Merge pull request #210 from hmcezar/main

Fix CI tests

.github/workflows/ci.yml

@@ -48,4 +48,6 @@ jobs:
         coverage report
         coverage xml
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

docs/docs_requirements.txt

@@ -6,3 +6,4 @@ sphinxcontrib.bibtex
 matplotlib
 numpy
 numpydoc
+jinja2<3.1

hymd/configure_runtime.py

@@ -8,6 +8,7 @@
 import cProfile
 import logging
 import pstats
+import tomli
 from .logger import Logger, print_header
 from .input_parser import read_config_toml, parse_config_toml
 
@@ -188,14 +189,14 @@ def profile_atexit():
         )
 
         if args.topol is not None:
-            topol = read_config_toml(args.topol)
+            topol = tomli.loads(read_config_toml(args.topol))
             # Check if we have single "itp" files and add their keys to topol
             if os.path.dirname(args.topol) == "":
                 args.topol = "./" + args.topol
             if "include" in topol["system"]:
                 for file in topol["system"]["include"]:
                     path = f"{os.path.dirname(args.topol)}/{file}"
-                    itps = read_config_toml(path)
+                    itps = tomli.loads(read_config_toml(path))
                     for mol, itp in itps.items():
                         topol[mol] = itp
         else:

hymd/input_parser.py

@@ -313,10 +313,9 @@ def __str__(self):
 
 
 def read_config_toml(file_path):
-    with open(file_path, "rb") as in_file:
-        toml_content = tomli.load(in_file)
-    return toml_content
-
+    with open(file_path, "r") as in_file:
+        file_content = in_file.read()
+    return file_content
 
 def propensity_potential_coeffs(x: float, comm):
     alpha_coeffs = np.array(
@@ -369,6 +368,9 @@ def propensity_potential_coeffs(x: float, comm):
 def parse_config_toml(toml_content, file_path=None, comm=MPI.COMM_WORLD):
     config_dict = {}
 
+    # read toml to a dictionary
+    toml_content = tomli.loads(toml_content)
+
     # Defaults = None
     for n in (
         "box_size",

pyproject.toml

@@ -1,4 +1,4 @@
 [build-system]
-requires = ["setuptools<60", "wheel", "numpy", "cython", "mpi4py"]
+requires = ["setuptools<60", "wheel", "numpy<1.24", "cython", "mpi4py"]
 [tool.black]
 exclude = "\\(./)"

requirements.txt

@@ -3,7 +3,7 @@ h5py
 mpi4py
 mpsort
 networkx
-numpy
+numpy<1.24
 pfft-python
 pmesh
 sympy

test/test_configure_runtime.py

@@ -15,54 +15,54 @@ def test_configure_runtime(h5py_molecules_file, config_toml,
 
     basearg = [config_toml_file, h5py_molecules_file]
 
-    parsed, config, prng = configure_runtime(basearg, comm)
+    parsed, config, prng, topol = configure_runtime(basearg, comm)
     assert isinstance(parsed, Namespace)
     assert isinstance(config, Config)
     assert isinstance(prng, np.random.Generator)
     assert parsed.destdir == "."
     assert parsed.logfile == "sim.log"
 
-    parsed, _, _ = configure_runtime(["-v", "2"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["-v", "2"]+basearg, comm)
     assert parsed.verbose == 2
 
-    parsed, _, _ = configure_runtime(["--disable-field"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--disable-field"]+basearg, comm)
     assert parsed.disable_field
 
-    parsed, _, _ = configure_runtime(["--disable-bonds"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--disable-bonds"]+basearg, comm)
     assert parsed.disable_bonds
 
-    parsed, _, _ = configure_runtime(["--disable-angle-bonds"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--disable-angle-bonds"]+basearg, comm)
     assert parsed.disable_angle_bonds
 
-    parsed, _, _ = configure_runtime(["--disable-dihedrals"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--disable-dihedrals"]+basearg, comm)
     assert parsed.disable_dihedrals
 
-    parsed, _, _ = configure_runtime(["--disable-dipole"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--disable-dipole"]+basearg, comm)
     assert parsed.disable_dipole
 
-    parsed, _, _ = configure_runtime(["--double-precision"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--double-precision"]+basearg, comm)
     assert parsed.double_precision
 
-    parsed, _, _ = configure_runtime(["--double-output"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--double-output"]+basearg, comm)
     assert parsed.double_output
 
-    parsed, _, _ = configure_runtime(["--dump-per-particle"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--dump-per-particle"]+basearg, comm)
     assert parsed.dump_per_particle
 
-    parsed, _, _ = configure_runtime(["--force-output"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--force-output"]+basearg, comm)
     assert parsed.force_output
 
-    parsed, _, _ = configure_runtime(["--velocity-output"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--velocity-output"]+basearg, comm)
     assert parsed.velocity_output
 
-    parsed, _, _ = configure_runtime(["--disable-mpio"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--disable-mpio"]+basearg, comm)
     assert parsed.disable_mpio
 
-    parsed, _, _ = configure_runtime(["--destdir", "testdir"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--destdir", "testdir"]+basearg, comm)
     assert parsed.destdir == "testdir"
 
-    parsed, _, _ = configure_runtime(["--seed", "54321"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--seed", "54321"]+basearg, comm)
     assert parsed.seed == 54321
 
-    parsed, _, _ = configure_runtime(["--logfile", "test.log"]+basearg, comm)
+    parsed, _, _, _ = configure_runtime(["--logfile", "test.log"]+basearg, comm)
     assert parsed.logfile == "test.log"

test/test_file_io.py

@@ -62,11 +62,12 @@ def test_setup_time_dependent_element(config_toml, tmp_path):
 
     assert isinstance(group, h5py.Group)
     assert group.name == "/test/position"
-    assert group.attrs["units"] == "nm"
 
     assert isinstance(step, h5py.Dataset)
     assert isinstance(time, h5py.Dataset)
+    assert time.attrs["unit"] == "ps"
     assert isinstance(value, h5py.Dataset)
+    assert value.attrs["unit"] == "nm"
 
     out.close_file()