Update auto-testing framework in CI

.coveragerc

@@ -3,8 +3,8 @@ omit =
     setup.py
     conf.py
     test/*
-    benchmarks/*
-    examples/*
     docs/*
     utils/*
-    hymd/__init__.py
+    hymd/__main__.py
+    hymd/main.py
+    hymd/gaussian_core.py

.github/workflows/ci.yml

@@ -25,25 +25,26 @@ jobs:
           ${{ runner.os }}-
     - name: Install dependencies
       run: |
-        sudo apt-get install libhdf5-openmpi-dev libfftw3-3 libfftw3-dev
-        python -m pip install --upgrade pip
-        pip install wheel
-        pip install pytest pytest-cov pytest-mpi coverage
-        pip install --upgrade numpy mpi4py cython
-        pip install -r requirements.txt
-    - name: Compile fortran modules
+        sudo apt-get update
+        sudo apt-get install -y python3-mpi4py python3-numpy
+        sudo apt-get install -y libhdf5-openmpi-dev libfftw3-3 libfftw3-dev
+    - name: Install python dependencies
       run: |
-        cd hymd/
-        make clean
-        make
-        cd ..
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade wheel numpy mpi4py cython
+        python3 -m pip install -r requirements.txt
+    - name: Install package
+      run: |
+        python3 -m pip install .
     - name: Test with pytest
       run: |
-        pytest -v --cov=./ --cov-report=
-        #### NPROCS=6
-        #### chmod +x pytest-mpi
-        #### ./pytest-mpi --nprocs ${NPROCS} --order-output --verbose
-        #### mpirun -n ${NPROCS} utils/mute_all_ranks_except.sh 0 pytest -v --only-mpi --cov=./ --cov-append --cov-report=
-    - name: Coverage report
+        python3 -m pip install pytest pytest-cov pytest-mpi coverage
+        pytest --cov=./
+        chmod +x pytest-mpi
+        ./pytest-mpi -c -ca -n 2 -ns -oo
+    - name: Coverage report and upload
       run: |
         coverage report
+        coverage xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2

hymd/force.py

@@ -154,7 +154,18 @@ def prepare_bonds_old(molecules, names, bonds, indices, config):
                         and name_mid_2 == a.atom_3
                         and name_j == a.atom_4
                     )
-                    if match_forward:
+                    if (
+                        match_forward
+                        and [
+                            bond_graph.nodes()[p[3]]["local_index"],
+                            bond_graph.nodes()[p[2]]["local_index"],
+                            bond_graph.nodes()[p[1]]["local_index"],
+                            bond_graph.nodes()[i]["local_index"],
+                            a.coeffs,
+                            a.dih_type,
+                        ]
+                        not in bonds_4
+                    ):
                         bonds_4.append(
                             [
                                 bond_graph.nodes()[i]["local_index"],
@@ -297,7 +308,7 @@ def compute_dihedral_forces__plain(f_dihedrals, r, bonds_4, box_size):
     f_dihedrals.fill(0.0)
     energy = 0.0
 
-    for a, b, c, d, coeff, phase in bonds_4:
+    for a, b, c, d, coeffs, phase in bonds_4:
         f = r[a, :] - r[b, :]
         g = r[b, :] - r[c, :]
         h = r[d, :] - r[c, :]
@@ -323,9 +334,9 @@ def compute_dihedral_forces__plain(f_dihedrals, r, bonds_4, box_size):
 
         df = 0
 
-        for m in range(len(coeff)):
-            energy += coeff[m] * (1 + np.cos(m * phi - phase[m]))
-            df += m * coeff[m] * np.sin(m * phi - phase[m])
+        for m in range(len(coeffs[0])):
+            energy += coeffs[0][m] * (1 + np.cos(m * phi - coeffs[1][m]))
+            df += m * coeffs[0][m] * np.sin(m * phi - coeffs[1][m])
 
         force_on_a = df * gn * v / vv
         force_on_d = df * gn * w / ww

hymd/version.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.0.1"

