pymt-lab · mcflugen · Jul 20, 2020 · Jul 20, 2020 · Jul 20, 2020 · Jul 20, 2020
diff --git a/.travis.yml b/.travis.yml
@@ -1,25 +1,15 @@
 language: generic
 os:
-- linux
 - osx
+- linux
 env:
   matrix:
-  - CONDA_ENV=3.7
-  - CONDA_ENV=3.6
+  - PYTHON="3.6"
+  - PYTHON="3.7"
+  - PYTHON="3.8"
+  global:
+  - CONDA_PREFIX=$HOME/miniconda
 sudo: false
-jobs:
-  include:
-  - stage: deploy
-    if: tag =~ v.*$
-    script: skip
-    os: linux
-    deploy:
-      on:
-        all_branches: true
-      provider: pypi
-      user: mcflugen
-      password:
-        secure: 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
 before_install:
 - |
   if [[ $TRAVIS_OS_NAME == "osx" ]]; then
@@ -29,21 +19,28 @@ before_install:
   fi
 - |
   if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-    curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > $HOME/miniconda.sh
+    OS="MacOSX-x86_64"
   else
-    curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > $HOME/miniconda.sh
+    OS="Linux-x86_64"
   fi
-- bash $HOME/miniconda.sh -b -p $HOME/anaconda
-- export PATH="$HOME/anaconda/bin:$PATH"
+- |
+  if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+    curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > $HOME/miniconda.sh
+  else
+    curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > $HOME/miniconda.sh
+  fi
+- bash $HOME/miniconda.sh -b -p $(pwd)/anaconda
+- export PATH="$(pwd)/anaconda/bin:$PATH"
 - hash -r
 - conda config --set always_yes yes --set changeps1 no
-- conda create -n test_env python=$CONDA_ENV
-- source activate test_env
+- conda config --add channels conda-forge
+- conda create -n _testing python=$PYTHON
+- source activate _testing
+- conda info -a && conda list
 install:
-- pip install bmi-tester model_metadata standard_names pytest
-- pip install . -r requirements.txt
+- pip install .
+- conda install -q --file=requirements-library.txt
 script:
+- conda install -q --file=requirements-testing.txt
 - python -c 'import pymt_rafem'
-- |
-  config_file=$(mmd-stage pymt_rafem/data/Rafem . > MANIFEST && mmd-query pymt_rafem/data/Rafem --var=run.config_file.path)
-  bmi-test pymt_rafem.bmi:Rafem --config-file=$config_file --manifest=MANIFEST --root-dir=. -v
+- bmi-test pymt_rafem.bmi:Rafem -vvv
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -0,0 +1,19 @@
+Changelog for pymt_rafem
+========================
+
+0.3 (unreleased)
+----------------
+
+- Nothing changed yet.
+
+
+0.2 (2020-07-20)
+----------------
+
+- Added rand_seed to parameters
+
+0.1.0 (2020-07-21)
+------------------
+
+- Initial release
+
diff --git a/CREDITS.rst b/CREDITS.rst
@@ -0,0 +1,4 @@
+Credits
+=======
+
+* csdms <csdms@colorado.edu>
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018, Eric Hutton
+Copyright (c) 2020, csdms
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,5 +1,13 @@
-include versioneer.py
-include _version.py
-include pymt_rafem/_version.py
-recursive-include pymt_rafem/data/ *
+recursive-include pymt_rafem/data *
 include LICENSE
+include requirements.txt
+include *.rst
+include *.txt
+include Makefile
+include babel.toml
+include pymt_rafem/data
+recursive-include docs *.py
+recursive-include docs *.rst
+recursive-include docs Makefile
+recursive-exclude meta *
+recursive-exclude recipe *
diff --git a/Makefile b/Makefile
@@ -58,8 +58,7 @@ pretty:
 	black setup.py pymt_rafem
 
 test: ## run tests quickly with the default Python
-	config_file=$(mmd-stage BmiRiverModule . > MANIFEST && mmd-query BmiRiverModule --var=run.config_file.path)
-	bmi-test pymt_rafem.bmi:BmiRiverModule --infile=$config_file --manifest=MANIFEST -v
+	bmi-test pymt_rafem.bmi:Rafem -vvv
 
 test-all: ## run tests on every Python version with tox
 	tox
@@ -90,4 +89,4 @@ dist: clean ## builds source and wheel package
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages
-	python setup.py develop
+	pip install -e .
diff --git a/README.rst b/README.rst
@@ -4,14 +4,14 @@ pymt_rafem
 
