rename xrsimlab to xsimlab

Also rename Dataset.simlab to Dataset.xsimlab
Also rename xrtopo to xtopo (doc: example)

Author: benbovy

.gitattributes

@@ -1 +1 @@
-xrsimlab/_version.py export-subst
+xsimlab/_version.py export-subst

MANIFEST.in

@@ -1,2 +1,2 @@
 include versioneer.py
-include xrsimlab/_version.py
+include xsimlab/_version.py

doc/api.rst

@@ -8,18 +8,18 @@ This page provides an auto-generated summary of xarray-simlab's API. For more
 details and examples, refer to the relevant sections in the main part of the
 documentation.
 
-Dataset.simlab (xarray accessor)
-================================
+Dataset.xsimlab (xarray accessor)
+=================================
 
 This accessor extends :py:class:`xarray.Dataset` with all the methods and
 properties listed below. Proper use of this accessor should be like:
 
 .. code-block:: python
 
    >>> import xarray as xr   # first import xarray
-   >>> import xrsimlab       # import xrsimlab (the simlab xarray accessor is registered)
+   >>> import xsimlab       # import xsimlab (the simlab xarray accessor is registered)
    >>> ds = xr.Dataset()
-   >>> ds.simlab.<meth_or_prop>   # access to the methods and properties listed below
+   >>> ds.xsimlab.<meth_or_prop>   # access to the methods and properties listed below
 
 .. currentmodule:: xarray
 
@@ -29,30 +29,30 @@ properties listed below. Proper use of this accessor should be like:
    :toctree: _api_generated/
    :template: autosummary/accessor_attribute.rst
 
-   Dataset.simlab.model
-   Dataset.simlab.dim_master_clock
-   Dataset.simlab.snapshot_vars
+   Dataset.xsimlab.model
+   Dataset.xsimlab.dim_master_clock
+   Dataset.xsimlab.snapshot_vars
 
 **Methods**
 
 .. autosummary::
    :toctree: _api_generated/
    :template: autosummary/accessor_method.rst
 
-   Dataset.simlab.use_model
-   Dataset.simlab.set_master_clock
-   Dataset.simlab.set_snapshot_clock
-   Dataset.simlab.set_input_vars
-   Dataset.simlab.set_snapshot_vars
-   Dataset.simlab.run
+   Dataset.xsimlab.use_model
+   Dataset.xsimlab.set_master_clock
+   Dataset.xsimlab.set_snapshot_clock
+   Dataset.xsimlab.set_input_vars
+   Dataset.xsimlab.set_snapshot_vars
+   Dataset.xsimlab.run
 
 Model
 =====
 
 Creating a model
 ----------------
 
-.. currentmodule:: xrsimlab
+.. currentmodule:: xsimlab
 .. autosummary::
    :toctree: _api_generated/
 
@@ -86,7 +86,7 @@ Running a model
 ---------------
 
 In most cases, the methods listed below should not be used directly.
-For running simulations, it is preferable to use the ``Dataset.simlab`` accessor
+For running simulations, it is preferable to use the ``Dataset.xsimlab`` accessor
 instead. These methods might be useful for debugging, though.
 
 .. autosummary::

doc/conf.py

@@ -32,8 +32,8 @@
 except ImportError:
     print("no xarray")
 
-import xrsimlab
-print("xrsimlab: %s, %s" % (xrsimlab.__version__, xrsimlab.__file__))
+import xsimlab
+print("xsimlab: %s, %s" % (xsimlab.__version__, xsimlab.__file__))
 
 # -- General configuration ------------------------------------------------
 
@@ -90,9 +90,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = xrsimlab.__version__
+version = xsimlab.__version__
 # The full version, including alpha/beta/rc tags.
-release = xrsimlab.__version__
+release = xsimlab.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/create_model.rst

@@ -4,8 +4,8 @@ Creating models
 ===============
 
 xarray-simlab's framework provides a few Python base classes, e.g.,
-:class:`~xrsimlab.Variable`, :class:`~xrsimlab.Process` and
-:class:`~xrsimlab.Model` that can used togheter to create fully operational
+:class:`~xsimlab.Variable`, :class:`~xsimlab.Process` and
+:class:`~xsimlab.Model` that can used togheter to create fully operational
 models.
 
