Fixing all mypy errors

.github/workflows/test.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [ master ]
   pull_request:
-    branches: [ master ]
+  #  branches: [ master ]
   release:
     types: [published]
 
@@ -22,7 +22,7 @@ jobs:
 
     - name: Build the wheel
       run: |
-        python -m pip install build
+        python -m pip install --group dev
         python -m build
 
     - name: Upload wheel
@@ -33,13 +33,10 @@ jobs:
 
     - name: Run the tests
       run: |
-        python -m pip install numpy pyparsing pytest pytest-cov
         pytest -v
 
     - name: Build the docs
       run: |
-        python -m pip install matplotlib sphinx
-        python -m pip install dist/periodictable*.whl
         make -j 4 -C doc/sphinx SPHINXOPTS="-W --keep-going" html
 
   # Test the wheel on different platforms
@@ -75,17 +72,22 @@ jobs:
       run: python -m pip install dist/periodictable*.whl
       shell: bash
 
-    - name: Install Python dependencies
+    # uncertainties and matplotlib are optional packages, but they are needed for mypy tests
+    - name: Install test dependencies
       run: |
-        python -m pip install pytest pytest-cov
+        python -m pip install --group test
 
+    # Use --pyargs --import-mode=append to target the installed package.
     # Change into the test directory to test the wheel so that the
-    # source directory is not on the path. Full tests with coverage are
-    # run before building the wheel.
+    # source directory is not on the path. We are running coverage tests
+    # because it shows that it is indeed the installed package that is tested.
+    # The mypy plugin fails when testing the installed package. Since there is no
+    # way to turn the option off, so we instead erase the addopts configuration
+    # and put them explicitly on the pytest command line below without --mypy.
     - name: Test wheel with pytest
       run: |
         cd test
-        pytest -v --pyargs --import-mode=append periodictable . ../doc/sphinx/guide
+        pytest -v --pyargs --import-mode=append periodictable --override-ini addopts= --doctest-modules --doctest-glob=*.rst --cov=periodictable . ../doc/sphinx/guide
 
   # Upload wheel to PyPI only when a tag is pushed, and its name begins with 'v'
   upload-to-pypi:

MANIFEST.in

@@ -3,6 +3,7 @@ include README.rst
 graft periodictable/xsf
 include periodictable/f0_WaasKirf.dat
 include periodictable/activation.dat
+include periodictable/py.typed
 prune doc
 prune doc/sphinx/_build
 prune doc/sphinx/build

periodictable/__init__.py

@@ -196,6 +196,9 @@ def __dir__():
 livermorium = Lv = elements.symbol("Lv")
 tennessine = Ts = elements.symbol("Ts")
 oganesson = Og = elements.symbol("Og")
+deuterium = D = elements.symbol("D")
+tritium = T = elements.symbol("T")
+neutron = n = elements.symbol("n")
 
 # Add element name and symbol (e.g. nickel and Ni) to the public attributes.
 __all__ += core.define_elements(elements, globals())

periodictable/core.py

@@ -651,7 +651,7 @@ def __init__(self, element: Union["Element", "Isotope"], charge: int):
     def __getattr__(self, attr: str) -> Any:
         return getattr(self.element, attr)
     @property
-    def mass(self) -> float:
+    def mass(self) -> float: # type: ignore[override]
         return getattr(self.element, 'mass') - constants.electron_mass*self.charge
     def __str__(self) -> str:
         sign = '+' if self.charge > 0 else '-'
@@ -661,12 +661,12 @@ def __str__(self) -> str:
     def __repr__(self) -> str:
         return repr(self.element)+'.ion[%d]'%self.charge
     def __reduce__(self):
-        try:
+        if isinstance(self.element, Isotope):
             return _make_isotope_ion, (self.element.table,
                                        self.element.number,
                                        self.element.isotope,
                                        self.charge)
-        except Exception:
+        else:
             return _make_ion, (self.element.table,
                                self.element.number,
                                self.charge)

periodictable/crystal_structure.py

@@ -40,9 +40,10 @@
 This data is from Ashcroft and Mermin.
 '''
 
+from typing import Any
 from .core import PeriodicTable
 
-crystal_structures = [
+crystal_structures: list[dict[str, Any]|None] = [
     {'symmetry': 'diatom', 'd': 0.74}, #H
     {'symmetry': 'atom'}, #He
     {'symmetry': 'BCC', 'a': 3.49}, #Li

periodictable/density.py

@@ -143,18 +143,18 @@ def init(table: PeriodicTable, reload: bool=False) -> None:
         return
     table.properties.append('density')
     Isotope.density \
-        = property(density, "density using inter-atomic spacing from naturally occurring form")
+        = property(density, doc="density using inter-atomic spacing from naturally occurring form")  # type: ignore[assignment]
     Element.density \
-        = property(density, "density using inter-atomic spacing from naturally occurring form")
+        = property(density, doc="density using inter-atomic spacing from naturally occurring form")  # type: ignore[assignment]
     Element.density_units = "g/cm^3"
 
