diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 0000000000000000000000000000000000000000..096ae14ebab27380feedb28bf923c29e112ab4ec
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,4 @@
+[run]
+omit =
+ *example.py
+ */usr/*
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1147c71c14b0dd9b485704e085cd0ecdd1e6f8d8..27b46ba817eb967e1f15d6cf89969048cf57f75e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -47,8 +47,8 @@ PEP8:
Pylint:
stage: linting
- allow_failure: true
- script: find . -type f -name '*.py' | xargs pylint -rn --fail-under=7 # Find all python files and check the code with pylint.
+ # 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
@@ -56,7 +56,7 @@ test:
- docker
script:
# - python -m unittest discover -s ./tests/ -p "test*" # deprecated unittest command
- - python runner_tests.py
+ - python tests/runner_tests.py
# - pip install tox flake8 # you can also use tox
# - tox -e py36,flake8
diff --git a/README.md b/README.md
index e873d62fc0f29ae08ed91cf1131273e856e1c5fe..8d481de3ce3336fb936684ef9f5748d771bc4c36 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,107 @@
-# plot_ID_python
+# PlotID for Python
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.
-To run the program python version 3.10 is required.
\ No newline at end of file
+**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.
diff --git a/create_id.py b/create_id.py
deleted file mode 100644
index 84f2b83202d84345531128ca24dbbc89e7248952..0000000000000000000000000000000000000000
--- a/create_id.py
+++ /dev/null
@@ -1,36 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Create an identifier to print it on a plot.
-
-Functions:
- create_id(int) -> string
-"""
-import time
-import uuid
-
-
-def create_id(id_method):
- """
- Create an Identifier (str).
-
- Creates an (sometimes unique) identifier based on the selected method
- if no method is selected method 1 will be the default method
-
- Returns
- -------
- ID
- """
- if id_method == 1:
- ID = time.time() # UNIX Time
- ID = hex(int(ID)) # convert time to hexadecimal
- time.sleep(0.5) # break for avoiding duplicate IDs
- elif id_method == 2:
- ID = str(uuid.uuid4()) # creates a random UUID
- ID = ID[0:8] # only use first 8 numbers
- else:
- raise ValueError(
- f'Your chosen ID method "{id_method}" is not supported.\n'
- 'At the moment these methods are available:\n'
- '"1": Unix time converted to hexadecimal\n'
- '"2": Random UUID')
- return ID
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..d0c3cbf1020d5c292abdedf27627c6abe25e2293
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# 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)
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000000000000000000000000000000000000..747ffb7b3033659bdd2d1e6eae41ecb00358a45e
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@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
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..7ca2459f4a60345e7602be2281fb6ed590a463be
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,58 @@
+# 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']
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..34d079234c933658bce40762274688153c631d04
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,19 @@
+.. 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`
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
new file mode 100644
index 0000000000000000000000000000000000000000..dd354c8698ea6d990ff1b421ad0822ef78a8bb65
--- /dev/null
+++ b/docs/source/modules.rst
@@ -0,0 +1,7 @@
+plotid
+======
+
+.. toctree::
+ :maxdepth: 4
+
+ plotid
diff --git a/docs/source/plotid.rst b/docs/source/plotid.rst
new file mode 100644
index 0000000000000000000000000000000000000000..005afcdb7f40bef97789edbedf0d42196589d5b4
--- /dev/null
+++ b/docs/source/plotid.rst
@@ -0,0 +1,85 @@
+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:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: plotid
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/example.py b/example.py
deleted file mode 100644
index b6302f7d7895616b2435d252b0c8a3777d1399e2..0000000000000000000000000000000000000000
--- a/example.py
+++ /dev/null
@@ -1,61 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Example workflow for integrating plotID.
-
-With tagplot an ID can be generated an printed on the plot. To export the plot
-along with the corresponding research data and the plot generating script use
-the function publish.
-"""
-
-# %% Import modules
-import numpy as np
-from numpy import random
-# import h5py as h5
-# import matplotlib
-import matplotlib.pyplot as plt
-from tagplot import tagplot
-from publish import publish
-
-# %% Project ID
-ProjectID = "MR04_"
-
-# %% Plot engine
-plot_engine = "matplotlib"
-
-# %% Create sample data
-x = np.linspace(0, 10, 100)
-y = random.rand(100) + 2
-y_2 = np.sin(x) + 2
-
-# %% Create figure
-
-# Create plot
-color1 = 'black'
-color2 = 'yellow'
-# 1.Figure
-fig1 = plt.figure()
-plt.plot(x, y, color=color1)
-plt.plot(x, y_2, color=color2)
-
-# 2.Figure
-fig2 = plt.figure()
-plt.plot(x, y, color=color2)
-plt.plot(x, y_2, color=color1)
-
-fig = [fig1, fig2]
-
-# %% TagPlot
-# p1 = PlotOptions(fig, plot_engine, prefix=ProjectID,
-# method='2', location='east')
-# [figs, ID] = p1.tagplot()
-[figs, ID] = tagplot(fig, plot_engine, prefix=ProjectID,
- id_method='2', location='west')
-
-# %% Figure als tiff-Datei abspeichern
-for i, figure in enumerate(figs):
- name = "Test"+str(i)+".tiff"
- figure.savefig(name)
-
-# %% Publish
-publish('tests', '/home/chief/Dokumente/fst/plotid_python/data',
- fig1, 'Bild', 'individual')
diff --git a/plotid/.pylintrc b/plotid/.pylintrc
new file mode 100644
index 0000000000000000000000000000000000000000..40743c0f4e5afcd7e44a1512d484bda76b655e1f
--- /dev/null
+++ b/plotid/.pylintrc
@@ -0,0 +1,4 @@
+[MASTER]
+init-hook='import sys; sys.path.append("./plotid")'
+fail-under=9
+ignore=conf.py
diff --git a/plotid/__init__.py b/plotid/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/plotid/create_id.py b/plotid/create_id.py
new file mode 100644
index 0000000000000000000000000000000000000000..450e2dae6c2608a210849d5120c692986c3a7da4
--- /dev/null
+++ b/plotid/create_id.py
@@ -0,0 +1,37 @@
+# -*- coding: utf-8 -*-
+"""
+Create an identifier to print it on a plot.
+
+Functions:
+ create_id(str) -> string
+"""
+import time
+import uuid
+
+
+def create_id(id_method):
+ """
+ Create an Identifier (str).
+
+ Creates an (sometimes unique) identifier based on the selected method
+ if no method is selected method 1 will be the default method
+
+ Returns
+ -------
+ figure_id
+ """
+ match id_method:
+ case 'time':
+ figure_id = time.time() # UNIX Time
+ figure_id = hex(int(figure_id)) # convert time to hexadecimal
+ time.sleep(0.5) # break for avoiding duplicate IDs
+ case 'random':
+ figure_id = str(uuid.uuid4()) # creates a random UUID
+ figure_id = figure_id[0:8] # only use first 8 numbers
+ case _:
+ raise ValueError(
+ f'Your chosen ID method "{id_method}" is not supported.\n'
+ 'At the moment these methods are available:\n'
+ '"time": Unix time converted to hexadecimal\n'
+ '"random": Random UUID')
+ return figure_id
diff --git a/plotid/example.py b/plotid/example.py
new file mode 100644
index 0000000000000000000000000000000000000000..fcf7713916dc9ffc92ff7b9508f8b2d8778dcb7a
--- /dev/null
+++ b/plotid/example.py
@@ -0,0 +1,58 @@
+# -*- coding: utf-8 -*-
+"""
+Example workflow for integrating plotID.
+
+With tagplot an ID can be generated an printed on the plot. To export the plot
+along with the corresponding research data and the plot generating script use
+the function publish.
+"""
+
+# %% Import modules
+import numpy as np
+# import h5py as h5
+import matplotlib.pyplot as plt
+from plotid.tagplot import tagplot
+from plotid.publish import publish
+
+# %% Set Project ID
+PROJECT_ID = "MR04_"
+
+# %% Choose Plot engine
+PLOT_ENGINE = "matplotlib"
+
+# %% Create sample data
+x = np.linspace(0, 10, 100)
+y = np.random.rand(100) + 2
+y_2 = np.sin(x) + 2
+
+# %% Create figures
+
+# 1. figure
+FIG1 = plt.figure()
+plt.plot(x, y, color='black')
+plt.plot(x, y_2, color='yellow')
+
+# 2. figure
+FIG2 = plt.figure()
+plt.plot(x, y, color='blue')
+plt.plot(x, y_2, color='red')
+
+# %% TagPlot
+
+# If multiple figures should be tagged, figures must be provided as list.
+FIGS_AS_LIST = [FIG1, FIG2]
+
+[TAGGED_FIGS, ID] = tagplot(FIGS_AS_LIST, PLOT_ENGINE, prefix=PROJECT_ID,
+ id_method='random', location='west')
+
+# %% Save figure as tiff-file, but publish also exports the plot to a picture
+# file in the destination folder.
+for i, figure in enumerate(TAGGED_FIGS):
+ NAME = "Test"+str(i)+".tiff"
+ figure.savefig(NAME)
+
+# %% Publish
+# Arguments: Source directory, destination directory, figure, plot name,
+# publish-mode).
