seppy 0.1.4__tar.gz → 0.4.0__tar.gz

seppy-0.4.0/.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

seppy-0.4.0/.github/release.yml

@@ -0,0 +1,10 @@
+# .github/release.yml
+
+changelog:
+  categories:
+    - title: Bugfixes 🛠
+      labels:
+        - bug
+    - title: New Features 🎉
+      labels:
+        - enhancement

seppy-0.4.0/.github/workflows/pytest.yml

@@ -0,0 +1,45 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: pytest
+
+on:
+  push:
+    # branches: [ "main" ]
+  pull_request:
+    # branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v5
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 nbmake pytest pytest-doctestplus pytest-cov
+        # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        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: Test with pytest
+      run: |
+        pytest --cov --nbmake .
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v5
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

seppy-0.4.0/.gitignore

@@ -0,0 +1,141 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# file generated by setuptools_scm
+_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tmp/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+.vscode/settings.json
+
+### MacOS: https://raw.githubusercontent.com/github/gitignore/master/Global/macOS.gitignore
+
+# General
+.DS_Store
+.AppleDouble
+.LSOverride

seppy-0.4.0/.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt

seppy-0.4.0/.zenodo.json

@@ -0,0 +1,53 @@
+{
+    "description": "A compendium of Python data loaders and analysis tools for in-situ measurements of Solar Energetic Particles (SEP).",
+    "license": "BSD-3-Clause",
+    "title": "SEPpy",
+    "grants": [
+        {
+            "id": "10.13039/501100000780::101004159"
+        }
+    ], 
+    "upload_type": "software",
+    "creators": [
+        {
+            "name": "Gieseler, Jan",
+            "orcid": "0000-0003-1848-7067",
+            "affiliation": "University of Turku"
+        },
+        {
+            "name": "Palmroos, Christian",
+            "orcid": "0000-0002-7778-5454",
+            "affiliation": "University of Turku"
+        },
+        {
+            "name": "Dresing, Nina",
+            "orcid": "0000-0003-3903-4649",
+            "affiliation": "University of Turku"
+        },
+        {
+            "name": "Morosan, Diana",
+            "orcid": "0000-0002-8416-1375",
+            "affiliation": "University of Turku"
+        },
+        {
+            "name": "Asvestari, Eleanna",
+            "orcid": "0000-0002-6998-7224",
+            "affiliation": "University of Helsinki"
+        },
+        {
+            "name": "Yli-Laurila, Aleksi",
+            "affiliation": "University of Turku"
+        },
+        {
+            "name": "Price, Daniel J.",
+            "orcid": "0000-0002-8065-2847",
+            "affiliation": "University of Helsinki"
+        },
+        {
+            "name": "Vainio, Rami",
+            "orcid": "0000-0002-3298-2067",
+            "affiliation": "University of Turku"
+        }
+    ],
+    "access_right": "open"
+}

