Merge pull request #61 from pysat/rc0_0_5

Release Candidate 0.0.5
pysat · Feb 6, 2025 · 8e18217 · 8e18217
2 parents e5d9c7d + ac39c36
commit 8e18217
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -16,9 +16,9 @@ jobs:
 
     name:
     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
@@ -12,40 +12,48 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.11", "3.12"]
         numpy_ver: ["latest"]
         test_config: ["latest"]
         include:
-          - python-version: "3.9"
-            numpy_ver: "1.21"
+          # SPEC-0 compliance settings w/ minimum supported pysat
+          - python-version: "3.10"
+            numpy_ver: "1.24"
+            pandas_ver: "1.5.0"
+            scipy_ver: "1.10.0"
+            xarray_ver: "2022.9.0"
+            pysat_ver: "3.2.1"
             os: ubuntu-latest
-            test_config: "NEP29"
-          - python-version: "3.6.8"
-            numpy_ver: "1.19.5"
+            test_config: "SPEC0"
+          # Operational compliance settings
+          - 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 }}
 
     - name: Install Operational dependencies
       if: ${{ matrix.test_config == 'Ops'}}
       run: |
-        pip install --no-cache-dir numpy==${{ matrix.numpy_ver }}
-        pip install -r requirements.txt
-        pip install -r test_requirements.txt
-        pip install .
+        pip install numpy==${{ matrix.numpy_ver }}
+        pip install --upgrade-strategy only-if-needed .[test]
 
-    - name: Install NEP29 dependencies
-      if: ${{ matrix.test_config == 'NEP29'}}
+    - name: Install SPEC-0 dependencies
+      if: ${{ matrix.test_config == 'SPEC0'}}
       run: |
         pip install numpy==${{ matrix.numpy_ver }}
+        pip install pandas==${{ matrix.pandas_ver }}
+        pip install scipy==${{ matrix.scipy_ver }}
+        pip install xarray==${{ matrix.xarray_ver }}
+        pip install pysat==${{ matrix.pysat_ver }}
         pip install --upgrade-strategy only-if-needed .[test]
 
     - name: Install standard dependencies
@@ -69,4 +77,18 @@ jobs:
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_PARALLEL: true
       run: coveralls --rcfile=pyproject.toml --service=github
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install --upgrade coveralls
+        coveralls --service=github --finish
+
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
@@ -10,35 +10,46 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.11"]
 
     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 }}
 
     - name: Install pysat RC
       run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pysat
 
-    - name: Install standard dependencies
-      run: |
-        pip install -r requirements.txt
-        pip install -r test_requirements.txt
+    - name: Install standard dependencies and package
+      run: pip install .[test]
 
     - name: Set up pysat
       run: |
         mkdir pysatData
         python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
 
     - name: Test with pytest
-      run: pytest
+      run: pytest -v
 
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_PARALLEL: true
       run: coveralls --rcfile=pyproject.toml --service=github
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install --upgrade coveralls
+        coveralls --service=github --finish
diff --git a/.zenodo.json b/.zenodo.json
@@ -6,7 +6,7 @@
         "orcid": "0000-0001-8321-6074"
       },
       {
-        "affiliation": "Stoneris LLC",
+        "affiliation": "Cosmic Studio",
         "name": "Stoneback, Russell",
         "orcid": "0000-0001-7216-4336"
       },
@@ -16,15 +16,21 @@
         "orcid": "0000-0001-8875-9326"
       },
       {
-        "affiliation": "Predictive Science",
-        "name": "Pembroke, Asher"
+        "affiliation": "Universities Space Research Association, Goddard Space Flight Center",
+        "name": "Govada, Aadarsh",
+        "orcid": "0009-0004-7873-5899"
       },
       {
         "affiliation": "Catholic University of America, Goddard Space Flight Center",
         "name": "Smith, Jonathon M.",
         "orcid": "0000-0002-8191-4765"
       },
       {
+        "affiliation": "Predictive Science",
+        "name": "Pembroke, Asher"
+      },
+      {
+        "affiliation": "The University of Texas at Dallas",
         "name": "Spence, Carey",
         "orcid": "0000-0001-8340-5625"
       }

diff --git a/ACKNOWLEDGEMENTS.md b/ACKNOWLEDGEMENTS.md
@@ -0,0 +1,34 @@
+Funding
+=======
+The following institutions, missions, and programs have provided funding
+for pysatCDAAC development.
+
+Institutions
+------------
+ - The Catholic University of America (CUA)
+ - Cosmic Studio
+ - Defense Advanced Research Projects Agency (DARPA) Defense Sciences Office
+ - National Aeronautics and Space Administration (NASA)
+ - National Oceanic and Atmospheric Administration (NOAA)
+ - National Science Foundation (NSF)
+ - Office of Naval Research (ONR)
+
+Missions
+--------
+ - NOAA Constellation Observing System for Meteorology Ionosphere and Climate
+   (COSMIC-2)
+
+Programs
+--------
+ - NSF 125908, AGS-1651393
+ - NASA Space Precipitation Impacts (SPI) project at Goddard Space Flight Center
+   through the Heliophysics Internal Science Funding Model.
+ - Naval Research Laboratory N00173191G016 and N0017322P0744
+
+Disclaimers
+===========
+Any opinions or actions taken by the listed funding institutions are those of
+the institutions and do not necessarily reflect the views of the pysatCDAAC
+development team or individual authors. Any opinions, findings, and conclusions
+or recommendations expressed in this material are those of the author(s) and do
+not necessarily reflect the views of the funding agencies.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,17 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.0.5] - 2025-02-06
+* Maintenance
+  * Update GitHub Actions standards, including SPEC-0 tests
+  * Add compatibility for numpy version>=3.2.0
+  * Update usage of 'Dataset.dims' to 'Dataset.sizes'
+  * Update compatibility with pysat 3.2.1
+  * Set minimum pysat version to 3.2.1
+  * Set minimum python version to 3.9
+  * Update operational environment
+  * Update controlled information statement for accuracy and clarity
+
 ## [0.0.4] - 2023-08-11
 * Bug fixes
   * Update metadata transfer for COSMIC GPS

