Unit tests (#12)

* Setup test framework using pytest

* Started adding tests for output module 

* Reformatted currently existing tests for geometry

* Minor refactor of parsing modules attributes and inheritance 

* Added pytest CI 

* Addresses #3, and #6

---------

Co-authored-by: lukashoermann200 <[email protected]>

.github/workflows/interrogate.yaml

@@ -0,0 +1 @@
+# TODO

.github/workflows/pypi.yaml

@@ -0,0 +1,65 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          poetry build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+
+    needs:
+      - release-build
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@6f7e8d9c0b1a2c3d4e5f6a7b8c9d0e1f2a3b4c5d

.github/workflows/pyright.yml → .github/workflows/pyright.yaml

@@ -1,4 +1,4 @@
-name: Run the pyright checker
+name: pyright
 
 on:
   push:

.github/workflows/pytest.yaml

@@ -0,0 +1,43 @@
+name: pytest
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+  # Only run after linting has finished
+  # workflow_run:
+  #   workflows: ['ruff']
+  #   types: [completed]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    # TODO run on all supported versions of the project
+    # strategy:
+    #   matrix:
+    #     python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - uses: abatilo/actions-poetry@v2
+      - name: Install the project dependencies
+        run: poetry install --with=dev
+      - name: Run the tests
+        run: poetry run -- pytest tests --cov=dfttools --cov-report xml
+
+      # TODO when approved for the maurergroup organisation
+      # - name: Coveralls GitHub Action
+      #   uses: coverallsapp/[email protected]
+      #   with:
+      #     github-token: ${{ secrets.GITHUB_TOKEN }}
+      #     parallel: true  # Enable parallel support for Coveralls if needed

.github/workflows/ruff.yml → .github/workflows/ruff.yaml

@@ -1,4 +1,4 @@
-name: Run the ruff linter and formatter
+name: ruff
 
 on:
   push:
@@ -12,6 +12,7 @@ on:
 jobs:
   ruff-lint:
     runs-on: ubuntu-latest
+
     steps:
       - uses: actions/checkout@v4
       - uses: chartboost/ruff-action@v1
@@ -22,6 +23,7 @@ jobs:
   ruff-format:
     runs-on: ubuntu-latest
     needs: ruff-lint
+
     steps:
       - uses: actions/checkout@v4
       - uses: chartboost/ruff-action@v1

.github/workflows/sphinx-docs.yml → .github/workflows/sphinx-docs.yaml

@@ -1,4 +1,4 @@
-name: Build and deploy Sphinx docs
+name: Sphinx
 
 on:
   # Runs on pushes targeting the default branch
@@ -32,14 +32,11 @@ jobs:
     permissions:
       contents: write
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Install Python
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.12"
-      - name: Install Poetry
-        uses: abatilo/actions-poetry@v2
+      - uses: abatilo/actions-poetry@v2
       - name: Install the project dependencies
         run: poetry install --with=docs
       - name: Build HTML

.gitignore

@@ -159,4 +159,9 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
+# Tests
+tests/.aims_bin_loc
+tests/fixtures/custom_bin_aims_calcs
+
+# Tutorials
 tutorials/temp/

dfttools/base_parser.py

@@ -1,4 +1,5 @@
 import os.path
+from typing import List
 
 
 class BaseParser:
@@ -39,3 +40,25 @@ def __init__(self, supported_files, **kwargs):
             else:
                 with open(kwargs[kwarg], "r") as f:
                     self.file_contents[kwarg] = f.readlines()
+
+    def __str__(self) -> str:
+        if self.lines is None or self.lines == "":
+            raise ValueError("Could not find file contents.")
+        else:
+            return "".join(self.lines)
+
+    @property
+    def lines(self) -> List[str]:
+        return self._lines
+
+    @lines.setter
+    def lines(self, value: List[str]):
+        self._lines = value
+
+    @property
+    def path(self) -> str:
+        return self._path
+
+    @path.setter
+    def path(self, value: str):
+        self._path = value