+publish('../../tests', '/home/chief/Dokumente/fst/plotid_python/data',
+ FIG1, 'Bild', 'individual')
diff --git a/filecompare.py b/plotid/filecompare.py
similarity index 100%
rename from filecompare.py
rename to plotid/filecompare.py
diff --git a/HDF5_externalLink.py b/plotid/hdf5_external_link.py
similarity index 100%
rename from HDF5_externalLink.py
rename to plotid/hdf5_external_link.py
diff --git a/plotid/plotoptions.py b/plotid/plotoptions.py
new file mode 100644
index 0000000000000000000000000000000000000000..6503422c73fe66f0fcd5a5fe9f44cdbd5ded1c7c
--- /dev/null
+++ b/plotid/plotoptions.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""Contains the PlotOption class."""
+
+
+class PlotOptions:
+ """
+ Container objects which include all plot options provided by plotid.
+
+ Methods
+ -------
+ __init__
+ validate_input: Check if input is correct type.
+
+ Attributes
+ ----------
+ figs : figure object
+ Figure that will be tagged.
+ prefix : str
+ Prefix that is placed before the ID.
+ id_method : int
+ Method that decides which method is used to generate the ID.
+ rotation : int
+ Rotation angle for the ID.
+ position : tuple
+ Relative position of the ID on the plot (x,y).
+ """
+
+ def __init__(self, figs, prefix, id_method, rotation, position):
+
+ self.figs = figs
+ self.prefix = prefix
+ self.id_method = id_method
+ self.rotation = rotation
+ self.position = position
+
+ def validate_input(self):
+ """
+ Validate if input for PlotOptions is correct type.
+
+ Raises
+ ------
+ TypeError
+ TypeError is thrown if one of the attributes is not the correct
+ type.
+
+ Returns
+ -------
+ 0, if all checks succeed.
+
+ """
+ # %% Validate inputs
+ # Input validation for figs is done in submodules tagplot_$engine.py
+ if isinstance(self.prefix, str):
+ pass
+ else:
+ raise TypeError("Prefix is not a string.")
+
+ if isinstance(self.id_method, str):
+ pass
+ else:
+ raise TypeError('The chosen id_method is not a string.')
+
+ return 0
diff --git a/publish.py b/plotid/publish.py
similarity index 90%
rename from publish.py
rename to plotid/publish.py
index 77486c82c5e465a771d89af3d03138c77337bece..c5c53dd58da59cca6e3adb56149b3ca9e071726b 100644
--- a/publish.py
+++ b/plotid/publish.py
@@ -15,10 +15,11 @@ import os
import shutil
import sys
import warnings
-from save_plot import save_plot
+from plotid.save_plot import save_plot
-def publish(src_datapath, dst_path, figure, plot_name, data_storage):
+def publish(src_datapath, dst_path, figure, plot_name,
+ data_storage='individual'):
"""
Save plot, data and measuring script.
@@ -37,7 +38,7 @@ def publish(src_datapath, dst_path, figure, plot_name, data_storage):
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.
+ every plot, respectively. This is the default value.
Returns
-------
@@ -55,10 +56,6 @@ def publish(src_datapath, dst_path, figure, plot_name, data_storage):
raise FileNotFoundError('The specified destination directory '
'does not exist.')
- # Check if handed over figure is not empty.
- if not figure:
- raise TypeError('No figure was given. ')
-
# If dst dir already exists ask user if it should be overwritten or not.
if os.path.isdir(dst_path):
warnings.warn(f'Folder "{dst_dirname}" already exists – '
@@ -87,15 +84,18 @@ def publish(src_datapath, dst_path, figure, plot_name, data_storage):
# Does nothing, not implemented yet
pass
case 'individual':
- # Copy data to invisible folder
+ # Copy all files to destination directory
print('Copying data has been started. Depending on the size of '
'your data this may take a while...')
+ # Copy data to invisible folder
shutil.copytree(src_datapath, dst_path_invisible)
# Copy script that calls this function to folder
shutil.copy2(sys.argv[0], dst_path_invisible)
# Copy plot file to folder
- shutil.move(plot_path, dst_path_invisible)
+ if os.path.isfile(plot_path):
+ shutil.copy2(plot_path, dst_path_invisible)
+ os.remove(plot_path)
case _:
raise ValueError('The data storage method {data_storage} '
'is not available.')
@@ -107,4 +107,3 @@ def publish(src_datapath, dst_path, figure, plot_name, data_storage):
print(f'Publish was successful.\nYour plot "{plot_path}",\n'
f'your data "{src_datapath}"\nand your script "{sys.argv[0]}"\n'
f'were copied to {dst_path}\nin {data_storage} mode.')
