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MAINT: NEP29 Apr 2024, zenodo updates #227

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Jul 8, 2024
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8b377f2
DOC: udpate zenodo
jklenzing Mar 28, 2024
0793fa5
MAINT: NEP29 apr 2024
jklenzing Mar 28, 2024
a7d3d35
DOC: update supported versions
jklenzing Mar 28, 2024
e968fec
DOC: update changelog
jklenzing Mar 28, 2024
b3ce91f
BUG: no new tests for ssusi
jklenzing Apr 9, 2024
379c4e3
BUG: comment out buggy tests
jklenzing Apr 11, 2024
8ed391b
BUG: turn off new tests for ICON FUV
jklenzing Apr 15, 2024
6fb8dfa
BUG: remove icon clean tests
jklenzing May 2, 2024
bb65a0b
BUG: manual install of git
jklenzing May 6, 2024
458f426
BUG: git branch
jklenzing May 6, 2024
b7b404c
BUG: spelling
jklenzing May 6, 2024
b198dea
BUG: use python setup
jklenzing May 6, 2024
9c5032e
BUG: hdf
jklenzing May 6, 2024
58af874
BUG: develop
jklenzing May 6, 2024
adae8e9
Update main.yml
jklenzing Jun 14, 2024
27cb538
Update main.yml
jklenzing Jun 14, 2024
d4bfcc2
BUG: always run finish
jklenzing Jun 14, 2024
ea02b89
BUG: GA syntax
jklenzing Jun 14, 2024
c49a879
BUG: turn off new tests for maven sep
jklenzing Jun 14, 2024
a53a469
Try coveralls app
jklenzing Jun 17, 2024
e1be3b6
BUG: switch to coveralls app
aburrell Jun 20, 2024
8c29804
BUG: fix yaml syntax
aburrell Jun 20, 2024
519f267
BUG: more yaml fixes
aburrell Jun 20, 2024
2012f63
BUG: re-added steps
aburrell Jun 20, 2024
4604d60
BUG: added if to yaml
aburrell Jun 20, 2024
5bdc4b5
BUG: fixed secret name
aburrell Jun 20, 2024
b0f6baf
BUG: specify coverage file
aburrell Jun 20, 2024
ed9ddd7
BUG: added debug line
aburrell Jun 20, 2024
86981a6
BUG: use coveralls repo token
aburrell Jun 20, 2024
8277eba
BUG: specify format
aburrell Jun 21, 2024
e35b977
BUG: remove "extra" options
aburrell Jun 21, 2024
a1a6baa
Revert "BUG: remove "extra" options"
aburrell Jun 21, 2024
ca2fe8a
BUG: add verbose mode
aburrell Jun 21, 2024
8220845
BUG: specify xml output
aburrell Jun 21, 2024
0abe87c
BUG: remove tabs from yaml
aburrell Jun 21, 2024
1d4c87b
BUG: update xml
aburrell Jun 21, 2024
090e4e1
BUG: made coveralls update
aburrell Jul 1, 2024
4086f8b
BUG: added debug
aburrell Jul 1, 2024
aa05825
NEP29 for June 2024
jklenzing Jul 8, 2024
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59 changes: 46 additions & 13 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,12 @@ 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"
- python-version: "3.10"
numpy_ver: "1.23"
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os: ubuntu-latest
test_config: "NEP29"
- python-version: "3.6.8"
Expand All @@ -40,10 +40,17 @@ 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 .

- name: Install NEP29 dependencies
Expand Down Expand Up @@ -71,20 +78,46 @@ jobs:
- name: Test with pytest
run: pytest

- name: Publish results to coveralls
- name: Coveralls Parallel (Ubuntu)
if: startsWith(matrix.os, 'ubuntu')
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
COVERALLS_PARALLEL: true
run: coveralls --rcfile=pyproject.toml --service=github
run: |
curl -sL https://coveralls.io/coveralls-linux.tar.gz | tar -xz
./coveralls report --parallel --repo-token=${{ 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

