Resolve merge conflicts.

.gitlab-ci.yml

-image: python:latest
+image: python:3.10
 stages:
 - linting
 - testing
@@ -14,16 +14,19 @@ before_script:
 - python --version  # For debugging
 - pip install --upgrade pip
 - pip install --user -r requirements.txt  # install dependencies from file
+
 PEP8:
   stage: linting
   script:
   - pip install flake8
   - flake8 --count .
+
 Pylint:
   stage: linting
   script:
   - pip install pylint
   - 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:
@@ -31,6 +34,7 @@ test:
   script:
   - python tests/runner_tests.py
   coverage: "/TOTAL.*\\s+(\\d+\\.\\d+%)$/"
+
 pages:
   stage: docs
   script:
@@ -44,7 +48,10 @@ pages:
   rules:
   - if: "$CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH"
   - when: manual
+
 sast:
+  before_script:
+      - echo "No before script pls"
   variables:
     SAST_EXCLUDED_PATHS: spec, test, tmp
   stage: security
@@ -52,6 +59,8 @@ sast:
   - docker
 
 dependency_scanning:
+  before_script:
+      - echo "No before script pls"
   stage: security
 
 include:

README.md

 # plotID for Python
 
+![The plotID logo](docs/source/_static/plotID_logo_small.png)
+
 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.

docs/source/conf.py

@@ -57,6 +57,7 @@ exclude_patterns = []
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
+html_logo = '_static/plotID.jpg'
 
 # 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,

docs/source/dependencies.rst

+Dependencies of plotID
+==================================
+
+The plotID package depends on other software for its full funcionality. Since plotID is a Python program, Python ≥ 3.10 is needed. A list of all dependencies and their connection to plotID is provided here.
+
+- `matplotlib <https://matplotlib.org/stable/index.html>`_: Famous plotting engine. matplotlib plots and figures can be tagged and published with plotID.
+- `Pillow <https://pillow.readthedocs.io/en/stable/>`_: Library for image processing. If no plotting engine was used that is supported by plotID, image files can be tagged as well. This is done with Pillow. Additionally, Pillow is used to print the QR codes on the plots.
+- `qrcode <https://github.com/lincolnloop/python-qrcode>`_: Creates QR codes from input data. qrcode is used to create the QR code which is printed on the plot in the end.
+- `numpy <https://numpy.org/doc/stable/>`_: Package for scientific computing. Right now it is only used to generate sample data in the examples. Since it is a dependency of matplotlib, it has to be installed anyway.
+
+Optional depedencies that are not necessary to run plotID but more to contribute to the code are the following:
+
+- `coverage <https://coverage.readthedocs.io/en/6.5.0/#>`_: Program to measure the code coverage. It is used in the development of plotID to monitor the coverage of the code when the unit tests are run.
+- `sphinx <https://www.sphinx-doc.org/en/master/>`_: Program to build documentation. For example, this documentatio is generated with the help of sphinx.
+- `sphinx-autoapi <https://sphinx-autoapi.readthedocs.io/en/latest/>`_: Generates documentation files automatically from documentation inside the code. This has the advantage that code can be documented inside the code but can also be read in the documentation without having two places with the same content.
+- `sphinx-rtd-theme <https://sphinx-rtd-theme.readthedocs.io/en/stable/>`_: Readthedocs theme for nicer documentation style.
+- `myst-parser <https://myst-parser.readthedocs.io/en/latest/>`_: Extenstion for sphinx, e.g. to include markdown files in the documentation. That allows to include plotID's README.md in the documentation without storing it at two different places.
\ No newline at end of file

docs/source/index.rst

@@ -12,6 +12,8 @@ Welcome to plotID's documentation!
 
     README <readme_link.rst>
     Structure and architecture <structure.rst>
+    Dependencies <dependencies.rst>
+
 
 
 Indices and tables

plotid/__init__.py

@@ -10,5 +10,5 @@ research data, the plot is based on. Additionally, the script that created the
 plot will also be copied to the directory.
 """
 
-__version__ = '0.2.1'
+__version__ = '0.2.2'
 __author__ = 'Institut Fluidsystemtechnik within nfdi4ing at TU Darmstadt'

plotid/publish.py

@@ -132,7 +132,7 @@ class PublishOptions:
                             overwrite_dir = input('Do you want to overwrite '
                                                   'the existing folder? '
                                                   '(yes/no[default])\n')
-                            if overwrite_dir in ('yes', 'y'):
+                            if overwrite_dir in ('yes', 'y', 'Yes', 'YES'):
                                 shutil.rmtree(dst_path)
                             else:
                                 raise RuntimeError('publish has finished '
@@ -150,7 +150,7 @@ class PublishOptions:
                                            'partially copied data at '
                                            f'{dst_path_invisible} be'
                                            ' removed? (yes/no[default])\n')
-                        if delete_dir in ('yes', 'y'):
+                        if delete_dir in ('yes', 'y', 'Yes', 'YES'):
                             shutil.rmtree(dst_path_invisible)
                         raise RuntimeError('Publishing was unsuccessful. '
                                            'Try re-running publish.') from exc

pyproject.toml

 [build-system]
 requires = ["setuptools>=43", "wheel"]
 build-backend = "setuptools.build_meta" 
+
+[project]
+name = "plotID"
+description = "The plotID toolkit supports researchers in tracking and storing relevant data in plots. Plots are labelled with an ID and the corresponding data is stored."
+readme = "README.md"
+license = {text = "Apache License, Version 2.0"}
+authors = [
+    {name = "Institut für Fluidsystemtechnik - TU Darmstadt", email = "nfdi4ing@fst.tu-darmstadt.de"},
+    {name = "Hannes Mayr", email = "hannes.mayr@stud.tu-darmstadt.de"},
+    {name = "Martin Hock", email = "Martin.Hock@fst.tu-darmstadt.de"},
+    {name = "Manuela Richter", email = "Manuela.Richter@fst.tu-darmstadt.de"},
+    
+]
+dynamic = ["version"]
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Visualization",
+]
+dependencies = [
+    "Pillow",
+    "matplotlib",
+    "numpy",
+    "qrcode",
+]
+
+[project.urls]
+Repository = "https://git.rwth-aachen.de/plotid/plotid_python"
+Documentation = "https://plotid.pages.rwth-aachen.de/plotid_python"
+"Bug Tracker" = "https://git.rwth-aachen.de/plotid/plotid_python/-/issues"
+
+[project.optional-dependencies]
+test = ["coverage"]
+docs = [
+    "sphinx",
+    "sphinx-autoapi",
+    "sphinx-rtd-theme",
+    "myst-parser",
+]
+
+[tool.setuptools]
+packages = ["plotid"]
+
+[tool.setuptools.dynamic]
+version = {attr = "plotid.__version__"}

requirements.txt

@@ -6,7 +6,7 @@ matplotlib==3.5.2
 myst-parser==0.18.0
 numpy==1.22.3
 packaging==21.3
-Pillow==9.1.0
+Pillow==9.1.1
 pyparsing==3.0.8
 python-dateutil==2.8.2
 qrcode==7.3.1

setup.cfg

-[metadata]
-name = plotID
-version = attr: plotid.__version__
-author = attr: plotid.__author__
-author_email = nfdi4ing@fst.tu-darmstadt.de
-description = The plotID toolkit supports researchers in tracking and storing relevant data in plots. Plots are labelled with an ID and the corresponding data is stored.
-license = Apache License, Version 2.0
-license_files = file: LICENSE
-long_description = file: README.md
-long_description_content_type = text/markdown
-url = https://git.rwth-aachen.de/plotid/plotid_python
-project_urls =
-    Bug Tracker = https://git.rwth-aachen.de/plotid/plotid_python/-/issues
-classifiers =
-    Programming Language :: Python
-    Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.10
-    License :: OSI Approved :: Apache Software License
-    Operating System :: OS Independent
-    Development Status :: 2 - Pre-Alpha
-    Intended Audience :: Science/Research
-    Topic :: Scientific/Engineering :: Visualization
-
-[options]
-packages = plotid
-python_requires = >=3.10
-install_requires =
-    Pillow
-    matplotlib
-    numpy
-    qrcode
-   
-[options.extras_require]
-test =
-    coverage
-docs =
-    sphinx
-    sphinx-autoapi
-    sphinx-rtd-theme
-    myst-parser