Merge pull request #9 from darothen/pyrcel_rename

Rename project from "parcel_model" to "pyrcel"

.travis.yml

@@ -48,7 +48,7 @@ before_install:
 
 install:
     - conda env create --file ci/requirements-$CONDA_ENV.yml
-    - source activate parcel_model
+    - source activate pyrcel
     # Build and install assimulo. If Python 3.5, we have to do this by hand
     # else we can rely on the existing conda package
     # - if [[ "$CONDA_ENV" == "py35" ]]; then

README.md

@@ -1,9 +1,9 @@
-Parcel Model
-============
+pyrcel: cloud parcel model
+==========================
 
 ![sample parcel model run](doc/figs/model_example.png)
 
-[![DOI](https://zenodo.org/badge/5050/darothen/parcel_model.svg)](https://zenodo.org/badge/latestdoi/5050/darothen/parcel_model)[![Build Status](https://travis-ci.org/darothen/parcel_model.svg?branch=master)](https://travis-ci.org/darothen/parcel_model)[![Documentation Status](https://readthedocs.org/projects/parcel-model/badge/?version=latest)](http://parcel-model.readthedocs.org/en/latest/?badge=latest)
+[![DOI](https://zenodo.org/badge/12927551.svg)](https://zenodo.org/badge/latestdoi/12927551)[![Build Status](https://travis-ci.org/darothen/pyrcel.svg?branch=master)](https://travis-ci.org/darothen/pyrcel)[![Documentation Status](https://readthedocs.org/projects/pyrcel/badge/?version=stable)](http://pyrcel.readthedocs.org/en/stable/?badge=stable)
 
 
 This is an implementation of a simple, adiabatic cloud parcel model for use in
@@ -24,9 +24,9 @@ to several different stiff integrators:
 
 among other details. It also includes a library of droplet activation routines and scripts/notebooks for evaluating those schemes against equivalent calculations done with the parcel model.
 
-Updated code can be found the project [github repository](https://github.com/darothen/parcel_model). If you'd like to use this code or have any questions about it, please [contact the author][author_email]. In particular, if you use this code for research purposes, be sure to carefully read through the model and ensure that you have tweaked/configured it for your purposes (i.e., modifying the accomodation coefficient); other derived quantities).
+Updated code can be found the project [github repository](https://github.com/darothen/pyrcel). If you'd like to use this code or have any questions about it, please [contact the author][author_email]. In particular, if you use this code for research purposes, be sure to carefully read through the model and ensure that you have tweaked/configured it for your purposes (i.e., modifying the accomodation coefficient); other derived quantities).
 
-[Detailed documentation is available](http://parcel-model.readthedocs.org/en/latest/index.html), including a [scientific description](http://parcel-model.readthedocs.org/en/latest/sci_descr.html), [installation details](http://parcel-model.readthedocs.org/en/latest/install.html), and a [basic example](http://parcel-model.readthedocs.org/en/latest/examples/basic_run.html) which produces a figure like the plot at the top of this page.
+[Detailed documentation is available](http://pyrcel.readthedocs.org/en/latest/index.html), including a [scientific description](http://pyrcel.readthedocs.org/en/latest/sci_descr.html), [installation details](http://pyrcel.readthedocs.org/en/latest/install.html), and a [basic example](http://pyrcel.readthedocs.org/en/latest/examples/basic_run.html) which produces a figure like the plot at the top of this page.
 
 Requirements
 ------------
@@ -63,7 +63,7 @@ the model and package can be used without Assimulo.
 Development
 -----------
 
-[http://github.com/darothen/parcel_model]()
+[http://github.com/darothen/pyrcel]()
 
 Please fork this repository if you intend to develop the model further so that the
 code's provenance can be maintained.

ci/requirements-py27.yml

@@ -1,4 +1,4 @@
-name: parcel_model
+name: pyrcel
 channels:
     - darothen
 dependencies:

ci/requirements-py34.yml

@@ -1,4 +1,4 @@
-name: parcel_model
+name: pyrcel
 channels:
     - darothen
 dependencies:

ci/requirements-py35.yml

@@ -1,4 +1,4 @@
-name: parcel_model
+name: pyrcel
 channels:
     - darothen
 dependencies:

doc/Makefile

@@ -96,17 +96,17 @@ qthelp:
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/parcel_model.qhcp"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pyrcel.qhcp"
 	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/parcel_model.qhc"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyrcel.qhc"
 
 devhelp:
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
 	@echo "Build finished."
 	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/parcel_model"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/parcel_model"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/pyrcel"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyrcel"
 	@echo "# devhelp"
 
 epub:

doc/conf.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# parcel_model documentation build configuration file, created by
+# pyrcel documentation build configuration file, created by
 # sphinx-quickstart on Wed Jul  2 15:49:19 2014.
 #
 # This file is execfile()d with the current directory set to its
@@ -61,15 +61,15 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'parcel_model'
+project = u'pyrcel'
 copyright = u'2016, Daniel Rothenberg'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-from parcel_model import __version__ as version
+from pyrcel import __version__ as version
 # The full version, including alpha/beta/rc tags.
 release = version
 
@@ -208,7 +208,7 @@
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'parcel_modeldoc'
+htmlhelp_basename = 'pyrceldoc'
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -228,7 +228,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'parcel_model.tex', u'parcel\\_model Documentation',
+  ('index', 'pyrcel.tex', u'pyrcel documentation',
    u'Daniel Rothenberg', 'manual'),
 ]
 
@@ -258,7 +258,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'parcel_model', u'parcel_model Documentation',
+    ('index', 'pyrcel', u'pyrcel Documentation',
      [u'Daniel Rothenberg'], 1)
 ]
 
@@ -272,8 +272,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'parcel_model', u'parcel_model Documentation',
-   u'Daniel Rothenberg', 'parcel_model',
+  ('index', 'pyrcel', u'pyrcel Documentation',
+   u'Daniel Rothenberg', 'pyrcel',
    'Adiabatic cloud parcel model for aerosol activation studies',
    'Miscellaneous'),
 ]

doc/environment.yml

@@ -1,4 +1,4 @@
-name: parcel_model
+name: pyrcel
 dependencies:
     - python=2.7
     - cython

doc/examples/README.md

@@ -1,7 +1,7 @@
 Because the Assimulo dependency is difficult to build on third-party content providers (travis, RTD, etc), I've opted to manually control the examples in this directory. Here are the steps to keep the examples up to date:
 
 1. Run each notebook independently, so that the results (figures, etc) it includes are pre-rendered and self-contained
-2. Execute the supplied Makefileto convert ipynb -> rst and generate hte rendered figures
+2. Execute the supplied Makefile to convert ipynb -> rst and generate hte rendered figures
 3. Commit the newly generated *_files/ folders and all new resources
 
 In the future, this can be simplified by packaging the entire parcel model install. However, that will require either (a) re-opening the ability to use third-party ODE solvers from SciPy, or (b) packaging Assimulo and Sundials into conda for easy access on a third-party server.

doc/examples/activate.ipynb

@@ -35,7 +35,7 @@
     "import warnings \n",
     "warnings.simplefilter('ignore')\n",
     "\n",
-    "import parcel_model as pm\n",
+    "import pyrcel as pm\n",
     "import numpy as np\n",
     "\n",
     "%matplotlib inline\n",
@@ -129,7 +129,7 @@
     }
    ],
    "source": [
-    "from parcel_model import binned_activation\n",
+    "from pyrcel import binned_activation\n",
     "\n",
     "Vs = np.logspace(-1, np.log10(10,), 11.)[::-1] # 0.1 - 5.0 m/s\n",
     "accom = 0.1\n",
@@ -181,7 +181,7 @@
     "    smaxes_arg.append(smax_arg)\n",
     "    act_fracs_arg.append(afs_arg[0])\n",
     "    smaxes_mbn.append(smax_mbn)\n",
-    "    act_fracs_mbn.append(afs_mbn[0])    "
+    "    act_fracs_mbn.append(afs_mbn[0])"
    ]
   },
   {
@@ -252,7 +252,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 3.0
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
@@ -264,4 +264,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}

doc/examples/activate.rst

@@ -15,7 +15,7 @@ activation of a lognormal ammonium sulfate accumulation mode aerosol.
     import warnings 
     warnings.simplefilter('ignore')
     
-    import parcel_model as pm
+    import pyrcel as pm
     import numpy as np
     
     %matplotlib inline
@@ -50,7 +50,7 @@ First, the parcel model calculations:
 
 .. code:: python
 
-    from parcel_model import binned_activation
+    from pyrcel import binned_activation
     
     Vs = np.logspace(-1, np.log10(10,), 11.)[::-1] # 0.1 - 5.0 m/s
     accom = 0.1
@@ -117,7 +117,7 @@ Now the activation parameterizations:
         smaxes_arg.append(smax_arg)
         act_fracs_arg.append(afs_arg[0])
         smaxes_mbn.append(smax_mbn)
-        act_fracs_mbn.append(afs_mbn[0])    
+        act_fracs_mbn.append(afs_mbn[0])
 
 Finally, we compile our results into a nice plot for visualization.
 

doc/examples/basic_run.ipynb

@@ -43,7 +43,7 @@
     "import warnings \n",
     "warnings.simplefilter('ignore')\n",
     "\n",
-    "import parcel_model as pm\n",
+    "import pyrcel as pm\n",
     "import numpy as np\n",
     "\n",
     "%matplotlib inline\n",
@@ -290,7 +290,7 @@
     }
    ],
    "source": [
-    "from parcel_model import binned_activation\n",
+    "from pyrcel import binned_activation\n",
     "\n",
     "sulf_trace = aerosol_traces['sulfate']\n",
     "sea_trace = aerosol_traces['sea salt']\n",
@@ -326,7 +326,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 3.0
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
@@ -338,4 +338,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}

doc/examples/basic_run.rst

@@ -17,7 +17,7 @@ aerosol and cloud droplets.
     import warnings 
     warnings.simplefilter('ignore')
     
-    import parcel_model as pm
+    import pyrcel as pm
     import numpy as np
     
     %matplotlib inline
@@ -195,7 +195,7 @@ from the ``activation`` package to perform these calculations for us:
 
 .. code:: python
 
-    from parcel_model import binned_activation
+    from pyrcel import binned_activation
     
     sulf_trace = aerosol_traces['sulfate']
     sea_trace = aerosol_traces['sea salt']

doc/index.rst

@@ -1,6 +1,16 @@
 
-Model/Package Overview
-======================
+pyrcel: cloud parcel model
+==========================
+
+|DOI|\ |Build Status|\ |Documentation Status|
+
+.. |DOI| image:: https://zenodo.org/badge/12927551.svg
+   :target: https://zenodo.org/badge/latestdoi/12927551
+.. |Build Status| image:: https://travis-ci.org/darothen/pyrcel.svg?branch=master
+   :target: https://travis-ci.org/darothen/pyrcel
+.. |Documentation Status| image:: https://readthedocs
+.org/projects/pyrcel/badge/?version=stable
+   :target: http://pyrcel.readthedocs.org/en/stable/?badge=stable
 
 This is an implementation of a simple, 0D adiabatic cloud parcel model tool (following `Nenes et al, 2001`_ and `Pruppacher and Klett, 1997`_). It allows flexible descriptions of an initial aerosol population, and simulates the evolution of a proto-cloud droplet population as the parcel ascends adiabatically at either a constant or time/height-dependent updraft speed. Droplet growth within the parcel is tracked on a Lagrangian grid.
 
