Add CI run without 'optional' deps installed (#3857)

* add CI run on macos-latest, python=3.12 with resolution: lowest and extras: '' to test pymatgen without any optional deps installed

* restore quotes around py version

* fix error: Failed to parse: `.[ci,]`
  Caused by: Couldn't parse requirement at position 5
  Caused by: Expected an alphanumeric character starting the extra name, found ']'
.[ci,]

* change uv resolution to lowest-direct on macos

* skip pwmat input tests that require seekpath if optional seekpath is not installed

* Trajectory class: raise ImportError with ASE installation instructions when reading .traj files

* fix TestTrajectory.test_from_file() when ase not installed, test expected error message

* Fix outdated NO_ASE_ERR attribute access in test_ase.py

* simplify ComputedEntry.__eq__

f-strings, better var names, fix ruff RUF002

.github/workflows/test.yml

@@ -31,8 +31,20 @@ jobs:
         # newest version (currently 3.12) on ubuntu (to get complete coverage on unix). We
         # ignore mac-os, which is assumed to be similar to ubuntu.
         config:
-          - { os: windows-latest, python: "3.9", resolution: highest }
-          - { os: ubuntu-latest, python: "3.12", resolution: lowest-direct }
+          - os: windows-latest
+            python: "3.9"
+            resolution: highest
+            extras: ci,optional
+          - os: ubuntu-latest
+            python: "3.12"
+            resolution: lowest-direct
+            extras: ci,optional
+          # test with lowest resolution and only required dependencies installed
+          - os: macos-latest
+            python: "3.10"
+            resolution: lowest-direct
+            extras: ci
+
         # pytest-split automatically distributes work load so parallel jobs finish in similar time
         split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
 
@@ -69,7 +81,7 @@ jobs:
           pip install torch
 
           uv pip install numpy cython
-          uv pip install --editable '.[dev,optional]' --resolution=${{ matrix.config.resolution }}
+          uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
 
       - name: pytest split ${{ matrix.split }}
         run: |

dev_scripts/update_pt_data.py

@@ -82,7 +82,7 @@ def parse_ionic_radii():
                 ionic_radii[int(header[tok_idx])] = float(match.group(1))
 
         if el in data:
-            data[el]["Ionic_radii" + suffix] = ionic_radii
+            data[el][f"Ionic_radii{suffix}"] = ionic_radii
             if suffix == "_hs":
                 data[el]["Ionic_radii"] = ionic_radii
         else:

pymatgen/analysis/magnetism/analyzer.py

@@ -614,7 +614,7 @@ def __init__(
         Args:
             structure: input structure
             default_magmoms: (optional, defaults provided) dict of
-                magnetic elements to their initial magnetic moments in µB, generally
+                magnetic elements to their initial magnetic moments in μB, generally
                 these are chosen to be high-spin since they can relax to a low-spin
                 configuration during a DFT electronic configuration
             strategies: different ordering strategies to use, choose from:

pymatgen/analysis/phase_diagram.py

@@ -2277,7 +2277,7 @@ def plot_element_profile(self, element, comp, show_label_index=None, xlim=5):
 
         X value is the negative value of the chemical potential reference to
         elemental chemical potential. For example, if choose Element("Li"),
-        X= -(µLi-µLi0), which corresponds to the voltage versus metal anode.
+        X= -(μLi-μLi0), which corresponds to the voltage versus metal anode.
         Y values represent for the number of element uptake in this composition
         (unit: per atom). All reactions are printed to help choosing the
         profile steps you want to show label in the plot.

pymatgen/command_line/gulp_caller.py

@@ -764,7 +764,7 @@ def __init__(self, msg):
         self.msg = msg
 
     def __str__(self):
-        return "GulpError : " + self.msg
+        return f"GulpError : {self.msg}"
 
 
 class GulpConvergenceError(Exception):

pymatgen/core/periodic_table.py

@@ -65,7 +65,7 @@ def __init__(self, symbol: SpeciesLike) -> None:
                 Data is obtained from http://wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page).
             van_der_waals_radius (float): Van der Waals radius for the element. This is the empirical value determined
                 from critical reviews of X-ray diffraction, gas kinetic collision cross-section, and other experimental
-                data by Bondi and later workers. The uncertainty in these values is on the order of 0.1 Å.
+                data by Bondi and later workers. The uncertainty in these values is on the order of 0.1 Å.
                 Data are obtained from "Atomic Radii of the Elements" in CRC Handbook of Chemistry and Physics,
                 91st Ed.; Haynes, W.M., Ed.; CRC Press: Boca Raton, FL, 2010.
             mendeleev_no (int): Mendeleev number from definition given by Pettifor, D. G. (1984). A chemical scale

pymatgen/core/trajectory.py

@@ -569,7 +569,7 @@ def from_file(cls, filename: str | Path, constant_lattice: bool = True, **kwargs
                     is_mol = True
 
             except ImportError as exc:
-                raise exc
+                raise ImportError("ASE is required to read .traj files. pip install ase") from exc
 
         else:
             supported_file_types = ("XDATCAR", "vasprun.xml", "*.traj")

pymatgen/entries/computed_entries.py

@@ -470,11 +470,8 @@ def __eq__(self, other: object) -> bool:
         if not math.isclose(self.energy, other.energy):
             return False
 