seppy-0.4.0/CITATION.cff

@@ -0,0 +1,81 @@
+# YAML 1.2
+# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
+cff-version: 1.0.3
+message: If you use this software, please cite it using these metadata.
+title: SEPpy
+doi: 10.5281/zenodo.15275445
+authors:
+- given-names: Jan
+  family-names: Gieseler
+  affiliation: University of Turku
+  orcid: https://orcid.org/0000-0003-1848-7067
+- given-names: Christian
+  family-names: Palmroos
+  affiliation: University of Turku
+  orcid: https://orcid.org/0000-0002-7778-5454
+- given-names: Nina
+  family-names: Dresing
+  affiliation: University of Turku
+  orcid: https://orcid.org/0000-0003-3903-4649
+- given-names: Diana
+  family-names: Morosan
+  affiliation: University of Turku
+  orcid: https://orcid.org/0000-0002-8416-1375
+- given-names: Eleanna
+  family-names: Asvestari
+  affiliation: University of Helsinki
+  orcid: https://orcid.org/0000-0002-6998-7224
+- given-names: Aleksi
+  family-names: Yli-Laurila
+  affiliation: University of Turku
+- given-names: Daniel
+  family-names: Price
+  name-particle: J.
+  affiliation: University of Helsinki
+  orcid: https://orcid.org/0000-0002-8065-2847
+- given-names: Rami
+  family-names: Vainio
+  affiliation: University of Turku
+  orcid: https://orcid.org/0000-0002-3298-2067
+version: 0.4.0
+date-released: 2025-04-24
+repository-code: https://github.com/serpentine-h2020/SEPpy
+license: BSD-3-Clause
+preferred-citation:
+  type: article
+  authors:
+  - given-names: Christian
+    family-names: Palmroos
+    orcid: https://orcid.org/0000-0002-7778-5454
+  - given-names: Jan
+    family-names: Gieseler
+    orcid: https://orcid.org/0000-0003-1848-7067
+  - given-names: Nina
+    family-names: Dresing
+    orcid: https://orcid.org/0000-0003-3903-4649
+  - given-names: Diana
+    family-names: Morosan
+    orcid: https://orcid.org/0000-0002-8416-1375
+  - given-names: Eleanna
+    family-names: Asvestari
+    affiliation: University of Helsinki
+    orcid: https://orcid.org/0000-0002-6998-7224
+  - given-names: Aleksi
+    family-names: Yli-Laurila
+    affiliation: University of Turku
+  - given-names: "Daniel J."
+    family-names: Price
+    orcid: https://orcid.org/0000-0003-2672-5491
+  - given-names: Saku
+    family-names: Valkila
+    affiliation: University of Turku
+  - given-names: Rami
+    family-names: Vainio
+    orcid: https://orcid.org/0000-0002-3298-2067
+  doi: 10.3389/fspas.2022.1073578
+  url: http://dx.doi.org/10.3389/fspas.2022.1073578
+  journal: Frontiers in Astronomy and Space Sciences
+  month: 12
+  title: 'Solar Energetic Particle Time Series Analysis with Python'
+  volume: 9
+  year: 2022

seppy-0.4.0/MANIFEST.in

@@ -0,0 +1,11 @@
+# Exclude specific files
+# All files which are tracked by git and not explicitly excluded here are included by setuptools_scm
+# Prune folders
+prune build
+prune docs/_build
+prune docs/api
+global-exclude *.pyc *.o
+
+# This subpackage is only used in development checkouts
+# and should not be included in built tarballs
+prune seppy/_dev

