Merge pull request #391 from xylar/update-to-0.9.0-alpha.4

Switch to `Tranche` config parser

Author: xylar

deploy/conda-dev-spec.template

@@ -6,6 +6,7 @@ cmocean
 esmf={{ esmf }}={{ mpi_prefix }}_*
 ffmpeg
 geometric_features={{ geometric_features }}
+gsw
 importlib_resources
 ipython
 jupyter
@@ -33,6 +34,7 @@ requests
 ruamel.yaml
 scipy>=1.8.0
 shapely>=2.0,<3.0
+tranche>=0.3.0
 xarray
 
 # Static typing

docs/conf.py

@@ -76,7 +76,8 @@
     'python': ('https://docs.python.org', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
     "sphinx": ("https://www.sphinx-doc.org/en/master", None),
-    'xarray': ('https://xarray.pydata.org/en/stable', None)
+    'xarray': ('https://xarray.pydata.org/en/stable', None),
+    'tranche': ('https://xylar.github.io/tranche/', None),
 }
 
 # -- MyST settings ---------------------------------------------------

docs/developers_guide/framework/config.md

@@ -2,10 +2,10 @@
 
 # Config files
 
-The primary documentation for the config parser is in
-[MPAS-Tools config parser](http://mpas-dev.github.io/MPAS-Tools/stable/config.html).
+The primary documentation for the config parser is in the
+[tranche documentation](https://xylar.github.io/tranche/).
 Here, we include some specific details relevant to using the
-{py:class}`mpas_tools.config.MpasConfigParser` in polaris.
+{py:class}`tranche.Tranche` in polaris.
 
 Here, we provide the {py:class}`polaris.config.PolarisConfigParser` that has
 almost the same functionality but also ensures that certain relative paths are
@@ -18,7 +18,7 @@ options) as part of setting up polaris tasks and steps.  These features are
 included to accommodate sharing config options across shared steps and/or
 multiple tasks.
 
-The {py:meth}`mpas_tools.config.MpasConfigParser.add_from_package()` method can
+The {py:meth}`tranche.Tranche.add_from_package()` method can
 be used to add the contents of a config file within a package to the config
 options. Examples of this can be found in many tasks as well as in the
 `polaris.setup` module. Here is a typical example from
@@ -71,11 +71,12 @@ for use by the framework rather than individual tasks.
 Other methods for the `MpasConfigParser` are similar to those for
 {py:class}`configparser.ConfigParser`.  In addition to `get()`,
 `getinteger()`, `getfloat()` and `getboolean()` methods, this class
-implements {py:meth}`mpas_tools.config.MpasConfigParser.getlist()`, which
+implements {py:meth}`tranche.Tranche.getlist()`, which
 can be used to parse a config value separated by spaces and/or commas into
-a list of strings, floats, integers, booleans, etc. Another useful method
-is {py:meth}`mpas_tools.config.MpasConfigParser.getexpression()`, which can
-be used to get python dictionaries, lists and tuples as well as a small set
+a list of strings, floats, integers, booleans, etc. Other useful methods
+are {py:meth}`tranche.Tranche.getexpression()`, which can
+be used to get python dictionaries, lists, and tuples, and
+{py:meth}`tranche.Tranche.getnumpy()`, which also suppports a small set
 of functions (`range()`, {py:meth}`numpy.linspace()`,
 {py:meth}`numpy.arange()`, and {py:meth}`numpy.array()`)
 
@@ -182,9 +183,10 @@ class Rpe(Task):
 
 ## Comments in config files
 
-One of the main advantages of {py:class}`mpas_tools.config.MpasConfigParser`
+One of the main advantages of {py:class}`tranche.Tranche`
 over {py:class}`configparser.ConfigParser` is that it keeps track of comments
 that are associated with config sections and options.
 
-See [comments in config files](http://mpas-dev.github.io/MPAS-Tools/stable/config.html#config_comments)
-in MPAS-Tools for more details.
+Comments must begin with the `#` character. They must be placed *before* the
+config section or option in question (preferably without blank lines between).
+The comments can be any number of lines long.

polaris/config.py

@@ -1,10 +1,10 @@
 import os
 from typing import Union
 
-from mpas_tools.config import MpasConfigParser
+from tranche import Tranche
 
 
-class PolarisConfigParser(MpasConfigParser):
+class PolarisConfigParser(Tranche):
     """
     A "meta" config parser that keeps a dictionary of config parsers and their
     sources to combine when needed.  The custom config parser allows provenance

polaris/job/__init__.py

@@ -244,7 +244,9 @@ def _get_job_options(
     wall_time : str
     filesystems : str
     """
-    partition_or_queue = config.get('job', partition_or_queue_option)
+    par_section = config['parallel']
+    job_section = config['job']
+    partition_or_queue = job_section.get(partition_or_queue_option)
     if partition_or_queue == '<<<default>>>':
         if machine == 'anvil' and partition_or_queue == 'partition':
             # choose the partition based on the number of nodes
@@ -254,37 +256,35 @@ def _get_job_options(
                 partition_or_queue = 'acme-medium'
             else:
                 partition_or_queue = 'acme-large'
-        elif config.has_option('parallel', partitions_or_queues):
+        elif par_section.has_option(partitions_or_queues):
             # get the first, which is the default
-            partition_or_queue = config.getlist(
-                'parallel', partitions_or_queues
-            )[0]
+            partition_or_queue = par_section.getlist(partitions_or_queues)[0]
         else:
             partition_or_queue = ''
 
