Merge pull request #14 from avrabyt/dev0.0.5.2

Dev0.0.5.2

.gitignore

@@ -1,9 +1,131 @@
-# production
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-dist
-# misc
+# C extensions
+*.so
 .DS_Store
-
+# Distribution / packaging
 *.egg-info
 __pycache__
-build/*
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/

README.md

@@ -39,7 +39,7 @@ Try the app, for different examples.
 ``` python
 import streamlit as st
 import glob
-from st_speckmol import spec_plot
+from st_speckmol import speck_plot
 
 # Example files path
 ex_files = glob.glob("examples/*.xyz")
@@ -48,7 +48,7 @@ with st.sidebar:
     f = open(example_xyz,"r")
     example_xyz = f.read()
 
-res = spec_plot(example_xyz)
+res = speck_plot(example_xyz)
 
 ```
 
@@ -69,7 +69,7 @@ res = spec_plot(example_xyz)
 
 ## Related library - [Stmol](https://github.com/napoles-uach/stmol) 
 
-During the development of the related and popular library [Stmol](https://github.com/napoles-uach/stmol), we introduced `speck_plot()` function for easy usage of both libraries simultaneously. However, the entire StSpeckmol has not yet been merged and extra(read new) functions such as `add_spec_param` is only available with this library.
+During the development of the related and popular library [Stmol](https://github.com/napoles-uach/stmol), we introduced `speck_plot()` function for easy usage of both libraries simultaneously. However, the entire StSpeckmol has not yet been merged and extra(read new) functions such as `add_speck_param` is only available with this library.
 
 ```python
 # Installation of Stmol

app.py

@@ -10,8 +10,8 @@
 st.sidebar.header(":sparkles: Install")
 st.sidebar.code('''pip install st-speckmol''')
 st.sidebar.subheader(':rocket: Usage')
-st.sidebar.code('from st_speckmol import spec_plot')
-st.sidebar.markdown(":heavy_check_mark: Quick Note: The module is **'spec_plot'** not ~~spec**k**_plot~~")
+st.sidebar.code('from st_speckmol import speck_plot')
+st.sidebar.markdown(":heavy_check_mark: Quick Note: The function `spec_plot` will be deprecated in furture release. Instead use `speck_plot`")
 
 st.sidebar.markdown(''' 
 ---------

pages/Example-1-Basic.py

@@ -1,6 +1,6 @@
 import streamlit as st
 import glob
-from st_speckmol import spec_plot
+from st_speckmol import speck_plot
 
 st.markdown('''# st-speckmol :package:
 _A Streamlit **Component** for creating Speck molecular structures within Streamlit Web app._
@@ -14,13 +14,13 @@
     example_xyz = f.read()
     st.sidebar.info(example_xyz.splitlines()[1])
 
-res = spec_plot(example_xyz)
+res = speck_plot(example_xyz)
 with st.sidebar.expander('Code', expanded=False):
     st.code(
         '''
         import streamlit as st
 import glob
-from st_speckmol import spec_plot
+from st_speckmol import speck_plot
 
 # Example files path
 ex_files = glob.glob("xyz_mol_examples/*.xyz")
@@ -30,6 +30,6 @@
     example_xyz = f.read()
     st.sidebar.info(example_xyz.splitlines()[1])
 
-res = spec_plot(example_xyz)
+res = speck_plot(example_xyz)
         '''
     )

pages/Example-2-Parameters-Usage.py

@@ -1,6 +1,6 @@
 import streamlit as st
 import glob
-from st_speckmol import spec_plot
+from st_speckmol import speck_plot
 
 st.markdown('''# st-speckmol :package:
 _A Streamlit **Component** for creating Speck molecular structures within Streamlit Web app._
@@ -26,14 +26,14 @@
                 'bonds': bond ,'bondShade' : bondShade,
                 'brightness': brightness, 'relativeAtomScale':relativeAtomScale,
                 }
-res = spec_plot(example_xyz,_PARAMETERS = _PARAMETERS,wbox_height="500px",wbox_width="500px")
+res = speck_plot(example_xyz,_PARAMETERS = _PARAMETERS,wbox_height="500px",wbox_width="500px")
 
 with st.expander('Code',expanded=False):
     st.code(
         '''
         import streamlit as st
     import glob
-    from st_speckmol import spec_plot
+    from st_speckmol import speck_plot
 
     # Example files path
     ex_files = glob.glob("xyz_mol_examples/*.xyz")
@@ -55,6 +55,6 @@
                     'bonds': bond ,'atomShade' : atomShade,
                     'brightness': brightness, 'relativeAtomScale':relativeAtomScale,
                     }
-    res = spec_plot(example_xyz,_PARAMETERS = _PARAMETERS,wbox_height="500px",wbox_width="500px")
+    res = speck_plot(example_xyz,_PARAMETERS = _PARAMETERS,wbox_height="500px",wbox_width="500px")
         '''
     )

pages/Example-3-Playground.py

@@ -1,5 +1,5 @@
 import streamlit as st
-from st_speckmol import spec_plot
+from st_speckmol import speck_plot
 
 st.markdown('''# st-speckmol :package:
 _A Streamlit **Component** for creating Speck molecular structures within Streamlit Web app._
@@ -18,7 +18,7 @@
                 value = example_xyz, height  = 200)
 
 st.code(_xyz.splitlines()[1])
-res = spec_plot(_xyz)
+res = speck_plot(_xyz)
 
 with st.sidebar.expander("Notes:",expanded=True):
 

setup.py

@@ -3,16 +3,17 @@
 # read the contents of your README file
 with open("README.md", "r", encoding='utf8') as fh:
     long_description = fh.read()
-
+exec(open('st_speckmol/version.py').read())
 setuptools.setup(
     name="st_speckmol",
-    version="0.0.5.1",
+    version=__version__,
     author="Avratanu Biswas",
     author_email="[email protected]",
     description="Streamlit component for for Speck molecule visualization.",
     long_description=long_description,
     long_description_content_type='text/markdown',
     url="https://github.com/avrabyt/Specklit",
+    # url = "https://github.com/avrabyt/st-speckmol/tree/dev0.0.5.2",
     packages=setuptools.find_packages(),
     include_package_data=True,
     classifiers=[],