Adds automatic deployment to Pypi

.github/workflows/CI.yaml

@@ -26,7 +26,7 @@ jobs:
         #os: [macOS-latest, ubuntu-latest, windows-latest]
         #python-version: [3.8, 3.9, "3.10"]
         os: [ubuntu-latest]
-        python-version: [3.8, 3.9, "3.10", "3.11"]
+        python-version: ["3.12", "3.13"]
     steps:
     - uses: actions/checkout@v1
 
@@ -92,44 +92,29 @@ jobs:
 
     #Install numpy first
     - name: Install numpy
+      shell: bash -l {0}
       run: |
-        conda install "numpy<2"
+        conda install "numpy"
 
-    #Install pydca
-    - name: Check out pydca
-      uses: actions/checkout@v3
-      with:
-        repository: cabb99/pydca
-        path: pydca_dir
+    # Install pyDCA from GitHub (optional – tests that need it will be skipped if this fails)
     - name: Install pydca
+      continue-on-error: true
+      shell: bash -l {0}
       run: |
-        cd pydca_dir
-        echo "numpy<2" > constraints.txt
-        conda run -n test pip install -r requirements.txt -c constraints.txt
-        conda run -n test python -m pip install . --no-deps
-        conda list
-        cd ..
-        pwd
-        conda run -n test python -c "import sys; print(sys.executable); print('\n'.join(sys.path))"
-        conda run -n test python -c "import pydca; print('pydca is installed and importable')"
-        conda run -n test pip freeze | grep pydca
+        python -m pip install "git+https://github.com/cabb99/pydca.git"
+        python -c "import pydca; print('pydca is installed and importable')"
+        pip freeze | grep pydca
 
     - name: Install package
 
       # conda setup requires this special shell
       shell: bash -l {0}
       run: |
-        conda install -c conda-forge --file requirements.txt
+        pip install -r requirements.txt
+        conda install -c conda-forge pdbfixer
         python -m pip install . --no-deps
         conda list
 
-    - name: Install pdbfixer
-
-      # conda setup requires this special shell
-      shell: bash -l {0}
-      run: |
-        conda install -c conda-forge pdbfixer
-
     - name: Run tests
 
       # conda setup requires this special shell
@@ -139,7 +124,7 @@ jobs:
         python -c "import sys; print(sys.executable); print('\n'.join(sys.path))"
         python -c "import pydca; print('pydca is installed and importable')"
         pip freeze | grep pydca
-        pytest -v --cov=frustratometer --cov-report=xml --color=yes tests/
+        pytest -v --skip-slow --skip-memory-heavy --cov=frustratometer --cov-report=xml --color=yes tests/
 
     - name: CodeCov
       uses: codecov/codecov-action@v3

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,124 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        persist-credentials: false
+        fetch-depth: 0  # versioneer needs full history
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+
+    - name: Install build dependencies
+      run: python3 -m pip install build --user
+
+    - name: Build wheel and source tarball
+      run: python3 -m build
+
+    - name: Store distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/frustratometer
+    permissions:
+      id-token: write  # mandatory for trusted publishing
+
+    steps:
+    - name: Download distributions
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+
+  test-from-testpypi:
+    name: Test install from TestPyPI
+    needs: publish-to-testpypi
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        persist-credentials: false
+
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        channels: conda-forge,defaults
+        activate-environment: test-publish
+        auto-update-conda: false
+        auto-activate-base: false
+
+    - name: Install conda dependencies
+      shell: bash -l {0}
+      run: |
+        conda install -c conda-forge openmm pdbfixer pytest
+
+    - name: Wait for TestPyPI to index the package
+      shell: bash -l {0}
+      run: sleep 30
+
+    - name: Install frustratometer from TestPyPI
+      shell: bash -l {0}
+      run: |
+        pip install --pre \
+          --index-url https://test.pypi.org/simple/ \
+          --extra-index-url https://pypi.org/simple/ \
+          frustratometer
+
+    - name: Verify import and version
+      shell: bash -l {0}
+      run: |
+        python -c "import frustratometer; print(frustratometer.__version__)"
+
+    - name: Run tests
+      shell: bash -l {0}
+      run: |
+        python -m pytest tests/ \
+          --ignore=tests/test_dca_frustratometer.py \
+          -x --tb=short
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: test-from-testpypi
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/frustratometer
+    permissions:
+      id-token: write  # mandatory for trusted publishing
+
+    steps:
+    - name: Download distributions
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -21,13 +21,25 @@ The frustratometer is based on the principle of minimal frustration postulated b
 
 Under most circunstances amino acids are minimally frustrated in the protein, but pockets where amino acids are of interest for protein function can remain frustrated, as they become minimally frustrated when achieving the corresponding function. In short, a frustrated residue or interaction indicates that the particular amino acid would be minimized under a different environment, which reveals possible competing evolutionary pressures on its selection. We have identified that these pockets usually correspond to regions of functional importance, for example, that may form part of a catalitic domain, a hinge domain, or a binding region.
 
