Re organize repository (#34)

* re-organize repository * Add .vscode/ to .gitignore * update pyproject.toml * update ci.yml * update ci.yml * typo * update action
haddocking · Apr 26, 2024 · cb1f282 · cb1f282
1 parent ad193a4
commit cb1f282
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -3,53 +3,28 @@ name: ci
 on: push
 
 jobs:
-  ci:
-    strategy:
-      matrix:
-        platform: [ubuntu-latest, macos-latest]
-        python-version: ["3.9.16", "3.10.9"]
+  test:
 
-    runs-on: ${{ matrix.platform }}
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
 
       - uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
-
-      # - name: cache poetry install
-      #   uses: actions/cache@v2
-      #   with:
-      #     path: ~/.local
-      #     key: poetry-1.1.12-0
+          python-version: "3.10"
 
       - uses: snok/install-poetry@v1
         with:
           version: 1.3.2
           virtualenvs-create: true
           virtualenvs-in-project: true
 
-      # - name: cache deps
-      #   id: cache-deps
-      #   uses: actions/cache@v2
-      #   with:
-      #     path: .venv
-      #     key: pydeps-${{ hashFiles('**/poetry.lock') }}
       - run: poetry install --no-interaction --no-root
-        # if: steps.cache-deps.outputs.cache-hit != 'true'
 
-      - run: |
-          poetry run coverage run -m unittest
-          poetry run 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
diff --git a/.gitignore b/.gitignore
@@ -157,4 +157,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+#.idea/
+
+.vscode/
+poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -23,17 +23,24 @@ biopython = "1.80"
 freesasa = "2.2.1"
 numpy = "^1.22.0"
 
+[tool.poetry.group.test.dependencies]
+pytest = "^8.1.1"
+coverage = "^7.4.4"
+pytest-cov = "^5.0.0"
+hypothesis = "^6.100.1"
+
 [tool.poetry.scripts]
 prodigy = "prodigy.predict_IC:main"
 
-[tool.poetry.group.test.dependencies]
-coverage = "^7.1.0"
-
 [tool.black]
 line-length = 79
 
 [tool.setuptools]
-packages = ["prodigy", "prodigy.lib"]
+include-package-data = true
+packages = ["src"]
+
+[tool.pytest.ini_options]
+pythonpath = ["src"]
 
 [build-system]
 requires = ["poetry-core"]

diff --git a/prodigy/__init__.py → src/prodigy/__init__.py b/prodigy/__init__.py → src/prodigy/__init__.py
diff --git a/prodigy/lib/__init__.py → src/prodigy/modules/__init__.py b/prodigy/lib/__init__.py → src/prodigy/modules/__init__.py
diff --git a/prodigy/lib/aa_properties.py → src/prodigy/modules/aa_properties.py b/prodigy/lib/aa_properties.py → src/prodigy/modules/aa_properties.py
diff --git a/prodigy/lib/freesasa_tools.py → src/prodigy/modules/freesasa_tools.py b/prodigy/lib/freesasa_tools.py → src/prodigy/modules/freesasa_tools.py
diff --git a/prodigy/lib/models.py → src/prodigy/modules/models.py b/prodigy/lib/models.py → src/prodigy/modules/models.py
diff --git a/prodigy/lib/nis_utils.py → src/prodigy/modules/nis_utils.py b/prodigy/lib/nis_utils.py → src/prodigy/modules/nis_utils.py
diff --git a/prodigy/lib/parsers.py → src/prodigy/modules/parsers.py b/prodigy/lib/parsers.py → src/prodigy/modules/parsers.py
diff --git a/prodigy/lib/utils.py → src/prodigy/modules/utils.py b/prodigy/lib/utils.py → src/prodigy/modules/utils.py
diff --git a/prodigy/naccess.config → src/prodigy/naccess.config b/prodigy/naccess.config → src/prodigy/naccess.config
diff --git a/prodigy/predict_IC.py → src/prodigy/predict_IC.py b/prodigy/predict_IC.py → src/prodigy/predict_IC.py
@@ -32,11 +32,11 @@
     )
     raise ImportError(e)
 
-from .lib import aa_properties
-from .lib.freesasa_tools import execute_freesasa_api
-from .lib.models import IC_NIS
-from .lib.parsers import parse_structure
-from .lib.utils import check_path, dg_to_kd
+from prodigy.modules import aa_properties
+from prodigy.modules.freesasa_tools import execute_freesasa_api
+from prodigy.modules.models import IC_NIS
+from prodigy.modules.parsers import parse_structure
+from prodigy.modules.utils import check_path, dg_to_kd
 
 
 def calculate_ic(struct, d_cutoff=5.5, selection=None):

diff --git a/tests/test_prodigy.py b/tests/test_prodigy.py
@@ -17,8 +17,8 @@
 import numpy as np
 from Bio.PDB import PDBParser, Structure
 
-from prodigy.lib.freesasa_tools import stdchannel_redirected
-from prodigy.lib.parsers import validate_structure
+from prodigy.modules.freesasa_tools import stdchannel_redirected
+from prodigy.modules.parsers import validate_structure
 from prodigy.predict_IC import Prodigy
 
 
@@ -66,7 +66,7 @@ def test_dataset(self):
             handle = dataset.extractfile(entry)
             # Wrap filehandle to ensure string file handle in Python 3
             if version_info[0] >= 3:
-                handle = TextIOWrapper(BufferedReader(handle))
+                handle = TextIOWrapper(BufferedReader(handle)) # type: ignore
             # Suppress gap warnings when parsing structure
             with stdchannel_redirected(stderr, devnull):
                 s = validate_structure(