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Documentation update for v0.10 #26

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Feb 3, 2022
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541d871
Doc WIP
jeandet Nov 4, 2021
34ed161
[Documentation] Rewrite in progress
jeandet Jan 19, 2022
f3ba3ea
[Documentation] More switch to numpydoc
jeandet Jan 20, 2022
211ed9e
[Documentation] Switch to numpydoc complete, AMDA introduction OK
jeandet Jan 22, 2022
a777b08
[Fix] it seems we can't change tzinfo on a datetime
jeandet Jan 22, 2022
0f7389d
Dynamic plot with Bokeh WIP
jeandet Jan 22, 2022
52008a2
[Documentation] Basic SSCWeb module documentation
jeandet Jan 24, 2022
69aa198
Removes Python 3.6 support and adds Python 3.10
jeandet Jan 24, 2022
bcbe975
Try to pass AMDA credentials to doctest in GH Actions
jeandet Jan 24, 2022
e72bb70
[Documentation] Skip AMDA user products access from doctest
jeandet Jan 24, 2022
7660873
[Documentation] Removes standalone examples since they are in API doc…
jeandet Jan 25, 2022
141cb9b
[Documentation] Make AMDA list_ examples more robust for doctest
jeandet Jan 25, 2022
42fa31b
[Documentation] Adds two more complete examples about AMDA usage
jeandet Jan 25, 2022
d5cd3db
[Documentation] Removes auto generated doc files
jeandet Jan 25, 2022
904c824
[Documentation] Adds citation file for GitHub https://docs.github.com…
jeandet Jan 25, 2022
78453aa
[Documentation] Adds missing entries into history file
jeandet Jan 25, 2022
ee235c5
[Documentation] Fix minor typos
jeandet Jan 25, 2022
2211818
[Documentation] Split back readme and doc index :/ plus some overall doc
jeandet Jan 25, 2022
382b8ce
[Documentation] Typo + rephrase AMDA Magnetic Cloud example
jeandet Jan 25, 2022
3bf9ee1
[Documentation] Better index page for RTD doc and some minor stuff
jeandet Jan 26, 2022
a59831f
[Documentation] Adds a notebooks gallery
jeandet Jan 26, 2022
ba23385
[Documentation] Adds ipywidgets and ipympl reqs for RTD and nbsphinx
jeandet Jan 26, 2022
80e9afd
[Documentation] GH Actions needs documentation packages too for doctest
jeandet Jan 27, 2022
f2f4fb4
[SSCWeb] restore get_orbit with a deprecation message
jeandet Jan 27, 2022
07cf307
[Documentation] GH Actions needs documentation packages too for doctest
jeandet Jan 27, 2022
450e6ed
[Documentation] Make code examples clickable, and update intersphinx …
jeandet Jan 27, 2022
eb90a5a
[Documentation] Adds some notes stating that Speasy isn't a plotting …
jeandet Jan 27, 2022
1f0a9a5
[Documentation] preinstall astropy from doc requirements to avoid usi…
jeandet Jan 27, 2022
4f91e7a
[Documentation] same with pandas...
jeandet Jan 27, 2022
83a550a
[Documentation] Use sphinxcontrib-apidoc module to auto-run apidoc on…
jeandet Jan 27, 2022
10c9a7a
[Documentation] fixes missing header with binderhub link
jeandet Jan 27, 2022
e4bfc0b
[Documentation] links update
jeandet Jan 27, 2022
ce84a50
[Documentation] Adds caches analysis notebook in gallery
jeandet Jan 27, 2022
f9f68ad
[GH Actions] fix typo
jeandet Jan 28, 2022
b6fe705
[Documentation] Forgot to update binder badges URLs
jeandet Jan 28, 2022
1930377
Fixes #33, until we have something more elegant
jeandet Feb 1, 2022
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15 changes: 9 additions & 6 deletions .github/workflows/PRs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,15 @@ on: [pull_request]

jobs:
build:
env:
SPEASY_AMDA_USERNAME: ${{ secrets.SPEASY_AMDA_USERNAME }}
SPEASY_AMDA_PASSWORD: ${{ secrets.SPEASY_AMDA_PASSWORD }}

runs-on: ubuntu-latest
strategy:
max-parallel: 4
matrix:
python-version: [3.6, 3.7, 3.8, 3.9]
python-version: ['3.7', '3.8', '3.9', '3.10']

steps:
- uses: actions/checkout@v2
Expand All @@ -29,13 +32,13 @@ jobs:
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: install texlive for Pandoc
run: sudo apt update && sudo apt install -y texlive pandoc && pip install wheel
- name: Test with pytest
env:
SPEASY_AMDA_USERNAME: ${{ secrets.SPEASY_AMDA_USERNAME }}
SPEASY_AMDA_PASSWORD: ${{ secrets.SPEASY_AMDA_PASSWORD }}
run: |
pip install pytest pytest-cov sphinx numpydoc sphinx-rtd-theme
SPEASY_AMDA_PASSWORD="${{ secrets.SPEASY_AMDA_PASSWORD }}" SPEASY_AMDA_USERNAME="${{ secrets.SPEASY_AMDA_USERNAME }}" pytest --cov=./ --cov-report=xml
pip install pytest pytest-cov sphinx pandoc
pip install -r docs/requirements.txt
pytest --cov=./ --cov-report=xml
make doctest
- name: Upload coverage to Codecov
if: matrix.python-version == '3.8'
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/pythonpublish.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ jobs:
strategy:
max-parallel: 4
matrix:
python-version: [3.6]
python-version: [3.7]
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
Expand Down
15 changes: 9 additions & 6 deletions .github/workflows/tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,15 @@ on: [push]

jobs:
build:
env:
SPEASY_AMDA_USERNAME: ${{ secrets.SPEASY_AMDA_USERNAME }}
SPEASY_AMDA_PASSWORD: ${{ secrets.SPEASY_AMDA_PASSWORD }}

runs-on: ubuntu-latest
strategy:
max-parallel: 4
matrix:
python-version: [3.6, 3.7, 3.8, 3.9]
python-version: ['3.7', '3.8', '3.9', '3.10']

steps:
- uses: actions/checkout@v2
Expand All @@ -29,13 +32,13 @@ jobs:
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: install texlive for Pandoc
run: sudo apt update && sudo apt install -y texlive pandoc && pip install wheel
- name: Test with pytest
env:
SPEASY_AMDA_USERNAME: ${{ secrets.SPEASY_AMDA_USERNAME }}
SPEASY_AMDA_PASSWORD: ${{ secrets.SPEASY_AMDA_PASSWORD }}
run: |
pip install pytest pytest-cov sphinx numpydoc sphinx-rtd-theme
SPEASY_AMDA_PASSWORD="${{ secrets.SPEASY_AMDA_PASSWORD }}" SPEASY_AMDA_USERNAME="${{ secrets.SPEASY_AMDA_USERNAME }}" pytest --cov=./ --cov-report=xml
pip install pytest pytest-cov sphinx pandoc
pip install -r docs/requirements.txt
pytest --cov=./ --cov-report=xml
make doctest
- name: Upload coverage to Codecov
if: matrix.python-version == '3.8'
Expand Down
16 changes: 16 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -103,3 +103,19 @@ ENV/

# IDE
.idea/

#auto generated doc files
/docs/dev/modules.rst
/docs/dev/speasy.common.rst
/docs/dev/speasy.config.rst
/docs/dev/speasy.core.cache.rst
/docs/dev/speasy.core.proxy.rst
/docs/dev/speasy.core.rst
/docs/dev/speasy.inventory.rst
/docs/dev/speasy.products.rst
/docs/dev/speasy.rst
/docs/dev/speasy.webservices.amda.rst
/docs/dev/speasy.webservices.cda.rst
/docs/dev/speasy.webservices.csa.rst
/docs/dev/speasy.webservices.rst
/docs/dev/speasy.webservices.ssc.rst
11 changes: 11 additions & 0 deletions CITATION.cff
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
@software{alexis_jeandet_2021_5727877,
author = {Alexis Jeandet and
Alexandre Schulz},
title = {{SciQLop/speasy: 0.9.1)}},
month = nov,
year = 2021,
publisher = {Zenodo},
version = {v0.9.1},
doi = {10.5281/zenodo.5727877},
url = {https://doi.org/10.5281/zenodo.5727877}
}
17 changes: 17 additions & 0 deletions HISTORY.rst
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,23 @@
History
=======

0.9.1 (2021-11-25)
==================

* Fix AMDA module bug `#24 downloading multidimensional data fails <https://github.com/SciQLop/speasy/issues/24>`_

0.9.0 (2021-07-29)
==================

* Adds SPWC migration tool
* Rename SpwcVariable to SpeasyVariable

0.8.3 (2021-07-28)
==================

* Package renamed from SPWC to SPEASY
* Some doc and CI improvements

0.8.2 (2021-04-20)
==================

Expand Down
6 changes: 3 additions & 3 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -69,9 +69,9 @@ coverage: ## check code coverage quickly with the default Python
$(BROWSER) htmlcov/index.html

docs: ## generate Sphinx HTML documentation, including API docs
rm -f docs/speasy.rst
rm -f docs/modules.rst
sphinx-apidoc -M -o docs/ speasy
rm -f docs/dev/speasy.rst
rm -f docs/dev/modules.rst
#sphinx-apidoc -M -o docs/dev speasy
$(MAKE) -C docs clean
$(MAKE) -C docs html
$(BROWSER) docs/_build/html/index.html
Expand Down
14 changes: 11 additions & 3 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ Space Physics made EASY
:alt: Zendoo DOI

.. image:: https://mybinder.org/badge_logo.svg
:target: https://mybinder.org/v2/gh/SciQLop/spwc/HEAD?filepath=examples%2Fdemo.ipynb
:target: https://mybinder.org/v2/gh/SciQLop/speasy/main?labpath=docs/examples
:alt: Discover on MyBinder

Speasy is an open source Python client for Space Physics web services such as `CDAWEB <https://cdaweb.gsfc.nasa.gov/index.html/>`_
Expand All @@ -47,7 +47,7 @@ Speasy aims to support as much as possible web services and also cover a maximum
Quickstart
----------

Installing Speasy with pip (:doc:`more details here <installation>`):
Installing Speasy with pip (`more details here <https://speasy.readthedocs.io/en/stable/installation.html>`_):

.. code-block:: console

Expand Down Expand Up @@ -99,7 +99,13 @@ Features

Examples
========
See `here <https://nbviewer.jupyter.org/github/SciQLop/speasy/blob/main/examples/demo.ipynb>`_ for a complete list of examples.
See `here <https://speasy.readthedocs.io/en/stable/examples/index.html`_ for a complete list of examples.

Caveats
=======
- installing speasy on both python 3.7 or less and python 3.8 or plus at the same time doesn't work since entries stored
in cache by python 3.8+ are not readable by python 3.7-.
- Speasy is not a plotting package, while it provides basic plot features, it is not meant to produce publication ready figures.

Credits
========
Expand All @@ -108,3 +114,5 @@ This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypack

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

The development of speasy is supported by the `CDPP <http://www.cdpp.eu/>`_.
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148 changes: 0 additions & 148 deletions docs/amda.rst

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23 changes: 0 additions & 23 deletions docs/amda_catalogs.rst

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23 changes: 0 additions & 23 deletions docs/amda_datasets.rst

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6 changes: 0 additions & 6 deletions docs/amda_example_1.rst

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6 changes: 0 additions & 6 deletions docs/amda_example_2.rst

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