seppy-0.4.0/PKG-INFO

@@ -0,0 +1,121 @@
+Metadata-Version: 2.4
+Name: seppy
+Version: 0.4.0
+Summary: SEPpy
+Author-email: Jan Gieseler <jan.gieseler@utu.fi>
+License-Expression: BSD-3-Clause
+Project-URL: repository, https://github.com/serpentine-h2020/SEPpy
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE.rst
+Requires-Dist: astropy
+Requires-Dist: astroquery
+Requires-Dist: bs4
+Requires-Dist: cdflib
+Requires-Dist: ipympl
+Requires-Dist: ipywidgets
+Requires-Dist: matplotlib
+Requires-Dist: mpl-animators>=1.0.0
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pooch
+Requires-Dist: psutil
+Requires-Dist: requests
+Requires-Dist: solo-epd-loader
+Requires-Dist: sunpy[all]>=4.1.0
+Requires-Dist: tqdm
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-doctestplus; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-automodapi; extra == "docs"
+Dynamic: license-file
+
+seppy
+=====
+
+|pypi Version| |python version| |pytest| |codecov| |docs| |repostatus| |zenodo doi|
+
+.. |pypi Version| image:: https://img.shields.io/pypi/v/seppy?style=flat&logo=pypi
+   :target: https://pypi.org/project/seppy/
+.. |python version| image:: https://img.shields.io/pypi/pyversions/seppy?style=flat&logo=python
+.. |zenodo doi| image:: https://zenodo.org/badge/451799504.svg
+   :target: https://zenodo.org/badge/latestdoi/451799504
+.. |pytest| image:: https://github.com/serpentine-h2020/SEPpy/actions/workflows/pytest.yml/badge.svg?branch=main
+.. |codecov| image:: https://codecov.io/gh/serpentine-h2020/SEPpy/branch/main/graph/badge.svg?token=FYELM4Y7DF 
+   :target: https://codecov.io/gh/serpentine-h2020/SEPpy
+.. |docs| image:: https://readthedocs.org/projects/seppy/badge/?version=latest
+   :target: https://seppy.readthedocs.io/en/latest/?badge=latest
+.. |repostatus| image:: https://www.repostatus.org/badges/latest/active.svg
+   :alt: Project Status: Active – The project has reached a stable, usable state and is being actively developed.
+   :target: https://www.repostatus.org/#active
+
+*This package is in development status! Intended for internal use only, as the syntax is in a floating state and the documentation is incomplete.*
+
+**A compendium of Python data loaders and analysis tools for in-situ measurements of Solar Energetic Particles (SEP)**
+
+So far combines loaders for the following instruments into one PyPI package:
+
+- BepiColombo: SIXS-P
+- Parker Solar Probe: ISOIS
+- SOHO: CELIAS, COSTEP-EPHIN, ERNE
+- Solar Orbiter: EPD (STEP, EPT, HET)*, MAG
+- STEREO: HET, LET, SEPT, MAG
+- Wind: 3DP
+
+(* Note that `solo-epd-loader <https://github.com/jgieseler/solo-epd-loader>`_ is a `PyPI package itself <https://pypi.org/project/solo-epd-loader/>`_ that just is loaded here for completeness.)
+
+
+Disclaimer
+----------
+This software is provided "as is", with no guarantee. It is no official data source, and not officially endorsed by the corresponding instrument teams. **Please always refer to the official data description of each instrument before using the data!**
+
+Installation
+------------
+
+seppy requires python >= 3.9.
+
+It can be installed from `PyPI <https://pypi.org/project/seppy/>`_ using:
+
+.. code:: bash
+
+    pip install seppy
+
+
+Usage
+-----
+
+The standard usecase is to utilize the ``***_load`` function, which returns Pandas dataframe(s) of the corresponding measurements and a dictionary containing information on the energy channels. For example the SOHO/ERNE data from Apr 16 to Apr 20, 2021, can be obtained as follows:
+
+.. code:: python
+
+   from seppy.loader.soho import soho_load
+
+   df, meta = soho_load(dataset="SOHO_ERNE-HED_L2-1MIN",
+                        startdate="2021/04/16",
+                        enddate="2021/04/20")
+
+Note that the syntax is different for each loader! `Please refer to this Notebook for more info and examples for the different data sets! <https://github.com/serpentine-h2020/serpentine/blob/main/notebooks/sep_analysis_tools/data_loader.ipynb>`_
+
+
+
+
+Citation
+--------
+
+Please cite the following paper if you use **seppy** in your publication:
+
+Palmroos, C., Gieseler, J., Dresing, N., Morosan, D.E., Asvestari, E., Yli-Laurila, A., Price, D.J., Valkila, S., Vainio, R. (2022).
+Solar Energetic Particle Time Series Analysis with Python. *Front. Astronomy Space Sci.* 9. `doi:10.3389/fspas.2022.1073578 <https://doi.org/10.3389/fspas.2022.1073578>`_ 

{seppy-0.1.4 → seppy-0.4.0}/README.rst

@@ -1,31 +1,37 @@
-SEPpy
+seppy
 =====
 
-|pypi Version| |python version| |zenodo doi|
+|pypi Version| |python version| |pytest| |codecov| |docs| |repostatus| |zenodo doi|
 
 .. |pypi Version| image:: https://img.shields.io/pypi/v/seppy?style=flat&logo=pypi
    :target: https://pypi.org/project/seppy/
 .. |python version| image:: https://img.shields.io/pypi/pyversions/seppy?style=flat&logo=python
 .. |zenodo doi| image:: https://zenodo.org/badge/451799504.svg
    :target: https://zenodo.org/badge/latestdoi/451799504
+.. |pytest| image:: https://github.com/serpentine-h2020/SEPpy/actions/workflows/pytest.yml/badge.svg?branch=main
+.. |codecov| image:: https://codecov.io/gh/serpentine-h2020/SEPpy/branch/main/graph/badge.svg?token=FYELM4Y7DF 
+   :target: https://codecov.io/gh/serpentine-h2020/SEPpy
+.. |docs| image:: https://readthedocs.org/projects/seppy/badge/?version=latest
+   :target: https://seppy.readthedocs.io/en/latest/?badge=latest
+.. |repostatus| image:: https://www.repostatus.org/badges/latest/active.svg
+   :alt: Project Status: Active – The project has reached a stable, usable state and is being actively developed.
+   :target: https://www.repostatus.org/#active
 
 *This package is in development status! Intended for internal use only, as the syntax is in a floating state and the documentation is incomplete.*
 
 **A compendium of Python data loaders and analysis tools for in-situ measurements of Solar Energetic Particles (SEP)**
 
-So far combines the following loaders into one PyPI package:
+So far combines loaders for the following instruments into one PyPI package:
 
-- `psp-isois-loader <https://github.com/jgieseler/psp-isois-loader>`_
-- `soho-loader <https://github.com/jgieseler/soho-loader>`_
-- `solo-epd-loader <https://github.com/jgieseler/solo-epd-loader>`_ *
-- `stereo-loader <https://github.com/jgieseler/stereo-loader>`_
-- `wind-3dp-loader <https://github.com/jgieseler/wind-3dp-loader>`_
+- BepiColombo: SIXS-P
+- Parker Solar Probe: ISOIS
+- SOHO: CELIAS, COSTEP-EPHIN, ERNE
+- Solar Orbiter: EPD (STEP, EPT, HET)*, MAG
+- STEREO: HET, LET, SEPT, MAG
+- Wind: 3DP
 
 (* Note that `solo-epd-loader <https://github.com/jgieseler/solo-epd-loader>`_ is a `PyPI package itself <https://pypi.org/project/solo-epd-loader/>`_ that just is loaded here for completeness.)
 
-Additional loaders:
-
-- `solo-mag-loader <https://github.com/jgieseler/solo-mag-loader>`_
 
 Disclaimer
 ----------
@@ -34,7 +40,7 @@ This software is provided "as is", with no guarantee. It is no official data sou
 Installation
 ------------
 
-SEPpy requires python >= 3.6.
+seppy requires python >= 3.9.
 
 It can be installed from `PyPI <https://pypi.org/project/seppy/>`_ using:
 
@@ -56,11 +62,15 @@ The standard usecase is to utilize the ``***_load`` function, which returns Pand
                         startdate="2021/04/16",
                         enddate="2021/04/20")
 
-Note that the syntax is different for each loader! Please refer to the independent packages for more details and the correct useage:
+Note that the syntax is different for each loader! `Please refer to this Notebook for more info and examples for the different data sets! <https://github.com/serpentine-h2020/serpentine/blob/main/notebooks/sep_analysis_tools/data_loader.ipynb>`_
+
+
+
+
+Citation
+--------
+
+Please cite the following paper if you use **seppy** in your publication:
 
-- `psp-isois-loader <https://github.com/jgieseler/psp-isois-loader>`_
-- `soho-loader <https://github.com/jgieseler/soho-loader>`_
-- `solo-epd-loader <https://github.com/jgieseler/solo-epd-loader>`_
-- `solo-mag-loader <https://github.com/jgieseler/solo-mag-loader>`_
-- `stereo-loader <https://github.com/jgieseler/stereo-loader>`_
-- `wind-3dp-loader <https://github.com/jgieseler/wind-3dp-loader>`_
+Palmroos, C., Gieseler, J., Dresing, N., Morosan, D.E., Asvestari, E., Yli-Laurila, A., Price, D.J., Valkila, S., Vainio, R. (2022).
+Solar Energetic Particle Time Series Analysis with Python. *Front. Astronomy Space Sci.* 9. `doi:10.3389/fspas.2022.1073578 <https://doi.org/10.3389/fspas.2022.1073578>`_ 

seppy-0.4.0/docs/api.rst

@@ -0,0 +1,87 @@
+#############
+API reference
+#############
+
+
+************
+seppy.loader
+************
+
+seppy.loader.bepi 
+=================
+
+.. automodule:: seppy.loader.bepi
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+seppy.loader.juice 
+=================
+
+.. automodule:: seppy.loader.juice
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+seppy.loader.psp
+================
+
+.. automodule:: seppy.loader.psp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+seppy.loader.soho
+=================
+
+.. automodule:: seppy.loader.soho
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+seppy.loader.solo
+=================
+
+.. automodule:: seppy.loader.solo
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+seppy.loader.stereo
+===================
+
+.. automodule:: seppy.loader.stereo
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+seppy.loader.wind
+=================
+
+.. automodule:: seppy.loader.wind
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+***********
+seppy.tools
+***********
+
+seppy.tools.Event
+=================
+
+.. autoclass:: seppy.tools.Event
+   :members:
+   :undoc-members:
+   :class-doc-from: both
+
+
+**********
+seppy.util
+**********
+
+.. automodule:: seppy.util
+   :members:
+   :undoc-members:
+   :show-inheritance: