Merge branch 'main' into joss

.github/workflows/pytest.yml

@@ -5,13 +5,13 @@ on:
     # Action will run when any changes to these paths are pushed or pr'ed to master
     branches: [ main ]
     paths:
-      - jankflow/**
+      - flowermd/**
       - environment-cpu.yml
       - .github/workflows/pytest.yml
   pull_request:
     branches: [ main ]
     paths:
-      - jankflow/**
+      - flowermd/**
       - environment-cpu.yml
       - .github/workflows/pytest.yml
   # Allows workflow to be manually triggered

.pre-commit-config.yaml

@@ -11,12 +11,12 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-        exclude: 'jankflow/tests/assets/.* | jankflow/assets/.*'
+        exclude: 'flowermd/tests/assets/.* | flowermd/assets/.*'
   - repo: https://github.com/psf/black
     rev: 23.9.1
     hooks:
@@ -29,7 +29,7 @@ repos:
         name: isort (python)
         args:
           [ --profile=black, --line-length=80 ]
-        exclude: 'cmeuitls/tests/assets/.* '
+        exclude: 'flowermd/tests/assets/.* '
 
   - repo: https://github.com/pycqa/flake8
     rev: 6.1.0
@@ -43,5 +43,5 @@ repos:
     rev: '6.3.0'
     hooks:
       - id: pydocstyle
-        exclude: ^(jankflow/tests/|jankflow/utils/|setup.py|jankflow/__version__.py|docs/)
+        exclude: ^(flowermd/tests/|flowermd/utils/|setup.py|flowermd/__version__.py|docs/)
         args: [ --convention=numpy ]

README.md

@@ -1,16 +1,16 @@
-[![pytest](https://github.com/cmelab/JankFlow/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/JankFlow/actions/workflows/pytest.yml)
-[![codecov](https://codecov.io/gh/cmelab/JankFlow/branch/main/graph/badge.svg?token=86LY9WHSH6)](https://codecov.io/gh/cmelab/JankFlow)
-## JankFlow: Flexible Library of Organic Workflows
-JankFlow is a modular “wrapper” package for molecular dynamics (MD)
+[![pytest](https://github.com/cmelab/flowerMD/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/flowerMD/actions/workflows/pytest.yml)
+[![codecov](https://codecov.io/gh/cmelab/flowerMD/branch/main/graph/badge.svg?token=86LY9WHSH6)](https://codecov.io/gh/cmelab/flowerMD)
+## flowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics
+flowerMD is a modular “wrapper” package for molecular dynamics (MD)
 simulation pipeline development, designed to enable fast, reproducible,
 end-to- end simulation workflows with minimal user effort. This package is a
 wrapper for [MoSDeF](https://github.com/mosdef-hub) packages and
 [Hoomd-Blue](https://github.com/glotzerlab/hoomd-blue) with a focus on
 simulating soft matter systems.
 
-An object-oriented design makes JankFlow extensible and highly flexible.
+An object-oriented design makes flowerMD extensible and highly flexible.
 This is bolstered by a library-based approach to system initialization, making
-JankFlow agnostic to system identity, forcefield, and thermodynamic
+flowerMD agnostic to system identity, forcefield, and thermodynamic
 ensemble, and allowing for growth on an as-needed basis.
 
 
@@ -20,24 +20,24 @@ ensemble, and allowing for growth on an as-needed basis.
 ### 1. Clone this repository: ###
 
 ```
-git clone [email protected]:cmelab/JankFlow.git
-cd JankFlow
+git clone [email protected]:cmelab/flowerMD.git
+cd flowerMD
 ```
 
 ### 2. Set up and activate environment: ###
 #### a. Using HOOMD-blue from conda:
 ```
 conda env create -f environment-cpu.yml
-conda activate jankflow
+conda activate flowermd
 python -m pip install .
 ```
 
 ## Basic Usage
 Please check out the [tutorials](tutorials) for a detailed description of
-how to use JankFlow and what functionalities it provides.
+how to use flowerMD and what functionalities it provides.
 
 ## Documentation
-Documentation is available at [https://jankflow.readthedocs.io](https://jankflow.readthedocs.io)
+Documentation is available at [https://flowermd.readthedocs.io](https://flowermd.readthedocs.io)
 
 [//]: # (#### Using the built in molecules, systems and forcefields:)
 

codecov.yml

@@ -7,8 +7,8 @@ comment:
     branches:               # branch names that can post comment
         - "main"
 ignore:
-    - "jankflow/tests"
-    - "jankflow/assets"
-    - "jankflow/__version__.py"
+    - "flowermd/tests"
+    - "flowermd/assets"
+    - "flowermd/__version__.py"
     - "tutorials"
     - "setup.py"

containers/dockerfile

@@ -7,11 +7,11 @@ RUN conda activate base
 WORKDIR /opt && chmod u+rwx .
 
 # install in base conda env
-RUN git clone https://github.com/cmelab/JankFlow && \
-    cd JankFlow && \
+RUN git clone https://github.com/cmelab/flowerMD && \
+    cd flowerMD && \
     conda env update -n base -f environment-gpu.yml && \
     conda clean --all --yes -f
 
-WORKDIR JankFlow
+WORKDIR flowerMD
 
 RUN python -m pip install --user -e .

docs/source/base.rst

@@ -3,11 +3,11 @@ Base
 
 .. rubric:: Overview
 
-.. py:currentmodule:: jankflow.base
+.. py:currentmodule:: flowermd.base
 
 .. rubric:: Details
 
-.. automodule:: jankflow.base
+.. automodule:: flowermd.base
 
 .. rubric:: Modules
 

docs/source/conf.py

@@ -9,7 +9,7 @@
 import os
 import sys
 
-project = "JankFlow"
+project = "flowerMD"
 copyright = (
     "2023, Chris Jones, Marjan Albooyeh, Rainier Barrett, Eric Jankowski"
 )

docs/source/forcefields.rst

@@ -1,9 +1,9 @@
 forcefields
 -----------
 
-.. py:currentmodule:jankflow.library
+.. py:currentmodule:flowermd.library
 
 .. rubric:: Details
 
-.. automodule:: jankflow.library.forcefields
+.. automodule:: flowermd.library.forcefields
     :members:

docs/source/index.rst

@@ -1,12 +1,12 @@
-JankFlow: Flexible Library of Organic Workflows
-===============================================
+flowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics
+=============================================================================================
 
 
-JankFlow is a modular “wrapper” package for molecular dynamics (MD)
+flowerMD is a modular “wrapper” package for molecular dynamics (MD)
 simulation pipeline development, designed to enable fast, reproducible, end-to-
 end simulation workflows with minimal user effort. An object-oriented design
-makes JankFlow extensible and highly flexible. This is bolstered by a
-library-based approach to system initialization, making JankFlow agnostic
+makes flowerMD extensible and highly flexible. This is bolstered by a
+library-based approach to system initialization, making flowerMD agnostic
 to system identity, forcefield, and thermodynamic ensemble, and allowing
 for growth on an as-needed basis.
 
@@ -19,9 +19,9 @@ Quick start
 Resources
 =========
 
-`GitHub Repository <https://github.com/cmelab/JankFlow>`_: Source code and issue tracker.
+`GitHub Repository <https://github.com/cmelab/flowerMD>`_: Source code and issue tracker.
 
-`Tutorials <https://github.com/cmelab/JankFlow/tree/main/tutorials>`_: Examples of how to use JankFlow.
+`Tutorials <https://github.com/cmelab/flowerMD/tree/main/tutorials>`_: Examples of how to use flowerMD.
 
 
 .. toctree::

docs/source/installation.rst

@@ -8,12 +8,12 @@ Install from source
 1. Clone this repository:
 ::
 
-    $ git clone [email protected]:cmelab/JankFlow.git
-    $ cd JankFlow
+    $ git clone [email protected]:cmelab/flowerMD.git
+    $ cd flowerMD
 
 2. Set up and activate environment:
 ::
 
     $ conda env create -f environment-cpu.yml
-    $ conda activate jankflow
+    $ conda activate flowermd
     $ python -m pip install .

docs/source/library.rst

@@ -3,11 +3,11 @@ Library
 
 .. rubric:: Overview
 
-.. py:currentmodule:: jankflow.library
+.. py:currentmodule:: flowermd.library
 
 .. rubric:: Details
 
-.. automodule:: jankflow.library
+.. automodule:: flowermd.library
 
 .. rubric:: Library
 

docs/source/modules.rst

@@ -3,11 +3,11 @@ Modules
 
 .. rubric:: Overview
 
-.. py:currentmodule:: jankflow.modules
+.. py:currentmodule:: flowermd.modules
 
 .. rubric:: Details
 
-.. automodule:: jankflow.modules
+.. automodule:: flowermd.modules
 
 .. rubric:: Modules
 

docs/source/molecule.rst

@@ -1,10 +1,10 @@
 Molecule
 -----------
 
-.. py:currentmodule:jankflow.base.molecule
+.. py:currentmodule:flowermd.base.molecule
 
 .. rubric:: Details
-.. automodule:: jankflow.base.molecule
+.. automodule:: flowermd.base.molecule
     :no-members:
     :show-inheritance:
 

docs/source/polymers.rst

@@ -1,10 +1,10 @@
 Polymers
 -----------
 
-.. py:currentmodule:jankflow.library
+.. py:currentmodule:flowermd.library
 
 .. rubric:: Details
 
-.. automodule:: jankflow.library.polymers
+.. automodule:: flowermd.library.polymers
     :members:
     :show-inheritance:

docs/source/simulation.rst

@@ -1,10 +1,10 @@
 Simulation
 -----------------
 
-.. py:currentmodule:jankflow.base.simulation
+.. py:currentmodule:flowermd.base.simulation
 
 .. rubric:: Details
 
-.. automodule:: jankflow.base.simulation
+.. automodule:: flowermd.base.simulation
     :members:
     :no-index:

docs/source/simulations.rst

@@ -1,10 +1,10 @@
 Simulations
 -----------
 
-.. py:currentmodule:jankflow.library.simulations
+.. py:currentmodule:flowermd.library.simulations
 
 .. rubric:: Details
 
-.. automodule:: jankflow.library.simulations.tensile
+.. automodule:: flowermd.library.simulations.tensile
     :members:
     :show-inheritance:

docs/source/system.rst

@@ -1,11 +1,11 @@
 System
 --------------
 
-.. py:currentmodule:jankflow.base.system
+.. py:currentmodule:flowermd.base.system
 
 .. rubric:: Details
 
-.. automodule:: jankflow.base.system
+.. automodule:: flowermd.base.system
     :no-members:
 
     .. autoclass:: System()

docs/source/welding.rst

@@ -1,11 +1,11 @@
 Welding
 -------
 
-.. py:currentmodule:jankflow.modules
+.. py:currentmodule:flowermd.modules
 
 .. rubric:: Details
 
-.. automodule:: jankflow.modules.welding
+.. automodule:: flowermd.modules.welding
     :no-members:
 
     .. autoclass:: Interface()

environment-cpu.yml

@@ -1,4 +1,4 @@
-name: jankflow
+name: flowermd
 channels:
   - conda-forge
 dependencies:

environment-gpu.yml

@@ -1,4 +1,4 @@
-name: jankflow
+name: flowermd
 channels:
   - conda-forge
 dependencies:

environment-readthedocs.yml

@@ -1,4 +1,4 @@
-name: jankflow-readthedocs
+name: flowermd-readthedocs
 channels:
   - conda-forge
 dependencies:

jankflow/__init__.py → flowermd/__init__.py

@@ -1,4 +1,4 @@
-"""JankFlow package."""
+"""flowerMD package."""
 from .base import (
     CoPolymer,
     Lattice,

jankflow/__version__.py → flowermd/__version__.py

@@ -1,3 +1,3 @@
-VERSION = (0, 0, 1)
+VERSION = (1, 0, 0)
 
 __version__ = ".".join(map(str, VERSION))

jankflow/assets/__init__.py → flowermd/assets/__init__.py

@@ -1,3 +1,3 @@
-"""Paths to the assets used by JankFlow."""
+"""Paths to the assets used by flowerMD."""
 from .forcefields import FF_DIR
 from .molecule_files import MON_DIR

jankflow/assets/forcefields/__init__.py → flowermd/assets/forcefields/__init__.py

@@ -1,4 +1,4 @@
-"""Forcefield files for JankFlow."""
+"""Forcefield files for flowerMD."""
 import os
 
 FF_DIR = os.path.abspath(os.path.dirname(__file__))

jankflow/assets/molecule_files/__init__.py → flowermd/assets/molecule_files/__init__.py

@@ -1,4 +1,4 @@
-"""Molecule files for JankFlow."""
+"""Molecule files for flowerMD."""
 import os
 
 MON_DIR = os.path.abspath(os.path.dirname(__file__))

jankflow/base/__init__.py → flowermd/base/__init__.py

@@ -1,4 +1,4 @@
-"""Base classes for JankFlow."""
+"""Base classes for flowerMD."""
 from .forcefield import BaseHOOMDForcefield, BaseXMLForcefield
 from .molecule import CoPolymer, Molecule, Polymer
 from .simulation import Simulation