Add pyproject.toml (#23)

* add pyproject

* Add .venv, .vscode, and poetry.lock to .gitignore

* update unittest

* update dockerfile

.github/workflows/unittests.yml

@@ -4,39 +4,29 @@ on: push
 
 jobs:
   build:
-    runs-on: ${{ matrix.platform }}
-    strategy:
-      matrix:
-        platform: [ubuntu-latest]
-        python-version: ["3.10.9"]
+    runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           submodules: recursive
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/[email protected]
+      - uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: "3.11"
 
-      - name: Install dependencies
-        run: |
-          pip install -r requirements.txt coverage
+      - uses: snok/install-poetry@v1
+        with:
+          version: 1.3.2
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - run: poetry install --no-interaction --no-root
 
-      - name: Test
-        run: |
-          coverage run -m unittest
-          coverage xml
+      - run: poetry run pytest --cov --cov-report xml:coverage.xml --cov-append -vv --hypothesis-show-statistics
 
       - name: Run codacy-coverage-reporter
         uses: codacy/codacy-coverage-reporter-action@v1
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: coverage.xml
-
-      - uses: codecov/codecov-action@v3
-        with:
-          fail_ci_if_error: false
-          token: ${{ secrets.CODECOV_TOKEN }}
-          files: ./coverage.xml
+          coverage-reports: coverage.xml

.gitignore

@@ -49,3 +49,8 @@ coverage.xml
 *.cover
 .hypothesis/
 .pytest_cache/
+
+
+.venv
+.vscode
+poetry.lock

Dockerfile

@@ -1,5 +1,5 @@
 #==============================================================================================
-FROM python:3.10
+FROM python:3.11
 WORKDIR /opt/software
 COPY . .
 RUN pip install .

pyproject.toml

@@ -0,0 +1,34 @@
+[tool.poetry]
+name = "prodigy-lig"
+version = "1.1.0"
+description = "Calculate protein-small molecule binding affinities."
+authors = ["BonvinLab <[email protected]>"]
+license = "Apache-2.0"
+readme = "README.md"
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "License :: OSI Approved :: Apache Software License",
+  "Programming Language :: Python :: 3.11",
+  "Topic :: Scientific/Engineering :: Chemistry",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Intended Audience :: Science/Research",
+]
+packages = [{ include = "prodigy_lig" }]
+
+[tool.poetry.dependencies]
+python = "^3.11"
+numpy = "^1.26.4"
+biopython = "^1.79"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.1.1"
+coverage = "^7.5.0"
+pytest-cov = "^5.0.0"
+hypothesis = "^6.100.1"
+
+[tool.poetry.scripts]
+prodigy_lig = "prodigy_lig.prodigy_lig:main"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"