pytest-mpi

@@ -17,6 +17,8 @@ while [[ "$#" -gt 0 ]]; do
     -s|--capture=no) CAPTURE=1 ;;
     -x|--exitfirst) EXITFIRST=1 ;;
     -ns|--no-summary) SUMMARY=1 ;;
+    -c|--coverage) COVERAGE=1 ;;
+    -ca|--cov-append) COVERAGE_APPEND=1 ;;
     -oo|--order-output) ORDEROUTPUT=1 ;;
     -h|--help) HELP=1 ;;
     *) echo "Unknown parameter passed: $1"; exit 1 ;;
@@ -38,6 +40,8 @@ then
   echo "    -s --capture=no                 Pass --capture=no to pytest."
   echo "    -x --exitfirst                  Pass --exitfirst to pytest."
   echo "    -ns --no-summary                Pass --no-summary to pytest."
+  echo "    -c  --coverage                  Pass --cov=./ to pytest."
+  echo "    -ca  --cov-append               Pass --cov-append to pytest."
   echo "    -oo --order-output              Dump output from ranks in order."
   echo "    -u --unmute                     Unmute (show output from) only a specfic MPI rank."
 else
@@ -60,6 +64,14 @@ else
     PYTEST_ARGS="${PYTEST_ARGS} --exitfirst"
   fi
 
+  if [ "${COVERAGE}" -eq 1 ]; then
+    PYTEST_ARGS="${PYTEST_ARGS} --cov=./"
+  fi
+
+  if [ "${COVERAGE_APPEND}" -eq 1 ]; then
+    PYTEST_ARGS="${PYTEST_ARGS} --cov-append"
+  fi
+
   if [ "${ORDEROUTPUT}" -eq 1 ]; then
     mpirun -n ${NPROCS} --output-filename outtest pytest ${PYTEST_ARGS} --only-mpi >/dev/null
     for ((RANK=0; RANK<${NPROCS}; RANK++)); do

requirements.txt

@@ -3,7 +3,6 @@ h5py
 mpi4py
 mpsort
 networkx
-numba
 numpy
 pfft-python
 pmesh

test/conftest.py

@@ -1,19 +1,10 @@
 from mpi4py import MPI
-import sys
-import os
+import sympy
 import numpy as np
 import h5py
 import pytest
 import collections
 
-# fmt: off
-# TODO: Remove this when we have a working pip installable main package and
-# can test against installed package by
-#
-# pip3 install -e . && python3 -m pytest
-curr_path = os.path.dirname(os.path.abspath(__file__))
-sys.path.insert(0, os.path.join(curr_path, os.pardir, 'hymd'))
-
 
 @pytest.fixture
 def three_atoms():
@@ -144,29 +135,29 @@ def alanine_octapeptide():
         dtype=np.float64)
     bonds = np.array(
         [
-            [ 1,  2, -1],  # BB(0)
-            [ 0, -1, -1],  # SC(1)
-            [ 0,  3,  4],  # BB(2)
-            [ 2, -1, -1],  # SC(3)
-            [ 2,  5,  6],  # BB(4)
-            [ 4, -1, -1],  # SC(5)
-            [ 4,  7,  8],  # BB(6)
-            [ 6, -1, -1],  # SC(7)
-            [ 6,  9, 10],  # BB(8)
-            [ 8, -1, -1],  # SC(9)
-            [ 8, 11, 12],  # BB(10)
-            [10, -1, -1],  # SC(11)
-            [10, 13, 14],  # BB(12)
-            [12, -1, -1],  # SC(13)
-            [12, 15, -1],  # BB(14)
-            [14, -1, -1],  # SC(15)
+            [1,   2,  -1],  # BB(0)
+            [0,  -1,  -1],  # SC(1)
+            [0,   3,   4],  # BB(2)
+            [2,  -1,  -1],  # SC(3)
+            [2,   5,   6],  # BB(4)
+            [4,  -1,  -1],  # SC(5)
+            [4,   7,   8],  # BB(6)
+            [6,  -1,  -1],  # SC(7)
+            [6,   9,  10],  # BB(8)
+            [8,  -1,  -1],  # SC(9)
+            [8,  11,  12],  # BB(10)
+            [10, -1,  -1],  # SC(11)
+            [10, 13,  14],  # BB(12)
+            [12, -1,  -1],  # SC(13)
+            [12, 15,  -1],  # BB(14)
+            [14, -1,  -1],  # SC(15)
         ],
         dtype=int)
     names = np.array(
         [
             b"BB", b"SC", b"BB", b"SC", b"BB", b"SC", b"BB", b"SC",
             b"BB", b"SC", b"BB", b"SC", b"BB", b"SC", b"BB", b"SC",
-        ], 
+        ],
         dtype="S5"
     )
     CONF = {}
@@ -177,7 +168,8 @@ def alanine_octapeptide():
         "Angle", ["atom_1", "atom_2", "atom_3", "equilibrium", "strength"]
     )
     Dihedral = collections.namedtuple(
-        "Dihedral", ["atom_1", "atom_2", "atom_3", "atom_4", "coeff", "phase"]
+        "Dihedral",
+        ["atom_1", "atom_2", "atom_3", "atom_4", "coeffs", "dih_type"]
     )
     # Values for bonds and angles taken from MARTINI 3 parameters.
     # Not used to test dihedral forces.
@@ -188,20 +180,25 @@ def alanine_octapeptide():
     CONF["bond_3"] = (
         Angle("BB", "BB", "BB", 127, 20),
         Angle("BB", "BB", "SC", 100, 25),
-        #Angle("SC", "BB", "BB", 100, 25), # In martini they have only the first angle of this type
     )
     # Symbolic arrays of 1s and 0s for analytical check
     CONF["bond_4"] = (
         Dihedral(
-            "BB", "BB", "BB", "BB", 
-            [1 for _ in range(5)], 
-            [0 for _ in range(5)],
+            "BB", "BB", "BB", "BB",
+            np.array([
+                [1, 1, 1, 1, 1],
+                [0, 0, 0, 0, 0]
+            ]),
+            0,
         ),
     )
-    for k, v in {"Np": 8, "types": 2, "mass": 72.0, "L": [5.0, 5.0, 5.0]}.items():
+    for k, v in {
+        "Np": 8, "types": 2, "mass": 72.0, "L": [5.0, 5.0, 5.0]
+    }.items():
         CONF[k] = v
     return indices, bonds, names, molecules, r, CONF
 
