Merge branch 'dev' into 'master'

Chores like formatting and packaging

See merge request ebi-biows/taxonomy-resolver!1

.github/workflows/package_and_publish.yml

@@ -0,0 +1,14 @@
+name: Publishing to PyPI
+on:
+  push:
+    tags:
+      - "v*.*.*"
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build and publish to pypi
+        uses: JRubics/[email protected]
+        with:
+          pypi_token: ${{ secrets.PYPI_TOKEN }}

.github/workflows/setup_and_test.yml

@@ -0,0 +1,58 @@
+name: Python package
+on: [push]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up python
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      #----------------------------------------------
+      #  -----  install & configure poetry  -----
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          virtualenvs-path: .venv
+          installer-parallel: true
+      #----------------------------------------------
+      # load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+      #----------------------------------------------
+      # install your root project, if required
+      #----------------------------------------------
+      - name: Install project
+        run: poetry install --no-interaction
+      #----------------------------------------------
+      # run test suite
+      #----------------------------------------------
+      - name: Test with pytest
+        run: |
+          source .venv/bin/activate
+          pytest tests/test_*.py
+      #----------------------------------------------
+      # packaging with poetry
+      #----------------------------------------------
+      - name: Build packages with Poetry
+        run: poetry build

.gitignore

@@ -128,4 +128,10 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# IDE
+.vscode/*
+!.vscode/settings.json
+.idea
+.history
+
 testdata/tree*

.gitlab-ci.yml

@@ -1,22 +1,28 @@
-# Author: Fábio Madeira <[email protected]>, 2020
-# test/run locally with
-# gitlab-runner exec docker test_pytest
-
-image: python:3.9
+---
+default:
+  image: python:3.11
+  tags:
+    - k8s-agent-runner
 
 before_script:
   - pip install --no-cache-dir -r requirements.txt
+  - pip install poetry
 
 stages:
   # Unit tests
   - test_pytest
   # Install Module
-  - setup_install
+  - poetry_install
+  - poetry_build
 
 test_pytest:
   stage: test_pytest
   script: pytest
 
-setup_install:
-  stage: setup_install
-  script: python setup.py install
+poetry_install:
+  stage: poetry_install
+  script: poetry install --no-interaction --no-root
+
+poetry_build:
+  stage: poetry_build
+  script: poetry build

.vscode/settings.json

@@ -0,0 +1,15 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter",
+        "editor.formatOnType": true,
+        "editor.formatOnSave": true,
+        "editor.codeActionsOnSave": {
+            "source.organizeImports.ruff": "explicit"
+        }
+    },
+}

__main__.py

@@ -4,11 +4,11 @@
 """
 Taxonomy Resolver
 
-:copyright: (c) 2020-2021.
+:copyright: (c) 2020-2024.
 :license: Apache 2.0, see LICENSE for more details.
 """
 
 from taxonresolver.cli import cli
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     cli()

pyproject.toml

@@ -0,0 +1,39 @@
+[tool.poetry]
+name = "taxonomy-resolver"
+version = "0.2.1"
+description = "Taxonomy Resolver builds NCBI Taxonomy Trees and lists of Taxonomy Identifiers (TaxIDs) based on the NCBI Taxonomy Database"
+authors = ["Fábio Madeira <[email protected]>"]
+readme = "README.rst"
+include = ["CHANGELOG.rst"]
+license = "Apache-2.0"
+packages = [{include = "taxonresolver"}]
+classifiers = [
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "Natural Language :: English",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
+        "Programming Language :: Python :: Implementation :: PyPy",
+        "Topic :: Internet",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+        "License :: OSI Approved :: Apache Software License",
+]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+click = ">=8.1.7"
+requests = ">=2.32.2"
+pytest = ">=8.2.1"
+pandas = ">=2.2.2"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]

requirements.txt

@@ -1,4 +1,4 @@
-click
-requests
-pytest
-pandas
+click>=8.1.7
+requests>=2.32.2
+pytest>=8.2.1
+pandas>=2.2.2

taxonomy-resolver.py

@@ -4,11 +4,11 @@
 """
 Taxonomy Resolver
 
-:copyright: (c) 2020-2021.
+:copyright: (c) 2020-2024.
 :license: Apache 2.0, see LICENSE for more details.
 """
 
 from taxonresolver.cli import cli
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     cli()

taxonresolver/__init__.py

@@ -4,13 +4,13 @@
 """
 Taxonomy Resolver
 
-:copyright: (c) 2020-2021.
+:copyright: (c) 2020-2024.
 :license: Apache 2.0, see LICENSE for more details.
 """
 
-__author__ = 'Fábio Madeira'
-__email__ = '[email protected]'
-__version__ = '0.2.1'
-__contributors__ = [u'Fábio Madeira', u'Adrian Tivey']
+__author__ = "Fábio Madeira"
+__email__ = "[email protected]"
+__version__ = "0.2.1"
+__contributors__ = ["Fábio Madeira"]
 
 from taxonresolver.tree import TaxonResolver