Merge branch 'develop' into maint/pysat_depr

.github/workflows/main.yml

@@ -41,6 +41,7 @@ jobs:
       if: ${{ matrix.test_config == 'Ops'}}
       run: |
         pip install --no-cache-dir numpy==${{ matrix.numpy_ver }}
+        pip install "cdflib<1.0"
         pip install -r requirements.txt
         pip install -r test_requirements.txt
         pip install .

CHANGELOG.md

@@ -59,6 +59,7 @@ This project adheres to [Semantic Versioning](https://semver.org/).
   * Set pysat 3.1.0 minimum
   * Use pysat logger to raise non-deprecation warnings
   * Update syntax based on latest pysat deprecations to make the code compatible with pysat 3.2.0.
+  * Updated syntax compliance with cdflib 1.0+
 
 ## [0.0.4] - 2022-11-07
 * Update instrument tests with new test class

README.md

@@ -24,7 +24,7 @@ Python 3.6+.
 
 | Common modules   | Community modules | Optional Modules |
 | ---------------- | ----------------- |------------------|
-| beautifulsoup4   | cdflib            | pysatCDF         |
+| beautifulsoup4   | cdflib>=0.4.4     | pysatCDF         |
 | lxml             | pysat>=3.1.0      |                  |
 | netCDF4          |                   |                  |
 | numpy            |                   |                  |

docs/installation.rst

@@ -14,7 +14,7 @@ Prerequisites
 
 pysatNASA uses common Python modules, as well as modules developed by
 and for the Space Physics community.  This module officially supports
-Python 3.8+ and pysat 3.1.0+.
+Python 3.6+ and pysat 3.1.0+.
 
  ================== =================
  Common modules     Community modules
@@ -25,7 +25,7 @@ Python 3.8+ and pysat 3.1.0+.
   numpy
   pandas
   requests
-  xarray<2022.11
+  xarray
  ================== =================
 
 

pyproject.toml

@@ -39,7 +39,7 @@ keywords = [
 dependencies = [
   "beautifulsoup4",
   "cdasws",
-  "cdflib >= 0.4.4, <1.0",
+  "cdflib >= 0.4.4",
   "lxml",
   "netCDF4",
   "numpy",

pysatNASA/instruments/methods/_cdf.py

@@ -91,8 +91,13 @@ def __init__(self, filename,
         self.meta = {}
         self._dependencies = {}
 
-        self._variable_names = (self._cdf_info['rVariables']
-                                + self._cdf_info['zVariables'])
+        if hasattr(self._cdf_info, 'rVariables'):
+            self._variable_names = (self._cdf_info.rVariables
+                                    + self._cdf_info.zVariables)
+        else:
+            # cdflib < 1.0 stores info as a dict
+            self._variable_names = (self._cdf_info['rVariables']
+                                    + self._cdf_info['zVariables'])
 
         self.load_variables()
 
@@ -156,8 +161,13 @@ def set_epoch(self, x_axis_var):
 
         """
 
-        data_type_description = self._cdf_file.varinq(
-            x_axis_var)['Data_Type_Description']
+        if hasattr(self._cdf_file.varinq(x_axis_var), 'Data_Type_Description'):
+            data_type_description = self._cdf_file.varinq(
+                x_axis_var).Data_Type_Description
+        else:
+            # cdflib < 1.0 stores this as a dict
+            data_type_description = self._cdf_file.varinq(
+                x_axis_var)['Data_Type_Description']
 
         center_measurement = self._center_measurement
         cdf_file = self._cdf_file
@@ -298,7 +308,12 @@ def load_variables(self):
             if not re.match(var_regex, variable_name):
                 # Skip this variable
                 continue
-            var_atts = self._cdf_file.varattsget(variable_name, to_np=True)
+            try:
+                var_atts = self._cdf_file.varattsget(variable_name, to_np=True)
+            except TypeError:
+                # cdflib 1.0+ drops to_np kwarg, assumes True
+                var_atts = self._cdf_file.varattsget(variable_name)
+
             for k in var_atts:
                 var_atts[k] = var_atts[k]  # [0]
 
@@ -319,13 +334,14 @@ def load_variables(self):
                 continue
 
             if "FILLVAL" in var_atts:
-                if (var_properties['Data_Type_Description'] == 'CDF_FLOAT'
-                    or var_properties['Data_Type_Description']
-                    == 'CDF_REAL4'
-                    or var_properties['Data_Type_Description']
-                    == 'CDF_DOUBLE'
-                    or var_properties['Data_Type_Description']
-                        == 'CDF_REAL8'):
+                if hasattr(var_properties, 'Data_Type_Description'):
+                    data_type_desc = var_properties.Data_Type_Description
+                else:
+                    # cdflib < 1.0 stores this as a dict
+                    data_type_desc = var_properties['Data_Type_Description']
+
+                if data_type_desc in ['CDF_FLOAT', 'CDF_REAL4', 'CDF_DOUBLE',
+                                      'CDF_REAL8']:
 
                     if ydata[ydata == var_atts["FILLVAL"]].size != 0:
                         ydata[ydata == var_atts["FILLVAL"]] = np.nan

pysatNASA/instruments/methods/cdaweb.py

@@ -7,7 +7,6 @@
 
 """
 
-import cdflib
 import datetime as dt
 import numpy as np
 import os
@@ -26,6 +25,13 @@
 from pysat.utils import io
 from pysatNASA.instruments.methods import CDF as libCDF
 
+try:
+    # cdflib 1.0 syntax
+    from cdflib.xarray import cdf_to_xarray
+except ModuleNotFoundError:
+    # cdflib 0.4 syntax required for backwards compatibility
+    from cdflib import cdf_to_xarray
+
 try:
     import pysatCDF
     auto_CDF = pysatCDF.CDF
@@ -372,7 +378,7 @@ def load_xarray(fnames, tag='', inst_id='',
             lfnames = fnames
 
         for lfname in lfnames:
-            temp_data = cdflib.cdf_to_xarray(lfname, to_datetime=True)
+            temp_data = cdf_to_xarray(lfname, to_datetime=True)
             if drop_dims:
                 temp_data = temp_data.drop_dims(drop_dims)
             if var_translation:

requirements.txt

@@ -1,6 +1,6 @@
 beautifulsoup4
 cdasws
-cdflib>=0.4.4,<1.0
+cdflib>=0.4.4
 lxml
 netCDF4
 numpy