datastock 0.0.49__tar.gz → 0.0.51__tar.gz

datastock-0.0.51/.github/workflows/python-publish.yml

@@ -0,0 +1,35 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  push:
+    tags:
+      - '*'
+    branches:
+      - main
+  release:
+    types: [created]
+
+jobs:
+  pypi:
+    name: Publish sdist to Pypi
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: '3.11'
+      - run: uv build
+      # Check that basic features work and we didn't miss to include crucial files
+      - name: import test (wheel)
+        run: uv run --isolated --no-project -p 3.11 --with dist/*.whl datastock/tests/prepublish.py
+      - name: import test (source distribution)
+        run: uv run --isolated --no-project -p 3.11 --with dist/*.tar.gz datastock/tests/prepublish.py
+      - run: uv publish -t ${{ secrets.PYPI_API_TOKEN }}

datastock-0.0.51/.github/workflows/python-testing-matrix.yml

@@ -0,0 +1,41 @@
+# 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: Testing matrix
+
+on:
+  push:
+    branches: [ devel ]
+  pull_request:
+    branches: [ devel ]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+
+    # git checkout
+    - uses: actions/checkout@v4
+
+    # Install uv
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+          python-version: ${{ matrix.python-version }}
+
+    # Install library
+    - name: Install the project
+      run: uv sync --all-extras --dev
+
+    # Run tests
+    - name: Run tests
+      # For example, using `pytest`
+      run: uv run pytest datastock/tests

datastock-0.0.51/.gitignore

@@ -0,0 +1,135 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# single sourcing verion file
+datastock/_version.py
+
+# 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
+
+# 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/
+.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/
+
+# vim swap file
+*.swp

datastock-0.0.51/CLASSIFIERS.txt

@@ -0,0 +1,10 @@
+Development Status :: 5 - Production/Stable
+Intended Audience :: Science/Research
+Programming Language :: Python :: 3
+Programming Language :: Python :: 3.6
+Programming Language :: Python :: 3.7
+Programming Language :: Python :: 3.8
+Programming Language :: Python :: 3.9
+Programming Language :: Python :: 3.10
+Programming Language :: Python :: 3.11
+Natural Language :: English

datastock-0.0.49/LICENSE → datastock-0.0.51/LICENSE.txt

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 ToFuProject
+Copyright (c) 2023 ToFuProject
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{datastock-0.0.49 → datastock-0.0.51}/MANIFEST.in

@@ -3,3 +3,4 @@
 include MANIFEST.in
 include LICENSE.txt
 include pyproject.toml
+include CLASSIFIERS.txt

{datastock-0.0.49/datastock.egg-info → datastock-0.0.51}/PKG-INFO

@@ -1,33 +1,12 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: datastock
-Version: 0.0.49
+Version: 0.0.51
 Summary: Generic handler for multiple heterogenous numpy arrays and subclasses
-Home-page: https://github.com/ToFuProject/datastock
-Author: Didier VEZINET
 Author-email: Didier VEZINET <didier.vezinet@gmail.com>
 Maintainer-email: Didier VEZINET <didier.vezinet@gmail.com>
-License: MIT License
-        
-        Copyright (c) 2022 ToFuProject
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
+License: MIT
+Project-URL: Homepage, https://github.com/ToFuProject/datastock
+Project-URL: Issues, https://github.com/ToFuProject/datastock/issues
 Keywords: data,analysis,interactive,heterogeneous arrays,numpy,Collection
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
@@ -38,12 +17,20 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.6
+Classifier: Natural Language :: English
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
-Provides-Extra: dev
+License-File: LICENSE.txt
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: PySide2; platform_system != "Windows"
+Requires-Dist: astropy
 Provides-Extra: linting
+Requires-Dist: ruff; extra == "linting"
 Provides-Extra: formatting
-License-File: LICENSE
+Requires-Dist: ruff; extra == "formatting"
+Dynamic: license-file
 
 [![Conda]( https://anaconda.org/conda-forge/datastock/badges/version.svg)](https://anaconda.org/conda-forge/datastock)
 [![](https://anaconda.org/conda-forge/datastock/badges/downloads.svg)](https://anaconda.org/conda-forge/datastock)
@@ -88,15 +75,15 @@ Examples:
 Straightforward array visualization:
 ------------------------------------
 
-```
+``
 import datastock as ds
 
 # any 1d, 2d or 3d array
-aa = np.np.random.random((100, 100, 100))
+aa = np.random((100, 100, 100))
 
 # plot interactive figure using shortcut to method
 dax = ds.plot_as_array(aa)
-```
+``
 
 Now do **shift + left clic** on any axes, the rest of the interactive commands are automatically printed in your python console
 
