Use pip requirements, add github actions

.github/workflows/main_actions.yml

@@ -0,0 +1,30 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: sodym.tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: windows-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.12"
+    - name: Install dependencies and run tests
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        python -m pytest

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        args: [--line-length=100]
+        language_version: python3.12
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+      - id: check-case-conflict
+      - id: end-of-file-fixer
+      - id: trailing-whitespace

README.md

@@ -16,23 +16,17 @@ https://github.com/IndEcol/ODYM<br>
 
 ## Installation
 
-sodym dependencies are managed with [poetry](https://python-poetry.org/), which creates a [virtual environment](https://docs.python.org/3/tutorial/venv.html) and installs dependencies automatically. The process is quite simple:
+sodym dependencies are managed with [pip](https://pypi.org/project/pip/).
 
-1. Clone the sodym repository using git.
-2. [Install poetry](https://python-poetry.org/docs/#installation)
-   - *Optional*: Configure poetry to create your virtual environment in the project folder via<br>`poetry config virtualenvs.in-project true`
-3. From the project main directory, run `poetry install` to obtain all the necessary dependencies.
-
-To execute python commands using the virtual environment of this project, use `poetry run <command>`, or activate the environment via `[/path/to/].venv/Scripts/activate`.
-Further information can be found in the documentations of poetry and virtual environments linked above.
+To install as a user: run `python -m pip install sodym@git+https://github.com/pik-piam/sodym.git`
 
-## Documentation
+To install as a developer, assuming you already have python installed:
 
-To build and view the documentation, follow these steps:
+1. Clone the sodym repository using git.
+2. From the project main directory, run `pip install -e ".[test]"` to obtain all the necessary
+dependencies, including those for running the tests.
 
-1. From the main directory, run `poetry install --with docs`
-2. Navigate to the `docs` subdirectory, and run `poetry run make html`.
-3. Open the file `docs/build/html/index.html` to view the documentation.
+Note that it is advisable to do this within a virtual environment.
 
 ## Examples
 

pyproject.toml

@@ -1,46 +1,40 @@
-[tool.poetry]
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
 name = "sodym"
 version = "0.1.0"
-description = ""
-authors = ["Jakob Dürrwächter, Merlin Hosak, Stefan Pauliuk"]
+authors = [
+    {name = "Jakob Dürrwächter"},
+    {name = "Merlin Hosak"},
+]
 readme = "README.md"
-packages = [{include = "sodym"}]
-
-[tool.poetry.dependencies]
-python = ">=3.10,<3.13"
-matplotlib = "^3.7.1"
-numpy = "^1.25.0"
-scipy = "^1.11.0"
-PyYAML = "^6.0"
-pandas = "^2.0.2"
-pickle4 = "^0.0.1"
-plotly = "^5.18.0"
-pydantic = "^2.8.2"
-ruff = "^0.5.6"
-docformatter = "^1.7.5"
-openpyxl = "^3.1.5"
-nbformat = "^5.10.4"
-
-[tool.poetry.group.examples.dependencies]
-jupyter = "^1.1.1"
-
-[tool.poetry.group.test]
-optional = true
+requires-python = ">= 3.10"
+dependencies = [
+    "matplotlib>=3.7.1",
+    "numpy>=1.25.0",
+    "scipy>=1.11.0",
+    "PyYAML>=6.0",
+    "pandas>=2.0.2",
+    "pickle4>=0.0.1",
+    "plotly>=5.18.0",
+    "pydantic>=2.8.2",
+    "docformatter>=1.7.5",
+    "openpyxl>=3.1.5",
+    "nbformat>=5.10.4",
+]
 
-[tool.poetry.group.test.dependencies]
-pytest = "^8.3.2"
-polyfactory = "^2.16.2"
-
-[tool.poetry.group.docs]
-optional = true
-
-[tool.poetry.group.docs.dependencies]
-sphinx = "^7.4.0"
-sphinx-pydantic = "^0.1.1"
-autodoc-pydantic = "^2.2.0"
-sphinx-rtd-theme = "^2.0.0"
-myst-parser = "^4.0.0"
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[project.optional-dependencies]
+examples = ["jupyter>=1.1.1"]
+test = [
+    "pytest>=8.3.2",
+    "polyfactory>=2.16.2",
+]
+docs = [
+    "sphinx>=7.4.0",
+    "sphinx-pydantic>=0.1.1",
+    "autodoc-pydantic>=2.2.0",
+    "sphinx-rtd-theme>=2.0.0",
+    "myst-parser>=4.0.0",
+]

requirements.txt

@@ -0,0 +1,46 @@
+annotated-types==0.7.0
+attrs==24.2.0
+charset-normalizer==3.4.0
+colorama==0.4.6
+contourpy==1.3.0
+cycler==0.12.1
+docformatter==1.7.5
+et-xmlfile==1.1.0
+Faker==30.8.0
+fastjsonschema==2.20.0
+fonttools==4.54.1
+iniconfig==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
+jupyter_core==5.7.2
+kiwisolver==1.4.7
+matplotlib==3.9.2
+nbformat==5.10.4
+numpy==2.1.2
+openpyxl==3.1.5
+packaging==24.1
+pandas==2.2.3
+pickle4==0.0.1
+pillow==11.0.0
+platformdirs==4.3.6
+plotly==5.24.1
+pluggy==1.5.0
+polyfactory==2.17.0
+pydantic==2.9.2
+pydantic_core==2.23.4
+pyparsing==3.2.0
+pytest==8.3.3
+python-dateutil==2.9.0.post0
+pytz==2024.2
+pywin32==308
+PyYAML==6.0.2
+referencing==0.35.1
+rpds-py==0.20.0
+scipy==1.14.1
+setuptools==75.2.0
+six==1.16.0
+tenacity==9.0.0
+traitlets==5.14.3
+typing_extensions==4.12.2
+tzdata==2024.2
+untokenize==0.1.1