- return
diff --git a/save_plot.py b/plotid/save_plot.py
similarity index 100%
rename from save_plot.py
rename to plotid/save_plot.py
diff --git a/tagplot.py b/plotid/tagplot.py
similarity index 77%
rename from tagplot.py
rename to plotid/tagplot.py
index ff089604f13caf96282e413c8f748e41d110e3f0..ba660b153fdfbd6fc6b17d02d9a5d156710a67bf 100644
--- a/tagplot.py
+++ b/plotid/tagplot.py
@@ -11,11 +11,11 @@ Functions:
"""
import warnings
-from plotoptions import PlotOptions
-from tagplot_matplotlib import tagplot_matplotlib
+from plotid.plotoptions import PlotOptions
+from plotid.tagplot_matplotlib import tagplot_matplotlib
-def tagplot(figs, engine, prefix='', id_method=1, location='east'):
+def tagplot(figs, engine, prefix='', id_method='time', location='east'):
"""
Tag your figure/plot with an ID.
@@ -30,9 +30,10 @@ def tagplot(figs, engine, prefix='', id_method=1, location='east'):
Plot engine which should be used to tag the plot.
prefix : string
Will be added as prefix to the ID.
- id_method : int, optional
+ id_method : string, optional
id_method for creating the ID. Create an ID by Unix time is referenced
- as 1, create a random ID with id_method=2. The default is 1.
+ 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'.
@@ -48,23 +49,6 @@ def tagplot(figs, engine, prefix='', id_method=1, location='east'):
figures were given. The first list contains the tagged figures.
The second list contains the corresponding IDs as strings.
"""
- # %% Validate inputs
- if isinstance(prefix, str):
- pass
- else:
- raise TypeError("Prefix is not a string.")
-
- if isinstance(figs, list):
- pass
- else:
- raise TypeError("Figures are not a list.")
-
- # TODO: Change id_method key from integer to (more meaningful) string.
- try:
- id_method = int(id_method)
- except ValueError:
- raise TypeError('The chosen ID id_method is not an integer.')
-
if isinstance(location, str):
pass
else:
@@ -99,6 +83,7 @@ def tagplot(figs, engine, prefix='', id_method=1, location='east'):
option_container = PlotOptions(figs, prefix, id_method,
rotation, position)
+ option_container.validate_input()
match engine:
case 'matplotlib' | 'pyplot':
diff --git a/tagplot_matplotlib.py b/plotid/tagplot_matplotlib.py
similarity index 73%
rename from tagplot_matplotlib.py
rename to plotid/tagplot_matplotlib.py
index a94e2b43d66a56fe7ed526a441f73d7d54ae6611..7230f884b99199ea22511509b787e6bcbf50d0ce 100644
--- a/tagplot_matplotlib.py
+++ b/plotid/tagplot_matplotlib.py
@@ -3,13 +3,13 @@
Tag your matplotlib plot with an ID.
Functions:
- TagPlot_matplotlib(figure object, string) -> list
+ tagplot_matplotlib(figure object, string) -> list
"""
import matplotlib
import matplotlib.pyplot as plt
-import create_id
-from plotoptions import PlotOptions
+import plotid.create_id as create_id
+from plotid.plotoptions import PlotOptions
def tagplot_matplotlib(plotid_object):
@@ -26,7 +26,7 @@ def tagplot_matplotlib(plotid_object):
'of PlotOptions.')
# Check if figs is a valid figure or a list of valid figures
if isinstance(plotid_object.figs, matplotlib.figure.Figure):
- pass
+ plotid_object.figs = [plotid_object.figs]
elif isinstance(plotid_object.figs, list):
for figure in plotid_object.figs:
if isinstance(figure, matplotlib.figure.Figure):
@@ -36,18 +36,18 @@ def tagplot_matplotlib(plotid_object):
fontsize = 'small'
color = 'grey'
- IDs = []
+ all_ids_as_list = []
# Loop to create and position the IDs
for fig in plotid_object.figs:
- ID = create_id.create_id(plotid_object.id_method)
- ID = plotid_object.prefix + str(ID)
- IDs.append(ID)
+ figure_id = create_id.create_id(plotid_object.id_method)
+ figure_id = plotid_object.prefix + str(figure_id)
+ all_ids_as_list.append(figure_id)
plt.figure(fig.number)
plt.figtext(x=plotid_object.position[0], y=plotid_object.position[1],
- s=ID, ha='left', wrap=True,
+ s=figure_id, ha='left', wrap=True,
rotation=plotid_object.rotation,
fontsize=fontsize, color=color)
fig.tight_layout()
- return [plotid_object.figs, IDs]
+ return [plotid_object.figs, all_ids_as_list]
diff --git a/plotoptions.py b/plotoptions.py
deleted file mode 100644
index 52699fb0b3c7e18c807febfca2c17992d8ac98ba..0000000000000000000000000000000000000000
--- a/plotoptions.py
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""Contains the PlotOption class."""
