Merge pull request #247 from pysat/rc_0_0_6

Pull RC 0.0.6 back into develop

.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

@@ -19,17 +19,17 @@ jobs:
             numpy_ver: "1.24"
             os: ubuntu-latest
             test_config: "NEP29"
-          - python-version: "3.6.8"
-            numpy_ver: "1.19.5"
+          - python-version: "3.9"
+            numpy_ver: "1.23.5"
             os: "ubuntu-20.04"
             test_config: "Ops"
 
     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 }}
 
@@ -40,18 +40,8 @@ jobs:
     - name: Install Operational dependencies
       if: ${{ matrix.test_config == 'Ops'}}
       run: |
-        sudo apt-get install libhdf5-serial-dev netcdf-bin libnetcdf-dev
         pip install --no-cache-dir numpy==${{ matrix.numpy_ver }}
-        pip install "cdflib<1.0"
-        pip install -r requirements.txt
-        pip install -r test_requirements.txt
-        cd ..
-        git clone https://github.com/pysat/pysat.git
-        cd pysat
-        git checkout pip_rc_install
-        python setup.py develop
-        cd ../pysatNASA
-        pip install .
+        pip install --upgrade-strategy only-if-needed .[test]
 
     - name: Install NEP29 dependencies
       if: ${{ matrix.test_config == 'NEP29'}}
@@ -78,46 +68,20 @@ jobs:
     - name: Test with pytest
       run: pytest
 
-    - name: Coveralls Parallel (Ubuntu)
-      if: startsWith(matrix.os, 'ubuntu')
-      env:
-        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-        COVERALLS_PARALLEL: true
-      run: |
-        curl -sL https://coveralls.io/coveralls-linux.tar.gz | tar -xz
-        ./coveralls report --parallel --repo-token=${{ secrets.COVERALLS_REPO_TOKEN }} --build-number ${{ github.run_number }}
-
-    - name: Coveralls Parallel (Windows)
-      if: startsWith(matrix.os, 'windows')
-      env:
-        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-        COVERALLS_PARALLEL: true
-      run: |
-        curl -L https://github.com/coverallsapp/coverage-reporter/releases/latest/download/coveralls-windows.exe -o coveralls.exe
-        ./coveralls.exe report --parallel --repo-token=${{ secrets.COVERALLS_REPO_TOKEN }} --build-number ${{ github.run_number }}
-
-    - name: Coveralls Parallel (MacOS)
-      if: startsWith(matrix.os, 'macos')
-      env:
-        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-        COVERALLS_PARALLEL: true
-      run: |
-        brew tap coverallsapp/coveralls --quiet
-        brew install coveralls --quiet
-        ls -lh .coverage
-        ls -lh coverage.xml
-        coveralls report coverage.xml --format=cobertura --verbose --parallel --repo-token=${{ secrets.COVERALLS_REPO_TOKEN }} --build-number ${{ github.run_number }} --debug --dry-run
+    - name: Coveralls Parallel
+      uses: coverallsapp/github-action@v2
+      with:
+        flag-name: run-${{ join(matrix.*, '-') }}
+        parallel: true
 
   finish:
     name: Finish Coverage Analysis
     needs: build
-    if: always()
-    runs-on: "ubuntu-latest"
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
     steps:
-      - name: Coveralls Finish
-        env:
-          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-          COVERALLS_PARALLEL: true
-        run: |
-          curl -sL https://coveralls.io/coveralls-linux.tar.gz | tar -xz
-          ./coveralls done --build-number ${{ github.run_number }}
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@v2
+      with:
+        parallel-finished: true
+

.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 }}
 
@@ -42,20 +42,20 @@ jobs:
     - name: Test with pytest
       run: pytest
 
-    - name: Publish results to coveralls
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        COVERALLS_PARALLEL: true
-      run: coveralls --rcfile=pyproject.toml --service=github
+    - name: Coveralls Parallel
+      uses: coverallsapp/github-action@v2
+      with:
+        flag-name: run-${{ join(matrix.*, '-') }}
+        parallel: true
 
   finish:
     name: Finish Coverage Analysis
     needs: build
+    if: ${{ always() }}
     runs-on: ubuntu-latest
     steps:
     - name: Coveralls Finished
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: |
-        pip install --upgrade coveralls
-        coveralls --service=github --finish
+      uses: coverallsapp/github-action@v2
+      with:
+        parallel-finished: true
+

.zenodo.json

@@ -5,6 +5,7 @@
     "atmosphere",
     "thermosphere",
     "magnetosphere",
+    "mars",
     "heliosphere",
     "observations",
     "models",
@@ -18,16 +19,16 @@
         "name": "Klenzing, Jeff",
         "orcid": "0000-0001-8321-6074"
       },
-      {
-        "affiliation": "Cosmic Studio",
-        "name": "Stoneback, Russell",
-        "orcid": "0000-0001-7216-4336"
-      },
       {
         "affiliation": "U.S. Naval Research Laboratory",
         "name": "Burrell, Angeline G.",
         "orcid": "0000-0001-8875-9326"
       },
+      {
+        "affiliation": "Cosmic Studio",
+        "name": "Stoneback, Russell",
+        "orcid": "0000-0001-7216-4336"
+      },
       {
         "affiliation": "Catholic University of America, Goddard Space Flight Center",
         "name": "Smith, Jonathon",
@@ -43,6 +44,11 @@
         "name": "Esman, Teresa",
         "orcid": "0000-0003-0382-6281"
       },
+      {
+        "affiliation": "Universities Space Research Association, Goddard Space Flight Center",
+        "name": "Govada, Aadarsh",
+        "orcid": "0009-0004-7873-5899"
+      },
       {
         "affiliation": "Predictive Science",
         "name": "Pembroke, Asher"

