Merge pull request #235 from pysat/maint/future_warn_2024

MAINT: Future Warnings for numpy, pandas, pysat

.github/workflows/docs.yml

@@ -16,9 +16,9 @@ jobs:
 
     name: Documentation tests
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/main.yml

@@ -27,9 +27,9 @@ jobs:
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with numpy ${{ matrix.numpy_ver }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/pip_rc_install.yml

@@ -17,9 +17,9 @@ jobs:
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/pysat_rc.yml

@@ -18,9 +18,9 @@ jobs:
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

CHANGELOG.md

@@ -38,6 +38,8 @@ This project adheres to [Semantic Versioning](https://semver.org/).
   * Added version cap for sphinx_rtd_theme
   * Include standard tests for ICON IVM-B
   * Update NEP29 standards for Jun 2024
+  * Updated standards for pandas, numpy, and pysat
+  * Updated versions in GitHub Actions
 
 ## [0.0.5] - 2023-06-27
 * New Instruments

pyproject.toml

@@ -84,6 +84,7 @@ markers = [
   "download",
   "no_download",
   "load_options",
+  "new_tests",
   "first",
   "second"
 ]

pysatNASA/instruments/de2_vefi.py

@@ -151,7 +151,7 @@ def load(fnames, tag='', inst_id='', **kwargs):
     if tag == '':
         # Warn user that e-field data is dropped.
         estr = 'E-field data dropped'
-        pysat.logger.warn(estr)
+        pysat.logger.warning(estr)
 
         # Drop E-field data
         if 'use_cdflib' in kwargs.keys():

pysatNASA/instruments/methods/cdaweb.py

@@ -164,7 +164,7 @@ def load(fnames, tag='', inst_id='', file_cadence=dt.timedelta(days=1),
     else:
         if not use_cdflib:
             estr = 'The `use_cdflib` option is not currently enabled for xarray'
-            pysat.logger.warn(estr)
+            pysat.logger.warning(estr)
 
         data, meta = load_xarray(fnames, tag=tag, inst_id=inst_id,
                                  epoch_name=epoch_name,
@@ -264,8 +264,8 @@ def load_pandas(fnames, tag='', inst_id='', file_cadence=dt.timedelta(days=1),
                         tdata = tdata.loc[date:date2, :]
                         ldata.append(tdata)
                     except ValueError as verr:
-                        logger.warn("unable to load {:}: {:}".format(fname,
-                                                                     str(verr)))
+                        logger.warning(
+                            "unable to load {:}: {:}".format(fname, str(verr)))
             else:
                 # Basic data return
                 with CDF(lfname) as cdf:
@@ -274,8 +274,8 @@ def load_pandas(fnames, tag='', inst_id='', file_cadence=dt.timedelta(days=1),
                             flatten_twod=flatten_twod)
                         ldata.append(temp_data)
                     except ValueError as verr:
-                        logger.warn("unable to load {:}: {:}".format(lfname,
-                                                                     str(verr)))
+                        logger.warning(
+                            "unable to load {:}: {:}".format(lfname, str(verr)))
 
         # Combine individual files together
         if len(ldata) > 0:
@@ -847,7 +847,7 @@ def list_remote_files(tag='', inst_id='', start=None, stop=None,
             if 'month' in search_dir['keys']:
                 search_times = pds.date_range(start,
                                               stop + pds.DateOffset(months=1),
-                                              freq='M')
+                                              freq='ME')
                 for time in search_times:
                     subdir = format_dir.format(year=time.year, month=time.month)
                     url_list.append('/'.join((remote_url, subdir)))
@@ -859,7 +859,7 @@ def list_remote_files(tag='', inst_id='', start=None, stop=None,
                 else:
                     search_times = pds.date_range(start, stop
                                                   + pds.DateOffset(years=1),
-                                                  freq='Y')
+                                                  freq='YE')
                 for time in search_times:
                     doy = int(time.strftime('%j'))
                     subdir = format_dir.format(year=time.year, day=doy)

pysatNASA/instruments/methods/jhuapl.py

@@ -282,15 +282,15 @@ def load_sdr_aurora(fnames, name='', tag='', inst_id='', pandas_format=False,
 
