Implement CI Pipeline:

- Updated CI.yaml to allow Github Actions to run:
 - tests
 - docs
 - pre-commit
- Moved the tests directory to the root of the repository, mentioned in issue #40

Author: harryswift01

.github/workflows/CI.yaml

@@ -1,82 +1,70 @@
-name: CI
+name: ci
 
 on:
-  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
-  # Existing codes likely still have "master" as the primary branch
-  # Both are tracked here to keep legacy and new codes working
   push:
-    branches:
-      - "master"
-      - "main"
+    branches: [main]
   pull_request:
-    branches:
-      - "master"
-      - "main"
-  schedule:
-    # Nightly tests run on master by default:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "0 0 * * *"
 
 jobs:
-  test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
+  tests:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
     strategy:
       matrix:
-        os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: ['3.9', '3.10']
-
+        python-version: ["3.11", "3.12", "3.13"]
+    name: Run tests
     steps:
-    - uses: actions/checkout@v1
-
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
-
+    - name: Checkout repo
+      uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Testing Dependencies
-      shell: bash
-      run: |
-        python -m pip install -U pytest pytest-cov codecov
-
-    - name: Install package
-
+    - name: Install CodeEntropy and its testing dependencies
       shell: bash
-      run: |
-        python -m pip install .
-
-
-    - name: Run tests
+      run: pip install -e .[testing]
 
+    - name: Run test suite
       shell: bash
+      run: pytest --cov CodeEntropy --cov-report term-missing --cov-append .
 
-      run: |
-        pytest -v --cov=CodeEntropy --cov-report=xml --color=yes CodeEntropy/tests/
+    - name: Coveralls GitHub Action
+      uses: coverallsapp/github-action@v2.3.6
+      with:
+        github-token: ${{ secrets.COVERALLS_REPO_TOKEN }}
 
-    - name: CodeCov
-      uses: codecov/codecov-action@v1
+  docs:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-    
-    - name: Testing executable capped protein
-      shell: bash
-      if: runner.os != 'Windows'
+        python-version: 3.12
+    - name: Install python dependencies
       run: |
-        CodeEntropyPoseidon -f "CodeEntropy/tests/data/poseidon_example.prmtop" "CodeEntropy/tests/data/poseidon_example.trr" -l "resname ARG" -b 0 -e 20 --wm --res --uatom --topog 2 --solwm --solres --soluatom --solContact
+        pip install --upgrade pip
+        pip install -e .[docs]
+    - name: Build docs
+      run: cd docs && make
 
-    - name: Testing executable lysozyme in water Multi-threading 
-      shell: bash
-      if: runner.os == 'Linux'
-      run: |
-        CodeEntropyPoseidon -f "CodeEntropy/tests/data/1AKI_prod_60.tpr" "CodeEntropy/tests/data/1AKI_prod_60.trr" -l "protein" -b 2 -e 12 -d 2 -t 2 --wm --res --uatom --topog 3 --solwm --solres --soluatom --solContact
+  pre-commit:
+   runs-on: ubuntu-latest
+   timeout-minutes: 15
+   steps:
+   - uses: actions/checkout@v4
+   - name: Set up Python 3.11
+     uses: actions/setup-python@v5
+     with:
+       python-version: 3.11
+   - name: Install python dependencies
+     run: |
+       pip install --upgrade pip
+       pip install -e .[pre-commit,docs,testing]
+   - name: Run pre-commit
+     run: |
+       pre-commit install
+       pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )