Merge pull request #11 from OceanParcels/fixes_evs

Updates to repository

.flake8

@@ -0,0 +1,12 @@
+[flake8]
+ignore =
+    # missing whitespace around arithmetic operator
+    E226,
+    # do not use bare except, specify exception instead
+    E722,
+    # line break before binary operator
+    W503,
+    # line too long (82 > 79 characters)
+    E501,
+    # ‘from module import *’ used; unable to detect undefined names
+    F403,

.gitignore

@@ -5,3 +5,5 @@ PlasticParcels/src/
 **.code-workspace*
 **.DS_store**
 **.pyc**
+**.nc
+**.zarr

paper/paper.md

@@ -23,7 +23,7 @@ link-bibliography: false
 # Summary
 `PlasticParcels` is a python package for simulating the transport and dispersion of plastics in the ocean. The tool is based on `v3.0.2` of the `Parcels` computational Lagrangian ocean analysis framework [@Lange2017,@Delandmeter2019], providing a modular and customizable collection of methods, notebooks, and tutorials for advecting virtual plastic particles with a wide range of physical properties. The tool applies a collection of physical processes to the virtual particles, such as Stokes drift, wind-induced drift, biofouling, and turbulent mixing, via custom particle behaviour programmed in the form of `Kernels`. In addition to the fine-scale physics parameterisations, `PlasticParcels` provides global particle initialisation maps that represent best estimates for plastic pollution emissions along coastlines [@Jambeck2015], from river sources [@Meijer2021], in the open-ocean from fishing-related activities [@Kroodsma2018], as well as a current best estimate of buoyant plastic concentrations globally [@Kaandorp2023]. We envisage PlasticParcels as a tool for easy-to-run plastic dispersal simulations; as well as for rapid prototyping, development, and testing of new fine-scale physics parameterisations.
 
-The current version supports nano- and microplastic behaviour, with support for macroplastics planned in the near-future. It has been designed for use with the Copernicus Marine Service platform [@CMEMS] **update .bib with full-details**, providing new plastic modelling capabilities as part of the NECCTON project. `PlasticParcels` is easily adapted to run on local machines and high-performance computing (HPC) architecture with various hydrodynamic, biogeochemical, and other model fields as inputs. A future goal is to embed `PlasticParcels` within a cloud platform to allow for even more rapid prototyping, development, and simulations.
+The current version supports nano- and microplastic behaviour, with support for macroplastics planned in the near-future. It has been designed for use with the Copernicus Marine Service platform [@CMEMS] **update .bib with full-details** <mark>EvS: I don't think they use the abbreviation CMEMS anymore</mark>, providing new plastic modelling capabilities as part of the NECCTON project. `PlasticParcels` is easily adapted to run on local machines and high-performance computing (HPC) architecture with various hydrodynamic, biogeochemical, and other model fields as inputs. A future goal is to embed `PlasticParcels` within a cloud platform to allow for even more rapid prototyping, development, and simulations.
 
 
 # Statement of need
@@ -38,7 +38,7 @@ The past decade has seen a growing number of community-developed software packag
 Here, we have developed `PlasticParcels` to unify plastic dispersion modelling into one easy-to-use code. While `PlasticParcels` has been designed for researchers who routinely perform plastic particle dispersion simulations, it is equally useful to novice users who are new to Lagrangian ocean analysis techniques.
 
 # Description of the software
-`PlasticParcels` has been designed as a layer over the `Parcels` Lagrangian framework [@Lange2017,@Delandmeter2019]. The core functionality of `Parcels` are its `FieldSets`, `Kernels` and `ParticleSets`. These objects are designed to be as flexible and customisable as possible so that users can perform Lagrangian simulations of a wide variety of particulates, such as tuna, plastic, plankton, **(etc. etc. + CITATIONS)**. However, due to the flexible nature of the software, there is a steep learning curve for new users, who often find it difficult to setup their simulations in a rapid fashion due to the complexity of modern hydrodynamic model output. We have developed `PlasticParcels` as user-friendly tool specifically designed for easy-to-generate plastic dispersal simulations. While `PlasticParcels` is primarily designed for use in the cloud and in HPC environments (due to the ever increasing size of hydrodynamic datasets generated from ocean general circulation models), it can be easily installed and run on local machines.
+`PlasticParcels` has been designed as a layer over the `Parcels` Lagrangian framework [@Lange2017,@Delandmeter2019]. The core functionality of `Parcels` are its `FieldSets`, `Kernels` and `ParticleSets`. These objects are designed to be as flexible and customisable as possible so that users can perform Lagrangian simulations of a wide variety of particulates, such as tuna, plastic, plankton, icebergs, turtles **(etc. etc. + CITATIONS)**. However, due to the flexible nature of the software, there is a steep learning curve for new users, who often find it difficult to setup their simulations in a rapid fashion due to the complexity of modern hydrodynamic model output. We have developed `PlasticParcels` as user-friendly tool specifically designed for easy-to-generate plastic dispersal simulations. While `PlasticParcels` is primarily designed for use in the cloud and in HPC environments (due to the ever increasing size of hydrodynamic datasets generated from ocean general circulation models), it can be easily installed and run on local machines.
 
 ![`PlasticParcels` schematic.\label{fig:schematic}](schematic.png){width=80%}
 

plasticparcels/__init__.py

@@ -0,0 +1,3 @@
+from plasticparcels.utils import *  # noqa
+from plasticparcels.constructors import *  # noqa
+from plasticparcels.particlefile import *  # noqa