Merge branch 'dev' into 'main'

v.0.1 for alpha release

See merge request !12

.coveragerc

+[run]
+omit = 
+    *example.py
+    */usr/*

.gitignore

@@ -90,7 +90,7 @@ celerybeat-schedule
 # Environments
 .env
 .venv
-env/
+env*/
 venv/
 ENV/
 env.bak/

.gitlab-ci.yml

+# 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

HDF5_externalLink.py

-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()
-

LICENSE

+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
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+      PARTICULAR PURPOSE. You are solely responsible for determining the
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+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
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+
+   Copyright 2022 PlotID
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

README.md

-# 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.

docs/Makefile

+# 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)

docs/make.bat

+@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

docs/source/conf.py

+# 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']

docs/source/index.rst

+.. 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`

docs/source/modules.rst

+plotid
+======
+
+.. toctree::
+   :maxdepth: 4
+
+   plotid

docs/source/plotid.rst

+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: