Merge branch 'rc_0_0_6' into no_remote_files

aburrell · web-flow · commit e8661963b634 · 2024-08-05T15:31:10.000-04:00
diff --git a/.github/workflows/docs.yml b/.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 }}
 
diff --git a/.github/workflows/main.yml b/.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 }}
 
diff --git a/.github/workflows/pip_rc_install.yml b/.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 }}
 
diff --git a/.github/workflows/pysat_rc.yml b/.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 }}
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,10 +2,10 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/).
 
-## [0.0.6] - 2024-XX-XX
+## [0.0.6] - 2024-07-31
 * New Instruments
   * DE2 VEFIMAGB - electric and magnetic field on the same cadence
-  * MAVEN mag
+  * MAVEN MAG
   * MAVEN SEP
   * MAVEN in situ key parameters
   * REACH Dosimeter
@@ -40,6 +40,8 @@ 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
diff --git a/docs/supported_instruments.rst b/docs/supported_instruments.rst
@@ -188,8 +188,8 @@ JPL GPS
 
 .. _maven_insitu_kp:
 
-MAVEN INSITU KP
----------------
+MAVEN IN SITU KP
+----------------
 
 .. automodule:: pysatNASA.instruments.maven_insitu_kp
    :members:
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pysatNASA"
-version = "0.0.5"
+version = "0.0.6"
 description = "pysat support for NASA Instruments"
 readme = "README.md"
 requires-python = ">=3.6"
@@ -44,7 +44,7 @@ dependencies = [
   "netCDF4",
   "numpy",
   "pandas",
-  "pysat >= 3.1",
+  "pysat >= 3.2",
   "requests",
   "scipy >= 1.4",
   "xarray"
@@ -84,6 +84,7 @@ markers = [
   "download",
   "no_download",
   "load_options",
+  "new_tests",
   "first",
   "second"
 ]
diff --git a/pysatNASA/instruments/de2_vefi.py b/pysatNASA/instruments/de2_vefi.py
@@ -43,7 +43,7 @@
 tag
     '', 'dca', 'ac'
 inst_id
-    none supported
+    None supported
 
 
 Warnings
@@ -133,7 +133,9 @@ def load(fnames, tag='', inst_id='', **kwargs):
     inst_id : str
         Instrument ID used to identify particular data set to be loaded.
         This input is nominally provided by pysat itself. (default='')
-
+    **kwargs : unpacked dict
+        Optional kwargs that will be passed to the
+        `pysatNASA.instruments.methods.cdaweb.load_xarray` function
     Returns
     -------
     data : pds.DataFrame
@@ -146,12 +148,16 @@ def load(fnames, tag='', inst_id='', **kwargs):
     Several variables relating to time stored in different formats are dropped.
     These are redundant and complicate the load procedure.
 
+    See Also
+    --------
+    pysatNASA.instruments.methods.cdaweb.load_xarray
+
     """
 
     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():
diff --git a/pysatNASA/instruments/de2_vefimagb.py b/pysatNASA/instruments/de2_vefimagb.py
@@ -111,7 +111,7 @@
 
 # Set the load routine
 def load(fnames, tag='', inst_id='', **kwargs):
-    """Load DE2 VEFI data.
+    """Load DE2 VEFI MAG B-field data.
 
     This routine is called as needed by pysat. It is not intended
     for direct user interaction.
diff --git a/pysatNASA/instruments/dmsp_ssusi.py b/pysatNASA/instruments/dmsp_ssusi.py
@@ -131,12 +131,12 @@ def clean(self):
 
 
 def concat_data(self, new_data, combine_times=False, **kwargs):
-    """Concatonate data to self.data for DMSP SSUSI data.
+    """Concatenate data to self.data for DMSP SSUSI data.
 
     Parameters
     ----------
     new_data : xarray.Dataset or list of such objects
-        New data objects to be concatonated
+        New data objects to be concatenated
     combine_times : bool
         For SDR data, optionally combine the different datetime coordinates
         into a single time coordinate (default=False)
@@ -155,7 +155,7 @@ def concat_data(self, new_data, combine_times=False, **kwargs):
     if self.tag in ['sdr-disk', 'sdr2-dist']:
         time_dims.append('time_auroral')
 
-    # Concatonate using the appropriate method for the number of time
+    # Concatenate using the appropriate method for the number of time
     # dimensions
     jhuapl.concat_data(self, time_dims, new_data, combine_times=combine_times,
                        **kwargs)
diff --git a/pysatNASA/instruments/maven_insitu_kp.py b/pysatNASA/instruments/maven_insitu_kp.py
@@ -7,9 +7,9 @@
 # DISTRIBUTION STATEMENT A: Approved for public release. Distribution is
 # unlimited.
 # ----------------------------------------------------------------------------
-"""Module for the MAVEN insitu instruments.
+"""Module for the MAVEN in situ instruments.
 
-Supports the in situ Key Parameter (kp) data from multiple instruments
+Supports the in situ Key Parameter (KP) data from multiple instruments
 onboard the Mars Atmosphere and Volatile Evolution (MAVEN) satellite.
 