         # Ensure identical day and night dimensions for GUVI
         if name == 'guvi':
-            if sdata.dims['nAlongDay'] != sdata.dims['nAlongNight']:
+            if sdata.sizes['nAlongDay'] != sdata.sizes['nAlongNight']:
                 raise ValueError('Along-track day and night dimensions differ')
 
             if 'nCrossDay' in rename_dims.keys():
-                if sdata.dims['nCrossDay'] != sdata.dims['nCrossNight']:
+                if sdata.sizes['nCrossDay'] != sdata.sizes['nCrossNight']:
                     raise ValueError(''.join([
                         'Cross-track day and night dimensions differ ',
-                        '{:} != {:}'.format(sdata.dims['nCrossDay'],
-                                            sdata.dims['nCrossNight'])]))
+                        '{:} != {:}'.format(sdata.sizes['nCrossDay'],
+                                            sdata.sizes['nCrossNight'])]))
 
         # Combine identical dimensions and rename some time dimensions
         sdata = sdata.rename_dims(rename_dims)

pysatNASA/instruments/methods/omni.py

@@ -51,15 +51,15 @@ def time_shift_to_magnetic_poles(inst):
 
     # Need to fill in Vx to get an estimate of what is going on.
     inst['Vx'] = inst['Vx'].interpolate('nearest')
-    inst['Vx'] = inst['Vx'].fillna(method='backfill')
-    inst['Vx'] = inst['Vx'].fillna(method='pad')
+    inst['Vx'] = inst['Vx'].bfill()
+    inst['Vx'] = inst['Vx'].ffill()
 
     inst['BSN_x'] = inst['BSN_x'].interpolate('nearest')
-    inst['BSN_x'] = inst['BSN_x'].fillna(method='backfill')
-    inst['BSN_x'] = inst['BSN_x'].fillna(method='pad')
+    inst['BSN_x'] = inst['BSN_x'].bfill()
+    inst['BSN_x'] = inst['BSN_x'].ffill()
 
     # Make sure there are no gaps larger than a minute.
-    inst.data = inst.data.resample('1T').interpolate('time')
+    inst.data = inst.data.resample('1min').interpolate('time')
 
     time_x = inst['BSN_x'] * 6371.2 / -inst['Vx']
     idx, = np.where(np.isnan(time_x))
@@ -164,12 +164,14 @@ def calculate_imf_steadiness(inst, steady_window=15, min_window_frac=0.75,
         if steady:
             del_min = int((inst.data.index[i]
                            - inst.data.index[i - 1]).total_seconds() / 60.0)
-            if np.isnan(cv) or np.isnan(ca_std[i]) or del_min > sample_rate:
+            if np.any([np.isnan(cv),
+                       np.isnan(ca_std.iloc[i]),
+                       del_min > sample_rate]):
                 # Reset the steadiness flag if fill values are encountered, or
                 # if an entry is missing
                 steady = False
 
-        if cv <= max_bmag_cv and ca_std[i] <= max_clock_angle_std:
+        if cv <= max_bmag_cv and ca_std.iloc[i] <= max_clock_angle_std:
             # Steadiness conditions have been met
             if steady:
                 imf_steady[i] = imf_steady[i - 1]

pysatNASA/tests/test_instruments.py

@@ -89,13 +89,13 @@ def test_load_cdflib(self, inst_dict):
             target = 'Fake Data to be cleared'
             test_inst.data = [target]
             try:
-                test_inst.load(date=date, use_header=True, use_cdflib=True)
+                test_inst.load(date=date, use_cdflib=True)
             except ValueError as verr:
                 # Check if instrument is failing due to strict time flag
                 if str(verr).find('Loaded data') > 0:
                     test_inst.strict_time_flag = False
                     with warnings.catch_warnings(record=True) as war:
-                        test_inst.load(date=date, use_header=True)
+                        test_inst.load(date=date)
                     assert len(war) >= 1
                     categories = [war[j].category for j in range(0, len(war))]
                     assert UserWarning in categories