-This principle of minimum frustration has been shown using the AWSEM forcefield but can be extended to any other forcefield, including atomistic forcefields, or a pseudo-forcefield like DCA, as implemented here.
+This principle of minimum frustration has been shown using the AWSEM forcefield but can be extended to any other forcefield, including atomistic forcefields, or energy models derived from coevolutionary analysis, such as DCA-based Potts models, as implemented here.
 
 ## Installation
 
-To install this modules please clone this repository and install it using the following commands.
+### Using conda (recommended)
 
-    git clone HanaJaafari/Frustratometer
+    conda install -c conda-forge frustratometer
+
+### Using pip
+
+    pip install frustratometer
+
+Note: `openmm` and `pdbfixer` are not available on PyPI and must be installed separately via conda:
+
+    conda install -c conda-forge openmm pdbfixer
+
+### From source
+
+    git clone https://github.com/HanaJaafari/Frustratometer
     cd Frustratometer
     conda install -c conda-forge --file requirements.txt
     pip install -e .

devtools/docker/Dockerfile

@@ -0,0 +1,35 @@
+ARG PYTHON_VERSION=3.12
+FROM condaforge/miniforge3:latest
+
+# Install OS-level deps
+RUN apt-get update -qq \
+    && apt-get install -qq -y --no-install-recommends \
+        gcc g++ gfortran git wget hmmer \
+    && rm -rf /var/lib/apt/lists/*
+
+# Create conda env with the requested Python version
+ARG PYTHON_VERSION
+RUN conda create -n test -y python=${PYTHON_VERSION} && conda clean -afy
+SHELL ["conda", "run", "-n", "test", "/bin/bash", "-c"]
+
+WORKDIR /repo
+
+# Install dependencies first (better layer caching)
+COPY requirements.txt .
+RUN pip install --quiet --no-cache-dir -r requirements.txt
+RUN pip install --quiet --no-cache-dir pytest pytest-cov
+RUN conda install -n test -y -c conda-forge pdbfixer \
+    || echo "WARNING: pdbfixer install failed – pdbfixer tests will be skipped"
+
+# On Python <3.10, old prody needs numpy<2; conda's pdbfixer may have upgraded it
+RUN python -c "import sys; sys.exit(0 if sys.version_info < (3,10) else 1)" \
+    && conda install -n test -y "numpy<2" \
+    || true
+
+# Install pyDCA (optional – continues on failure)
+RUN pip install --quiet --no-cache-dir "git+https://github.com/cabb99/pydca.git" \
+    || echo "WARNING: pydca install failed – pyDCA tests will be skipped"
+
+# Install the package itself
+COPY . .
+RUN pip install --quiet --no-cache-dir --no-deps -e .