     Element.interatomic_distance \
         = property(interatomic_distance,
-                   "interatomic distance estimated from density")
+                   doc="interatomic distance estimated from density")  # type: ignore[assignment]
     Element.interatomic_distance_units = "angstrom"
     Element.number_density \
         = property(number_density,
-                   "number density estimated from mass and density")
+                   doc="number density estimated from mass and density")  # type: ignore[assignment]
     Element.number_density_units = "1/cm^3"
 
     for k, v in element_densities.items():

periodictable/fasta.py

@@ -73,7 +73,7 @@
 from pathlib import Path
 # Warning: name clash with Sequence
 from collections.abc import Iterator
-from typing import IO
+from typing import IO, cast
 
 from .formulas import formula as parse_formula, Formula, FormulaInput
 from .nsf import neutron_sld
@@ -82,7 +82,7 @@
 from .constants import avogadro_number
 
 # CRUFT 1.5.2: retaining fasta.isotope_substitution for compatibility
-def isotope_substitution(formula: Formula, source: Atom, target: Atom, portion: float=1):
+def isotope_substitution(formula: Formula, source: Atom, target: Atom, portion: float=1.0):
     """
     Substitute one atom/isotope in a formula with another in some proportion.
 
@@ -188,6 +188,7 @@ def __init__(
             M.density = 1e24*M.molecular_mass/cell_volume if cell_volume > 0 else 0
             #print name, M.molecular_mass, cell_volume, M.density
         else:
+            assert M.density is not None, "Need density to compute cell volume"
             cell_volume = 1e24*M.molecular_mass/M.density
 
         H = M.replace(elements.H[1], elements.H)
@@ -590,9 +591,9 @@ def fasta_table() -> None:
     for v in rows:
         protons = sum(num*el.number for el, num in v.natural_formula.atoms.items())
         electrons = protons - v.charge
-        Xsld = xray_sld(v.formula, wavelength=elements.Cu.K_alpha)
+        Xsld = xray_sld(v.formula, wavelength=cast(float, elements.Cu.K_alpha))
         print("%25s %7.1f %7.1f %7.1f %5.2f %5d %5.2f %5.2f %5.2f %5.1f"%(
-            v.name, v.mass, v.Dmass, v.cell_volume, v.natural_formula.density,
+            v.name, v.mass, v.Dmass, v.cell_volume, v.natural_formula.density or 0.,
             electrons, Xsld[0], v.sld, v.Dsld, v.D2Omatch))
 
 beta_casein = "RELEELNVPGEIVESLSSSEESITRINKKIEKFQSEEQQQTEDELQDKIHPFAQTQSLVYPFPGPIPNSLPQNIPPLTQTPVVVPPFLQPEVMGVSKVKEAMAPKHKEMPFPKYPVEPFTESQSLTLTDVENLHLPLPLLQSWMHQPHQPLPPTVMFPPQSVLSLSQSKVLPVPQKAVPYPQRDMPIQAFLLYQEPVLGPVRGPFPIIV"

periodictable/formulas.py

@@ -108,7 +108,7 @@ def _mix_by_weight_pairs(pairs: list[tuple["Formula", float]]) -> "Formula":
             result += ((q/f.mass)/scale) * f
         if all(f.density for f, _ in pairs):
             # Tested that densities are not None, so the following will work
-            volume = sum(q/f.density for f, q in pairs)/scale
+            volume = sum(q/cast(float, f.density) for f, q in pairs)/scale
             result.density = result.mass/volume
     return result
 
@@ -193,9 +193,9 @@ def _mix_by_volume_pairs(pairs: list[tuple["Formula", float]]) -> "Formula":
         #        = q / (mass/density)
         #        = q * density / mass
         # scale this so that n = 1 for the smallest quantity
-        scale = min(q*f.density/f.mass for f, q in pairs)
+        scale = min(q*cast(float, f.density)/f.mass for f, q in pairs)
         for f, q in pairs:
-            result += ((q*f.density/f.mass)/scale) * f
+            result += ((q*cast(float, f.density)/f.mass)/scale) * f
 
         volume = sum(q for _, q in pairs)/scale
         result.density = result.mass/volume
@@ -298,7 +298,7 @@ def formula(
         structure = ((1, cast(Atom, compound)), )
     elif isinstance(compound, dict):
         structure = _convert_to_hill_notation(cast(dict[Atom, float], compound))
-    elif _is_string_like(compound):
+    elif isinstance(compound, str):
         try:
             chem = parse_formula(compound, table=table)
             if name:
@@ -403,14 +403,16 @@ def natural_mass_ratio(self) -> float:
         return (total_natural_mass + charge_correction)/(total_isotope_mass + charge_correction)
 
