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Models","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# Pyroms\n\nWelcome to Pyroms!\n\nPyroms is a collection of tools to process input and output files\nfrom the Regional Ocean Modeling System, [ROMS](https://www.myroms.org/). It was originally\nstarted by Rob Hetland as a googlecode project, then he morphed it\ninto octant, also at googlecode. Frederic Castruccio then created a\nfork and renamed it back to pyroms.\n\nPyroms is now hosted on GitHub.com in the [ESMG/pyroms](https://github.com/ESMG/pyroms) repository. This version is on the [python3](https://github.com/ESMG/pyroms/tree/python3) branch. It requires Python 3.4 or later.\n\n## Installation\n\nPyroms is still a bit rough around the edges, particularly with regard to installation. Recent development has been done in Python environments managed by [Conda](https://docs.conda.io/en/latest/). However Pyroms itself cannot yet be installed with Conda.\n\nIf you are starting from scratch, we recommend that you install\n[Anaconda](https://www.anaconda.com/) or\n[Miniconda](https://docs.conda.io/en/latest/miniconda.html) and create a Python 3 environment (as of December 2020, version 3.8 is your best bet) for Pyroms and your other scientific software. You should also consider making conda-forge your default channel. See the [conda-forge tips and tricks page](https://conda-forge.org/docs/user/tipsandtricks.html).\n\nIf you don't want to use Conda, that's fine, but you will have to do more of the work yourself.\n\n## Prerequisites\n\nThe following are required and are all available from [Conda-Forge](https://conda-forge.org/).\n\n   * Python \u003e= 3.4 (Python 3.8 currently recommended for new environments)\n   * [numpy](https://numpy.org/)\n   * [scipy](https://www.scipy.org/)\n   * [matplotlib](https://matplotlib.org/)\n   * [basemap](https://matplotlib.org/basemap/)\n   * [netcdf4](https://unidata.github.io/netcdf4-python/netCDF4/index.html)\n   * [cftime](https://unidata.github.io/cftime/)\n   * [lpsolve55](https://github.com/chandu-atina/lp_solve_python_3x)\n   * [pip](https://pypi.org/project/pip/)\n\nThe following is optional: Pyroms can be built and run without it but some of the functionality will be missing.\n\n   * scrip, a Python implementation of [SCRIP](https://github.com/SCRIP-Project/SCRIP),\n     the Spherical Coordinate Remapping and Interpolation Package. This is used by the pyroms\n     module. The Python scrip code (a rather old version) is\n     [bundled in pyroms](https://github.com/ESMG/pyroms/tree/python3/pyroms/external/scrip)\n     and can be built and installed separately as described below. In future we plan to\n     move from the bundled scrip code to a stand-alone package like\n     [ESMF/ESMPy](https://www.earthsystemcog.org/projects/esmpy/) or\n     [PySCRIP](https://github.com/dchandan/PySCRIP).\n\nThe following is optional and provides high-resolution coastlines for basemap:\n\n   * [basemap-data-hires](https://anaconda.org/conda-forge/basemap-data-hires/)\n\n## Install from source\n\nTo clone a copy of the source and install the pyroms packages, you can use the following commands\n```\n# Cd to a convenient directory\n$ git clone https://github.com/ESMG/pyroms.git\n$ pip install -e pyroms/pyroms\n$ pip install -e pyroms/pyroms_toolbox\n$ pip install -e pyroms/bathy_smoother\n```\n\nThis installs three PIP packages with the names pyroms, pyroms\\_toolbox and bathy\\_smoother,\neach with an [eponymous](https://en.wiktionary.org/wiki/eponymous) module.\n\nAn [editable-mode](https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs) installation is recommended becauses it means changes you make to your copy of the source code will take effect when you import the modules. If you don't want this you can omit the \"-e\" option\n\nThe \"pip install\" command runs \"python setup.py install\" (or \"python setup.py develop\" with the \"-e\" switch) in each of the subdirectories listed. The \"pip install\" form is recommended because it allow easy removal (see below)\n\nThe above should work on most Linuces and on OSX with the system gcc and gfortran compilers.\nThey have also been verified to work in a Conda environment on Windows,\nprovided you install the\n[m2w64-gcc](https://anaconda.org/msys2/m2w64-gcc) and [m2w64-gfortran](https://anaconda.org/msys2/m2w64-gcc-fortran) compilers.\n\n## Install scrip\n\nIf you install as above and try to import the three Pyroms modules without having installed\nscrip you will get a warning like this:\n\n```\n$ python\nPython 3.8.5 | packaged by conda-forge | (default, Aug 29 2020, 01:22:49)\n[GCC 7.5.0] on linux\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\n\u003e\u003e\u003e import pyroms\nWARNING:root: scrip could not be imported. Remapping functions will not be available\n\u003e\u003e\u003e import pyroms_toolbox\n\u003e\u003e\u003e import bathy_smoother\n```\n\nThe scrip module is not available via Conda or any other package repository and we are looking at alternatives. In the meantime, scrip can be built and installed from source as follows\n\n```\n# Start in the directory into which you cloned pyroms and cd to the SCRIP\n# source directory\n$ cd pyroms/pyroms/external/scrip/source/\n\n# Print the location of the active Conda environment (which is called \"python38\"\n# in this case). The active environment location is used to find the netCDF and\n# other libraries.\n$ conda info | grep \"active env location\"\n    active env location : /home/hadfield/miniconda3/envs/python38\n\n# Run make to build the scrip Python extension and install it into the Conda\n# environment. The makefile calculates a variable called SCRIP_EXT_DIR, into\n# which it installs the scrip Python extension. If pyroms has been installed\n# in editable (development) mode, set the DEVELOP variable to a non-empty value.\n$ export PREFIX=/home/hadfield/miniconda3/envs/python38\n$ make DEVELOP=1 PREFIX=$PREFIX install\n$ mv -vf scrip*.so ../../../pyroms\n‘scrip.cpython-38-x86_64-linux-gnu.so’ -\u003e ‘../../../pyroms/scrip.cpython-38-x86_64-linux-gnu.so’\n```\n\n## Removal\n\nTo remove the three Pyroms packages you can use the \"pip uninstall\" command, referring to the packages by their package names\n\n```\n# Run from any directory in the same environment as you installed\n# and use the package name\n$ pip uninstall pyroms\n$ pip uninstall pyroms_toolbox\n$ pip uninstall bathy_smoother\n```\n\nIf you have built and installed the scrip extension from the makefile as above, you can also uninstall it with the makefile. The PREFIX does not need to be set in this case.\n\n```\n# Start in the directory into which you cloned pyroms and cd to the SCRIP\n# source directory\n$ cd pyroms/pyroms/external/scrip/source/\n\n# Remove with make.\n$ make DEVELOP=1 uninstall\n```\n\n## Running Pyroms\n\nWe have a gridid.txt file that's pointed to by the PYROMS\\_GRIDID\\_FILE\nenvironment variable. If you are operating on files containing\nsufficient grid information already, you won't need to use this.\nAn example is provided in the examples directory.\n\n\n## Doxygen\n\nRunning \"doxygen .doxygen\" in any of pyroms, pyroms\\_toolbox or\nbathy\\_smoother will generate doxygen files. Edit the .doxygen files to\nspecify html vs. some other output format.\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["numerical-modeling","ocean-circulation-models","climate-modeling","ocean-modelling","oceanography"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/712","html_url":"https://ost.ecosyste.ms/projects/712"}