Update installation, fix some warning move to src layout (#93)

- I have transitioned from setup.py to pyproject.toml . #89
- Changed the layout from flat to source. [See here for advantages](https://packaging.python.org/en/latest/discussions/src-layout-vs-flat-layout/)
- Updated the installation description in the README.md
- Fixed a couple of deprecation and future warnings, reported in #91
---------

Co-authored-by: Julian Belina <j.belina@fz-juelich.de>

Author: julian-belina

.github/workflows/daily_tests.yml

@@ -34,11 +34,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest
-        pip install pytest-cov
-        pip install codecov
-        pip install -r requirements.txt
-        pip install --no-cache-dir -e .
+        pip install --no-cache-dir -e .[dev]
         
     - name: Test with pytest
       working-directory: ./test/

.github/workflows/test_on_push_and_pull.yml

@@ -29,11 +29,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest
-        pip install pytest-cov
-        pip install codecov
-        pip install -r requirements.txt
-        pip install --no-cache-dir -e .
+        pip install --no-cache-dir -e .[dev]
         
     - name: Test with pytest
       working-directory: ./test/
@@ -58,11 +54,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install numpy==${{matrix.python-numpy-version.numpy}} --upgrade pip
-        pip install pytest
-        pip install pytest-cov
-        pip install codecov
-        pip install -r requirements.txt
-        pip install --no-cache-dir -e .
+        pip install --no-cache-dir -e .[dev]
         
     - name: Test with pytest
       working-directory: ./test/

.readthedocs.yml

@@ -11,5 +11,6 @@ build:
 
 python:
   install:
+  - requirements: requirements.txt
   - requirements: requirements_dev.txt
   system_packages: false

README.md

@@ -19,28 +19,50 @@ The documentation of the tsam code can be found [**here**](https://tsam.readthed
 
 
 ## Installation
+It is recommended to install tsam within its own environment. If you are no familiar with python environments, plaese consider to read some [external documentation](https://realpython.com/python-virtual-environments-a-primer/). In the following we assume you have a [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) or [conda](https://www.anaconda.com/) installation.  All conda and mamba command are interchangeable.
+
+### Direct Installations from Package Manager Repositories
+
+If you want to prevent any possible dependency conflicts create a new environment using the following command:
+
+	mamba create -n tsam_env python pip
+
+Activate an existing or the newly create environment afterward
+
+	mamba activate tsam_env
+
 Directly install via pip from pypi as follows:
 
 	pip install tsam
 
-of install from conda forge with the following command:
+or install from conda forge with the following command:
 
 	conda install tsam -c conda-forge
 
+### Local Installation for Development
 Alternatively, clone a local copy of the repository to your computer
 
 	git clone https://github.com/FZJ-IEK3-VSA/tsam.git
-	
-Then install tsam via pip as follow
-	
+
+Change the directory of your shell into the root folder of the repository
+
 	cd tsam
-	pip install . 
-	
-Or install directly via python as 
 
-	python setup.py install
+For development, it is recommended to install tsam into its own environment using conda e.g.
+
+	conda env create --file=requirement.yml
+
+Afterward activate the environment
+
+	conda activate tsam_env
+
+Then install tsam via pip as follows
+	
+	
+	pip install -e .[dev]
 
-In order to use the k-medoids clustering, make sure that you have installed a MILP solver. As default [HiGHS](https://github.com/ERGO-Code/HiGHS) is used. Nevertheless, in case you have access to a license we recommend commercial solvers (e.g. Gurobi or CPLEX) since they have a better performance.
+### Installation of MILP Solver for k-medoids	
+In order to use the k-medoids clustering, make sure that you have installed a MILP solver. As default [HiGHS](https://github.com/ERGO-Code/HiGHS) is installed and used. Nevertheless, in case you have access to a license we recommend commercial solvers (e.g. Gurobi or CPLEX) since they have a better performance.
 
 ### Developer installation
 

pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+requires = ["setuptools>=64.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "tsam"
+version = "2.3.6"
+description = "Time series aggregation module (tsam) to create typical periods"
+authors = [
+    { name = "Leander Kotzur", email = "leander.kotzur@googlemail.com" },
+    { name = "Maximilian Hoffmann", email = "maximilian.hoffmann@julumni.fz-juelich.de" },
+]
+maintainers = [
+  {name = "Julian Belina", email = "j.belina@fz-juelich.de"}
+]
+license = { file = "LICENSE.txt" }
+keywords = ["clustering", "optimization"]
+requires-python = ">=3.9,<3.13"
+readme = "README.md"
+classifiers=[
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: End Users/Desktop",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: MIT License",
+        "Natural Language :: English",
+        "Operating System :: OS Independent",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 2",
+        "Programming Language :: Python :: 3",
+        "Topic :: Scientific/Engineering :: Mathematics",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+    ]
+dynamic = ["dependencies", "optional-dependencies"]
+
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+optional-dependencies = {dev = { file = ["requirements_dev.txt"] }}
+
+
+#Configureation options
+# https://docs.pytest.org/en/7.1.x/reference/reference.html#configuration-options
+
+[tool.pytest.ini_options]
+testpaths = ["test"] # Sets the path where to look for tests
+pythonpath =["test"] # Sets the path which should be prepended to pythonpath relative to the root folder
+console_output_style = "count"
+
+

requirements.yml

@@ -1,8 +1,6 @@
-name: tsam
+name: tsam_env
 channels:
   - conda-forge
 dependencies:
   - python>=3.9,<3.13
   - pip
-  - pip:
-    - -r requirements.txt

requirements_dev.txt

@@ -1,8 +1,7 @@
--r requirements.txt
-
 # Testing
 pytest
 pytest-cov
+codecov
 
 # Documentation
 sphinx