Replace pyparsing with lark for better error messages by pkienzle · Pull Request #124 · python-periodictable/periodictable

pkienzle · 2026-03-05T21:01:15Z

This PR replaces pyparsing with lark.

It does a better job of error messages (#34), and it is more robust than the existing parser.

The syntax is represented as a string using EBNF notation. This nicely separates it from parsing and interpretation. The format is clean enough to use directly in the documentation.

periodictable/periodictable/lark_parse.py

Lines 23 to 89 in cc49581

    
           grammar = """ 
        
           start      : SPACE? formula SPACE?  # strip blank space from start and end 
        
           # formula: composite @ density | str:sequence @ density | mixture 
        
           formula    : compound | mixture 
        
           compound   : (composite | fasta) [density] 
        
           # Density applies to the entire composite, such as "NaCl + 29.2H2O @ 1.07n" 
        
           # For the density of a mixture you need parentheses: "(10 wt% NaCl // H2O)@1.07n" 
        
           # Activation only cares about total mass, so you can freely mix masses and volumes if 
        
           # you have the density for each component. For scattering you need the density of the 
        
           # mixture. When this is different from the mixture of densities use (mixture)@density. 
        
           # For thin film samples, allow stacking of layers with the thickness of each layer. 
        
           # With density for each layer the relative quantities of each element in the stack can 
        
           # be calculated. Convert to mass by multiplying density by thickness (cm) and area (cm²). 
        
           # mixture:  quantity compound // quantity compound // quantity compound 
        
           mixture    : byamount | byvolume | byweight | layers 
        
           byamount   : quantity compound (MIX quantity compound)* 
        
           byvolume   : volumepct compound (MIX percentage compound)* MIX compound 
        
           byweight   : weightpct compound (MIX percentage compound)* MIX compound 
        
           layers     : thickness compound (MIX thickness compound)* 
        
           quantity   : NUMBER SPACE? (MASS | VOLUME) SPACE 
        
           weightpct  : NUMBER SPACE? WEIGHTPCT SPACE 
        
           volumepct  : NUMBER SPACE? VOLUMEPCT SPACE 
        
           thickness  : NUMBER SPACE? LENGTH SPACE 
        
           percentage : NUMBER SPACE? "%" SPACE  # Allows "3 % " 
        
           MIX        : SPACE? "//" SPACE? 
        
           WEIGHTPCT  : /%w((eigh)?t)?/ | /w((eigh)?t)?%/ | /%m(ass)?/ | /m(ass)?%/ 
        
           VOLUMEPCT  : /%v(ol(ume)?)?/ | /v(ol(ume)?)?%/ 
        
           MASS       : "kg" | "g" | "mg" | "ug" | "μg" | "ng" 
        
           VOLUME     : "L" | "mL" | "uL" | "μL" | "nL" 
        
           LENGTH     : "cm" | "mm" | "um" | "μm" | "nm" | "Ang" | "Å" 
        
           # FASTA sequence:   (rna|dna|aa):SEQUENCE @ density 
        
           fasta      : FASTA ":" SEQUENCE 
        
           FASTA      : /[a-z]+/  # str:sequence reports better errors than /dna|rna|aa/:sequence 
        
           SEQUENCE   : /[-A-Z *]+/ 
        
           # composite: number group number group ... @density 
        
           # group: El count El count ... 
        
           # Note: optional `[token]` leaves a None placeholder in the tree, unlike `token?` 
        
           composite  : [NUMBER] group (SEPARATOR [NUMBER] group)* 
        
           group      : ((atom | isoatom | "(" formula ")") [COUNT])+ 
        
           atom       : SYMBOL [isotope] [valence] 
        
           isoatom    : SUPERINT SYMBOL [valence]    # For example ²H for deuterium 
        
           isotope    : "[" INTEGER "]" 
        
           valence    : "{" [INTEGER] CHARGE "}" | [SUPERINT] SUPERCHARGE 
        
           density    : SPACE? "@" SPACE? DENSITY [DENSITYMODE] 
        