finish:
name: Finish Coverage Analysis
needs: build
runs-on: ubuntu-latest
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
- 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 }}
25 changes: 19 additions & 6 deletions .zenodo.json
Original file line number Diff line number Diff line change
@@ -1,12 +1,25 @@
{
"keywords": [
"pysat",
"ionosphere",
"atmosphere",
"thermosphere",
"magnetosphere",
"heliosphere",
"observations",
"models",
"space",
"satellites",
"analysis"
],
"creators": [
{
"affiliation": "Goddard Space Flight Center",
"name": "Klenzing, Jeff",
"orcid": "0000-0001-8321-6074"
},
{
"affiliation": "The University of Texas at Dallas",
"affiliation": "Cosmic Studio",
"name": "Stoneback, Russell",
"orcid": "0000-0001-7216-4336"
},
Expand All @@ -25,18 +38,18 @@
"name": "Navarro, Luis",
"orcid": "0000-0002-6362-6575"
},
{
"affiliation": "NASA Postdoctoral Program, Goddard Space Flight Center",
"name": "Esman, Teresa",
"orcid": "0000-0003-0382-6281"
},
{
"affiliation": "Predictive Science",
"name": "Pembroke, Asher"
},
{
"name": "Spence, Carey",
"orcid": "0000-0001-8340-5625"
},
{
"affiliation": "NASA Postdoctoral Program, Goddard Space Flight Center",
"name": "Esman, Teresa",
"orcid": "0000-0003-0382-6281"
}
]
}
2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ This project adheres to [Semantic Versioning](https://semver.org/).
* Documentation
* Added example of how to export data for archival
* Updated documentation refs
* Add keywords to zenodo
* Deprecations
* Deprecated '' tag for de2_vefi module, support moved to de2_vefimagb
* Maintenance
Expand All @@ -35,6 +36,7 @@ This project adheres to [Semantic Versioning](https://semver.org/).
* Use standard clean routine for C/NOFS VEFI mag data
* Added version cap for sphinx_rtd_theme
* Include standard tests for ICON IVM-B
* Update NEP29 standards for Apr 2024
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## [0.0.5] - 2023-06-27
* New Instruments
Expand Down
4 changes: 2 additions & 2 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,9 @@ classifiers = [
"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"
Expand Down Expand Up @@ -78,7 +78,7 @@ Source = "https://github.com/pysat/pysatNASA"
omit = ["*/instruments/templates/"]

[tool.pytest.ini_options]
addopts = "--cov=pysatNASA"
addopts = "--cov=pysatNASA --cov-report xml"
markers = [
"all_inst",
"download",
Expand Down
12 changes: 8 additions & 4 deletions pysatNASA/instruments/dmsp_ssusi.py
Original file line number Diff line number Diff line change
Expand Up @@ -84,17 +84,21 @@

_test_dates = {inst_id: {tag: dt.datetime(2015, 1, 1) for tag in tags.keys()}
for inst_id in inst_ids.keys()}
_clean_warn = {inst_id: {tag: mm_nasa.clean_warnings
for tag in inst_ids[inst_id]
if tag not in ['sdr-disk', 'sdr2-disk']}
for inst_id in inst_ids.keys()}
# TODO(pysat#1196): Un-comment when pysat bug is fixed and released
# _clean_warn = {inst_id: {tag: mm_nasa.clean_warnings
# for tag in inst_ids[inst_id]
# if tag not in ['sdr-disk', 'sdr2-disk']}
# for inst_id in inst_ids.keys()}

# ----------------------------------------------------------------------------
# Instrument methods


# Use standard init routine
init = functools.partial(mm_nasa.init, module=mm_dmsp, name=name)
# TODO(#218, #222): Remove when compliant with multi-day load tests
_new_tests = {inst_id: {tag: False for tag in tags.keys()}
for inst_id in inst_ids.keys()}


def clean(self):
Expand Down
6 changes: 3 additions & 3 deletions pysatNASA/instruments/icon_fuv.py
Original file line number Diff line number Diff line change
Expand Up @@ -67,9 +67,9 @@

_test_dates = {'': {kk: dt.datetime(2020, 1, 1) for kk in tags.keys()}}
_test_load_opt = {'': {kk: {'keep_original_names': True} for kk in tags.keys()}}
_clean_warn = {inst_id: {tag: mm_icon.fuv_clean_warnings
for tag in inst_ids[inst_id]}
for inst_id in inst_ids.keys()}
# TODO(#218, #222): Remove when compliant with multi-day load tests
_new_tests = {inst_id: {tag: False for tag in tags.keys()}
for inst_id in inst_ids.keys()}

# ----------------------------------------------------------------------------
# Instrument methods
Expand Down
3 changes: 3 additions & 0 deletions pysatNASA/instruments/maven_sep.py
Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,9 @@
# Instrument test attributes

_test_dates = {id: {'': dt.datetime(2020, 1, 1)} for id in inst_ids.keys()}
# TODO(#218, #222): Remove when compliant with multi-day load tests
_new_tests = {inst_id: {tag: False for tag in tags.keys()}
for inst_id in inst_ids.keys()}

# ----------------------------------------------------------------------------
# Instrument methods
Expand Down
7 changes: 4 additions & 3 deletions pysatNASA/instruments/timed_guvi.py
Original file line number Diff line number Diff line change
Expand Up @@ -97,9 +97,10 @@
for iid in ['high_res', 'low_res']}
# TODO(#218): Remove when compliant with multi-day load tests
_new_tests = {'high_res': {tag: False for tag in inst_ids['high_res']}}
_clean_warn = {inst_id: {tag: mm_nasa.clean_warnings
for tag in inst_ids[inst_id] if tag != 'sdr-imaging'}
for inst_id in inst_ids.keys()}
# TODO(pysat#1196): Un-comment when pysat bug is fixed and released
# _clean_warn = {inst_id: {tag: mm_nasa.clean_warnings
# for tag in inst_ids[inst_id] if tag != 'sdr-imaging'}
# for inst_id in inst_ids.keys()}

# ----------------------------------------------------------------------------
# Instrument methods
Expand Down
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