refactor

envs/brendapyrser-dev.yml

@@ -0,0 +1,19 @@
+name: brendapyrser-dev
+channels:
+  - defaults
+  - bioconda
+  - conda-forge
+dependencies:
+  - python >= 3.8
+  - poetry >= 1.3
+  - pip
+  - pip:
+    - mkdocs
+    - mkdocs-gen-files
+    - pymdown-extensions
+    - mkdocs-jupyter
+    - mkdocstrings[python]
+    - ruff
+    - black
+    - argmark
+    - coverage

pyproject.toml

@@ -0,0 +1,46 @@
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "brendapyrser"
+version = "0.0.4"
+description = "Tools to parse the BRENDA database"
+license = "Apache-2.0"
+authors = ["Semidán Robaina Estévez <semidan.robaina@gmail.com>"]
+maintainers = ["Semidán Robaina Estévez <semidan.robaina@gmail.com>"]
+readme = "README.md"
+homepage = "https://github.com/robaina/BRENDApyrser"
+repository = "https://github.com/robaina/BRENDApyrser"
+documentation = "https://robaina.github.io/BRENDApyrser"
+keywords = ["BRENDA", "metabolism", "enzymes", "bioinformatics"]
+classifiers = [
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Natural Language :: English",
+]
+packages = [{ include = "brendapyrser", from = "src" }]
+[tool.poetry.dependencies]
+python = "^3.8"
+numpy = "^1.20.2"
+pandas = "^1.2.4"
+importlib-metadata = "^4.0.1"
+
+[tool.ruff]
+select = [
+    "E", # pycodestyle errors
+    "W", # pycodestyle warnings
+    "F", # pyflakes
+    "I", # isort
+]
+ignore = [
+    "E501", # line too long, handled by black
+    "B008", # do not perform function calls in argument defaults
+    "C901", # mccabe complexity
+    "E999", # match statement is not yet supported
+    "W605", # ASCII art, verbatim text
+]
+
+[tool.ruff.isort]
+known-first-party = ["brendapyrser"]