+
 @pytest.fixture()
 def h5py_molecules_file(mpi_file_name):
     n_particles = 1000
@@ -557,3 +554,55 @@ def molecules_with_solvent():
                      dtype=int)
     return (np.arange(0, r.shape[0]), r, molecules, velocities, bonds, names,
             types)
+
+
+@pytest.fixture
+def filter(sigma):
+    k = sympy.var('k:%d' % (3))
+
+    def H1(k):
+        return sympy.functions.elementary.exponential.exp(
+            -0.5 * sigma**2 * (k0**2 + k1**2 + k2**2)  # noqa: F821
+        )
+    H1 = sympy.lambdify([k], H1(k))
+
+    def H(k, v):
+        return v * H1(k)
+
+    return sigma, H
+
+
+@pytest.fixture
+def v_ext(types, kappa, rho0, sigma):
+    n_types = len(types)
+    phi = sympy.var('phi:%d' % (n_types))
+
+    def w(phi):
+        return 0.5 / (kappa * rho0) * (sum(phi) - rho0)**2
+
+    v_external = [
+        sympy.lambdify([phi], sympy.diff(w(phi), "phi%d" % (i)))
+        for i in range(n_types)
+    ]
+
+    w = sympy.lambdify([phi], w(phi))
+    return types, n_types, kappa, rho0, sigma, w, v_external
+    """
+    k = sympy.var("k:%d" % (3))
+
+    def H1(k):
+        return sympy.functions.elementary.exponential.exp(
+            -0.5 * sigma**2 * (k0**2 + k1**2 + k2**2)  # noqa: F821
+        )
+
+    kdHdk = [
+        k0 * sympy.diff(H1(k), "k0"),  # noqa: F821
+        k1 * sympy.diff(H1(k), "k1"),  # noqa: F821
+        k2 * sympy.diff(H1(k), "k2")   # noqa: F821
+    ]
+    kdHdk = [sympy.lambdify([k], kdHdk[i]) for i in range(3)]
+    H1 = sympy.lambdify([k], H1(k))
+
+    def H(k, v):
+        return v * H1(k)
+    """

test/test_distribute_input.py

@@ -1,6 +1,6 @@
 import numpy as np
 import h5py
-from file_io import distribute_input
+from hymd.file_io import distribute_input
 
 
 def _distribute_nranks(size, in_path, n_particles):

test/test_field.py

@@ -4,9 +4,9 @@
 import pmesh
 import logging
 import numpy as np
-from input_parser import Config
-from file_io import distribute_input
-from field import domain_decomposition
+from hymd.input_parser import Config
+from hymd.file_io import distribute_input
+from hymd.field import domain_decomposition
 
 
 @pytest.mark.mpi()