 
 .. image:: https://img.shields.io/badge/CSDMS-Basic%20Model%20Interface-green.svg
-        :target: https://bmi-forum.readthedocs.io/
+        :target: https://bmi.readthedocs.io/
         :alt: Basic Model Interface
 
 .. image:: https://img.shields.io/badge/recipe-pymt_rafem-green.svg
         :target: https://anaconda.org/conda-forge/pymt_rafem
 
-.. image:: https://img.shields.io/travis/mcflugen/pymt_rafem.svg
-        :target: https://travis-ci.org/mcflugen/pymt_rafem
+.. image:: https://img.shields.io/travis/pymt-lab/pymt_rafem.svg
+        :target: https://travis-ci.org/pymt-lab/pymt_rafem
 
 .. image:: https://readthedocs.org/projects/pymt_rafem/badge/?version=latest
         :target: https://pymt_rafem.readthedocs.io/en/latest/?badge=latest
@@ -25,10 +25,18 @@ pymt_rafem
 PyMT plugin for Rafem
 
 
-* Free software: MIT license
+* Free software: MIT License
 * Documentation: https://rafem.readthedocs.io.
 
 
+
+
+========= ===================================
+Component PyMT
+========= ===================================
+Rafem     `from pymt.models import Rafem`
+========= ===================================
+
 ---------------
 Installing pymt
 ---------------
@@ -45,7 +53,7 @@ into which to install it. This can be done with,
 
 .. code::
 
-  conda create -n pymt python=3.6
+  conda create -n pymt python=3
   conda activate pymt
 
 Once the `conda-forge` channel has been enabled, `pymt` can be installed with:

diff --git a/babel.toml b/babel.toml
@@ -0,0 +1,23 @@
+[build]
+define_macros = []
+extra_compile_args = []
+include_dirs = []
+libraries = []
+library_dirs = []
+undef_macros = []
+
+[info]
+github_username = "pymt-lab"
+plugin_author = "csdms"
+plugin_author_email = "csdms@colorado.edu"
+plugin_license = "MIT"
+summary = "PyMT plugin for Rafem"
+
+[library]
+entry_point = ["Rafem=rafem:BmiRiverModule"]
+language = "python"
+
+[plugin]
+name = "rafem"
+requirements = ["rafem"]
+
diff --git a/docs/conf.py b/docs/conf.py
@@ -48,8 +48,8 @@
 
 # General information about the project.
 project = u'pymt_rafem'
-copyright = u"2018, Eric Hutton"
-author = u"Eric Hutton"
+copyright = u"2020, csdms"
+author = u"csdms"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -130,7 +130,7 @@
 latex_documents = [
     (master_doc, 'pymt_rafem.tex',
      u'pymt_rafem Documentation',
-     u'Eric Hutton', 'manual'),
+     u'csdms', 'manual'),
 ]
 
 

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -39,13 +39,13 @@ You can either clone the public repository:
 
 .. code-block:: console
 
-    $ git clone git://github.com/mcflugen/pymt_rafem
+    $ git clone git://github.com/pymt-lab/pymt_rafem
 
 Or download the `tarball`_:
 
 .. code-block:: console
 
-    $ curl  -OL https://github.com/mcflugen/pymt_rafem/tarball/master
+    $ curl  -OL https://github.com/pymt-lab/pymt_rafem/tarball/master
 
 Once you have a copy of the source, you can install it with:
 
@@ -55,5 +55,5 @@ Once you have a copy of the source, you can install it with:
     $ python setup.py install
 