 A ``Model`` is a collection of processes that each define an interface with the

doc/examples/landscape-evolution-model.ipynb

@@ -19,7 +19,7 @@
    "source": [
     "import numpy as np\n",
     "import xarray as xr\n",
-    "import xrsimlab"
+    "import xsimlab"
    ]
   },
   {
@@ -28,7 +28,7 @@
    "source": [
     "## Import and inspect a model\n",
     "\n",
-    "The model (i.e., the `xrsimlab.Model` object) that we use here is provided by the [xarray-topo](https://gitext.gfz-potsdam.de/sec55-public/xarray-topo) package."
+    "The model (i.e., the `xsimlab.Model` object) that we use here is provided by the [xarray-topo](https://gitext.gfz-potsdam.de/sec55-public/xarray-topo) package."
    ]
   },
   {
@@ -39,7 +39,7 @@
    },
    "outputs": [],
    "source": [
-    "from xrtopo.models.fastscape_base import fastscape_base_model"
+    "from xtopo.models.fastscape_base import fastscape_base_model"
    ]
   },
   {
@@ -67,7 +67,7 @@
     {
      "data": {
       "text/plain": [
-       "<xrsimlab.Model (9 processes, 13 inputs)>\n",
+       "<xsimlab.Model (9 processes, 13 inputs)>\n",
        "grid\n",
        "    x_size     (in) nb. of nodes in x\n",
        "    y_size     (in) nb. of nodes in y\n",
@@ -144,7 +144,7 @@
     {
      "data": {
       "text/plain": [
-       "<xrsimlab.Process 'xrtopo.models.fastscape_base.StackedGridXY'>\n",
+       "<xsimlab.Process 'xtopo.models.fastscape_base.StackedGridXY'>\n",
        "Variables:\n",
        "    x_size     IntegerVariable ()\n",
        "    y_size     IntegerVariable ()\n",
@@ -175,7 +175,7 @@
    "source": [
     "## Create a model setup\n",
     "\n",
-    "With a few lines of code, using the `Dataset.simlab` extension (accessor), we create the setup of a new simulation, starting from an empty `Dataset`."
+    "With a few lines of code, using the `Dataset.xsimlab` extension (accessor), we create the setup of a new simulation, starting from an empty `Dataset`."
    ]
   },
   {
@@ -190,16 +190,16 @@
     "ds = xr.Dataset()   \n",
     "\n",
     "# use the model above with this Dataset\n",
-    "ds.simlab.use_model(fastscape_base_model) \n",
+    "ds.xsimlab.use_model(fastscape_base_model) \n",
     "\n",
     "# populate Dataset with input variable values (per process in the model)\n",
-    "ds.simlab.set_input_vars('grid', x_size=101, y_size=101, x_length=1e5, y_length=1e5)\n",
-    "ds.simlab.set_input_vars('topography', elevation=('node', np.random.rand(101 * 101)))\n",
-    "ds.simlab.set_input_vars('spower', k_coef=7e-5, m_exp=0.4, n_exp=1)\n",
-    "ds.simlab.set_input_vars('uplift', u_coef=2e-3)\n",
+    "ds.xsimlab.set_input_vars('grid', x_size=101, y_size=101, x_length=1e5, y_length=1e5)\n",
+    "ds.xsimlab.set_input_vars('topography', elevation=('node', np.random.rand(101 * 101)))\n",
+    "ds.xsimlab.set_input_vars('spower', k_coef=7e-5, m_exp=0.4, n_exp=1)\n",
+    "ds.xsimlab.set_input_vars('uplift', u_coef=2e-3)\n",
     "\n",
     "# set the clock coordinate where labels are time steps (here in years)\n",
-    "ds.simlab.set_master_clock('time', end=1e6, step=1e3)"
+    "ds.xsimlab.set_master_clock('time', end=1e6, step=1e3)"
    ]
   },
   {
@@ -218,10 +218,10 @@
    "outputs": [],
    "source": [
     "# set another time coordinate for snapshots with much larger steps than for 'time'\n",
-    "ds.simlab.set_snapshot_clock('out', end=1e6, step=1e5)\n",
+    "ds.xsimlab.set_snapshot_clock('out', end=1e6, step=1e5)\n",
     "\n",
     "# use the last created time coordinate to save topographic elevation values\n",
-    "ds.simlab.set_snapshot_vars('out', topography='elevation')"
+    "ds.xsimlab.set_snapshot_vars('out', topography='elevation')"
    ]
   },
   {
@@ -240,7 +240,7 @@
    "outputs": [],
    "source": [
     "# use None for saving time-independent outputs\n",
-    "ds.simlab.set_snapshot_vars(None, grid=['x', 'y'])"
+    "ds.xsimlab.set_snapshot_vars(None, grid=['x', 'y'])"
    ]
   },
   {
@@ -279,7 +279,7 @@
        "    spower__n_exp          int64 1\n",
        "    uplift__u_coef         float64 0.002\n",
        "Attributes:\n",
-       "    _simlab_snapshot_vars: grid__x,grid__y"
+       "    _xsimlab_snapshot_vars: grid__x,grid__y"
       ]
      },
      "execution_count": 9,
@@ -327,7 +327,7 @@
    "source": [
     "## Run the model\n",
     "\n",
-    "We run the model simply by calling `Dataset.simlab.run()`, which returns a new Dataset with both the inputs and the outputs. Note the additional variables `grid__x` and `grid__y` and the `topography__elevation` variable which has now also the `out` dimension. "
+    "We run the model simply by calling `Dataset.xsimlab.run()`, which returns a new Dataset with both the inputs and the outputs. Note the additional variables `grid__x` and `grid__y` and the `topography__elevation` variable which has now also the `out` dimension. "
    ]
   },
   {
@@ -368,7 +368,7 @@
     }
    ],
    "source": [
-    "out_ds = ds.simlab.run()\n",
+    "out_ds = ds.xsimlab.run()\n",
     "\n",
     "out_ds"
    ]
@@ -1403,7 +1403,7 @@
        "    spower__n_exp          int64 1\n",
        "    uplift__u_coef         float64 0.002\n",
        "Attributes:\n",
-       "    _simlab_snapshot_vars: grid__x,grid__y"
+       "    _xsimlab_snapshot_vars: grid__x,grid__y"
       ]
      },
      "execution_count": 20,
@@ -1415,9 +1415,9 @@
     "ds_kt = ds.copy()\n",
     "\n",
     "# we copied the dataset so we need to explicitly re-assign the Model\n",
-    "ds_kt.simlab.use_model(fastscape_base_model)\n",
+    "ds_kt.xsimlab.use_model(fastscape_base_model)\n",
     "\n",
-    "ds_kt.simlab.set_input_vars('spower', k_coef=da_k_time, m_exp=0.4, n_exp=1)\n",
+    "ds_kt.xsimlab.set_input_vars('spower', k_coef=da_k_time, m_exp=0.4, n_exp=1)\n",
     "\n",
     "ds_kt"
    ]
@@ -1446,7 +1446,7 @@
     }
    ],
    "source": [
-    "out_ds_kt = ds_kt.simlab.run()\n",
+    "out_ds_kt = ds_kt.xsimlab.run()\n",
     "\n",
     "out_ds_kt_unstack = out_ds_kt.set_index(node=['grid__x', 'grid__y']).unstack('node')\n",
     "\n",
@@ -1484,13 +1484,13 @@
     "datasets_k = []\n",
     "    \n",
     "ds_in = ds.copy()\n",
-    "ds_in.simlab.use_model(fastscape_base_model)\n",
+    "ds_in.xsimlab.use_model(fastscape_base_model)\n",
     "\n",
     "for k in k_values:\n",
     "    print('run k=%f' % k)\n",
     "\n",
-    "    ds_in.simlab.set_input_vars('spower', k_coef=k, m_exp=0.4, n_exp=1)\n",
-    "    out_ds = ds_in.simlab.run()\n",
+    "    ds_in.xsimlab.set_input_vars('spower', k_coef=k, m_exp=0.4, n_exp=1)\n",
+    "    out_ds = ds_in.xsimlab.run()\n",
     "\n",
     "    datasets_k.append(out_ds)\n",
     "\n",
@@ -1985,11 +1985,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from xrtopo.models.fastscape_base import StackedGridXY, BoundaryFacesXY\n",
-    "from xrsimlab import Process, FloatVariable, Variable, ForeignVariable\n",
+    "from xtopo.models.fastscape_base import StackedGridXY, BoundaryFacesXY\n",
+    "from xsimlab import Process, FloatVariable, Variable, ForeignVariable\n",
     "\n",
     "\n",
-    "class VariableUplift(xrsimlab.Process):\n",
+    "class VariableUplift(xsimlab.Process):\n",
     "    \"\"\"Compute spatially variable uplift as a linear function of x.\"\"\"\n",
     "    \n",
     "    x_coef = FloatVariable((), description='uplift function x coefficient')\n",
@@ -2023,7 +2023,7 @@
     {
      "data": {
       "text/plain": [
-       "<xrsimlab.Model (9 processes, 13 inputs)>\n",
+       "<xsimlab.Model (9 processes, 13 inputs)>\n",
        "grid\n",
        "    x_size     (in) nb. of nodes in x\n",
        "    y_size     (in) nb. of nodes in y\n",
@@ -2076,10 +2076,10 @@
     "\n",
     "alt_ds = ds.drop('uplift__u_coef')\n",
     "\n",
-    "alt_ds.simlab.use_model(alt_model)\n",
-    "alt_ds.simlab.set_input_vars('uplift', x_coef=1e-7)\n",
+    "alt_ds.xsimlab.use_model(alt_model)\n",
+    "alt_ds.xsimlab.set_input_vars('uplift', x_coef=1e-7)\n",
     "\n",
-    "out_alt_ds = alt_ds.simlab.run()"
+    "out_alt_ds = alt_ds.xsimlab.run()"
    ]
   },
   {

doc/installing.rst

@@ -56,4 +56,4 @@ Import xarray-simlab
 To make sure that ``xarray-simlab`` is correctly installed, try import it in a
 Python console::
 
-    >>> import xrsimlab
+    >>> import xsimlab

setup.cfg

@@ -13,7 +13,7 @@ max-line-length = 80
 [versioneer]
 VCS = git
 style = pep440
-versionfile_source = xrsimlab/_version.py
-versionfile_build = xrsimlab/_version.py
+versionfile_source = xsimlab/_version.py
+versionfile_build = xsimlab/_version.py
 tag_prefix =
 parentdir_prefix = xarray-simlab-

setup.py

@@ -15,7 +15,7 @@
       maintainer_email='[email protected]',
       license='BSD-Clause3',
       keywords='python xarray modelling simulation-framework',
-      packages=['xrsimlab', 'xrsimlab.variable'],
+      packages=['xsimlab', 'xsimlab.variable'],
       long_description=(open('README.md').read() if exists('README.md')
                         else ''),
       python_requires='>=3.4',

xrsimlab/__init__.py renamed to xsimlab/__init__.py

@@ -2,7 +2,7 @@
 xarray-simlab.
 
 """
-from .xr_accessor import SimLabAccessor
+from .xr_accessor import SimlabAccessor
 from .variable.base import (Variable, ForeignVariable, VariableList,
                             VariableGroup, diagnostic, ValidationError)
 from .variable.custom import NumberVariable, FloatVariable, IntegerVariable