Implement CI pipeline pre-commit hooks

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,12 +1,20 @@
-## Description
-Provide a brief description of the PR's purpose here.
+### Summary
+<!-- Provide a brief description of the PR's purpose here. -->
 
-## Todos
-Notable points that this PR has either accomplished or will accomplish.
-  - [ ] TODO 1
+### Changes
+<!-- List all the changes introduced in this PR. -->
+Change 1 <!-- Rename Change 1 to reflect change title -->:
+- <!-- Bullet point the changes in update 1. -->
+-  
 
-## Questions
-- [ ] Question1
+Change 2 <!-- Rename Change 2 to reflect change title -->:
+- <!-- Bullet point the changes in update 2. -->
+-  
 
-## Status
-- [ ] Ready to go
+Change 3 <!-- Rename Change 3 to reflect change title -->:
+- <!-- Bullet point the changes in update 3. -->
+-  
+
+### Impact
+- <!-- Bullet point the expected impact this PR will have on the codebase. -->
+-  

.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 )

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies: [flake8-pyproject]
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile=black"]

CodeEntropy/ConformationFunctions.py

@@ -1,14 +1,19 @@
-import numpy as nmp
-from MDAnalysis.analysis.dihedrals import Dihedral
+import numpy as np
 
-def assign_conformation(data_container, dihedral, number_frames, bin_width, start, end, step):
+# from MDAnalysis.analysis.dihedrals import Dihedral
+
+
+def assign_conformation(
+    data_container, dihedral, number_frames, bin_width, start, end, step
+):
     """
     Create a state vector, showing the state in which the input dihedral is
-    as a function of time. The function creates a histogram from the timeseries of the 
-    dihedral angle values and identifies points of dominant occupancy 
+    as a function of time. The function creates a histogram from the timeseries of the
+    dihedral angle values and identifies points of dominant occupancy
     (called CONVEX TURNING POINTS).
-    Based on the identified TPs, states are assigned to each configuration of the dihedral.
-
+    Based on the identified TPs, states are assigned to each configuration of the
+    dihedral.
+
     Input
     -----
     dihedral_atom_group : the group of 4 atoms defining the dihedral
@@ -21,25 +26,26 @@ def assign_conformation(data_container, dihedral, number_frames, bin_width, star
     Return
     ------
     A timeseries with integer labels describing the state at each point in time.
-    
+
     """
-    conformations = nmp.zeros(number_frames)
-    phi = nmp.zeros(number_frames)
+    conformations = np.zeros(number_frames)
+    phi = np.zeros(number_frames)
 
     # get the values of the angle for the dihedral
     # dihedral angle values have a range from -180 to 180
     for timestep in data_container.trajectory[start:end:step]:
         value = dihedral.value()
         # we want postive values in range 0 to 360 to make the peak assignment work
-        # using the fact that dihedrals have circular symetry (i.e. -15 degrees = +345 degrees)
+        # using the fact that dihedrals have circular symetry
+        # (i.e. -15 degrees = +345 degrees)
         if value < 0:
             value += 360
         phi[timestep.frame] = value
 
     # create a histogram using numpy
-    number_bins = int(360/bin_width)
-    popul, bin_edges = nmp.histogram(a=phi, bins=number_bins, range=(0,360))
-    bin_value = [0.5 * (bin_edges[i] + bin_edges[i+1]) for i in range(0,len(popul))]
+    number_bins = int(360 / bin_width)
+    popul, bin_edges = np.histogram(a=phi, bins=number_bins, range=(0, 360))
+    bin_value = [0.5 * (bin_edges[i] + bin_edges[i + 1]) for i in range(0, len(popul))]
 
     # identify "convex turning-points" and populate a list of peaks
     # peak : a bin whose neighboring bins have smaller population
@@ -50,19 +56,30 @@ def assign_conformation(data_container, dihedral, number_frames, bin_width, star
         # if there is no dihedrals in a bin then it cannot be a peak
         if popul[bin_index] == 0:
             pass
-        # being careful of the last bin (dihedrals have circular symmetry, the histogram does not)
-        elif bin_index == number_bins-1: # the -1 is because the index starts with 0 not 1
-            if popul[bin_index] >= popul[bin_index-1] and popul[bin_index] >= popul[0]:
+        # being careful of the last bin
+        # (dihedrals have circular symmetry, the histogram does not)
+        elif (
+            bin_index == number_bins - 1
+        ):  # the -1 is because the index starts with 0 not 1
+            if (
+                popul[bin_index] >= popul[bin_index - 1]
+                and popul[bin_index] >= popul[0]
+            ):
                 peak_values.append(bin_value[bin_index])
         else:
-            if popul[bin_index] >= popul[bin_index-1] and popul[bin_index] >= popul[bin_index+1]:
+            if (
+                popul[bin_index] >= popul[bin_index - 1]
+                and popul[bin_index] >= popul[bin_index + 1]
+            ):
                 peak_values.append(bin_value[bin_index])
 
     # go through each frame again and assign conformation state
     for frame in range(number_frames):
         # find the TP that the snapshot is least distant from
         distances = [abs(phi[frame] - peak) for peak in peak_values]
-        conformations[frame] = nmp.argmin(distances)
+        conformations[frame] = np.argmin(distances)
 
     return conformations
-#END assign_conformation
+
+
+# END assign_conformation