           # could list all elements, but better error reporting if element symbol lookup fails 
        
           SYMBOL     : /[A-Z][a-z]*/ 
        
           CHARGE     : /[+]+|[-]+/  # allow valence using {++} or {--} 
        
           SUPERCHARGE: /\u207A+|\u207B+/ # unicode valence such as Ca⁺⁺ and O²⁻ 
        
           DENSITY    : NUMBER  # using alias DENSITY for number for better error reporting 
        
           DENSITYMODE: /[ni]/       # n=natural density, i=isotopic density 
        
           COUNT      : NUMBER | SUBNUM  # atom counts can be normal numbers or unicode subscripts 
        
           SEPARATOR  : SPACE? /[+•·]/ SPACE? | SPACE   # For example, CaCO₃·6H₂O 
        
           SPACE      : /[ \\t\\n\\r]+/ 
        
           NUMBER     : INTEGER | FRACTION 
        
           INTEGER    : /[1-9][0-9]*/ 
        
           FRACTION   : /([1-9][0-9]*|0)?[.][0-9]*/  # allow all floats? 
        
           SUBNUM     : SUBINT | SUBFRAC 
        
           SUBINT     : /(\u2080|[\u2081-\u2089][\u2080-\u2089]*)/ 
        
           SUBFRAC    : /(\u2080|[\u2081-\u2089][\u2080-\u2089]*|)([.][\u2080-\u2089]*)/ 
        
           SUPERINT   : /(\u2070|[\u00B9\u00B2\u00B3\u2074-\u2079][\u2070\u00B9\u00B2\u00B3\u2074-\u2079]*)/ 
        
           """

…hints

pkienzle · 2026-05-22T16:16:24Z

Most of the error messages are an improvement over the old parser, though some of them are still confusing.

Here's a mix of accepted and rejected formulas along with the associated error messages. Note that lines marked with ## didn't parse in the old parser.

$ python -m periodictable.lark_parse

!!!  DNA:CAGT  # incorrect case for FASTA type not properly identified
Expected one of @DENSITY[ni] COUNT SYMBOL in
 DNA:CAGT  
    ^

!!!  dna CAGT  # missing colon in FASTA
Expected :SEQ in
 dna CAGT  
    ^

!!!  O²  # SUPERCHARGE should be the only valid token here
Expected SYMBOL in
 O²  
   ^

!!!  ₃H2O  # badly placed subscript
Expected one of NUMBER SYMBOL aa:SEQ in
 ₃H2O  
 ^

!!!  // 3g Ca  # // is not a comment
Expected one of NUMBER SYMBOL aa:SEQ in
 // 3g Ca  
 ^

!!!  3g Ca@ // 5g Si # missing density value
Expected @DENSITY[ni] in
 3g Ca@ // 5g Si 
        ^

!!!  Ca@i  # missing density value  ##
Expected @DENSITY[ni] in
 Ca@i  
    ^

!!!  Ca ⁺⁺  # extra space before valence
Expected one of @DENSITY[ni] NUMBER SYMBOL in
 Ca ⁺⁺  
    ^

!!!  Ca++  # missing braces in valence: the + is acting as SEPARATOR
Expected one of NUMBER SYMBOL in
 Ca++  
    ^

!!!  Ca2+  # missing braces in valence: the 2 is acting as COUNT and the + as SEPARATOR
Expected one of NUMBER SYMBOL in
 Ca2+  
      ^

!!!  Ca{2}  # missing charge in valence
Expected CHARGE[+-] in
 Ca{2}  
     ^

!!!  37 vol% H2O@1 / 5% D2O@1  # missing /
Expected one of // @DENSITY[ni] in
 37 vol% H2O@1 / 5% D2O@1  
              ^

!!!  37 vol% H2O@1 /// 5% D2O@1  # extra /
Expected one of NUMBER SYMBOL aa:SEQ in
 37 vol% H2O@1 /// 5% D2O@1  
                 ^

!!!  H2O@1h  # bad density mode
Expected @DENSITY[ni] in
 H2O@1h  
      ^

!!!  37 vol% NaCl@2.16 // H2O@1 // D2O@1  # percent missing in middle part
Expected end of formula in
 37 vol% NaCl@2.16 // H2O@1 // D2O@1  
                            ^

!!!  37 vol% H2O@1 // 5% D2O@1  # percent not allowed in last part
Expected one of // @DENSITY[ni] in
 37 vol% H2O@1 // 5% D2O@1  
                          ^

!!!  37 vol% H2O@1 // 5 vol% D2O@1  # only % in subsequent parts
Expected % in
 37 vol% H2O@1 // 5 vol% D2O@1  
                    ^

!!!  37% H2O@1 // D2O@1  # missing vol% or wt%
Expected one of SYMBOL UNIT[mL] UNIT[mg] UNIT[mm] vol% wt% in
 37% H2O@1 // D2O@1  
   ^

!!!  37 val% H2O@1 // D2O@1  # bad spelling of vol%
Expected one of UNIT[mL] UNIT[mg] UNIT[mm] vol% wt% in
 37 val% H2O@1 // D2O@1  
    ^

!!!  Fe[56O2 # bad isotope syntax
Expected ] in
 Fe[56O2 
      ^

!!!  Co[181]  # bad isotope
'181 is not an isotope of Co'

!!!  Ca{2+O2  # bad valence syntax
Expected } in
 Ca{2+O2  
      ^

!!!  Co{17-}  # bad valence
valence 17- is not valid for Co

!!!  3..5 mg NaCl
Expected one of SYMBOL UNIT[mL] UNIT[mg] UNIT[mm] vol% wt% in
 3..5 mg NaCl
   ^

!!!  3.5 fm Si # bad units at the start; could be wt%/vol% or LENGTH, VOLUME, MASS 
Expected one of UNIT[mL] UNIT[mg] UNIT[mm] vol% wt% in
 3.5 fm Si 
     ^

!!!  3.5 mm Si // 2.5 nm SiO2 //
Expected NUMBER in
 3.5 mm Si // 2.5 nm SiO2 //
                           ^

!!!  3.5 mm Si // 2.5 nm SiO2 // 35 mm cG
Expected :SEQ in
 3.5 mm Si // 2.5 nm SiO2 // 35 mm cG
                                    ^

!!!  ((Co) # mismatched LPAR
Expected one of @DENSITY[ni] NUMBER SYMBOL in
 ((Co) 
      ^

!!!  Co)  # mismatched RPAR
Expected one of @DENSITY[ni] COUNT SYMBOL in
 Co)  
   ^

!!!  bad:CAGT  # bad sequence type
Invalid fasta sequence type 'bad:'