ACKNOWLEDGEMENTS.md

@@ -19,6 +19,7 @@ Missions
 - NASA Scintillation Observations and Response of the Ionosphere to
   Electrodynamics (SORTIE)
 - NASA Scintillation Prediction Observations Research Task (SPORT)
+- NOAA Constellation Observing System for Meteorology Ionosphere and Climate (COSMIC-2)
 
 Disclaimers
 ===========

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] - 2024-10-03
 * 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
@@ -14,6 +14,7 @@ This project adheres to [Semantic Versioning](https://semver.org/).
   * Allow files to be unzipped after download
   * Added custom `concat_data` method to JHUAPL methods, for TIMED-GUVI and
     DMSP-SSUSI data
+  * Added time-dependent, file format function for DMSP SSUSI to DMSP methods
   * Added cleaning to TIMED-GUVI SDR imaging data
 * Bug Fixes
   * Fix general clean routine to skip transformation matrices
@@ -23,10 +24,13 @@ This project adheres to [Semantic Versioning](https://semver.org/).
   * Allow graceful failure with no files in jhuapl load functions
   * New window needs to be integer for calculate_imf_steadiness
   * Fixed a bug where cdas_download may drop the requested end date file
+  * Reverted the coveralls integration to the GitHub service for MacOS runs
+  * Fixed a bug where cdas_list_remote_files errored without remote data
 * Documentation
   * Added example of how to export data for archival
   * Updated documentation refs
   * Add keywords to zenodo
+  * Fixed broken links
 * Deprecations
   * Deprecated '' tag for de2_vefi module, support moved to de2_vefimagb
 * Maintenance
@@ -38,6 +42,10 @@ 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
+  * Implement coveralls app in GitHub Actions
+  * Cycled Operational Environment testing
 
 ## [0.0.5] - 2023-06-27
 * New Instruments

docs/archival.rst

@@ -52,7 +52,11 @@ preferred formats.  An example of this is:
 In this case, note that the pysat 'name' label is output to three different
 metadata values required by the ITSP standards. Additionally, the
 :py:attr:`export_pysat_info` option is set to false here. This drops several
-internal :py:mod:`pysat` metadata values before writing to file.
+internal :py:mod:`pysat` metadata values before writing to file. Note that
+this includes the default acknowledgements and references objects. These
+are set manually to avoid conflicts between the original dataset and the
+new dataset, as well as keeping in line with requirements with potentially
+different data servers. An example can be found in the [REACH Operational Software](https://github.com/jklenzing/ops_reach/blob/main/ops_reach/instruments/methods/reach.py).
 
 A full guide to SPDF metadata standards can be found 
 `at SPDF <https://spdf.gsfc.nasa.gov/istp_guide/istp_guide.html>`_.

docs/supported_instruments.rst

@@ -125,6 +125,8 @@ DMSP SSUSI
 
 FORMOSAT-1 IVM
 --------------
+Note that the Ion Velocity Meter data product is managed here since the repository is
+at CDAWeb. For other FORMOSAT-X data products, please see pysatCDAAC.
 
 .. automodule:: pysatNASA.instruments.formosat1_ivm
   :members:
@@ -188,8 +190,8 @@ JPL GPS
 
 .. _maven_insitu_kp:
 
-MAVEN INSITU KP
----------------
+MAVEN IN SITU KP
+----------------
 
 .. automodule:: pysatNASA.instruments.maven_insitu_kp
    :members:

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"
@@ -53,7 +53,6 @@ dependencies = [
 [project.optional-dependencies]
 pysatcdf = ["pysatCDF"]
 test = [
-  "coveralls",
   "flake8",
   "flake8-docstrings",
   "hacking >= 1.0",
@@ -84,6 +83,7 @@ markers = [
   "download",
   "no_download",
   "load_options",
+  "new_tests",
   "first",
   "second"
 ]

pysatNASA/instruments/cnofs_vefi.py

@@ -23,7 +23,7 @@
 spacecraft is to enable an accurate V x B measurement along the spacecraft
 trajectory.  In order to provide an in-flight calibration of the magnetic field
 data, we compare the most recent POMME model (the POtsdam Magnetic Model of the
-Earth, https://geomag.us/models/pomme5.html) with the actual magnetometer
+Earth, https://geomag.org/models/pomme5.html) with the actual magnetometer
 measurements to help determine a set of calibration parameters for the gains,
 offsets, and non-orthogonality matrix of the sensor axes.  The calibrated
 magnetic field measurements are provided in the data file here. The VEFI

pysatNASA/instruments/de2_vefi.py

@@ -43,12 +43,14 @@
 tag
     '', 'dca', 'ac'
 inst_id
-    none supported
+    None supported
 
 
 Warnings
 --------
 - Currently no cleaning routine.
+- The deprecated '' tag will drop the E-field data. To use this data
+  product, please use the new de2_vefimagb instrument.
 
 
 """
@@ -133,7 +135,9 @@ 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 +150,16 @@ 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():

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.