     @property
-    def natural_density(self) -> float:
+    def natural_density(self) -> float | None:
         """
         |g/cm^3|
 
         Density of the formula with specific isotopes of each element
         replaced by the naturally occurring abundance of the element
         without changing the cell volume.
         """
+        if self.density is None:
+            return None
         return self.density*self.natural_mass_ratio()
 
     @natural_density.setter
@@ -455,7 +457,7 @@ def mass_fraction(self) -> dict[Atom, float]:
         return dict((a, m*a.mass/total_mass) for a, m in self.atoms.items())
 
     # TODO: Remove compound._pf. It is unused and wrong.
-    def _pf(self) -> float:
+    def _pf(self) -> float | None:
         """
         packing factor  | unitless
 
@@ -531,6 +533,7 @@ def volume(self, *args, **kw) -> float:
         # Compute atomic volume
         V = 0.
         for atom, count in self.atoms.items():
+            assert atom.covalent_radius is not None, "Need covalent radius for "+str(atom)
             radius = atom.covalent_radius
             #if el.number == 1 and H_radius is not None:
             #    radius = H_radius
@@ -607,7 +610,7 @@ def change_table(self, table: PeriodicTable) -> "Formula":
         self.structure = _change_table(self.structure, table)
         return self
 
-    def replace(self, source, target, portion=1):
+    def replace(self, source, target, portion=1.0):
         """
         Create a new formula with one atom/isotope substituted for another.
 
@@ -688,6 +691,7 @@ def _isotope_substitution(compound: "Formula", source: Atom, target: Atom, porti
     """
     # TODO: fails if density is not defined
     atoms = compound.atoms
+    assert compound.density is not None, "Need density for isotope substitution"
     if source in atoms:
         mass = compound.mass
         mass_reduction = atoms[source]*portion*(source.mass - target.mass)
@@ -1099,13 +1103,6 @@ def _str_atoms(seq) -> str:
 
     return ret
 
-def _is_string_like(val: Any) -> bool:
-    """Returns True if val acts like a string"""
-    try:
-        val+''
-    except Exception:
-        return False
-    return True
 
 def from_subscript(value: str) -> str:
     """

periodictable/mass.py

@@ -61,6 +61,7 @@
     materials (IUPAC Technical Report). Pure and Applied Chemistry, 93(1), 155-166.
     https://doi.org/10.1515/pac-2018-0916
 """
+from typing import cast
 from .core import Element, Isotope, PeriodicTable, default_table
 from .util import parse_uncertainty
 
@@ -94,10 +95,10 @@ def init(table: PeriodicTable, reload: bool=False) -> None:
     if 'mass' in table.properties and not reload:
         return
     table.properties.append('mass')
-    Element.mass = property(mass, doc=mass.__doc__)
+    Element.mass = property(mass, doc=mass.__doc__) # type: ignore[assignment]
     Element.mass_units = "u"
-    Isotope.mass = property(mass, doc=mass.__doc__)
-    Isotope.abundance = property(abundance, doc=abundance.__doc__)
+    Isotope.mass = property(mass, doc=mass.__doc__) # type: ignore[assignment]
+    Isotope.abundance = property(abundance, doc=abundance.__doc__) # type: ignore[assignment]
     Isotope.abundance_units = "%"
 
     # Parse isotope mass table where each line looks like:
@@ -113,9 +114,9 @@ def init(table: PeriodicTable, reload: bool=False) -> None:
         iso = el.add_isotope(int(astr))
         # Note: new mass table doesn't include nominal values for transuranics
         # so use old masses here and override later with new masses.
-        el._mass, el._mass_unc = parse_uncertainty(el_mass)
+        el._mass, el._mass_unc = cast(tuple[float, float], parse_uncertainty(el_mass))
         #el._mass, el._mass_unc = None, None
-        iso._mass, iso._mass_unc = parse_uncertainty(iso_mass)
+        iso._mass, iso._mass_unc = cast(tuple[float, float], parse_uncertainty(iso_mass))
         #iso._abundance, iso._abundance_unc = parse_uncertainty(p)
         iso._abundance, iso._abundance_unc = 0, 0
 
