlette
+    # via watchfiles
+ase==3.23.0
+    # via toma
+attrs==23.2.0
+    # via aiohttp
+    # via jsonschema
+    # via referencing
+bidict==0.23.1
+    # via python-socketio
+blinker==1.8.2
+    # via streamlit
+cachetools==5.3.3
+    # via streamlit
+certifi==2024.7.4
+    # via httpcore
+    # via httpx
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via streamlit
+    # via uvicorn
+colour==0.1.5
+    # via toma
+configparser==7.0.0
+    # via toma
+contourpy==1.2.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+docutils==0.19
+    # via nicegui
+    # via readme-renderer
+eagerpy==0.30.0
+    # via toma
+fastapi==0.109.2
+    # via justpy
+    # via nicegui
+fonttools==4.53.1
+    # via matplotlib
+frozenlist==1.4.1
+    # via aiohttp
+    # via aiosignal
+gitdb==4.0.11
+    # via gitpython
+gitpython==3.1.43
+    # via streamlit
+h11==0.14.0
+    # via httpcore
+    # via uvicorn
+    # via wsproto
+hjson==3.1.0
+    # via justpy
+httpcore==1.0.5
+    # via httpx
+httptools==0.6.1
+    # via uvicorn
+httpx==0.27.0
+    # via justpy
+    # via nicegui
+idna==3.7
+    # via anyio
+    # via httpx
+    # via requests
+    # via yarl
+ifaddr==0.2.0
+    # via nicegui
+importlib-metadata==8.0.0
+    # via twine
+itsdangerous==2.2.0
+    # via justpy
+    # via nicegui
+jaraco-classes==3.4.0
+    # via keyring
+jaraco-context==5.3.0
+    # via keyring
+jaraco-functools==4.0.1
+    # via keyring
+jinja2==3.1.4
+    # via altair
+    # via justpy
+    # via nicegui
+    # via pydeck
+jsonschema==4.22.0
+    # via altair
+jsonschema-specifications==2023.12.1
+    # via jsonschema
+justpy==0.14.0
+    # via toma
+keyring==25.2.1
+    # via twine
+kiwisolver==1.4.5
+    # via matplotlib
+markdown-it-py==3.0.0
+    # via rich
+markdown2==2.4.13
+    # via nicegui
+markupsafe==2.1.5
+    # via jinja2
+matplotlib==3.9.1
+    # via ase
+    # via toma
+    # via vtk
+mdurl==0.1.2
+    # via markdown-it-py
+more-itertools==10.3.0
+    # via jaraco-classes
+    # via jaraco-functools
+    # via trame-server
+msgpack==1.0.8
+    # via wslink
+multidict==6.0.5
+    # via aiohttp
+    # via yarl
+nh3==0.2.18
+    # via readme-renderer
+nicegui==1.4.28
+    # via toma
+numpy==2.0.0
+    # via altair
+    # via ase
+    # via contourpy
+    # via eagerpy
+    # via matplotlib
+    # via pandas
+    # via pyarrow
+    # via pydeck
+    # via scipy
+    # via streamlit
+    # via toma
+orjson==3.10.6
+    # via nicegui
+packaging==24.1
+    # via altair
+    # via matplotlib
+    # via plotly
+    # via streamlit
+pandas==2.2.2
+    # via altair
+    # via streamlit
+    # via toma
+pillow==10.4.0
+    # via matplotlib
+    # via streamlit
+pip==24.1.1
+    # via toma
+pkginfo==1.10.0
+    # via twine
+plotly==5.22.0
+    # via toma
+protobuf==5.27.2
+    # via streamlit
+pscript==0.7.7
+    # via vbuild
+psutil==6.0.0
+    # via justpy
+pyarrow==16.1.0
+    # via streamlit
+pydantic==2.8.2
+    # via fastapi
+pydantic-core==2.20.1
+    # via pydantic
+pydeck==0.9.1
+    # via streamlit
+pygments==2.18.0
+    # via nicegui
+    # via readme-renderer
+    # via rich
+pyparsing==3.1.2
+    # via matplotlib
+python-dateutil==2.9.0.post0
+    # via matplotlib
+    # via pandas
+python-dotenv==1.0.1
+    # via uvicorn
+python-engineio==4.9.1
+    # via python-socketio
+python-multipart==0.0.9
+    # via nicegui
+python-socketio==5.11.3
+    # via nicegui
+pytz==2024.1
+    # via pandas
+pyyaml==6.0.1
+    # via uvicorn
+readme-renderer==43.0
+    # via twine
+referencing==0.35.1
+    # via jsonschema
+    # via jsonschema-specifications
+requests==2.32.3
+    # via nicegui
+    # via requests-toolbelt
+    # via streamlit
+    # via twine
+requests-toolbelt==1.0.0
+    # via twine
+rfc3986==2.0.0
+    # via twine
+rich==13.7.1
+    # via streamlit
+    # via twine
+rpds-py==0.18.1
+    # via jsonschema
+    # via referencing
+scipy==1.14.0
+    # via ase
+simple-websocket==1.0.0
+    # via python-engineio
+six==1.16.0
+    # via python-dateutil
+smmap==5.0.1
+    # via gitdb
+sniffio==1.3.1
+    # via anyio
+    # via httpx
+starlette==0.36.3
+    # via fastapi
+    # via justpy
+streamlit==1.36.0
+    # via toma
+tenacity==8.5.0
+    # via plotly
+    # via streamlit
+toml==0.10.2
+    # via streamlit
+toolz==0.12.1
+    # via altair
+tornado==6.4.1
+    # via streamlit
+trame==3.6.3
+    # via toma
+trame-client==3.2.1
+    # via trame
+    # via trame-vtk
+    # via trame-vuetify
+trame-server==3.0.3
+    # via trame
+trame-vtk==2.8.9
+    # via toma
+trame-vuetify==2.6.1
+    # via toma
+twine==5.1.1
+    # via justpy
+typing-extensions==4.12.2
+    # via eagerpy
+    # via fastapi
+    # via nicegui
+    # via pydantic
+    # via pydantic-core
+    # via streamlit
+tzdata==2024.1
+    # via pandas
+urllib3==2.2.2
+    # via requests
+    # via twine
+uvicorn==0.30.1
+    # via justpy
+    # via nicegui
+uvloop==0.19.0
+    # via uvicorn
+vbuild==0.8.2
+    # via nicegui
+vtk==9.3.1
+    # via toma
+watchdog==4.0.1
+    # via toma
+watchfiles==0.22.0
+    # via nicegui
+    # via uvicorn
+websockets==12.0
+    # via justpy
+    # via uvicorn
+wheel==0.43.0
+    # via justpy
+wslink==2.1.1
+    # via trame-server
+wsproto==1.2.0
+    # via simple-websocket
+yarl==1.9.4
+    # via aiohttp
+zipp==3.19.2
+    # via importlib-metadata