diff --git a/README.md b/README.md
@@ -15,13 +15,13 @@ pysatCDAAC uses common Python modules, as well as modules developed by
 and for the Space Physics community.  This module officially supports
 Python 3.7+.
 
-| Common modules | Community modules |
-| -------------- | ----------------- |
-| netCDF4        | pysat>=3.0.4      |
-| numpy          |                   |
-| pandas         |                   |
-| requests       |                   |
-| xarray         |                   |
+| Common modules | Community modules   |
+| -------------- | ------------------- |
+| netCDF4        | pysat>=3.2.1        |
+| numpy          |                     |
+| pandas         |                     |
+| requests       |                     |
+| xarray         |                     |
 
 # Installation
 

diff --git a/docs/acknowledgements.rst b/docs/acknowledgements.rst
@@ -0,0 +1 @@
+.. mdinclude:: ../ACKNOWLEDGEMENTS.md
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,4 +1,12 @@
 # -*- coding: utf-8 -*-
+# Full author list can be found in .zenodo.json file
+# DOI:10.5281/zenodo.3475493
+#
+# Review Status for Classified or Controlled Information by NRL
+# -------------------------------------------------------------
+# DISTRIBUTION STATEMENT A: Approved for public release. Distribution is
+# unlimited.
+# ----------------------------------------------------------------------------
 """Configuration file for the Sphinx documentation builder.
 
 Note

diff --git a/docs/index.rst b/docs/index.rst
@@ -18,6 +18,13 @@ Center (CDAAC) as pysat.Instrument objects.
    examples.rst
    develop_guide.rst
    history.rst
+   acknowledgements.rst
+
+
+.. admonition:: Review Status for Classified or Controlled Information by NRL
+
+   DISTRIBUTION STATEMENT A: Approved for public release.
+   Distribution is unlimited.
 
 
 Indices and tables

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -14,18 +14,17 @@ Prerequisites
 
 pysatCDAAC uses common Python modules, as well as modules developed by
 and for the Space Physics community.  This module officially supports
-Python 3.6+ and pysat 3.0.4+.
+Python 3.9+ and pysat 3.2.1+.
 
- ================== =================
+ ================== ====================
  Common modules     Community modules
- ================== =================
-  netCDF4            pysat>=3.0.4
+ ================== ====================
+  netCDF4            pysat>=3.2.1
   numpy
   pandas
   requests
   xarray
- ================== =================
-
+ ================== ====================
 
 Installation Options
 --------------------
@@ -56,11 +55,14 @@ Installation Options
 
         pip install --user -e .
 
-.. extras-require:: test
-    :pyproject:
 
-.. extras-require:: doc
-    :pyproject:
+..
+    .. extras-require:: test
+        :pyproject:
+
+..
+    .. extras-require:: doc
+        :pyproject:
 
 .. _post-install:
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -4,10 +4,10 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pysatCDAAC"
-version = "0.0.4"
+version = "0.0.5"
 description = "pysat support for CDAAC Instruments"
 readme = "README.md"
-requires-python = ">=3.6"
+requires-python = ">=3.9"
 license = {file = "LICENSE"}
 authors = [
     {name = "Jeff Klenzing, et al.", email = "[email protected]"},
@@ -21,10 +21,10 @@ classifiers = [
   "License :: OSI Approved :: BSD License",
   "Natural Language :: English",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.6",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Operating System :: POSIX :: Linux",
   "Operating System :: MacOS :: MacOS X",
   "Operating System :: Microsoft :: Windows"
@@ -39,7 +39,7 @@ dependencies = [
   "netCDF4",
   "numpy",
   "pandas",
-  "pysat >= 3.0.4",
+  "pysat >= 3.2.1",
   "requests",
   "xarray"
 ]
@@ -61,7 +61,7 @@ doc = [
   "numpydoc",
   "sphinx < 7.0",
   "sphinx-autoapi",
-  "sphinx_rtd_theme >= 1.2.2"
+  "sphinx_rtd_theme >= 1.2.2, <2.0.0"
 ]
 
 [project.urls]
@@ -71,12 +71,13 @@ Source = "https://github.com/pysat/pysatCDAAC"
 [tool.coverage.report]
 
 [tool.pytest.ini_options]
-addopts = "--cov=pysatCDAAC"
+addopts = "--cov=pysatCDAAC --cov-report xml"
 markers = [
   "all_inst",
   "download",
   "no_download",
   "load_options",
+  "new_tests",
   "first",
   "second"
 ]