-
-
-class PlotOptions:
- """
- Container objects which include all plot options provided by plotid.
-
- Methods
- -------
- __init__figs : figure object
- Figure that will be tagged.
- prefix : str
- Prefix that is placed before the ID.
- id_method : int
- Method that decides which method is used to generate the ID.
- rotation : int
- Rotation angle for the ID.
- position : tuple
- Relative position of the ID on the plot (x,y).
- """
-
- def __init__(self, figs, prefix, id_method, rotation, position):
-
- self.figs = figs
- self.prefix = prefix
- self.id_method = id_method
- self.rotation = rotation
- self.position = position
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000000000000000000000000000000000000..b519f7854682b15071afddae1cb25b862aa48f2b
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=43", "wheel"]
+build-backend = "setuptools.build_meta"
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000000000000000000000000000000000000..cf36c1f25ffc3e5e220ee13d3aa140f91f33c470
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,31 @@
+[metadata]
+name = plotID
+version = 0.1.0
+author = Institut Fluidsystemtechnik within nfdi4ing at TU Darmstadt
+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.
+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 :: 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 =
+ matplotlib
+ numpy
+
+[options.extras_require]
+test =
+ coverage
+
+
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/runner_tests.py b/tests/runner_tests.py
similarity index 85%
rename from runner_tests.py
rename to tests/runner_tests.py
index cb159c4f6d24d86dddab007a15675160b5bdc835..de973b1e9d01e9c67946cb520ee063c7a59cd660 100644
--- a/runner_tests.py
+++ b/tests/runner_tests.py
@@ -6,17 +6,21 @@ Includes starting all tests and measuring the code coverage.
"""
import sys
+import os
import unittest
import coverage
+path = os.path.abspath('plotid')
+sys.path.append(path)
+
cov = coverage.Coverage()
cov.start()
loader = unittest.TestLoader()
-tests = loader.discover('tests')
+tests = loader.discover('.')
testRunner = unittest.runner.TextTestRunner(verbosity=2)
-
result = testRunner.run(tests)
+
cov.stop()
cov.save()
cov.report(show_missing=True)
diff --git a/tests/test_create_id.py b/tests/test_create_id.py
index 68a8a8d77d9acba6dd1444e1c3a5585e7e62f803..589405785640b5cd8ba74f69b9c8245ddfb92190 100644
--- a/tests/test_create_id.py
+++ b/tests/test_create_id.py
@@ -1,27 +1,34 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
-'''
+"""
Unittests for CreateID
-'''
+"""
+
import unittest
-from create_id import create_id
+import plotid.create_id as cid
class TestCreateID(unittest.TestCase):
+ """
+ Class for all unittests of the create_id module.
+ """
def test_existence(self):
- self.assertIsInstance(create_id(1), str)
- self.assertIsInstance(create_id(2), str)
+ """Test if create_id returns a string."""
+ self.assertIsInstance(cid.create_id('time'), str)
+ self.assertIsInstance(cid.create_id('random'), str)
def test_errors(self):
+ """ Test if Errors are raised when id_method is wrong. """
with self.assertRaises(ValueError):
- create_id(3)
+ cid.create_id(3)
with self.assertRaises(ValueError):
- create_id('h')
+ cid.create_id('h')
def test_length(self):
- self.assertEqual(len(create_id(1)), 10)
- self.assertEqual(len(create_id(2)), 8)
+ """ Test if figure_id has the correct length. """
+ self.assertEqual(len(cid.create_id('time')), 10)
+ self.assertEqual(len(cid.create_id('random')), 8)
if __name__ == '__main__':
diff --git a/tests/test_publish.py b/tests/test_publish.py
index a01e727cad948944ee6e55f196d7c1b9d1b3b280..d09b7419f1793f9bae0a47788ebc06a1b1b60c74 100644
--- a/tests/test_publish.py
+++ b/tests/test_publish.py
@@ -1,20 +1,19 @@
# -*- coding: utf-8 -*-
-'''
-Unittests for Publish
-'''
+"""
+Unittests for publish
+"""
import unittest
import os
import sys
import shutil
-import base64
-import matplotlib.pyplot as plt
from unittest.mock import patch
-from publish import publish
+import matplotlib.pyplot as plt
+from plotid.publish import publish
+
SRC_DIR = 'test_src_folder'
-IMG_DATA = b'iVBORw0KGgoAAAANSUhEUgAAAUAAAAFAAgMAAACw/k05AAAACXBIWXMAAA7DAAAOwwHHb6hkAAAAGXRFWHRTb2Z0d2FyZQB3d3cuaW5rc2NhcGUub3Jnm+48GgAAAAxQTFRFAAAAHBwcVFRU////6irJIAAAAIVJREFUeNrt3TERACAQBLHTgQlMU6GQDkz8MF9kBcTCJmrY2IWtJPMWdoBAIBAIBAKBQCAQCAQCgUAgEAgEAoFAIBAIBAKBQCAQCAQCgUAgEAgEAoFAIBAIBAKBQCAQCAQCgUAgEAgEAoFAIBAIBAKBQCAQCAQCgUAgEAgEAv+A5RMHtesBZRvjTSF8ofkAAAAASUVORK5CYII=' # noqa: E501
PIC_NAME = 'test_picture'
DST_DIR = 'test_dst_folder'
DST_PARENT_DIR = 'test_parent'
@@ -24,27 +23,32 @@ fig = plt.figure()
class TestPublish(unittest.TestCase):
+ """
+ Class for all unittests of the publish module.
+ """
def setUp(self):
+ """ Generate source and destination directory and test image. """
os.makedirs(SRC_DIR, exist_ok=True)
os.makedirs(DST_PARENT_DIR, exist_ok=True)
- with open(PIC_NAME, "wb") as test_pic:
- test_pic.write(base64.decodebytes(IMG_DATA))
# Skip test if tests are run from command line.
@unittest.skipIf(not os.path.isfile(sys.argv[0]), 'Publish is not called '
'from a Python script. Therefore, the script cannot be '
'copied.')
def test_publish(self):
+ """ Test publish and check if an exported picture file exists. """
publish(SRC_DIR, DST_PATH, fig, PIC_NAME, 'individual')
assert os.path.isfile(os.path.join(DST_PATH, PIC_NAME + '.png'))
def test_src_directory(self):
+ """ Test if Error is raised when source directory does not exist."""
with self.assertRaises(FileNotFoundError):
publish('not_existing_folder', DST_PATH, fig,
PIC_NAME, 'individual')
def test_dst_directory(self):
+ """ Test if Error is raised when destination dir does not exist."""
with self.assertRaises(FileNotFoundError):
publish(SRC_DIR, 'not_existing_folder',
fig, PIC_NAME, 'individual')
@@ -54,6 +58,10 @@ class TestPublish(unittest.TestCase):
'from a Python script. Therefore, the script cannot be '
'copied.')
def test_dst_already_exists_yes(self):
+ """
+ Test if publish succeeds if the user wants to overwrite an existing
+ destination directory.
+ """
os.mkdir(DST_PATH)
# Mock user input as 'yes'
with patch('builtins.input', return_value='yes'):
@@ -64,6 +72,10 @@ class TestPublish(unittest.TestCase):
'from a Python script. Therefore, the script cannot be '
'copied.')
def test_dst_already_exists_no(self):
+ """
+ Test if publish exits with error if the user does not want to overwrite
+ an existing destination directory by user input 'no'.
+ """
os.mkdir(DST_PATH)
# Mock user input as 'no'
with patch('builtins.input', return_value='no'):
@@ -75,6 +87,10 @@ class TestPublish(unittest.TestCase):
'from a Python script. Therefore, the script cannot be '
'copied.')
def test_dst_already_exists_empty(self):
+ """
+ Test if publish exits with error if the user does not want to overwrite
+ an existing destination directory by missing user input.
+ """
os.mkdir(DST_PATH)
# Mock user input as empty (no should be default).
with patch('builtins.input', return_value=''):
@@ -86,21 +102,24 @@ class TestPublish(unittest.TestCase):
'from a Python script. Therefore, the script cannot be '
'copied.')
def test_dst__invisible_already_exists(self):
+ """
+ Test if publish succeeds when there is already an invisible
+ directory from a previous run (delete the folder and proceed).
+ """
os.mkdir(INVISIBLE_PATH)
publish(SRC_DIR, DST_PATH, fig, PIC_NAME, 'individual')
- def test_picture(self):
- with self.assertRaises(TypeError):
- publish(SRC_DIR, DST_PATH, 'fig', PIC_NAME, 'individual')
-
def test_data_storage(self):
+ """
+ Test if Error is raised when unsupported storage method was chosen.
+ """
with self.assertRaises(ValueError):
publish(SRC_DIR, DST_PATH, fig, PIC_NAME, 'none_existing_method')
def tearDown(self):
+ """ Delete all files created in setUp. """
shutil.rmtree(SRC_DIR)
shutil.rmtree(DST_PARENT_DIR)
- os.remove(PIC_NAME)
if __name__ == '__main__':
diff --git a/tests/test_save_plot.py b/tests/test_save_plot.py
index 767875110242c2613087b6ba4f087ac74dd9fbf7..0f28ae73c00ffffc2deb9d178ea277b2a8730667 100644
--- a/tests/test_save_plot.py
+++ b/tests/test_save_plot.py
@@ -1,25 +1,30 @@
# -*- coding: utf-8 -*-
-'''
+"""
Unittests for save_plot
-'''
+"""
import os
import unittest
import matplotlib.pyplot as plt
-from save_plot import save_plot
+from plotid.save_plot import save_plot
-figure = plt.figure()
-plot_name = 'PLOT_NAME'
+FIGURE = plt.figure()
+PLOT_NAME = 'PLOT_NAME'
-class TestSave_Plot(unittest.TestCase):
+class TestSavePlot(unittest.TestCase):
+ """
+ Class for all unittests of the save_plot module.
+ """
def test_save_plot(self):
- save_plot(figure, plot_name, extension='jpg')
- os.remove(plot_name + '.jpg')
+ """ Test if save_plot succeeds with valid arguments. """
+ save_plot(FIGURE, PLOT_NAME, extension='jpg')
+ os.remove(PLOT_NAME + '.jpg')
def test_wrong_fig_type(self):
+ """ Test if Error is raised when not a figure object is given. """
with self.assertRaises(TypeError):
save_plot('figure', 'PLOT_NAME', extension='jpg')
diff --git a/tests/test_tagplot.py b/tests/test_tagplot.py
index 25c1ee2aa59bef2305bba0227938e8f8bb743ecd..cb71137911a71cccc28e348985a6f8973273f664 100644
--- a/tests/test_tagplot.py
+++ b/tests/test_tagplot.py
@@ -1,72 +1,63 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
-'''
+"""
Unittests for tagplot
-'''
+"""
+
import unittest
-import numpy as np
import matplotlib.pyplot as plt
from tagplot import tagplot
-
-# %% Create data
-x = np.linspace(0, 10, 100)
-y = np.random.rand(100) + 2
-y_2 = np.sin(x) + 2
-
-# %% Create figure
-color1 = 'black'
-color2 = 'yellow'
-
-# 1.Figure
-fig1 = plt.figure()
-plt.plot(x, y, color=color1)
-plt.plot(x, y_2, color=color2)
-
-# 2.Figure
-fig2 = plt.figure()
-plt.plot(x, y, color=color2)
-plt.plot(x, y_2, color=color1)
-
-fig = [fig1, fig2]
-
# Constants for tests
-ProjectID = "MR01"
-plot_engine = "matplotlib"
-method = 1
+FIG1 = plt.figure()
+FIG2 = plt.figure()
+FIGS_AS_LIST = [FIG1, FIG2]
+PROJECT_ID = "MR01"
+PLOT_ENGINE = "matplotlib"
+METHOD = 'time'
-class Test_tagplot(unittest.TestCase):
- def test_figures(self):
- with self.assertRaises(TypeError):
- tagplot('fig', ProjectID, plot_engine, method)
- with self.assertRaises(TypeError):
- tagplot(fig1, plot_engine, prefix=ProjectID)
+class TestTagplot(unittest.TestCase):
+ """
+ Class for all unittests of the tagplot module.
+ """
def test_prefix(self):
+ """ Test if Error is raised if prefix is not a string. """
with self.assertRaises(TypeError):
- tagplot(fig, plot_engine, 3, method)
+ tagplot(FIGS_AS_LIST, PLOT_ENGINE, 3, METHOD, location='southeast')
def test_plotengine(self):
+ """
+ Test if Errors are raised if the provided plot engine is not supported.
+ """
with self.assertRaises(ValueError):
- tagplot(fig, 1, ProjectID, method)
+ tagplot(FIGS_AS_LIST, 1, PROJECT_ID, METHOD, location='north')
with self.assertRaises(ValueError):
- tagplot(fig, 'xyz', ProjectID, method)
+ tagplot(FIGS_AS_LIST, 'xyz', PROJECT_ID, METHOD, location='south')
def test_idmethod(self):
+ """
+ Test if Errors are raised if the id_method is not an string.
