Merge pull request #3 from kevinshen56714/kshen-v1.0.0

Add args for `setup` and bump to v1.0.0

README.md

@@ -1,23 +1,18 @@
 # Enhanced Monte Carlo (EMC) Python Interface
+
 [![PyPI version shields.io](https://img.shields.io/pypi/v/emc-pypi.svg?style=for-the-badge&logo=PyPI&logoColor=blue)](https://pypi.python.org/pypi/emc-pypi/)
 [![PyPI download month](https://img.shields.io/pypi/dm/emc-pypi.svg?style=for-the-badge&logo=PyPI)](https://pypi.python.org/pypi/emc-pypi/)
 [![PyPI download day](https://img.shields.io/pypi/dd/emc-pypi.svg?style=for-the-badge&logo=PyPI)](https://pypi.python.org/pypi/emc-pypi/)
 
-This module is a thin Python wrapper library of the [EMC](http://montecarlo.sourceforge.net/emc/Welcome.html) package that allows you to use all EMC functionalities with Python interface. 
+This module is a thin Python wrapper library of the [EMC](http://montecarlo.sourceforge.net/emc/Welcome.html) package that allows you to use all EMC functionalities with Python interface.
+
+EMC creates input structures from SMILES strings and LAMMPS input files for particle simulations with atomistic force fields - Born, COMPASS, PCFF, CHARMM, OPLS, TraPPE or coarse-grained force fields - DPD, Martini, SDK.
 
 - See the [example input files](https://github.com/kevinshen56714/emc-pypi/tree/main/pyemc/emc/examples/setup) on how to prepare EMC input (.esh) files.
 - See the [docs](https://github.com/kevinshen56714/emc-pypi/blob/main/pyemc/emc/docs/emc.pdf) to understand more about EMC.
 
 The package works out of the box without pre-installation of EMC or any configuration. Please open an issue if you find something missing or not working as expected.
 
-## About EMC
-EMC creates input structures from SMILES strings and LAMMPS input files for particle simulations. Supported force fields are
-- Atomistic: Born, COMPASS, PCFF, CHARMM, OPLS, TraPPE
-- Coarse-grained: DPD, Martini, SDK
-
-In any publication of scientific results based in part or completely on the use of EMC, please cite the original paper: 
-P.J. in 't Veld and G.C. Rutledge, Macromolecules 2003, 36, 7358 [[link](https://pubs.acs.org/doi/full/10.1021/ma0346658)] [[pdf](https://pubs.acs.org/doi/pdf/10.1021/ma0346658)]
-
 ## Installation
 
 ```bash
@@ -29,10 +24,15 @@ pip install emc-pypi
 ```python
 import pyemc
 
-# Run the emc_setup.pl and prepare the build.emc file for the following build command
+# Run the emc_setup.pl and generate the build.emc file for the build command
 pyemc.setup('your-setup-file.esh')
 
-# Run the emc executable
+# Or you can pass in arguments like this
+pyemc.setup('your-setup-file.esh', '-ntotal=1000', '-field=opls-aa')
+
+# Finally, run the emc executable to create simulation input files
 pyemc.build('build.emc')
 ```
 
+In any publication of scientific results based in part or completely on the use of EMC, please cite the original paper:
+P.J. in 't Veld and G.C. Rutledge, Macromolecules 2003, 36, 7358 [[link](https://pubs.acs.org/doi/full/10.1021/ma0346658)] [[pdf](https://pubs.acs.org/doi/pdf/10.1021/ma0346658)]

pyemc/runner.py

@@ -38,7 +38,7 @@ def _get_path() -> str:
     return os.path.dirname(__file__)
 
 
-def setup(esh_file: str):
+def setup(esh_file: str, *args):
     '''Method to run emc_setup.pl of EMC
 
     Attributes:
@@ -50,7 +50,10 @@ def setup(esh_file: str):
     emc_setup_file = os.path.join(_get_path(), 'emc', 'scripts',
                                   'emc_setup.pl')
 
-    subprocess.run(['perl', str(emc_setup_file), esh_file])
+    command = ['perl', str(emc_setup_file), esh_file]
+    for arg in args:
+        command.append(arg)
+    subprocess.run(command)
 
 
 def build(build_file: str):
@@ -62,7 +65,6 @@ def build(build_file: str):
     Returns:
         None
     '''
-    emc_exec = _get_exec()
-    emc_bin_file = os.path.join(_get_path(), 'emc', 'bin', emc_exec)
+    emc_bin_file = os.path.join(_get_path(), 'emc', 'bin', _get_exec())
 
     subprocess.run([str(emc_bin_file), build_file])

setup.py

@@ -20,7 +20,7 @@ def package_files(directory):
 
 setup(
     name='emc-pypi',
-    version='0.1.2',
+    version='1.0.0',
     long_description=LONG_DESCRIPTION,
     long_description_content_type='text/markdown',
     description='Python interface for the Enhanced Monte Carlo (EMC) package',