@@ -9,7 +19,10 @@ This is an implementation of a simple, 0D adiabatic cloud parcel model tool (fol
 
 .. image:: figs/model_example.png
 
-You are invited to use the model (in accordance with the `licensing <https://raw.githubusercontent.com/darothen/parcel_model/master/LICENSE>`_), but please get in touch with the author via `e-mail <mailto:[email protected]>`_ or on `twitter <https://twitter.com/darothen>`_. Up-to-date versions can be obtained through the model's `github repository <https://github.com/darothen/parcel_model>`_ or directly from the author. If you use the model for research, please cite `this journal article <http://journals.ametsoc.org/doi/abs/10.1175/JAS-D-15-0223.1>`_ which details the original model formulation:
+You are invited to use the model (in accordance with the `licensing <https://raw
+.githubusercontent.com/darothen/pyrcel/master/LICENSE>`_), but please get in touch with
+ the author via `e-mail <mailto:[email protected]>`_ or on `twitter <https://twitter.com/darothen>`_. Up-to-date versions can be obtained through the model's `github repository <https://github.com/darothen/pyrcel>`_ or directly from the
+ author. If you use the model for research, please cite `this journal article <http://journals.ametsoc.org/doi/abs/10.1175/JAS-D-15-0223.1>`_ which details the original model formulation:
 
 
 | Daniel Rothenberg and Chien Wang, 2016: Metamodeling of Droplet Activation for Global Climate Models. *J. Atmos. Sci.*, **73**, 1255–1272. doi: http://dx.doi.org/10.1175/JAS-D-15-0223.1

doc/install.rst

@@ -8,7 +8,7 @@ point it to the source code `repository`_ on github:
 
 .. code-block:: bash
 
-    $ pip install git+git://github.com/darothen/parcel_model.git
+    $ pip install git+git://github.com/darothen/pyrcel.git
 
 This should automatically build the necessary Cython modules and export the
 code package to your normal package installation directory. If you wish to
@@ -29,7 +29,7 @@ points directly to the git-monitored code:
 
 .. code-block:: bash
 
-    $ cd path/to/parcel_model/
+    $ cd path/to/pyrcel/
     $ pip install -e .
 
 
@@ -44,7 +44,7 @@ scientific python distribution, such as
 out-of-the box with almost all dependencies filled (exception being numerical
 solvers) on a recent version (1.2+) of this distribution. To faciliate this,
 `conda <http://conda.pydata.org/docs/>`_ environments for Python versions 2.7
-and 3.4+ are provided in the ``parcel_model/ci`` directory.
+and 3.4+ are provided in the ``pyrcel/ci`` directory.
 
 Necessary dependencies
 ^^^^^^^^^^^^^^^^^^^^^^
@@ -101,19 +101,19 @@ version of the model with the pre-packed simple run case:
 
 .. code-block:: bash
 
-    $ cd path/to/parcel_model/
+    $ cd path/to/pyrcel/
     $ ./run_parcel examples/simple.yml
 
 
 Bugs / Suggestions
 ------------------
 
 The code has an
-`issue tracker on github <https://github.com/darothen/parcel_model/issues>`_
+`issue tracker on github <https://github.com/darothen/pyrcel/issues>`_
 and I strongly encourage you to note any problems with the model there, such
 as typos or weird behavior and results. Furthermore, I'm looking for ways to
 expand and extend the model, so if there is something you might wish to see
 added, please note it there or `send me an e-mail <mailto:[email protected]>`_.
 The code was written in such a way that it should be trivial to add physics in a modular fashion.
 
-.. _repository: http://github.com/darothen/parcel_model
+.. _repository: http://github.com/darothen/pyrcel

doc/parcel.rst

@@ -1,6 +1,6 @@
 .. _parcel:
 
-.. currentmodule:: parcel_model
+.. currentmodule:: pyrcel
 
 Parcel Model Details
 ====================