Merge pull request #19 from ericbarefoot/separate_bmi

Separate BMI wrapper from core model
DeltaRCM · Apr 23, 2020 · 8117c2d · 8117c2d
2 parents 4088c68 + 9a328b6
commit 8117c2d
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Showing 34 changed files with 1,197 additions and 811 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,36 @@
+deltaRCM_Output/
+
+### a standard OSX .gitignore ###
+
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+#################
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

diff --git a/.travis.yml b/.travis.yml
@@ -5,9 +5,11 @@ python:
 # command to install dependencies
 install:
   - pip install pytest
+  - pip install -r requirements.txt
 # command to run tests
 script:
   - python setup.py install
+  # - pip install -e .
   - pytest
 
 jobs:
@@ -16,14 +18,16 @@ jobs:
       python: "3.8"
       install: 
         - pip install -r requirements.txt 
+        - pip install -e .
         - pip install pytest pytest-cov coveralls
       script: pytest --cov=pyDeltaRCM/
       after_success: 
         - coveralls
     - stage: docs
       python: "3.8"
       install: 
-        - pip install -r requirements.txt 
+        - pip install -r requirements.txt
+        - pip install -e .
         - pip install sphinx sphinx-automodapi
         - sudo apt update -y && sudo apt install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended dvipng
       script: (cd docs && make html)

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,2 @@
+recursive-include pyDeltaRCM *.yml
+exclude *.yml
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # pyDeltaRCM_WMT
 
-[![Build Status](https://travis-ci.com/DeltaRCM/pyDeltaRCM_WMT.svg?branch=develop)](https://travis-ci.org/DeltaRCM/pyDeltaRCM_WMT)
+[![Build Status](https://travis-ci.com/DeltaRCM/pyDeltaRCM_WMT.svg?branch=develop)](https://travis-ci.com/DeltaRCM/pyDeltaRCM_WMT)
 
 [![Coverage Status](https://coveralls.io/repos/github/DeltaRCM/pyDeltaRCM_WMT/badge.svg?branch=develop)](https://coveralls.io/github/DeltaRCM/pyDeltaRCM_WMT?branch=develop)
 

diff --git a/deltaRCM.yaml b/deltaRCM.yaml
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -35,7 +35,6 @@
 # ones.
 extensions = ['sphinx.ext.autodoc', 
               'sphinx.ext.autosummary',
-              'sphinx_automodapi.automodapi',
               'sphinx.ext.napoleon',
               'sphinx.ext.graphviz',
               'sphinx.ext.imgmath',

diff --git a/docs/source/reference/10min.rst → docs/source/guides/10min.rst b/docs/source/reference/10min.rst → docs/source/guides/10min.rst
diff --git a/docs/source/reference/devguide.rst → docs/source/guides/devguide.rst b/docs/source/reference/devguide.rst → docs/source/guides/devguide.rst
diff --git a/docs/source/reference/getting_started.rst → docs/source/guides/getting_started.rst b/docs/source/reference/getting_started.rst → docs/source/guides/getting_started.rst
diff --git a/docs/source/guides/userguide.rst b/docs/source/guides/userguide.rst
@@ -0,0 +1,27 @@
+**********
+User Guide
+**********
+
+Guide to users!
+
+
+Configuring the input yaml file
+===============================
+
+The configuration for a pyDeltaRCM run is set up by a parameter set, described in the ``yaml`` markup format.
+To configure a run, you should create a file called, for example, ``run_parameters.yml``. 
+Inside this file you can specify parameters for your run, with each parameter on a new line. For example, if ``run_parameters.yml`` contained the line: 
+
+.. code-block:: yaml
+
+    S0: 0.005
+
+then a :obj:`~pyDeltaRCM.deltaRCM_driver.pyDeltaRCM` model instance initialized with this file specified as ``input_file`` will have a slope of 0.005.
+Multiple parameters can be specified line by line.
+
+Default values are substituted for any parameter not explicitly given in the ``input_file`` ``.yaml`` file.
+Default values are defined as:
+
+.. literalinclude:: ../../../pyDeltaRCM/default.yml
+   :language: yaml
+   :linenos: 
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -18,8 +18,8 @@ User documentation
 .. toctree::
    :maxdepth: 2
 
-   reference/getting_started
-   reference/userguide
+   guides/getting_started
+   guides/userguide
 
 
 Developer documentation
@@ -28,5 +28,5 @@ Developer documentation
 .. toctree::
    :maxdepth: 2
 
-   reference/devguide
+   guides/devguide
    reference/index
diff --git a/docs/source/meta/conduct.rst b/docs/source/meta/conduct.rst
@@ -1,2 +1,6 @@
+***************
+Code of Conduct
+***************
+
 
 .. include:: ../../../CODE_OF_CONDUCT.rst
diff --git a/docs/source/reference/userguide.rst b/docs/source/reference/userguide.rst
diff --git a/ez_setup.py b/ez_setup.py
@@ -232,7 +232,8 @@ def download_file_powershell(url, target):
     ps_cmd = (
         "[System.Net.WebRequest]::DefaultWebProxy.Credentials = "
         "[System.Net.CredentialCache]::DefaultCredentials; "
-        '(new-object System.Net.WebClient).DownloadFile("%(url)s", "%(target)s")'
+        '(new-object System.Net.WebClient).DownloadFile("%(url)s", \
+        "%(target)s")'
         % locals()
     )
     cmd = [
@@ -254,6 +255,8 @@ def has_powershell():
         except Exception:
             return False
     return True
+
+
 download_file_powershell.viable = has_powershell
 
 
@@ -270,6 +273,8 @@ def has_curl():
         except Exception:
             return False
     return True
+
+
 download_file_curl.viable = has_curl
 
 
@@ -286,6 +291,8 @@ def has_wget():
         except Exception:
             return False
     return True
+
+
 download_file_wget.viable = has_wget
 
 
@@ -301,6 +308,8 @@ def download_file_insecure(url, target):
     # Write all the data in one block to avoid creating a partial file.
     with open(target, "wb") as dst:
         dst.write(data)
+
+
 download_file_insecure.viable = lambda: True