@@ -122,7 +109,7 @@ Thanks to dref, the class knows the relationaships between all numpy arrays.
 In particular it knows which arrays share the same references / dimensions
 
 
-```
+```python
 import numpy as np
 import datastock as ds
 
@@ -143,24 +130,24 @@ lprof = [(1 + np.cos(t)[:, None]) * x[None, :] for t in lt]
 # Populate DataStock
 
 # instanciate 
-st = ds.DataStock()
+coll = ds.DataStock()
 
 # add references (i.e.: store size of each dimension under a unique key)
-st.add_ref(key='nc', size=nc)
-st.add_ref(key='nx', size=nx)
+coll.add_ref(key='nc', size=nc)
+coll.add_ref(key='nx', size=nx)
 for ii, nt in enumerate(lnt):
-    st.add_ref(key=f'nt{ii}', size=nt)
+    coll.add_ref(key=f'nt{ii}', size=nt)
 
 # add data dependening on these references
 # you can, optionally, specify units, physical dimensionality (ex: distance, time...), quantity (ex: radius, height, ...) and name (to your liking)
 
-st.add_data(key='x', data=x, dimension='distance', quant='radius', units='m', ref='nx')
+coll.add_data(key='x', data=x, dimension='distance', quant='radius', units='m', ref='nx')
 for ii, nt in enumerate(lnt):
-    st.add_data(key=f't{ii}', data=lt[ii], dimension='time', units='s', ref=f'nt{ii}')
-    st.add_data(key=f'prof{ii}', data=lprof[ii], dimension='velocity', units='m/s', ref=(f'nt{ii}', 'x'))
+    coll.add_data(key=f't{ii}', data=lt[ii], dimension='time', units='s', ref=f'nt{ii}')
+    coll.add_data(key=f'prof{ii}', data=lprof[ii], dimension='velocity', units='m/s', ref=(f'nt{ii}', 'x'))
 