@@ -139,7 +140,7 @@ def init(table: PeriodicTable, reload: bool=False) -> None:
             #from uncertainties import ufloat as U
             #if delta > 0.01:
             #    print(f"{el.number}-{el.symbol} mass changed by {delta:.2f}% to {U(v,dv):fS} from {U(el._mass,el._mass_unc):fS}")
-            el._mass, el._mass_unc = parse_uncertainty(valstr)
+            el._mass, el._mass_unc = cast(tuple[float, float], parse_uncertainty(valstr))
 
     #Li_ratio = table.Li[7]._abundance/table.Li[6]._abundance
 
@@ -176,25 +177,25 @@ def init(table: PeriodicTable, reload: bool=False) -> None:
             #print(line)
             parts = line.strip().split()
             #print(parts)
-            value[int(parts[0])] = parse_uncertainty(parts[1])
+            value[int(parts[0])] = cast(tuple[float, float], parse_uncertainty(parts[1]))
 
     #new_Li_ratio = table.Li[7]._abundance/table.Li[6]._abundance
     #print(f"Li6:Li7 ratio changed from {Li_ratio:.1f} to {new_Li_ratio:.1f}")
 
 
 def print_natural_mass(table: PeriodicTable|None=None) -> None:
-    from uncertainties import ufloat as U
+    from uncertainties import ufloat as U  # type: ignore[import-untyped]
     table = default_table(table)
     for el in table:
         iso_mass = [
-            U(iso.abundance, iso._abundance_unc)/100*U(iso.mass, iso._mass_unc)
+            U(iso.abundance, iso._abundance_unc)/100*U(iso.mass, iso._mass_unc)  # type: ignore[operator]
             for iso in el if iso.abundance>0]
         if iso_mass:
             el_mass = U(el.mass, el._mass_unc)
             iso_sum = sum(iso_mass)
-            delta = el_mass - iso_sum
+            delta = el_mass - iso_sum # type: ignore[operator]
             # python 3.6 and above only
-            if abs(delta.n) > 1e-3 or delta.s/iso_sum.n > 0.01:
+            if abs(delta.n) > 1e-3 or delta.s/iso_sum.n > 0.01:  # type: ignore[operator,union-attr]
                 print(f"{el.number}-{el}: {el_mass:fS}, sum: {iso_sum:fS}, Δ={delta:fS}")
                 #print(f"{el.number}-{el}: {delta:fS}")
             #print(f"{el.number}-{el}: {el_mass:fS}, sum: {iso_sum:fS}, Δ=")

periodictable/mass_2001.py

@@ -55,6 +55,7 @@
        and High-Energy Physics, Amsterdam, The Netherlands.
 """
 
+from typing import cast
 from .core import Element, Isotope, PeriodicTable
 from .mass import mass, abundance
 from .util import parse_uncertainty
@@ -64,10 +65,10 @@ def init(table: PeriodicTable, reload: bool=False) -> None:
     if 'mass' in table.properties and not reload:
         return
     table.properties.append('mass')
-    Element.mass = property(mass, doc=mass.__doc__)
+    Element.mass = property(mass, doc=mass.__doc__) # type: ignore
     Element.mass_units = "u"
-    Isotope.mass = property(mass, doc=mass.__doc__)
-    Isotope.abundance = property(abundance, doc=abundance.__doc__)
+    Isotope.mass = property(mass, doc=mass.__doc__) # type: ignore
+    Isotope.abundance = property(abundance, doc=abundance.__doc__) # type: ignore
     Isotope.abundance_units = "%"
 
     for line in massdata.split('\n'):
@@ -77,9 +78,9 @@ def init(table: PeriodicTable, reload: bool=False) -> None:
         assert el.symbol == sym, \
             "Symbol %s does not match %s"%(sym, el.symbol)
         iso = el.add_isotope(int(a))
-        el._mass, el._mass_unc = parse_uncertainty(avg)
-        iso._mass, iso._mass_unc = parse_uncertainty(m)
-        iso._abundance,iso._abundance_unc = parse_uncertainty(p) if p else (0,0)
+        el._mass, el._mass_unc = cast(tuple[float, float], parse_uncertainty(avg))
+        iso._mass, iso._mass_unc = cast(tuple[float, float], parse_uncertainty(m))
+        iso._abundance, iso._abundance_unc = cast(tuple[float, float], parse_uncertainty(p)) if p else (0, 0)
 
     # # A single neutron is an isotope of element 0
     # from .constants import neutron_mass