-    qos = config.get('job', 'qos')
+    qos = job_section.get('qos')
     if qos == '<<<default>>>':
-        if config.has_option('parallel', 'qos'):
-            qos = config.getlist('parallel', 'qos')[0]
+        if par_section.has_option('qos'):
+            qos = par_section.getlist('qos')[0]
         else:
             qos = ''
 
-    constraint = config.get('job', 'constraint')
+    constraint = job_section.get('constraint')
     if constraint == '<<<default>>>':
-        if config.has_option('parallel', 'constraints'):
-            constraint = config.getlist('parallel', 'constraints')[0]
+        if par_section.has_option('constraints'):
+            constraint = par_section.getlist('constraints')[0]
         else:
             constraint = ''
 
-    if config.has_option('parallel', 'gpus_per_node'):
-        gpus_per_node = config.get('parallel', 'gpus_per_node')
+    if par_section.has_option('gpus_per_node'):
+        gpus_per_node = par_section.get('gpus_per_node')
     else:
         gpus_per_node = ''
 
-    wall_time = config.get('job', 'wall_time')
+    wall_time = job_section.get('wall_time')
 
-    if config.has_option('job', 'filesystems'):
-        filesystems = config.get('job', 'filesystems')
+    if job_section.has_option('filesystems'):
+        filesystems = job_section.get('filesystems')
     else:
         filesystems = ''
 

polaris/ocean/model/ocean_model_step.py

@@ -303,13 +303,14 @@ def update_namelist_eos(self):
         Modify the namelist to make it consistent with eos config options
         """
         config = self.config
-
-        eos_type = config.get('ocean', 'eos_type')
-        eos_linear_alpha = config.getfloat('ocean', 'eos_linear_alpha')
-        eos_linear_beta = config.getfloat('ocean', 'eos_linear_beta')
-        eos_linear_rhoref = config.getfloat('ocean', 'eos_linear_rhoref')
-        eos_linear_Tref = config.getfloat('ocean', 'eos_linear_Tref')
-        eos_linear_Sref = config.getfloat('ocean', 'eos_linear_Sref')
+        section = config['ocean']
+
+        eos_type = section.get('eos_type')
+        eos_linear_alpha = section.getfloat('eos_linear_alpha')
+        eos_linear_beta = section.getfloat('eos_linear_beta')
+        eos_linear_rhoref = section.getfloat('eos_linear_rhoref')
+        eos_linear_Tref = section.getfloat('eos_linear_Tref')
+        eos_linear_Sref = section.getfloat('eos_linear_Sref')
 
         replacements = {
             'config_eos_type': eos_type,

polaris/version.py

@@ -1 +1 @@
-__version__ = '0.9.0-alpha.3'
+__version__ = '0.9.0-alpha.4'

polaris/viz/spherical.py

@@ -326,9 +326,11 @@ def _setup_colormap(config, colormap_section):
 
     colormap = plt.get_cmap(config.get(colormap_section, 'colormap_name'))
 
-    norm_type = config.get(colormap_section, 'norm_type')
+    section = config[colormap_section]
 
-    kwargs = config.getexpression(colormap_section, 'norm_args')
+    norm_type = section.get('norm_type')
+
+    kwargs = section.getnumpy('norm_args')
 
     if norm_type == 'symlog':
         norm = cols.SymLogNorm(**kwargs)
@@ -342,17 +344,15 @@ def _setup_colormap(config, colormap_section):
         )
 
     try:
-        ticks = config.getexpression(
-            colormap_section, 'colorbar_ticks', use_numpyfunc=True
-        )
+        ticks = section.getnumpy('colorbar_ticks')
     except configparser.NoOptionError:
         ticks = None
 
-    if config.has_option(colormap_section, 'under_color'):
-        under_color = config.get(colormap_section, 'under_color')
+    if section.has_option('under_color'):
+        under_color = section.get('under_color')
         colormap.set_under(under_color)
-    if config.has_option(colormap_section, 'over_color'):
-        over_color = config.get(colormap_section, 'over_color')
+    if section.has_option('over_color'):
+        over_color = section.get('over_color')
         colormap.set_over(over_color)
 
     return colormap, norm, ticks

pyproject.toml

@@ -30,6 +30,7 @@ classifiers = [
 dependencies = [
     "cartopy",
     "cmocean",
+    "gsw",
     "importlib_resources",
     "ipython",
     "jigsawpy",
@@ -45,6 +46,7 @@ dependencies = [
     "requests",
     "scipy>=1.8.0",
     "shapely>=2.0,<3.0",
+    "tranche>=0.3.0",
     "xarray",
 ]