-        if self.composition != other.composition:
-            return False
-
         # assumes that data, parameters are equivalent
-        return True
+        return self.composition == other.composition
 
     @classmethod
     def from_dict(cls, dct: dict) -> Self:

pymatgen/io/abinit/pseudos.py

@@ -144,7 +144,7 @@ def to_str(self, verbose=0) -> str:
         lines: list[str] = []
         lines += (
             f"<{type(self).__name__}: {self.basename}>",
-            "  summary: " + self.summary.strip(),
+            f"  summary: {self.summary.strip()}",
             f"  number of valence electrons: {self.Z_val}",
             f"  maximum angular momentum: {l2str(self.l_max)}",
             f"  angular momentum for local part: {l2str(self.l_local)}",
@@ -1512,7 +1512,7 @@ def plot_projectors(self, ax: plt.Axes = None, fontsize=12, **kwargs):
     #    ax.annotate("$r_c$", xy=(self.paw_radius + 0.1, 0.1))
 
     #    for state, rfunc in self.potentials.items():
-    #        ax.plot(rfunc.mesh, rfunc.values, label="TPROJ: " + state)
+    #        ax.plot(rfunc.mesh, rfunc.values, label=f"TPROJ: {state}")
 
     #    ax.legend(loc="best")
 

pymatgen/io/abinit/variable.py

@@ -112,7 +112,7 @@ def __str__(self):
 
         # Add units
         if self.units:
-            line += " " + self.units
+            line += f" {self.units}"
 
         return line
 

pymatgen/io/ase.py

@@ -114,8 +114,8 @@ def get_atoms(structure: SiteCollection, msonable: bool = True, **kwargs) -> MSO
         if msonable:
             atoms = MSONAtoms(atoms)
 
-        if "tags" in structure.site_properties:
-            atoms.set_tags(structure.site_properties["tags"])
+        if tags := structure.site_properties.get("tags"):
+            atoms.set_tags(tags)
 
         # Set the site magmoms in the ASE Atoms object
         # Note: ASE distinguishes between initial and converged

pymatgen/io/cif.py

@@ -1073,7 +1073,7 @@ def get_matching_coord(
 
         if any(occu > 1 for occu in _sum_occupancies):
             msg = (
-                f"Some occupancies ({list(filter(lambda x: x>1, _sum_occupancies))}) sum to > 1! If they are within "
+                f"Some occupancies ({list(filter(lambda x: x > 1, _sum_occupancies))}) sum to > 1! If they are within "
                 "the occupancy_tolerance, they will be rescaled. "
                 f"The current occupancy_tolerance is set to: {self._occupancy_tolerance}"
             )

pymatgen/io/lammps/inputs.py

@@ -504,7 +504,7 @@ def get_str(self, ignore_comments: bool = False, keep_stages: bool = True) -> st
                 # Print first the name of the stage in a comment.
                 # We print this even if ignore_comments is True.
                 if "Comment" not in stage["stage_name"] and len(self.stages) > 1:
-                    lammps_input += "\n# " + stage["stage_name"] + "\n"
+                    lammps_input += f"\n# {stage['stage_name']}\n"
 
                 # In case of a block of comment, the header is not printed (useless)
                 else:

pymatgen/io/nwchem.py

@@ -373,7 +373,7 @@ def molecule(self):
     def __str__(self):
         out = []
         if self.memory_options:
-            out.append("memory " + self.memory_options)
+            out.append(f"memory {self.memory_options}")
         for d in self.directives:
             out.append(f"{d[0]} {d[1]}")
         out.append("geometry " + " ".join(self.geometry_options))

pymatgen/symmetry/analyzer.py

@@ -1554,8 +1554,8 @@ def generate_full_symmops(symmops: Sequence[SymmOp], tol: float) -> Sequence[Sym
     # Uses an algorithm described in:
     # Gregory Butler. Fundamental Algorithms for Permutation Groups.
     # Lecture Notes in Computer Science (Book 559). Springer, 1991. page 15
-    UNIT = np.eye(4)
-    generators = [op.affine_matrix for op in symmops if not np.allclose(op.affine_matrix, UNIT)]
+    identity = np.eye(4)
+    generators = [op.affine_matrix for op in symmops if not np.allclose(op.affine_matrix, identity)]
     if not generators:
         # C1 symmetry breaks assumptions in the algorithm afterwards
         return symmops
@@ -1574,9 +1574,9 @@ def generate_full_symmops(symmops: Sequence[SymmOp], tol: float) -> Sequence[Sym
                     " and rerun with a different tolerance."
                 )
 
-    d = np.abs(full - UNIT) < tol
+    d = np.abs(full - identity) < tol
     if not np.any(np.all(np.all(d, axis=2), axis=1)):
-        full.append(UNIT)
+        full.append(identity)
     return [SymmOp(op) for op in full]
 
 

setup.py

@@ -61,7 +61,11 @@
             "pytest-split>=0.8",
             "pytest>8",
             "ruff>=0.4",
-            "typing-extensions>=4",
+        ],
+        "ci": [
+            "pytest>=8",
+            "pytest-cov>=4",
+            "pytest-split>=0.8",
         ],
         "docs": [
             "sphinx",
@@ -83,7 +87,7 @@
             "matgl>=1.1.1",
             "netCDF4>=1.6.5",
             "phonopy>=2.23",
-            "seekpath>=1.9.4",
+            "seekpath>=2.0.1",
             # don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175
             "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'",
             # "hiphive>=0.6",

tests/core/test_trajectory.py

@@ -474,14 +474,18 @@ def test_xdatcar_write(self):
         self._check_traj_equality(self.traj, written_traj)
 
     def test_from_file(self):
-        traj = Trajectory.from_file(f"{TEST_DIR}/LiMnO2_chgnet_relax.traj")
-        assert isinstance(traj, Trajectory)
+        try:
+            traj = Trajectory.from_file(f"{TEST_DIR}/LiMnO2_chgnet_relax.traj")
+            assert isinstance(traj, Trajectory)
 
-        # Check length of the trajectory
-        assert len(traj) == 2
+            # Check length of the trajectory
+            assert len(traj) == 2
 
-        # Check composition of the first frame of the trajectory
-        assert traj[0].formula == "Li2 Mn2 O4"
+            # Check composition of the first frame of the trajectory
+            assert traj[0].formula == "Li2 Mn2 O4"
+        except ImportError:
+            with pytest.raises(ImportError, match="ASE is required to read .traj files. pip install ase"):
+                Trajectory.from_file(f"{TEST_DIR}/LiMnO2_chgnet_relax.traj")
 
     def test_index_error(self):
         with pytest.raises(IndexError, match="index=100 out of range, trajectory only has 100 frames"):

tests/io/pwmat/test_inputs.py

@@ -80,6 +80,7 @@ def test_write_file(self):
 
 class TestGenKpt(PymatgenTest):
     def test_from_structure(self):
+        pytest.importorskip("seekpath")
         filepath = f"{TEST_DIR}/atom.config"
         structure = Structure.from_file(filepath)
         gen_kpt = GenKpt.from_structure(structure, dim=2, density=0.01)
@@ -88,6 +89,7 @@ def test_from_structure(self):
         assert gen_kpt.kpath["path"] == [["GAMMA", "M", "K", "GAMMA"]]
 
     def test_write_file(self):
+        pytest.importorskip("seekpath")
         filepath = f"{TEST_DIR}/atom.config"
         structure = Structure.from_file(filepath)
         dim = 2
@@ -103,6 +105,7 @@ def test_write_file(self):
 
 class TestHighSymmetryPoint(PymatgenTest):
     def test_from_structure(self):
+        pytest.importorskip("seekpath")
         filepath = f"{TEST_DIR}/atom.config"
         structure = Structure.from_file(filepath)
         high_symmetry_points = HighSymmetryPoint.from_structure(structure, dim=2, density=0.01)
@@ -112,6 +115,7 @@ def test_from_structure(self):
         assert high_symmetry_points.reciprocal_lattice.shape == (3, 3)
 
     def test_write_file(self):
+        pytest.importorskip("seekpath")
         filepath = f"{TEST_DIR}/atom.config"
         structure = Structure.from_file(filepath)
         dim = 2
@@ -123,3 +127,12 @@ def test_write_file(self):
         with zopen(tmp_filepath, "rt") as file:
             tmp_high_symmetry_points_str = file.read()
         assert tmp_high_symmetry_points_str == high_symmetry_points.get_str()
+
+
+# simulate and test error message when seekpath is not installed
+def test_err_msg_on_seekpath_not_installed(monkeypatch):
+    try:
+        import seekpath  # noqa: F401
+    except ImportError:
+        with pytest.raises(RuntimeError, match="SeeK-path needs to be installed to use the convention of Hinuma et al"):
+            GenKpt.from_structure(Structure.from_file(f"{TEST_DIR}/atom.config"), dim=2, density=0.01)

tests/io/test_ase.py

@@ -359,6 +359,6 @@ def test_no_ase_err():
 
     import pymatgen.io.ase
 
-    expected_msg = str(pymatgen.io.ase.no_ase_err)
+    expected_msg = str(pymatgen.io.ase.NO_ASE_ERR)
     with pytest.raises(PackageNotFoundError, match=expected_msg):
         pymatgen.io.ase.MSONAtoms()