*** Co
 => Co @ 8.90

*** dna:CAGT
 => C₃₉H₃₇¹H₁₀N₁₅O₂₅P₄ @ 1.69

*** (Co@5) ##
 => Co @ 5.00

*** (((Co@5)@6)) ##
 => Co @ 6.00

*** CaCO3
 => CaCO₃

*** CaCO₃
 => CaCO₃

*** CaCO3+6H2O
 => CaCO₃(H₂O)₆

*** CaCO3 6H2O
 => CaCO₃(H₂O)₆

*** CaCO3(H2O)6
 => CaCO₃(H₂O)₆

*** CaCO3 (H2O)6
 => CaCO₃(H₂O)₆

*** (Ca(CO3)((H2O)6))
 => CaCO₃(H₂O)₆

*** CaCO₃·6H₂O  ##
 => CaCO₃(H₂O)₆

*** DHO
 => DHO

!!! Ca{2++}  # bad valence string
Use 2+ instead of 2++ for valence

*** Ca⁺⁺  # also Ca{2+}  ##
 => Ca²⁺ @ 1.55

*** O²⁻   ##
 => O²⁻ @ 1.14

*** H[1]
 => ¹H @ 0.07

*** ²H⁺    # D{+} ##
 => D⁺ @ 0.14

*** O²H⁻   # OD{-} ##
 => OD⁻

*** O²⁻H⁺  # O{2-}H{+} ##
 => O²⁻H⁺

*** O²⁻²H⁺ # O{2-}D{+} ##
 => O²⁻D⁺

*** H2O@1
 => H₂O @ 1.00

*** D2O@1n
 => D₂O @ 1.11

*** D2O @ 1.11  ##
 => D₂O @ 1.11

*** D2O@1.11i
 => D₂O @ 1.11

*** HO{1-}
 => HO⁻

*** H[1]{1-}O
 => ¹H⁻O

*** H2SO4
 => H₂SO₄

*** C3H4H[1]NO@1.29n
 => C₃H₄¹HNO @ 1.29

*** 78.2H2O[16] + 21.8H2O[18] @1n  # density applies to composite
 => (H₂¹⁶O)₇₈.₂(H₂¹8O)₂₁.₈ @ 1.02

*** dna:CAGT @1n  # fasta density override
 => C₃₉H₃₇¹H₁₀N₁₅O₂₅P₄ @ 1.00

*** 50 wt% Co // Ti
 => CoTi₁.₂₃₁₁₈₆₂₈₇₀₀₃₅₇₂₆ @ 6.01

*** 33 wt% Co // 33% Fe // Ti
 => CoFe₁.₀₅₅₂₉₉₃₈₂₂₁₈₆₄₁Ti₁.₂₆₈₄₉₄₉₆₂₃₆₇₃₁₇₂ @ 6.50

!!!  93 wt% Co // 33% Fe // Ti  # More than 100 wt%
Total weight 126% is more than 100% in wt% mixture

!!!  93 vol% Co // 33% Fe // Ti  # More than 100 vol%
Total volume 126% is more than 100% in vol% mixture

*** 20 vol% (10 wt% NaCl@2.16 // H2O@1) // D2O@1n
 => NaCl(H₂O)₂₉.₁₉₅₅₅₅₀₁₀₈₂₄₃₁(D₂O)₁₂₂.₇₈₉₅₃₅₈₈₉₁₄₅₈₅ @ 1.10

*** NaCl(H2O)29.1966(D2O)122.794@1.10i
 => NaCl(H₂O)₂₉.₁₉₆₆(D₂O)₁₂₂.₇₉₄ @ 1.10

*** 5g NaCl // 50mL H2O@1
 => NaCl(H₂O)₃₂.₄₃₉₅₀₅₅₆₇₅₈₂₅₇

*** 5g NaCl@2.16 // 50mL H2O@1
 => NaCl(H₂O)₃₂.₄₃₉₅₀₅₅₆₇₅₈₂₅₇ @ 1.05

!!!  5g NaCl // 50mL H2O   # Need density for H2O to convert volume to mass
Need the mass density of H2O

*** (10 wt% NaCl // H2O)@1.07n # set density of a mixture
 => NaCl(H₂O)₂₉.₁₉₅₅₅₅₀₁₀₈₂₄₃₁ @ 1.07

*** 50 mL (45 mL H2O@1 // 5 g NaCl)@1.0707 // 20 mL D2O@1n
 => (H₂O)₂₉.₁₉₅₅₅₅₀₁₀₈₂₄₃₁NaCl(D₂O)₁₂.₁₁₈₉₈₉₆₅₈₁₉₈₄₀₂ @ 1.08

*** 1 cm Si // 5 nm Cr // 10 nm Au
 => Si₁₁₉₉₉₂₂.₉₇₃₇₄₆₂₄₉₅CrAu₁.₄₁₇₂₁₈₀₀₉₃₁₂₁₃₆ @ 2.33

*** aa:RELEELNVPGEIVESLSSSEESITRINKKIEKFQSEEQQQTEDELQDKIHPFAQTQSLVYPFPGPIPNSLPQNIPPLTQTPVVVPPFLQPEVMGVSKVKEAMAPKHKEMPFPKYPVEPFTESQSLTLTDVENLHLPLPLLQSWMHQPHQPLPPTVMFPPQSVLSLSQSKVLPVPQKAVPYPQRDMPIQAFLLYQEPVLGPVRGPFPIIV
 => C₁₀₈₀H₁₃₇₀¹H₃₁₉N₂₆₈O₃₁₀S₆ @ 1.27

!!!  Bl2Oh   # Bad symbol
Element Bl doesn't exist

!!!  5 Mg NaCl // 50mL H2O@1  # Bad units
Expected one of UNIT[mL] UNIT[mg] UNIT[mm] vol% wt% in
 5 Mg NaCl // 50mL H2O@1  
   ^

!!!  4 nm NaCl@2.17// 50 g Si  # Can't use mass in layer mixture
Expected UNIT[mm] in
 4 nm NaCl@2.17// 50 g Si  
                     ^

pkienzle · 2026-05-22T16:34:58Z

Here are the error messages from pyparsing for comparison:

!!!  DNA:CAGT  # incorrect case for FASTA type not properly identified
unknown element A

!!!  dna CAGT  # missing colon in FASTA
Expected end of text, found 'dna'  (at char 1), (line:1, col:2)

!!!  O²  # SUPERCHARGE should be the only valid token here
Expected end of text, found '²'  (at char 2), (line:1, col:3)

!!!  ₃H2O  # badly placed subscript
Expected end of text, found '₃'  (at char 1), (line:1, col:2)

!!!  // 3g Ca  # // is not a comment
Expected end of text, found '/'  (at char 1), (line:1, col:2)

!!!  3g Ca@ // 5g Si # missing density value
Expected end of text, found '3g'  (at char 1), (line:1, col:2)

!!!  Ca@i  # missing density value  ##
!!! pyparsing fails

!!!  Ca ⁺⁺  # extra space before valence
Expected end of text, found '⁺'  (at char 4), (line:1, col:5)

!!!  Ca++  # missing braces in valence: the + is acting as SEPARATOR
Expected end of text, found '+'  (at char 3), (line:1, col:4)

!!!  Ca2+  # missing braces in valence: the 2 is acting as COUNT and the + as SEPARATOR
Expected end of text, found '+'  (at char 4), (line:1, col:5)

!!!  Ca{2}  # missing charge in valence
Expected end of text, found '{'  (at char 3), (line:1, col:4)

!!!  37 vol% H2O@1 / 5% D2O@1  # missing /
Expected end of text, found '37'  (at char 1), (line:1, col:2)

!!!  37 vol% H2O@1 /// 5% D2O@1  # extra /
Expected end of text, found '37'  (at char 1), (line:1, col:2)

!!!  H2O@1h  # bad density mode
Expected end of text, found 'h'  (at char 6), (line:1, col:7)

!!!  37 vol% NaCl@2.16 // H2O@1 // D2O@1  # percent missing in middle part
Expected end of text, found '37'  (at char 1), (line:1, col:2)

!!!  37 vol% H2O@1 // 5% D2O@1  # percent not allowed in last part
Expected end of text, found '37'  (at char 1), (line:1, col:2)

!!!  37 vol% H2O@1 // 5 vol% D2O@1  # only % in subsequent parts
Expected end of text, found '37'  (at char 1), (line:1, col:2)

!!!  37% H2O@1 // D2O@1  # missing vol% or wt%
Expected end of text, found '37'  (at char 1), (line:1, col:2)

!!!  37 val% H2O@1 // D2O@1  # bad spelling of vol%
Expected end of text, found '37'  (at char 1), (line:1, col:2)

!!!  Fe[56O2 # bad isotope syntax
Expected end of text, found '['  (at char 3), (line:1, col:4)

!!!  Co[181]  # bad isotope
'181 is not an isotope of Co'

!!!  Ca{2+O2  # bad valence syntax
Expected end of text, found '{'  (at char 3), (line:1, col:4)

!!!  Co{17-}  # bad valence
valence 17- is not valid for Co

!!!  3..5 mg NaCl
Expected end of text, found '3'  (at char 1), (line:1, col:2)

!!!  3.5 fm Si # bad units at the start; could be wt%/vol% or LENGTH, VOLUME, MASS 
Expected end of text, found '3'  (at char 1), (line:1, col:2)

!!!  3.5 mm Si // 2.5 nm SiO2 //
Expected end of text, found '3'  (at char 1), (line:1, col:2)

!!!  3.5 mm Si // 2.5 nm SiO2 // 35 mm cG
Expected end of text, found '3'  (at char 1), (line:1, col:2)

!!!  ((Co) # mismatched LPAR
Expected end of text, found '('  (at char 1), (line:1, col:2)

!!!  Co)  # mismatched RPAR
Expected end of text, found ')'  (at char 3), (line:1, col:4)

!!!  bad:CAGT  # bad sequence type
Expected end of text, found 'bad'  (at char 1), (line:1, col:2)

*** Co
 => Co @ 8.90

*** dna:CAGT
 => C₃₉H₃₇¹H₁₀N₁₅O₂₅P₄ @ 1.69

*** (Co@5) ##
!!! pyparsing fails

*** (((Co@5)@6)) ##
!!! pyparsing fails

*** CaCO3
 => CaCO₃

*** CaCO₃
 => CaCO₃

*** CaCO3+6H2O
 => CaCO₃(H₂O)₆

*** CaCO3 6H2O
 => CaCO₃(H₂O)₆

*** CaCO3(H2O)6
 => CaCO₃(H₂O)₆

*** CaCO3 (H2O)6
 => CaCO₃(H₂O)₆

*** (Ca(CO3)((H2O)6))
 => CaCO₃(H₂O)₆

*** CaCO₃·6H₂O  ##
!!! pyparsing fails

*** DHO
 => DHO

!!! Ca{2++}  # bad valence string
Expected end of text, found '{'  (at char 2), (line:1, col:3)

*** Ca⁺⁺  # also Ca{2+}  ##
!!! pyparsing fails

*** O²⁻   ##
!!! pyparsing fails

*** H[1]
 => ¹H @ 0.07

*** ²H⁺    # D{+} ##
!!! pyparsing fails

*** O²H⁻   # OD{-} ##
!!! pyparsing fails

*** O²⁻H⁺  # O{2-}H{+} ##
!!! pyparsing fails

*** O²⁻²H⁺ # O{2-}D{+} ##
!!! pyparsing fails

*** H2O@1
 => H₂O @ 1.00

*** D2O@1n
 => D₂O @ 1.11

*** D2O @ 1.11  ##
!!! pyparsing fails

*** D2O@1.11i
 => D₂O @ 1.11

*** HO{1-}
 => HO⁻

*** H[1]{1-}O
 => ¹H⁻O

*** H2SO4
 => H₂SO₄

*** C3H4H[1]NO@1.29n
 => C₃H₄¹HNO @ 1.29

*** 78.2H2O[16] + 21.8H2O[18] @1n  # density applies to composite
 => (H₂¹⁶O)₇₈.₂(H₂¹8O)₂₁.₈ @ 1.02

*** dna:CAGT @1n  # fasta density override
 => C₃₉H₃₇¹H₁₀N₁₅O₂₅P₄ @ 1.00

*** 50 wt% Co // Ti
 => CoTi₁.₂₃₁₁₈₆₂₈₇₀₀₃₅₇₂₆ @ 6.01

*** 33 wt% Co // 33% Fe // Ti
 => CoFe₁.₀₅₅₂₉₉₃₈₂₂₁₈₆₄₁Ti₁.₂₆₈₄₉₄₉₆₂₃₆₇₃₁₇₂ @ 6.50

!!!  93 wt% Co // 33% Fe // Ti  # More than 100 wt%
Expected end of text, found '93'  (at char 1), (line:1, col:2)

!!!  93 vol% Co // 33% Fe // Ti  # More than 100 vol%
Expected end of text, found '93'  (at char 1), (line:1, col:2)

*** 20 vol% (10 wt% NaCl@2.16 // H2O@1) // D2O@1n
 => NaCl(H₂O)₂₉.₁₉₅₅₅₅₀₁₀₈₂₄₃₁(D₂O)₁₂₂.₇₈₉₅₃₅₈₈₉₁₄₅₈₅ @ 1.10

*** NaCl(H2O)29.1966(D2O)122.794@1.10i
 => NaCl(H₂O)₂₉.₁₉₆₆(D₂O)₁₂₂.₇₉₄ @ 1.10

*** 5g NaCl // 50mL H2O@1
 => NaCl(H₂O)₃₂.₄₃₉₅₀₅₅₆₇₅₈₂₅₇

*** 5g NaCl@2.16 // 50mL H2O@1
 => NaCl(H₂O)₃₂.₄₃₉₅₀₅₅₆₇₅₈₂₅₇ @ 1.05

!!!  5g NaCl // 50mL H2O   # Need density for H2O to convert volume to mass
Expected end of text, found '5g'  (at char 1), (line:1, col:2)

*** (10 wt% NaCl // H2O)@1.07n # set density of a mixture
 => NaCl(H₂O)₂₉.₁₉₅₅₅₅₀₁₀₈₂₄₃₁ @ 1.07

*** 50 mL (45 mL H2O@1 // 5 g NaCl)@1.0707 // 20 mL D2O@1n
 => (H₂O)₂₉.₁₉₅₅₅₅₀₁₀₈₂₄₃₁NaCl(D₂O)₁₂.₁₁₈₉₈₉₆₅₈₁₉₈₄₀₂ @ 1.08

*** 1 cm Si // 5 nm Cr // 10 nm Au
 => Si₁₁₉₉₉₂₂.₉₇₃₇₄₆₂₄₉₅CrAu₁.₄₁₇₂₁₈₀₀₉₃₁₂₁₃₆ @ 2.33

*** aa:RELEELNVPGEIVESLSSSEESITRINKKIEKFQSEEQQQTEDELQDKIHPFAQTQSLVYPFPGPIPNSLPQNIPPLTQTPVVVPPFLQPEVMGVSKVKEAMAPKHKEMPFPKYPVEPFTESQSLTLTDVENLHLPLPLLQSWMHQPHQPLPPTVMFPPQSVLSLSQSKVLPVPQKAVPYPQRDMPIQAFLLYQEPVLGPVRGPFPIIV
 => C₁₀₈₀H₁₃₇₀¹H₃₁₉N₂₆₈O₃₁₀S₆ @ 1.27

!!!  Bl2Oh   # Bad symbol
unknown element Bl

!!!  5 Mg NaCl // 50mL H2O@1  # Bad units
Expected end of text, found '5'  (at char 1), (line:1, col:2)

!!!  4 nm NaCl@2.17// 50 g Si  # Can't use mass in layer mixture
Expected end of text, found '4'  (at char 1), (line:1, col:2)

Paul Kienzle added 14 commits March 5, 2026 15:45

Explore lark as replacement for the pyparsing formula parser

1cec0b9

improve error display for lark parser

e2b5aec

better formatting of invalid valence error

c3c0ced

Allow Ang when defining layered samples

a31ce46

check failure text in pyparsing

1390132

display and parse unicode superscripts for isotopes

ee2fc98

fix tests

a30069e

add output type hints to ast transforms

f8cecea

adjust imports; improve :SEQ error message

3412542

move unicode superscript/subscript conversion to util; clean up type …

a1579af

…hints

fix tests and doc build

0efb666

remove pyparsing dependency

42278e6

tweak formula docs

1ccb4a3

improve output of error handling demo python -m periodictable.lark_parse

40a1b6c

Paul Kienzle added 3 commits May 22, 2026 12:22

attempt to fix missing lark on CI

abe5058

attempt to fix missing lark on CI

e2ce8f7

attempt to fix missing lark on CI

cc49581

pkienzle marked this pull request as ready for review May 22, 2026 16:26

pkienzle changed the title ~~Explore lark as replacement for the pyparsing formula parser~~ Replace pyparsing with lark for better error messages May 22, 2026

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Replace pyparsing with lark for better error messages#124

Replace pyparsing with lark for better error messages#124
pkienzle wants to merge 17 commits into
masterfrom
use-lark-parse

pkienzle commented Mar 5, 2026 •

edited

Loading

Uh oh!

pkienzle commented May 22, 2026 •

edited

Loading

Uh oh!

pkienzle commented May 22, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

	grammar = """
	start : SPACE? formula SPACE? # strip blank space from start and end

	# formula: composite @ density \| str:sequence @ density \| mixture
	formula : compound \| mixture
	compound : (composite \| fasta) [density]
	# Density applies to the entire composite, such as "NaCl + 29.2H2O @ 1.07n"
	# For the density of a mixture you need parentheses: "(10 wt% NaCl // H2O)@1.07n"

	# Activation only cares about total mass, so you can freely mix masses and volumes if
	# you have the density for each component. For scattering you need the density of the
	# mixture. When this is different from the mixture of densities use (mixture)@density.
	# For thin film samples, allow stacking of layers with the thickness of each layer.
	# With density for each layer the relative quantities of each element in the stack can
	# be calculated. Convert to mass by multiplying density by thickness (cm) and area (cm²).

	# mixture: quantity compound // quantity compound // quantity compound
	mixture : byamount \| byvolume \| byweight \| layers
	byamount : quantity compound (MIX quantity compound)*
	byvolume : volumepct compound (MIX percentage compound)* MIX compound
	byweight : weightpct compound (MIX percentage compound)* MIX compound
	layers : thickness compound (MIX thickness compound)*
	quantity : NUMBER SPACE? (MASS \| VOLUME) SPACE
	weightpct : NUMBER SPACE? WEIGHTPCT SPACE
	volumepct : NUMBER SPACE? VOLUMEPCT SPACE
	thickness : NUMBER SPACE? LENGTH SPACE
	percentage : NUMBER SPACE? "%" SPACE # Allows "3 % "
	MIX : SPACE? "//" SPACE?
	WEIGHTPCT : /%w((eigh)?t)?/ \| /w((eigh)?t)?%/ \| /%m(ass)?/ \| /m(ass)?%/
	VOLUMEPCT : /%v(ol(ume)?)?/ \| /v(ol(ume)?)?%/
	MASS : "kg" \| "g" \| "mg" \| "ug" \| "μg" \| "ng"
	VOLUME : "L" \| "mL" \| "uL" \| "μL" \| "nL"
	LENGTH : "cm" \| "mm" \| "um" \| "μm" \| "nm" \| "Ang" \| "Å"

	# FASTA sequence: (rna\|dna\|aa):SEQUENCE @ density
	fasta : FASTA ":" SEQUENCE
	FASTA : /[a-z]+/ # str:sequence reports better errors than /dna\|rna\|aa/:sequence
	SEQUENCE : /[-A-Z *]+/

	# composite: number group number group ... @density
	# group: El count El count ...
	# Note: optional `[token]` leaves a None placeholder in the tree, unlike `token?`
	composite : [NUMBER] group (SEPARATOR [NUMBER] group)*
	group : ((atom \| isoatom \| "(" formula ")") [COUNT])+
	atom : SYMBOL [isotope] [valence]
	isoatom : SUPERINT SYMBOL [valence] # For example ²H for deuterium
	isotope : "[" INTEGER "]"
	valence : "{" [INTEGER] CHARGE "}" \| [SUPERINT] SUPERCHARGE
	density : SPACE? "@" SPACE? DENSITY [DENSITYMODE]
	# could list all elements, but better error reporting if element symbol lookup fails
	SYMBOL : /[A-Z][a-z]*/
	CHARGE : /[+]+\|[-]+/ # allow valence using {++} or {--}
	SUPERCHARGE: /\u207A+\|\u207B+/ # unicode valence such as Ca⁺⁺ and O²⁻
	DENSITY : NUMBER # using alias DENSITY for number for better error reporting
	DENSITYMODE: /[ni]/ # n=natural density, i=isotopic density
	COUNT : NUMBER \| SUBNUM # atom counts can be normal numbers or unicode subscripts
	SEPARATOR : SPACE? /[+•·]/ SPACE? \| SPACE # For example, CaCO₃·6H₂O

	SPACE : /[ \\t\\n\\r]+/
	NUMBER : INTEGER \| FRACTION
	INTEGER : /[1-9][0-9]*/
	FRACTION : /([1-9][0-9]\|0)?[.][0-9]/ # allow all floats?
	SUBNUM : SUBINT \| SUBFRAC
	SUBINT : /(\u2080\|[\u2081-\u2089][\u2080-\u2089]*)/
	SUBFRAC : /(\u2080\|[\u2081-\u2089][\u2080-\u2089]\|)([.][\u2080-\u2089])/
	SUPERINT : /(\u2070\|[\u00B9\u00B2\u00B3\u2074-\u2079][\u2070\u00B9\u00B2\u00B3\u2074-\u2079]*)/
	"""

Conversation

pkienzle commented Mar 5, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

pkienzle commented May 22, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

pkienzle commented May 22, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

pkienzle commented Mar 5, 2026 •

edited

Loading

pkienzle commented May 22, 2026 •

edited

Loading