 Accesses local data in CDF format.
@@ -32,9 +32,9 @@
 ::
     import pysat
 
-    insitu = pysat.Instrument(platform='maven', name='insitu_kp')
-    insitu.download(dt.datetime(2020, 1, 1), dt.datetime(2020, 1, 31))
-    insitu.load(2020, 1, use_header=True)
+    insitukp = pysat.Instrument(platform='maven', name='insitu_kp')
+    insitukp.download(dt.datetime(2020, 1, 1), dt.datetime(2020, 1, 31))
+    insitukp.load(2020, 1, use_header=True)
 
 """
 
diff --git a/pysatNASA/instruments/maven_mag.py b/pysatNASA/instruments/maven_mag.py
@@ -7,7 +7,7 @@
 # DISTRIBUTION STATEMENT A: Approved for public release. Distribution is
 # unlimited.
 # ----------------------------------------------------------------------------
-"""Module for the MAVEN mag instrument.
+"""Module for the MAVEN magnetometer.
 
 Supports the Magnetometer (MAG) onboard the Mars Atmosphere
 and Volatile Evolution (MAVEN) satellite.
diff --git a/pysatNASA/instruments/maven_sep.py b/pysatNASA/instruments/maven_sep.py
@@ -7,7 +7,7 @@
 # DISTRIBUTION STATEMENT A: Approved for public release. Distribution is
 # unlimited.
 # ----------------------------------------------------------------------------
-"""Module for the MAVEN sep instrument.
+"""Module for the MAVEN Solar Energetic Particle instrument.
 
 Supports the Solar Energetic Particle (SEP) data from
 onboard the Mars Atmosphere and Volatile Evolution (MAVEN) satellite.
@@ -31,9 +31,9 @@
 ::
     import pysat
 
-    insitu = pysat.Instrument(platform='maven', name='sep', inst_id='s1')
-    insitu.download(dt.datetime(2020, 1, 1), dt.datetime(2020, 1, 31))
-    insitu.load(2020, 1, use_header=True)
+    sep = pysat.Instrument(platform='maven', name='sep', inst_id='s1')
+    sep.download(dt.datetime(2020, 1, 1), dt.datetime(2020, 1, 31))
+    sep.load(2020, 1, use_header=True)
 
 """
 
diff --git a/pysatNASA/instruments/methods/cdaweb.py b/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)
diff --git a/pysatNASA/instruments/methods/jhuapl.py b/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)
diff --git a/pysatNASA/instruments/methods/maven.py b/pysatNASA/instruments/methods/maven.py
@@ -7,12 +7,7 @@
 # DISTRIBUTION STATEMENT A: Approved for public release. Distribution is
 # unlimited.
 # ----------------------------------------------------------------------------
-"""Provides non-instrument specific routines for MAVEN data.
-
-Created on Thu Jul 13 11:21:01 2023
-
-@author: tesman
-"""
+"""Provides non-instrument specific routines for MAVEN data."""
 
 ackn_str = ''.join(('Jakosky, B.M., Lin, R.P., Grebowsky, J.M. et al.',
                     ' The Mars Atmosphere and Volatile Evolution',
diff --git a/pysatNASA/instruments/methods/omni.py b/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]
diff --git a/pysatNASA/instruments/reach_dosimeter.py b/pysatNASA/instruments/reach_dosimeter.py
@@ -14,7 +14,7 @@
 
 The Responsive Environmental Assessment Commercially Hosted (REACH)
 constellation is collection of 32 small sensors hosted on six orbital planes of
-the Iridium-Next space vehicles in low earth orbit. Each sensor contains two
+the Iridium-Next space vehicles in Low Earth Orbit. Each sensor contains two
 micro-dosimeters sensitive to the passage of charged particles from the Earth's
 radiation belts. There are six distinct dosimeter types spread among the 64
 individual sensors, which are unique in shielding and electronic threshold.
@@ -33,8 +33,6 @@
     '101', '102', '105', '108', '113', '114', '115', '116', '133', '134', '135',
     '136', '137', '138', '139', '140', '148', '149', '162', '163', '164', '165',
     '166', '169', '170', '171', '172', '173', '175', '176', '180', '181'
-
-
 """
 
 import datetime as dt
@@ -69,8 +67,6 @@
 
 # ----------------------------------------------------------------------------
 # Instrument methods
-
-
 # Use standard init routine
 init = functools.partial(mm_nasa.init, module=mm_reach, name=name)
 
@@ -84,8 +80,6 @@ def preprocess(self):
     self.acknowledgements = self.meta.header.Acknowledgement
 
     return
-
-
 # ----------------------------------------------------------------------------
 # Instrument functions
 #
diff --git a/pysatNASA/instruments/timed_guvi.py b/pysatNASA/instruments/timed_guvi.py
diff --git a/pysatNASA/tests/test_instruments.py b/pysatNASA/tests/test_instruments.py
diff --git a/setup.cfg b/setup.cfg