devtools/scripts/smoke_test.sh

@@ -0,0 +1,125 @@
+#!/usr/bin/env bash
+# smoke_test.sh – build and run the fast test suite for one or more Python versions.
+#
+# By default all versions run in PARALLEL.  Set PARALLEL=0 to run sequentially.
+#
+# Usage:
+#   devtools/scripts/smoke_test.sh [PYTHON_VERSION ...]
+#
+# Examples:
+#   devtools/scripts/smoke_test.sh                     # defaults: 3.12 3.13
+#   devtools/scripts/smoke_test.sh 3.10 3.11 3.12 3.13 3.14
+#
+# Environment variables:
+#   TEST_FLAGS   – pytest flags (default: --skip-slow --skip-stochastic --skip-network)
+#   LOG_DIR      – directory for per-version log files (default: devtools/logs)
+#   PARALLEL     – set to 0 to run sequentially (default: 1)
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
+DOCKERFILE="$REPO_ROOT/devtools/docker/Dockerfile"
+TEST_FLAGS="${TEST_FLAGS:---skip-slow --skip-stochastic --skip-network}"
+LOG_DIR="${LOG_DIR:-$REPO_ROOT/devtools/logs}"
+PARALLEL="${PARALLEL:-1}"
+
+# Default to testing Python 3.7 through 3.14, but allow overriding via command-line args
+if [ $# -gt 0 ]; then
+    VERSIONS=("$@")
+else
+    VERSIONS=(3.7 3.8 3.9 3.10 3.11 3.12 3.13 3.14)
+fi
+
+mkdir -p "$LOG_DIR"
+
+# ---------- worker function (one per Python version) ----------
+run_one() {
+    local PY="$1"
+    local LOG="$LOG_DIR/smoke_py${PY}.log"
+    local IMAGE="frustratometer-test:py${PY}"
+
+    {
+        echo "════════════════════════════════════════"
+        echo " Python ${PY} – started $(date '+%H:%M:%S')"
+        echo "════════════════════════════════════════"
+
+        echo "--- docker build ---"
+        if ! docker build \
+            --build-arg PYTHON_VERSION="${PY}" \
+            -f "$DOCKERFILE" \
+            -t "$IMAGE" \
+            "$REPO_ROOT" ; then
+            echo "BUILD FAILED for Python ${PY}"
+            return 1
+        fi
+
+        echo ""
+        echo "--- pytest ---"
+        if docker run --rm "$IMAGE" \
+            conda run -n test --no-capture-output \
+            python -m pytest tests/ $TEST_FLAGS -v --tb=short --color=no ; then
+            echo ""
+            echo "RESULT: PASS (Python ${PY})"
+            return 0
+        else
+            echo ""
+            echo "RESULT: FAIL (Python ${PY})"
+            return 1
+        fi
+    } > "$LOG" 2>&1
+}
+
+# ---------- launch ----------
+PIDS=()
+for PY in "${VERSIONS[@]}"; do
+    if [ "$PARALLEL" = "1" ]; then
+        run_one "$PY" &
+        PIDS+=("$!:$PY")
+    else
+        run_one "$PY" || true
+    fi
+done
+
+# ---------- wait & collect ----------
+PASS=()
+FAIL=()
+
+if [ "$PARALLEL" = "1" ]; then
+    for entry in "${PIDS[@]}"; do
+        PID="${entry%%:*}"
+        PY="${entry##*:}"
+        if wait "$PID"; then
+            PASS+=("$PY")
+        else
+            FAIL+=("$PY")
+        fi
+    done
+else
+    for PY in "${VERSIONS[@]}"; do
+        if grep -q "^RESULT: PASS" "$LOG_DIR/smoke_py${PY}.log" 2>/dev/null; then
+            PASS+=("$PY")
+        else
+            FAIL+=("$PY")
+        fi
+    done
+fi
+
+# ---------- summary ----------
+echo ""
+echo "════════════════════════════════════════"
+echo " Summary"
+echo "════════════════════════════════════════"
+[ ${#PASS[@]} -gt 0 ] && echo "  PASSED: ${PASS[*]}"
+[ ${#FAIL[@]} -gt 0 ] && echo "  FAILED: ${FAIL[*]}"
+echo "  Logs:   $LOG_DIR/"
+echo ""
+
+# Print failures inline for convenience
+for PY in "${FAIL[@]+"${FAIL[@]}"}"; do
+    echo ""
+    echo "──── FAILURES for Python ${PY} (last 50 lines) ────"
+    tail -50 "$LOG_DIR/smoke_py${PY}.log"
+done
+
+[ ${#FAIL[@]} -eq 0 ]   # exit 0 only if nothing failed

docs/frustratometer.rst

@@ -20,7 +20,7 @@ The frustratometer is based on the principle of minimal frustration postulated b
 
 Under most circumstances, amino acids are minimally frustrated in the protein, but pockets where amino acids are of interest for protein function. In short, a frustrated residue or interaction indicates that the particular amino acid would be minimized under a different configuration, or a different sequence, which reveals possible competing evolutionary pressures on its selection. We have identified that these pockets usually correspond to regions of functional importance, for example, that may form part of a catalytic domain, a hinge domain, or a binding region.
 
-This principle of minimum frustration has been shown using the AWSEM forcefield but can be extended to any other forcefield, including atomistic forcefields, or a pseudo-forcefield like DCA, as implemented here.
+This principle of minimum frustration has been shown using the AWSEM forcefield but can be extended to any other forcefield, including atomistic forcefields, or energy models derived from coevolutionary analysis, such as DCA-based Potts models, as implemented here.
 
 In this module, we implement a version of the frustratometer based on Direct Coupling analysis.