+ """
with self.assertRaises(TypeError):
- tagplot(fig, plot_engine, ProjectID, method='(0,1)')
+ tagplot(FIGS_AS_LIST, PLOT_ENGINE, PROJECT_ID, id_method=(0, 1),
+ location='west')
with self.assertRaises(TypeError):
- tagplot(fig, plot_engine, ProjectID, method='h')
+ tagplot(FIGS_AS_LIST, PLOT_ENGINE, PROJECT_ID, id_method=1)
with self.assertRaises(TypeError):
- tagplot(fig, plot_engine, ProjectID, method='[0,1]')
+ tagplot(FIGS_AS_LIST, PLOT_ENGINE, PROJECT_ID, id_method=[0, 1])
def test_location(self):
+ """
+ Test if Errors are raised if the provided location is not supported.
+ """
with self.assertRaises(TypeError):
- tagplot(fig, plot_engine, ProjectID, method, location=1)
+ tagplot(FIGS_AS_LIST, PLOT_ENGINE, PROJECT_ID, METHOD, location=1)
with self.assertWarns(Warning):
- tagplot(fig, plot_engine, ProjectID, method, location='up')
+ tagplot(FIGS_AS_LIST, PLOT_ENGINE, PROJECT_ID, METHOD,
+ location='up')
if __name__ == '__main__':
diff --git a/tests/test_tagplot_matplotlib.py b/tests/test_tagplot_matplotlib.py
index a73c95591591eeae6f4cf2ea3edfb15d5f725645..8f81b6f742b3c6f0b8d176341a9e643afec44f8e 100644
--- a/tests/test_tagplot_matplotlib.py
+++ b/tests/test_tagplot_matplotlib.py
@@ -5,54 +5,55 @@ Unittests for TagPlot_matplotlib
"""
import unittest
-from tagplot_matplotlib import tagplot_matplotlib
-import numpy as np
import matplotlib.pyplot as plt
from matplotlib.figure import Figure
-from tagplot import PlotOptions
+from plotid.tagplot_matplotlib import tagplot_matplotlib
+from plotid.plotoptions import PlotOptions
-# %% Create data
-x = np.linspace(0, 10, 100)
-y = np.random.rand(100) + 2
-y_2 = np.sin(x) + 2
-# %% Create figure
-color1 = 'black'
-color2 = 'yellow'
-
-# 1.Figure
-fig1 = plt.figure()
-plt.plot(x, y, color=color1)
-plt.plot(x, y_2, color=color2)
-
-# 2.Figure
-fig2 = plt.figure()
-plt.plot(x, y, color=color2)
-plt.plot(x, y_2, color=color1)
-
-fig = [fig1, fig2]
+FIG1 = plt.figure()
+FIG2 = plt.figure()
+FIGS_AS_LIST = [FIG1, FIG2]
# Constants for tests
-ProjectID = "MR01"
-method = 1
-rotation = 90
-position = (0.975, 0.35)
+PROJECT_ID = "MR01"
+METHOD = 'time'
+ROTATION = 90
+POSITION = (0.975, 0.35)
-class Test_tagplot_matplotlib(unittest.TestCase):
+class TestTagplotMatplotlib(unittest.TestCase):
+ """
+ Class for all unittests of the tagplot_matplotlib module.
+ """
def test_mplfigures(self):
- options = PlotOptions(fig, ProjectID, method, rotation, position)
- [figs, ID] = tagplot_matplotlib(options)
+ """ Test of returned objects. Check if they are matplotlib figures. """
+ options = PlotOptions(FIGS_AS_LIST, PROJECT_ID, METHOD, ROTATION,
+ POSITION)
+ [figs, _] = tagplot_matplotlib(options)
self.assertIsInstance(figs[0], Figure)
self.assertIsInstance(figs[1], Figure)
+ def test_single_mplfigure(self):
+ """
+ Test of returned objects. Check if matplotlib figures are returned,
+ if a single matplot figure is given (not as a list).
+ """
+ options = PlotOptions(FIG1, PROJECT_ID, METHOD, ROTATION, POSITION)
+ [figs, _] = tagplot_matplotlib(options)
+ self.assertIsInstance(figs[0], Figure)
+
def test_mplerror(self):
- options = PlotOptions(3, ProjectID, method, rotation, position)
+ """ Test if Error is raised if wrong type of figures is given. """
+ options = PlotOptions(3, PROJECT_ID, METHOD, ROTATION, POSITION)
with self.assertRaises(TypeError):
tagplot_matplotlib(options)
def test_mpl_plotoptions(self):
+ """
+ Test if Error is raised if not an instance of PlotOptions is passed.
+ """
with self.assertRaises(TypeError):
tagplot_matplotlib('wrong_object')