Reconcile 2.0-pre with master

.github/workflows/test.yml

@@ -7,9 +7,44 @@ on:
     branches: [ master ]
 
 jobs:
-  test:
+  build-wheel:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Build the wheel
+      run: |
+        python -m pip install build
+        python -m build
+
+    - name: Upload wheel
+      uses: actions/upload-artifact@v4
+      with:
+        name: wheel
+        path: dist/*.whl
+
+    - 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
+  test:
     runs-on: ${{ matrix.cfg.os }}
+    needs: build-wheel
+
     strategy:
       matrix:
         cfg:
@@ -19,27 +54,34 @@ jobs:
           - { os: ubuntu-latest, py: 3.11, doc: 1 }
           - { os: windows-latest, py: 3.11 }
           - { os: macos-latest, py: 3.11 }
+      fail-fast: false
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.cfg.py }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.cfg.py }}
 
-    - name: Install Python dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install wheel setuptools
-        python -m pip install numpy scipy matplotlib pytest pytest-cov
+    - name: Download the wheel
+      uses: actions/download-artifact@v4
+      with:
+        name: wheel
+        path: dist
+
+    - name: Install the wheel
+      run: python -m pip install dist/periodictable*.whl
+      shell: bash
 
-    - name: Test with pytest
+    - name: Install Python dependencies
       run: |
-        pytest -v
+        python -m pip install pytest pytest-cov
 
-    - name: check that the docs build (linux only)
-      if: matrix.cfg.doc == 1
+    # 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.
+    - name: Test wheel with pytest
       run: |
-        python -m pip install sphinx
-        make -j 4 -C doc/sphinx SPHINXOPTS="-W --keep-going" html
+        cd test
+        pytest -v --pyargs --import-mode=append periodictable . ../doc/sphinx/guide

MANIFEST.in

@@ -1,8 +1,8 @@
 include LICENSE.txt
 include README.rst
-graft doc
 graft periodictable/xsf
 include periodictable/activation.dat
+prune doc
 prune doc/sphinx/_build
 prune doc/sphinx/build
 prune */__pycache__

doc/sphinx/Makefile

@@ -31,7 +31,7 @@ help:
 clean:
 	-rm -rf _build/* build/* plots/*.pyc plots/*.png
 
-html: build
+html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html
 	@echo
 	@echo "Build finished. The HTML pages are in _build/html."
@@ -66,7 +66,7 @@ qthelp:
 	@echo "To view the help file:"
 	@echo "# assistant -collectionFile _build/qthelp/Periodic Table.qhc"
 
-latex: build
+latex:
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex
 	@echo
 	@echo "Build finished; the LaTeX files are in _build/latex."
@@ -92,5 +92,3 @@ doctest:
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in _build/doctest/output.txt."
 
-build:
-	cd ../.. && python setup.py build

doc/sphinx/guide/extending.rst

@@ -25,7 +25,7 @@ The simplest solution is to load it directly when your package is imported.
 In the current example, this could be done by adding the following
 line to the end of the file::
 
-    init(periodictable.core.elements)
+    init(periodictable.core.default_table())
 
 This would be fine for the current example because the table size is
 small and load time is fast.  For large tables, you may wish to

doc/sphinx/guide/using.rst

@@ -56,15 +56,12 @@ Import all elements:
     >>> print(periodictable.H.mass)
     1.008
 
-Deuterium and tritium are special isotopes named D and T
-some neutron information is available as 'n':
+Deuterium and tritium are special isotopes named D and T:
 
 .. doctest::
 
     >>> print("D mass %s"%D.mass)
     D mass 2.01410177784
-    >>> print("neutron mass %s"%n.mass)
-    neutron mass 1.0086649159
 
 Process all the elements:
 
@@ -73,7 +70,6 @@ Process all the elements:
     >>> import periodictable
     >>> for el in periodictable.elements: # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
     ...     print("%s %s"%(el.symbol,el.name))
-    n neutron
     H hydrogen
     He helium
        ...
@@ -86,7 +82,6 @@ Another example for processing all elements:
     >>> from periodictable import elements
     >>> for el in elements: # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
     ...     print("%s %s"%(el.symbol,el.number))
-    n 0
     H 1
     He 2
        ...

periodictable/activation.dat

@@ -569,7 +569,7 @@ Tl	505	81	Tl	205	Tl-205	70.5	Tl-206	4.19	m			act	n	0.1		0.7	0.069833333	4.19 m
 Pb	506	82	Pb	204	Pb-204	1.4	Pb-203	51.88	h			"n,2n"	y	0.00245			51.88	51.88 h				"IAEA156, fission averaged"
 Pb	507	82	Pb	204	Pb-204	1.4	Pb-204m	66.9	m			"n,n'"	y	0.38			1.115	66.90 m				"IAEA156, fission averaged"
 Pb	508	82	Pb	204	Pb-204	1.4	Pb-205	14000000	y			act	n	0.661		1.7	1.2264E+11	14.0 My				
-Pb	509	82	Pb	208	Pb-208	52.3	Pb-209	3.3	h			act	n	0.487			3.3	3.30 h				
+Pb	509	82	Pb	208	Pb-208	52.3	Pb-209	3.3	h			act	n	0.000487			3.3	3.30 h				
 Bi	510	83	Bi	209	Bi-209	100	Bi-210ms	3500000	y	ms	0	act	n	0.019			30660000000	3.5 My				
 Bi	511	83	Bi	209	Bi-209	100	Bi-210t	5.01	d	t		act	n	0.014			120.24	5.01 d		0.054	0.2	
 Bi	512	83	Bi	209	Bi-209	100	Po-210	138.38	d			b	n	0.014			3321.12	138.4 d	120.24			

periodictable/activation.py

@@ -412,6 +412,7 @@ def activity(isotope, mass, env, exposure, rest_times):
     * AK1495 (Au-198 => Au-199 2n) target should be Au-197
     * AN1428 (Tm-169 => Tm-171 2n) t1/2 updated to Tm-171 rather than Tm-172
     * AN1420 (Er-162 => Ho-163 b) t1/2 updated to 4570 y from 10 y
+    * AT1508 (Pb-208 => Pb-209 act) Thermal (b) x1000 to convert from mbarns to barns
     """
     # TODO: is the table missing 1-H => 3-H ?
     # 0nly activations which produce radioactive daughter products are

periodictable/constants.py

@@ -25,7 +25,6 @@
 neutron_mass_unc = 0.00000000047
 #neutron_mass = 1.00866491597 #(43) u [CODATA 2010?]
 #neutron_mass = 1.00866491595 #(49) u [CODATA 2018]
-
 #: atomic mass constant (kg / u)
 atomic_mass_constant = 1.660538782e-27 #(83) kg / u
 #: electron mass (u)

periodictable/core.py

@@ -188,8 +188,7 @@ class PeriodicTable(object):
         56-Fe
 
 
-    Deuterium and tritium are defined as 'D' and 'T'.  Some
-    neutron properties are available in ``elements[0]``.
+    Deuterium and tritium are defined as 'D' and 'T'.
 
     To show all the elements in the table, use the iterator:
 
@@ -198,7 +197,6 @@ class PeriodicTable(object):
         >>> from periodictable import *
         >>> for el in elements:  # lists the element symbols
         ...     print("%s %s"%(el.symbol, el.name))  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
-        n neutron
         H hydrogen
         He helium
         ...
@@ -606,7 +604,7 @@ def _make_isotope_ion(table, Z, n, c):
 element_base = {
     # number: name symbol common_ions uncommon_ions
     # ion info comes from Wikipedia: list of oxidation states of the elements.
-    0: ['Neutron',     'n',  [],         []],
+    # 0: ['Neutron',     'n',  [],         []],
     1: ['Hydrogen',    'H',  [-1, 1],    []],
     2: ['Helium',      'He', [],         [1, 2]],  # +1,+2  http://periodic.lanl.gov/2.shtml
     3: ['Lithium',     'Li', [1],        []],

periodictable/covalent_radius.py

@@ -75,7 +75,8 @@ def init(table, reload=False):
         return
     table.properties.append('covalent_radius')
 
-    table[0].covalent_radius = 0.20
+    # neutron covalent radius of 0.20 A ? Not sure where that value came from
+    # table[0].covalent_radius = 0.20
     Element.covalent_radius_units = 'angstrom'
     Element.covalent_radius = None
     Element.covalent_radius_uncertainty = None

periodictable/crystal_structure.py

@@ -42,7 +42,6 @@
 
 
 crystal_structures = [\
-    None, #X
     {'symmetry': 'diatom', 'd': 0.74}, #H
     {'symmetry': 'atom'}, #He
     {'symmetry': 'BCC', 'a': 3.49}, #Li
@@ -155,5 +154,5 @@ def init(table, reload=False):
         return
     table.properties.append('crystal_structure')
 
-    for Z, struct in enumerate(crystal_structures):
-        table[Z].crystal_structure = struct
+    for k, struct in enumerate(crystal_structures):
+        table[k+1].crystal_structure = struct

periodictable/density.py

@@ -170,8 +170,7 @@ def init(table, reload=False):
             el.density_caveat = ""
 
 element_densities = dict(
-    # TODO: stop pretending that a bare neutron is element zero.
-    n=None,
+    # n=None,  # No longer using element 0 for a bare neutron
     H=(0.0708, "T=-252.87"),
     He=(0.122, "T=-268.93"),
     Li=0.534,

periodictable/fasta.py

@@ -538,17 +538,32 @@ def fasta_table():
         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)
-        print("%20s %7.1f %7.1f %7.1f %5.2f %5d %5.2f %5.2f %5.2f %5.1f"%(
+        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,
             electrons, Xsld[0], v.sld, v.Dsld, v.D2Omatch))
 
 beta_casein = "RELEELNVPGEIVESLSSSEESITRINKKIEKFQSEEQQQTEDELQDKIHPFAQTQSLVYPFPGPIPNSLPQNIPPLTQTPVVVPPFLQPEVMGVSKVKEAMAPKHKEMPFPKYPVEPFTESQSLTLTDVENLHLPLPLLQSWMHQPHQPLPPTVMFPPQSVLSLSQSKVLPVPQKAVPYPQRDMPIQAFLLYQEPVLGPVRGPFPIIV"
 
+## Uncomment to show package path on CI infrastructure
+#def doctestpath():
+#    """
+#    Checking import path for doctests::
+#
+#        >>> import periodictable
+#        >>> print(f"Path to imported periodictable in docstr is {periodictable.__file__}")
+#        some path printed here
+#    """
+
 def test():
     from periodictable.constants import avogadro_number
     from .formulas import formula
     elements = default_table()
 
+    ## Uncomment to show package path on CI infrastructure
+    #import periodictable
+    #print(f"Path to imported periodictable in package is {periodictable.__file__}")
+    #print(fail_test)
+
     # Beta casein results checked against Duncan McGillivray's spreadsheet
     # name        Hmass   Dmass   vol     den   #el   xray  Hsld  Dsld
     # =========== ======= ======= ======= ===== ===== ===== ===== =====

periodictable/mass.py

@@ -119,13 +119,13 @@ def init(table, reload=False):
         #iso._abundance, iso._abundance_unc = parse_uncertainty(p)
         iso._abundance, iso._abundance_unc = 0, 0
 
-    # A single neutron is an isotope of element 0
-    from .constants import neutron_mass, neutron_mass_unc
-    el = table[0]
-    el._mass, el._mass_unc = neutron_mass, neutron_mass_unc
-    iso = el.add_isotope(1)
-    iso._mass, iso._mass_unc = neutron_mass, neutron_mass_unc
-    iso._abundance, iso._abundance_unc = 100, 0
+    # # A single neutron is an isotope of element 0
+    # from .constants import neutron_mass, neutron_mass_unc
+    # el = table[0]
+    # el._mass, el._mass_unc = neutron_mass, neutron_mass_unc
+    # iso = el.add_isotope(1)
+    # iso._mass, iso._mass_unc = neutron_mass, neutron_mass_unc
+    # iso._abundance, iso._abundance_unc = 100, 0
 
     # Parse element mass table where each line looks like:
     #    z  El  element mass(unc)|[low,high]|- note note ...

periodictable/mass_2001.py

@@ -81,13 +81,13 @@ def init(table, reload=False):
         iso._mass, iso._mass_unc = parse_uncertainty(m)
         iso._abundance,iso._abundance_unc = parse_uncertainty(p) if p else (0,0)
 
-    # A single neutron is an isotope of element 0
-    from .constants import neutron_mass
-    el = table[0]
-    el._mass = neutron_mass
-    iso = el.add_isotope(1)
-    iso._mass = neutron_mass
-    iso._abundance = 100
+    # # A single neutron is an isotope of element 0
+    # from .constants import neutron_mass
+    # el = table[0]
+    # el._mass = neutron_mass
+    # iso = el.add_isotope(1)
+    # iso._mass = neutron_mass
+    # iso._abundance = 100
 
 # z-El-n,iso_mass(unc),abundance%(unc),element_mass(unc)
 massdata = """\

periodictable/nsf.py

@@ -567,6 +567,9 @@ def init(table, reload=False):
         symbol = parts[1]
         isotope_number = int(parts[2]) if len(parts) == 3 else 0
 
+        if Z == 0: # Skip row 0-n-1
+            continue
+
         # Fetch element from the table and check that the symbol matches
         element = table[Z]
         assert element.symbol == symbol, \
@@ -576,13 +579,6 @@ def init(table, reload=False):
         # it can calculate sld.
         nsf._number_density = element.number_density # N/cm^3 = N/cm^3
 
-
-        # For new elements, clear out 'neutron' attribute for isotopes
-        # This protects against isotope using the element data when
-        # they don't have any specific neutron data.
-        #if isotope_number == 0 or not hasattr(element,'neutron'):
-        #    for iso in element: iso.neutron = None
-
         if isotope_number == 0:
             # Bulk values using laboratory abundances of isotopes
             element.neutron = nsf
@@ -1876,8 +1872,6 @@ def coherent_comparison_table(table=None, tol=None):
 
         >>> coherent_comparison_table (tol=0.5) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
         Comparison of (4 pi |b_c|^2/100) and coherent
-                 n   172.03    43.01 300.0%
-               1-n   172.03    43.01 300.0%
                 Sc    18.40    19.00  -3.2%
              45-Sc    18.40    19.00  -3.2%
              65-Cu    13.08    14.10  -7.2%
@@ -1908,8 +1902,6 @@ def total_comparison_table(table=None, tol=None):
 
         >>> total_comparison_table (tol=0.1)
         Comparison of total cross section to (coherent + incoherent)
-                 n    43.01     ----
-               1-n    43.01     ----
              84-Kr     6.60     ----
             149-Sm   200.00   200.50  -0.2%
                 Eu     9.20     9.07   1.4%
@@ -1999,3 +1991,5 @@ def main():
 
 if __name__ == "__main__":
     main()
+    #coherent_comparison_table(tol=0.5)
+    #incoherent_comparison_table(tol=0.5)