 
-.. _Github repo: https://github.com/mcflugen/pymt_rafem
-.. _tarball: https://github.com/mcflugen/pymt_rafem/tarball/master
+.. _Github repo: https://github.com/pymt-lab/pymt_rafem
+.. _tarball: https://github.com/pymt-lab/pymt_rafem/tarball/master
diff --git a/pymt_rafem/data/Rafem/api.yaml → meta/Rafem/api.yaml b/pymt_rafem/data/Rafem/api.yaml → meta/Rafem/api.yaml
diff --git a/pymt_rafem/data/Rafem/info.yaml → meta/Rafem/info.yaml b/pymt_rafem/data/Rafem/info.yaml → meta/Rafem/info.yaml
diff --git a/pymt_rafem/data/Rafem/input.yaml → meta/Rafem/input.yaml b/pymt_rafem/data/Rafem/input.yaml → meta/Rafem/input.yaml
@@ -13,7 +13,7 @@ max_rand: 0.1  # multiply by slope for max height of a random perturbation
 dt_day: {{ time_step }}  # timestep (days)
 
 # Random seed
-rand_seed: 1988  # seed for random number generator
+rand_seed: {{ rand_seed }}  # seed for random number generator
 
 # Sea level and subsidence parameters
 Initial_SL: {{ sea_level_initial }}  # initial sea level

diff --git a/pymt_rafem/data/Rafem/parameters.yaml → meta/Rafem/parameters.yaml b/pymt_rafem/data/Rafem/parameters.yaml → meta/Rafem/parameters.yaml
@@ -63,6 +63,16 @@ time_step:
       max: 1.0
     units: day
 
+rand_seed:
+  description: Seed for random number generator
+  value:
+    type: int
+    default: 1988
+    range:
+      min: 1
+      max: 65536
+    units: '-'
+
 sea_level_initial:
   description: Initial sea level
   value:

diff --git a/pymt_rafem/data/Rafem/run.yaml → meta/Rafem/run.yaml b/pymt_rafem/data/Rafem/run.yaml → meta/Rafem/run.yaml
diff --git a/plugin.yaml b/plugin.yaml
diff --git a/pymt_rafem/__init__.py b/pymt_rafem/__init__.py
@@ -1,11 +1,11 @@
 #! /usr/bin/env python
+import pkg_resources
 
-from .bmi import (Rafem,
-)
+__version__ = pkg_resources.get_distribution("pymt_rafem").version
 
-__all__ = ["Rafem",
-]
 
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+from .bmi import Rafem
+
+__all__ = [
+    "Rafem",
+]
diff --git a/pymt_rafem/bmi.py b/pymt_rafem/bmi.py
@@ -1,11 +1,11 @@
 from __future__ import absolute_import
 
-import os
-
 import pkg_resources
 from rafem import BmiRiverModule as Rafem
 
 Rafem.__name__ = "Rafem"
-Rafem.METADATA = os.path.abspath(
-    pkg_resources.resource_filename("pymt_rafem", "data/Rafem")
-)
+Rafem.METADATA = pkg_resources.resource_filename(__name__, "data/Rafem")
+
+__all__ = [
+    "Rafem",
+]
diff --git a/pymt_rafem/data b/pymt_rafem/data
@@ -0,0 +1 @@
+../meta
diff --git a/pymt_rafem/rafem.py b/pymt_rafem/rafem.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,33 @@
+[build-system]
+requires = ["cython", "numpy", "setuptools", "wheel"]
+
+[tool.pytest.ini_options]
+minversion = "5.0"
+testpaths = ["pymt_rafem", "tests"]
+norecursedirs = [".*", "*.egg*", "build", "dist"]
+addopts = """
+    --ignore setup.py
+    --tb native
+    --strict
+    --durations 16
+    --doctest-modules
+    -vvv
+"""
+doctest_optionflags = [
+    "NORMALIZE_WHITESPACE",
+    "IGNORE_EXCEPTION_DETAIL",
+    "ALLOW_UNICODE"
+]
+
+[tool.isort]
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+combine_as_imports = true
+line_length = 88
+
+[tool.check-manifest]
+ignore = [
+  "pymt_rafem/data",
+  "pymt_rafem/data/**/*",
+]