finish poetry setup

INSTALL.md

@@ -0,0 +1,43 @@
+# Installation for development
+
+### Clone this repository to a location on your computer
+```
+git clone https://git.io-warnemuende.de/sperlea/microbiome_ML_benchmark.git
+```
+or 
+```
+git@git.io-warnemuende.de:sperlea/microbiome_ML_benchmark.git
+```
+
+### Install poetry
+Full instructions can be found on [https://python-poetry.org/docs/](https://python-poetry.org/docs/).
+
+Short version (Unix/Win-WSL):
+```
+curl -sSL https://install.python-poetry.org | python3 -
+```
+
+Short version (Win-Powershell):
+```
+(Invoke-WebRequest -Uri https://install.python-poetry.org -UseBasicParsing).Content | py -
+```
+
+Check for success: `poetry --version`.
+
+### Install project
+Run `poetry install` in the folder with the `pyproject.toml`.
+This will read the `pyproject.toml` file from the current project, resolves the dependencies, 
+and installs them to the (possibly newly created) virtual environment `.venv` in your project folder.
+
+In your IDE use `project_dir/.venv/bin/python`.
+
+To activate/deactivate the virtual environment from command line use `poetry shell` and `deactivate`.
+
+### Install dependencies
+Instead of `pip install ...` or `conda install ...` use `poetry add ...`.  
+Use `poetry add ... -G dev` for adding a development dependency.  
+This will check if there are any conflicts with other dependencies 
+and (on success) add the dependency to the `pyproject.toml` as well as installing it.
+
+See [here](https://python-poetry.org/docs/cli/#add) for further details, 
+e.g. adding repositories or local sources. 

README.md

@@ -1,5 +1,8 @@
 # Benchmark of Supervised ML methods for the analysis of envicronmental microbiomes and a python package that is not named yet
 
+## Installation
+See [Instructions](INSTALL.md).
+
 ## Organizational matters
 ### Contribute to this Repository
 Please coordinate contributions with Henning Schröder (henning.schroeder@planet-ai.de) or Theodor Sperlea (theodor.sperlea@io-warnemuende.de).

pyproject.toml

@@ -0,0 +1,87 @@
+[tool.poetry]
+name = "microbiome-ml-benchmark"
+version = "0.1.0"
+description = ""
+authors = [
+    "Planet artificial intelligence GmbH <legal@planet-ai.de>",
+    "IOW"
+]
+license = "LICENSE"
+readme = "README.md"
+
+
+documentation = "https://www.io-warnemuende.de/"
+homepage = "https://www.io-warnemuende.de/"
+
+classifiers = [
+  "Development Status :: 2 - Pre-Alpha",
+  "Intended Audience :: Science/Research",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.8",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+
+packages = [{include = "mbmbm"}]
+
+[tool.poetry.dependencies]
+python = "^3.8"
+numpy = "^1.23.4"
+
+[tool.poetry.group.dev.dependencies]
+autoflake = "*"
+black = "*"
+flake8 = "*"
+flake8-bugbear = "*"
+flake8-builtins = "*"
+flake8-comprehensions = "*"
+flake8-debugger = "*"
+flake8-eradicate = "*"
+flake8-logging-format = "*"
+isort = "*"
+mypy = "*"
+pep8-naming = "*"
+pre-commit = "*"
+pymdown-extensions = "*"
+pytest = "*"
+pytest-cov = "*"
+python-kacl = "*"
+pyupgrade = "*"
+tryceratops = "*"
+
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.isort]
+profile = "black"
+src_paths = ["src", "tests"]
+
+[tool.black]
+target-version = ["py38", "py39"]
+include = '\.pyi?$'
+
+[tool.coverage.report]
+fail_under = 100
+exclude_lines = [
+    'if TYPE_CHECKING:',
+    'pragma: no cover'
+]
+
+[tool.mypy]
+disallow_any_unimported = true
+disallow_untyped_defs = true
+no_implicit_optional = true
+strict_equality = true
+warn_unused_ignores = true
+warn_redundant_casts = true
+warn_return_any = true
+check_untyped_defs = true
+show_error_codes = true
+
+
+
+