Commit 8abe8e6a authored by Hock, Martin's avatar Hock, Martin 🤹
Browse files

Merge branch 'dev' into 'main'

v.0.1 for alpha release

See merge request !12
parents 242b4af5 d116be05
Pipeline #740282 passed with stages
in 57 seconds
[run]
omit =
*example.py
*/usr/*
......@@ -90,7 +90,7 @@ celerybeat-schedule
# Environments
.env
.venv
env/
env*/
venv/
ENV/
env.bak/
......
# This file is a template, and might need editing before it works on your project.
# To contribute improvements to CI/CD templates, please follow the Development guide at:
# https://docs.gitlab.com/ee/development/cicd/templates.html
# This specific template is located at:
# https://gitlab.com/gitlab-org/gitlab/-/blob/master/lib/gitlab/ci/templates/Python.gitlab-ci.yml
# Official language image. Look for the different tagged releases at:
# https://hub.docker.com/r/library/python/tags/
image: python:latest
stages:
- linting
- testing
# Change pip's cache directory to be inside the project directory since we can
# only cache local items.
variables:
PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
# Pip's cache doesn't store the python packages
# https://pip.pypa.io/en/stable/reference/pip_install/#caching
#
# If you want to also cache the installed packages, you have to install
# them in a virtualenv and cache it as well.
cache:
paths:
# - .cache/pip #
# - venv/ #
before_script:
- python --version # For debugging
- pip install -r requirements.txt # install dependencies from file
- pip install flake8
- pip install pylint
# - pip install virtualenv
# - virtualenv venv
# - source venv/bin/activate
PEP8:
stage: linting
# allow_failure: true
script: flake8 --count . # PEP8 linting
Pylint:
stage: linting
# allow_failure: true
script: find . -type f -name '*.py' | xargs pylint -rn --rcfile='plotid/.pylintrc' # Find all python files and check the code with pylint.
test:
stage: testing
tags:
- docker
script:
# - python -m unittest discover -s ./tests/ -p "test*" # deprecated unittest command
- python tests/runner_tests.py
# - pip install tox flake8 # you can also use tox
# - tox -e py36,flake8
# Commenting out all other stages and jobs
#run:
# script:
# - python setup.py bdist_wheel
# # an alternative approach is to install and run:
# - pip install dist/*
# # run the command here
# artifacts:
# paths:
# - dist/*.whl
#pages:
# script:
# - pip install sphinx sphinx-rtd-theme
# - cd doc
# - make html
# - mv build/html/ ../public/
# artifacts:
# paths:
# - public
# rules:
# - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
import h5py
#Shows how to create an externalLink (symbolic) to a hdf5 File
#Documentation available at: https://docs.h5py.org/en/stable/high/group.html#external-links
myfile = h5py.File('./example.h5','w')
myfile['ext link'] = h5py.ExternalLink("testdata_2.h5", "/")
myfile.close()
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END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
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See the License for the specific language governing permissions and
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# plot_ID_python
# PlotID for Python
This is the python PlotID project
\ No newline at end of file
This is the python PlotID project.
PlotID is a program connected to Research Data Management (RDM). It has two main functionalities:
1. Tag your plot with an identifier.
2. Export the resulting file to a specified directory along the corresponding research data, the plot is based on. Additionally, the script that created the plot will also be copied to the directory.
**Note:** To run PlotID python version ≥ 3.10 is required.
## Installation
Currently there are two options to run PlotID. Either install it via pip from the Python Package Index (PyPi) or install PlotID from the source code.
### From PyPi with pip
1. [Optional] Create a virtual environment and activate it:
```bash
pip install venv
mkdir venv
python3 -m venv
source venv/bin/activate
```
2. Install PlotID
`pip install --upgrade --index-url https://test.pypi.org/simple/ example-package-plotid-test`
### From source
1. Download the source code from [Gitlab](https://git.rwth-aachen.de/plotid/plotid_python):
`git clone https://git.rwth-aachen.de/plotid/plotid_python.git`
`cd plotid_python`
2. [Optional] Create a virtual environment:
```bash
pip install venv
mkdir venv
python3 -m venv
source venv/bin/activate
```
3. Install dependencies
`pip install -r requirements.txt`
4. Install PlotID
`pip install .`
## Usage
PlotID has two main functionalities:
1. Tag your plot with an identifier.
2. Export the resulting file to a specified directory along the corresponding research data, the plot is based on. Additionally, the script that created the plot will also be copied to the directory.
### tagplot()
Tag your figure/plot with an ID.
`tagplot(figures, plot_engine)`
The variable "figures" can be a single figure or a list of multiple figures.
The argument "plot_engine" defines which plot engine was used to create the figures. It also determines which plot engine PlotID uses to place the ID on the plot. Currently supported plot engines are:
- 'matplotlib'
tagplot returns a list that contains two lists each with as many entries as figures were given. The first list contains the tagged figures. The second list contains the corresponding IDs as strings
Optional parameters can be used to customize the tag process.
- prefix : str, optional
Will be added as prefix to the ID.
- id_method : str, optional
id_method for creating the ID. Create an ID by Unix time is referenced as 'time', create a random ID with id_method='random'. The default is 'time'.
- location : string, optional
Location for ID to be displayed on the plot. Default is 'east'.
Example:
```python
FIG1 = plt.figure()
FIG2 = plt.figure()
FIGS_AS_LIST = [FIG1, FIG2]
[TAGGED_FIGS, ID] = tagplot(FIGS_AS_LIST, 'matplotlib', prefix='XY23_', id_method='random', location='west')
```
### publish()
Save plot, data and measuring script.
`publish(src_datapath, dst_path, figure, plot_name)`
- "src_datapath" specifies the path to (raw) data that should be published.
- "dst_path" is the path to the destination directory, where all the data should be copied/exported to.
- "figure" expects the figure that was tagged and now should be saved as picture.
- "plot_name" will be the file name for the exported plot.
Optional parameters can be used to customize the publish process.
- data_storage: str, optional
Method how the data should be stored. Available options:
- centralized: The raw data will copied only once. All other plots will reference this data via sym link.
- individual: The complete raw data will be copied to a folder for every plot, respectively.
Example:
`publish('/home/user/Documents/research_data', '/home/user/Documents/exported_data', FIG1, 'EnergyOverTime-Plot')
## Build
If you want to build PlotID yourself, follow these steps:
1. Download the source code from [Gitlab](https://git.rwth-aachen.de/plotid/plotid_python):
`git clone https://git.rwth-aachen.de/plotid/plotid_python.git`
`cd plotid_python`
2. [Optional] Create a virtual environment:
```bash
pip install venv
mkdir venv
python3 -m venv
source venv/bin/activate
```
3. [Optional] Run unittests and coverage:
`python3 tests/runner_tests.py`
4. Build the package
`python3 -m build`
## Documentation
If you have more questions about PlotID, please have a look at the [documentation](link-to-docs).
Also have a look at the example.py that is shipped with PlotID.
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = source
BUILDDIR = build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
@ECHO OFF
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set SOURCEDIR=source
set BUILDDIR=build
%SPHINXBUILD% >NUL 2>NUL
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.https://www.sphinx-doc.org/
exit /b 1
)
if "%1" == "" goto help
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
goto end
:help
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
:end
popd
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('../../plotid'))
# -- Project information -----------------------------------------------------
project = 'PlotID'
copyright = '2022, Example Author'
author = 'Example Author'
# The full version, including alpha/beta/rc tags
release = '0.0.6'
# -- General configuration ---------------------------------------------------
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'autoapi.extension'
]
autoapi_type = 'python'
autoapi_dirs = ['../../plotid', '../../tests']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'alabaster'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
.. PlotID documentation master file, created by
sphinx-quickstart on Tue Jun 21 14:09:27 2022.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to PlotID's documentation!
==================================
.. toctree::
:maxdepth: 2
:caption: Contents:
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
plotid
======
.. toctree::
:maxdepth: 4
plotid
plotid package
==============
Submodules
----------
plotid.create\_id module
------------------------
.. automodule:: plotid.create_id
:members:
:undoc-members:
:show-inheritance:
plotid.example module
---------------------
.. automodule:: plotid.example
:members:
:undoc-members:
:show-inheritance:
plotid.filecompare module
-------------------------
.. automodule:: plotid.filecompare
:members:
:undoc-members:
:show-inheritance:
plotid.hdf5\_external\_link module
----------------------------------
.. automodule:: plotid.hdf5_external_link
:members:
:undoc-members:
:show-inheritance:
plotid.plotoptions module
-------------------------
.. automodule:: plotid.plotoptions
:members:
:undoc-members:
:show-inheritance:
plotid.publish module
---------------------
.. automodule:: plotid.publish
:members:
:undoc-members:
:show-inheritance:
plotid.save\_plot module
------------------------
.. automodule:: plotid.save_plot
:members:
:undoc-members:
:show-inheritance:
plotid.tagplot module
---------------------
.. automodule:: plotid.tagplot
:members:
:undoc-members:
:show-inheritance:
plotid.tagplot\_matplotlib module
---------------------------------
.. automodule:: plotid.tagplot_matplotlib
:members: