Merge pull request #110 from bird-house/implement-date-of-year-inputs

- Implement `before_date` and `mid_date` inputs
- Remove realization from csv output
- Update to xclim 0.15.2
- Refresh notebooks

CHANGES.rst

@@ -6,6 +6,8 @@ Changes
 ==================
 
 * fix to remove realization coordinate from ensembles
+* added chunk datasets for local files also
+* update xclim to == 0.15.2
 
 0.5.1 (2020-04-18)
 ==================
@@ -23,7 +25,7 @@ Changes
 
 * fix #103 (drs_filename) add defaults when `project_id` is unknown
 * drs_filenames: use dash instead of underscores in variable names
-* fix #80 frequency attrs of computed datasets 
+* fix #80 frequency attrs of computed datasets
 
 0.4.0 (2020-03-10)
 ==================

docs/source/notebooks/dap_subset.ipynb

@@ -553,7 +553,7 @@
        "Attributes:\n",
        "    units:          mm/day\n",
        "    cell_methods:   time: mean (interval: 30 minutes)\n",
-       "    history:        pr=max(0,pr) applied to raw data;\\n[2020-04-04 16:13:21] ...\n",
+       "    history:        pr=max(0,pr) applied to raw data;\\n[2020-04-05 10:27:31] ...\n",
        "    standard_name:  lwe_thickness_of_precipitation_amount\n",
        "    long_name:      Average precipitation during wet days (sdii)\n",
        "    description:    Annual simple daily intensity index (sdii) : annual avera...</pre>"
@@ -576,7 +576,7 @@
        "Attributes:\n",
        "    units:          mm/day\n",
        "    cell_methods:   time: mean (interval: 30 minutes)\n",
-       "    history:        pr=max(0,pr) applied to raw data;\\n[2020-04-04 16:13:21] ...\n",
+       "    history:        pr=max(0,pr) applied to raw data;\\n[2020-04-05 10:27:31] ...\n",
        "    standard_name:  lwe_thickness_of_precipitation_amount\n",
        "    long_name:      Average precipitation during wet days (sdii)\n",
        "    description:    Annual simple daily intensity index (sdii) : annual avera..."
@@ -610,7 +610,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.8.2"
   }
  },
  "nbformat": 4,

docs/source/notebooks/finch-usage.ipynb

@@ -54,7 +54,7 @@
       "    ----------\n",
       "    tasmin : ComplexData:mimetype:`application/x-netcdf`, :mimetype:`application/x-ogc-dods`\n",
       "        NetCDF Files or archive (tar/zip) containing netCDF files.\n",
-      "    freq : {'YS', 'MS', 'QS-DEC', 'AS-JUL'}string\n",
+      "    freq : string\n",
       "        Resampling frequency\n",
       "    \n",
       "    Returns\n",
@@ -104,7 +104,7 @@
      "output_type": "stream",
      "text": [
       "Process status:  ProcessSucceeded\n",
-      "Link to process output:  https://pavics.ouranos.ca/wpsoutputs/be502914-76b0-11ea-9d75-0800276e9ee6/frost-days_SRES-A2-experiment_20460101-20650101.nc\n"
+      "Link to process output:  https://pavics.ouranos.ca/wpsoutputs/98bd37b6-7749-11ea-bda5-0800276e9ee6/frost-days_SRES-A2-experiment_20460101-20650101.nc\n"
      ]
     }
    ],
@@ -228,7 +228,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.8.2"
   }
  },
  "nbformat": 4,

environment.yml

@@ -14,6 +14,6 @@ dependencies:
   - xarray>=0.14
   - sentry-sdk
   - siphon
-  - xclim>=0.15.0, <0.16
+  - xclim==0.15.2
   - pywps==4.2.4
   - parse

finch/processes/__init__.py

@@ -34,14 +34,11 @@ def get_indicators(module):
 
 for i in indicators:
     # Todo: remove me after xclim fixes the identifier name
-    if i.compute.__name__ == 'hot_spell_max_length':
-        i.identifier = 'hot_spell_max_length'
+    if i.compute.__name__ == "hot_spell_max_length":
+        i.identifier = "hot_spell_max_length"
 
 not_implemented = [
     "DC",  # lat input type is not implemented and start_up_mode argument seems to be missing?
-    "growing_season_length",  # mid_date parameter not implemented
-    "growing_season_end",  # mid_date parameter not implemented
-    "last_spring_frost",  # before_date parameter not implemented
 ]
 indicators = [i for i in indicators if i.identifier not in not_implemented]
 ensemble_indicators = [i for i in indicators if uses_accepted_netcdf_variables(i)]
@@ -114,7 +111,9 @@ def _build_xclim():
     processes = get_processes(all_processes=True)
     objs = {p.__class__.__name__: p.__class__ for p in processes}
 
-    mod = xclim.indicators.build_module("finch.processes.xclim", objs, doc="""XCLIM Processes""")
+    mod = xclim.indicators.build_module(
+        "finch.processes.xclim", objs, doc="""XCLIM Processes"""
+    )
     sys.modules["finch.processes.xclim"] = mod
     return mod
 

finch/processes/wps_base.py

@@ -2,7 +2,6 @@
 from typing import Dict, List
 
 from dask.diagnostics import ProgressBar
-from dask.diagnostics.progress import format_time
 from pywps import ComplexInput, FORMATS, LiteralInput, Process
 from pywps.app.Common import Metadata
 from sentry_sdk import configure_scope
@@ -121,9 +120,11 @@ def convert_xclim_inputs_to_pywps(params: Dict) -> List[PywpsInput]:
         elif name in ["thresh"]:
             inputs.append(make_thresh(name, attrs["default"], attrs["desc"]))
         elif name in ["freq"]:
-            inputs.append(make_freq(name, attrs["default"]))
+            inputs.append(make_freq(name, attrs["default"], attrs["desc"]))
         elif name in ["window"]:
             inputs.append(make_window(name, attrs["default"], attrs["desc"]))
+        elif name in ["mid_date", "before_date"]:
+            inputs.append(make_date_of_year(name, attrs["default"], attrs["desc"]))
         else:
             # raise NotImplementedError(name)
             LOGGER.warning("not implemented: {}".format(name))
@@ -168,6 +169,18 @@ def make_window(name, default, abstract=""):
     )
 
 
+def make_date_of_year(name, default, abstract=""):
+    return LiteralInput(
+        name,
+        "Date of the year",
+        abstract=abstract,
+        data_type="string",
+        min_occurs=0,
+        max_occurs=1,
+        default=default,
+    )
+
+
 def make_nc_input(name):
     return ComplexInput(
         name,

requirements.txt

@@ -1,5 +1,5 @@
 pywps>=4.2.0<4.3
-xclim>=0.13.0
+xclim==0.15.2
 geopandas
 jinja2
 click

tests/test_wps_xclim_indices.py

@@ -43,6 +43,8 @@ def test_processes(client, netcdf_datasets):
     literal_inputs = {
         "freq": "MS",
         "window": "3",
+        "mid_date": "07-01",
+        "before_date": "07-01",
     }
     keep_defaults = ["thresh", "thresh_tasmin", "thresh_tasmax"]