 # print in the console the content of st
-st
+coll
 ```
 
 <p align="center">
@@ -171,22 +158,22 @@ You can see that DataStock stores the relationships between each array and each
 Specifying explicitly the references is only necessary if there is an ambiguity (i.e.: several references have the same size, like nx and nt2 in our case)
 
 
-```
+``
 # plot any array interactively
-dax = st.plot_as_array('x')
-dax = st.plot_as_array('t0')
-dax = st.plot_as_array('prof0')
-dax = st.plot_as_array('prof0', keyX='t0', keyY='x', aspect='auto')
-```
+dax = coll.plot_as_array('x')
+dax = coll.plot_as_array('t0')
+dax = coll.plot_as_array('prof0')
+dax = coll.plot_as_array('prof0', keyX='t0', keyY='x', aspect='auto')
+``
 
 You can then decide to store any object category
 Let's create a 'campaign' category to store the characteristics of each measurements campaign
 and let's add a 'campaign' parameter to each profile data
 
-```
+``
 # add arbitrary object category as sub-dict of self.dobj
 for ii in range(nc):
-    st.add_obj(
+    coll.add_obj(
         which='campaign',
 	    key=f'c{ii}',
         start_date=f'{ii}.04.2022',
@@ -197,16 +184,16 @@ for ii in range(nc):
     )
 
 # create new 'campaign' parameter for data arrays
-st.add_param('campaign', which='data')
+coll.add_param('campaign', which='data')
 
 # tag each data with its campaign
 for ii in range(nc):
-    st.set_param(which='data', key=f't{ii}', param='campaign', value=f'c{ii}')	
-    st.set_param(which='data', key=f'prof{ii}', param='campaign', value=f'c{ii}')	
+    coll.set_param(which='data', key=f't{ii}', param='campaign', value=f'c{ii}')	
+    coll.set_param(which='data', key=f'prof{ii}', param='campaign', value=f'c{ii}')	
 
 # print in the console the content of st
-st
-```
+coll
+``
 
 <p align="center">
 <img align="middle" src="https://github.com/ToFuProject/datastock/blob/devel/README_figures/DataStock_Obj.png" width="600" alt="Direct 3d array visualization"/>
@@ -215,31 +202,31 @@ st
 DataStock also provides built-in object selection method to allow return all
 objects matching a criterion, as lits of int indices, bool indices or keys.
 
-```
-In [9]: st.select(which='campaign', index=2, returnas=int)
+``
+In [9]: coll.select(which='campaign', index=2, returnas=int)
 Out[9]: array([2])
 
 # list of 2 => return all matches inside the interval
-In [10]: st.select(which='campaign', index=[2, 4], returnas=int)
+In [10]: coll.select(which='campaign', index=[2, 4], returnas=int)
 Out[10]: array([2, 3, 4])
 
 # tuple of 2 => return all matches outside the interval
-In [11]: st.select(which='campaign', index=(2, 4), returnas=int)
+In [11]: coll.select(which='campaign', index=(2, 4), returnas=int)
 Out[11]: array([0, 1])
 
 # return as keys
-In [12]: st.select(which='campaign', index=(2, 4), returnas=str)
+In [12]: coll.select(which='campaign', index=(2, 4), returnas=str)
 Out[12]: array(['c0', 'c1'], dtype='<U2')
 
 # return as bool indices
-In [13]: st.select(which='campaign', index=(2, 4), returnas=bool)
+In [13]: coll.select(which='campaign', index=(2, 4), returnas=bool)
 Out[13]: array([ True,  True, False, False, False])
 
 # You can combine as many constraints as needed
-In [17]: st.select(which='campaign', index=[2, 4], operator='Barnaby', returnas=str)
+In [17]: coll.select(which='campaign', index=[2, 4], operator='Barnaby', returnas=str)
 Out[17]: array(['c3', 'c4'], dtype='<U2')
 
-```
+``
 
 You can also decide to sub-class DataStock to implement methods and visualizations specific to your needs
 
@@ -252,6 +239,6 @@ DataStock provides built-in methods like:
     - size is the total size of all data stored in the instance in bytes
     - dsize is a dict with the detail (size for each item in each sub-dict of the instance)
 * `save()`: will save the instance
-* `ds.load()`: will load a saved instance
+* `coll.load()`: will load a saved instance
 
 

{datastock-0.0.49 → datastock-0.0.51}/README.md

@@ -41,15 +41,15 @@ Examples:
 Straightforward array visualization:
 ------------------------------------
 
-```
+``
 import datastock as ds
 
 # any 1d, 2d or 3d array
-aa = np.np.random.random((100, 100, 100))
+aa = np.random((100, 100, 100))
 
 # plot interactive figure using shortcut to method
 dax = ds.plot_as_array(aa)
-```
+``
 
 Now do **shift + left clic** on any axes, the rest of the interactive commands are automatically printed in your python console
 
@@ -75,7 +75,7 @@ Thanks to dref, the class knows the relationaships between all numpy arrays.
 In particular it knows which arrays share the same references / dimensions
 
 
-```
+```python
 import numpy as np
 import datastock as ds
 
@@ -96,24 +96,24 @@ lprof = [(1 + np.cos(t)[:, None]) * x[None, :] for t in lt]
 # Populate DataStock
 
 # instanciate 
-st = ds.DataStock()
+coll = ds.DataStock()
 
 # add references (i.e.: store size of each dimension under a unique key)
-st.add_ref(key='nc', size=nc)
-st.add_ref(key='nx', size=nx)
+coll.add_ref(key='nc', size=nc)
+coll.add_ref(key='nx', size=nx)
 for ii, nt in enumerate(lnt):
-    st.add_ref(key=f'nt{ii}', size=nt)
+    coll.add_ref(key=f'nt{ii}', size=nt)
 
 # add data dependening on these references
 # you can, optionally, specify units, physical dimensionality (ex: distance, time...), quantity (ex: radius, height, ...) and name (to your liking)
 
-st.add_data(key='x', data=x, dimension='distance', quant='radius', units='m', ref='nx')
+coll.add_data(key='x', data=x, dimension='distance', quant='radius', units='m', ref='nx')
 for ii, nt in enumerate(lnt):
-    st.add_data(key=f't{ii}', data=lt[ii], dimension='time', units='s', ref=f'nt{ii}')
-    st.add_data(key=f'prof{ii}', data=lprof[ii], dimension='velocity', units='m/s', ref=(f'nt{ii}', 'x'))
+    coll.add_data(key=f't{ii}', data=lt[ii], dimension='time', units='s', ref=f'nt{ii}')
+    coll.add_data(key=f'prof{ii}', data=lprof[ii], dimension='velocity', units='m/s', ref=(f'nt{ii}', 'x'))
 
 # print in the console the content of st
-st
+coll
 ```
 
 <p align="center">
@@ -124,22 +124,22 @@ You can see that DataStock stores the relationships between each array and each
 Specifying explicitly the references is only necessary if there is an ambiguity (i.e.: several references have the same size, like nx and nt2 in our case)
 
 
-```
+``
 # plot any array interactively
-dax = st.plot_as_array('x')
-dax = st.plot_as_array('t0')
-dax = st.plot_as_array('prof0')
-dax = st.plot_as_array('prof0', keyX='t0', keyY='x', aspect='auto')
-```
+dax = coll.plot_as_array('x')
+dax = coll.plot_as_array('t0')
+dax = coll.plot_as_array('prof0')
+dax = coll.plot_as_array('prof0', keyX='t0', keyY='x', aspect='auto')
+``
 
 You can then decide to store any object category
 Let's create a 'campaign' category to store the characteristics of each measurements campaign
 and let's add a 'campaign' parameter to each profile data
 
-```
+``
 # add arbitrary object category as sub-dict of self.dobj
 for ii in range(nc):
-    st.add_obj(
+    coll.add_obj(
         which='campaign',
 	    key=f'c{ii}',
         start_date=f'{ii}.04.2022',
@@ -150,16 +150,16 @@ for ii in range(nc):
     )
 
 # create new 'campaign' parameter for data arrays
-st.add_param('campaign', which='data')
+coll.add_param('campaign', which='data')
 
 # tag each data with its campaign
 for ii in range(nc):
-    st.set_param(which='data', key=f't{ii}', param='campaign', value=f'c{ii}')	
-    st.set_param(which='data', key=f'prof{ii}', param='campaign', value=f'c{ii}')	
+    coll.set_param(which='data', key=f't{ii}', param='campaign', value=f'c{ii}')	
+    coll.set_param(which='data', key=f'prof{ii}', param='campaign', value=f'c{ii}')	
 
 # print in the console the content of st
-st
-```
+coll
+``
 
 <p align="center">
 <img align="middle" src="https://github.com/ToFuProject/datastock/blob/devel/README_figures/DataStock_Obj.png" width="600" alt="Direct 3d array visualization"/>
@@ -168,31 +168,31 @@ st
 DataStock also provides built-in object selection method to allow return all
 objects matching a criterion, as lits of int indices, bool indices or keys.
 
-```
-In [9]: st.select(which='campaign', index=2, returnas=int)
+``
+In [9]: coll.select(which='campaign', index=2, returnas=int)
 Out[9]: array([2])
 
 # list of 2 => return all matches inside the interval
-In [10]: st.select(which='campaign', index=[2, 4], returnas=int)
+In [10]: coll.select(which='campaign', index=[2, 4], returnas=int)
 Out[10]: array([2, 3, 4])
 
 # tuple of 2 => return all matches outside the interval
-In [11]: st.select(which='campaign', index=(2, 4), returnas=int)
+In [11]: coll.select(which='campaign', index=(2, 4), returnas=int)
 Out[11]: array([0, 1])
 
 # return as keys
-In [12]: st.select(which='campaign', index=(2, 4), returnas=str)
+In [12]: coll.select(which='campaign', index=(2, 4), returnas=str)
 Out[12]: array(['c0', 'c1'], dtype='<U2')
 
 # return as bool indices
-In [13]: st.select(which='campaign', index=(2, 4), returnas=bool)
+In [13]: coll.select(which='campaign', index=(2, 4), returnas=bool)
 Out[13]: array([ True,  True, False, False, False])
 
 # You can combine as many constraints as needed
-In [17]: st.select(which='campaign', index=[2, 4], operator='Barnaby', returnas=str)
+In [17]: coll.select(which='campaign', index=[2, 4], operator='Barnaby', returnas=str)
 Out[17]: array(['c3', 'c4'], dtype='<U2')
 
-```
+``
 
 You can also decide to sub-class DataStock to implement methods and visualizations specific to your needs
 
@@ -205,6 +205,6 @@ DataStock provides built-in methods like:
     - size is the total size of all data stored in the instance in bytes
     - dsize is a dict with the detail (size for each item in each sub-dict of the instance)
 * `save()`: will save the instance
-* `ds.load()`: will load a saved instance
+* `coll.load()`: will load a saved instance
 
 

datastock-0.0.51/datastock/__init__.py

@@ -0,0 +1,31 @@
+# ###############
+# __version__
+# ###############
+
+
+from . import _version
+__version__ = _version.version
+__version_tuple__ = _version.version_tuple
+
+
+# from setuptools_scm import get_version
+# __version__ = get_version(root='..', relative_to=__file__)
+
+
+# from importlib.metadata import version
+# __version__ = version(__package__)
+# cleanup
+# del get_version
+
+
+# ###############
+# sub-packages
+# ###############
+
+
+from . import _generic_check
+from ._generic_utils_plot import *
+from ._class import DataStock
+from ._saveload import load, get_files
+from ._direct_calls import *
+from . import tests