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Broken references in Python Module index with latexpdf #4764

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peterjc opened this issue Jun 28, 2024 · 0 comments
Open

Broken references in Python Module index with latexpdf #4764

peterjc opened this issue Jun 28, 2024 · 0 comments
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@peterjc
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peterjc commented Jun 28, 2024

Noticed building the PDF docs for Biopython 1.84 using c6120cd on Ubuntu (under WSL), using sphinx versions as per e1987f0

$ make -C Doc/ latexpdf
...
Output written on Biopython_doc.pdf (1108 pages, 5334003 bytes).
Transcript written on Biopython_doc.log.
Latexmk: Examining 'Biopython_doc.log'
=== TeX engine is 'pdfTeX'
Latexmk: Index file 'Biopython_doc.idx' was written
Latexmk: Log file says output to 'Biopython_doc.pdf'
Latexmk: List of undefined refs and citations:
  Reference `api/Bio.Align.AlignInfo:module-Bio.Align.AlignInfo' on page 1039 undefined on input line 109816
  Reference `api/Bio.Align.Applications:module-Bio.Align.Applications' on page 1039 undefined on input line 109818
  Reference `api/Bio.Align.a2m:module-Bio.Align.a2m' on page 1039 undefined on input line 109815
  Reference `api/Bio.Align.analysis:module-Bio.Align.analysis' on page 1039 undefined on input line 109817
  Reference `api/Bio.Align.bed:module-Bio.Align.bed' on page 1039 undefined on input line 109819
  Reference `api/Bio.Align.bigbed:module-Bio.Align.bigbed' on page 1039 undefined on input line 109820
  Reference `api/Bio.Align.bigmaf:module-Bio.Align.bigmaf' on page 1039 undefined on input line 109821
  Reference `api/Bio.Align.bigpsl:module-Bio.Align.bigpsl' on page 1039 undefined on input line 109822
  Reference `api/Bio.Align.chain:module-Bio.Align.chain' on page 1039 undefined on input line 109823
  Reference `api/Bio.Align.clustal:module-Bio.Align.clustal' on page 1039 undefined on input line 109824
  Reference `api/Bio.Align.emboss:module-Bio.Align.emboss' on page 1039 undefined on input line 109825
  Reference `api/Bio.Align.exonerate:module-Bio.Align.exonerate' on page 1039 undefined on input line 109826
  Reference `api/Bio.Align.fasta:module-Bio.Align.fasta' on page 1039 undefined on input line 109827
  Reference `api/Bio.Align.hhr:module-Bio.Align.hhr' on page 1039 undefined on input line 109828
  Reference `api/Bio.Align.interfaces:module-Bio.Align.interfaces' on page 1039 undefined on input line 109829
  Reference `api/Bio.Align.maf:module-Bio.Align.maf' on page 1039 undefined on input line 109830
  Reference `api/Bio.Align.mauve:module-Bio.Align.mauve' on page 1039 undefined on input line 109831
  Reference `api/Bio.Align.msf:module-Bio.Align.msf' on page 1039 undefined on input line 109832
  Reference `api/Bio.Align.nexus:module-Bio.Align.nexus' on page 1039 undefined on input line 109833
  Reference `api/Bio.Align.phylip:module-Bio.Align.phylip' on page 1039 undefined on input line 109834
  Reference `api/Bio.Align.psl:module-Bio.Align.psl' on page 1039 undefined on input line 109835
  Reference `api/Bio.Align.sam:module-Bio.Align.sam' on page 1039 undefined on input line 109836
  Reference `api/Bio.Align.stockholm:module-Bio.Align.stockholm' on page 1039 undefined on input line 109837
  Reference `api/Bio.Align.substitution_matrices:module-Bio.Align.substitution_matrices' on page 1039 undefined on input line 109838
  Reference `api/Bio.Align.tabular:module-Bio.Align.tabular' on page 1039 undefined on input line 109839
  Reference `api/Bio.Align:module-Bio.Align' on page 1039 undefined on input line 109814
  Reference `api/Bio.AlignIO.ClustalIO:module-Bio.AlignIO.ClustalIO' on page 1039 undefined on input line 109841
  Reference `api/Bio.AlignIO.EmbossIO:module-Bio.AlignIO.EmbossIO' on page 1039 undefined on input line 109842
  Reference `api/Bio.AlignIO.FastaIO:module-Bio.AlignIO.FastaIO' on page 1039 undefined on input line 109843
  Reference `api/Bio.AlignIO.Interfaces:module-Bio.AlignIO.Interfaces' on page 1039 undefined on input line 109844
  Reference `api/Bio.AlignIO.MafIO:module-Bio.AlignIO.MafIO' on page 1039 undefined on input line 109845
  Reference `api/Bio.AlignIO.MauveIO:module-Bio.AlignIO.MauveIO' on page 1039 undefined on input line 109846
  Reference `api/Bio.AlignIO.MsfIO:module-Bio.AlignIO.MsfIO' on page 1039 undefined on input line 109847
  Reference `api/Bio.AlignIO.NexusIO:module-Bio.AlignIO.NexusIO' on page 1039 undefined on input line 109848
  Reference `api/Bio.AlignIO.PhylipIO:module-Bio.AlignIO.PhylipIO' on page 1039 undefined on input line 109849
  Reference `api/Bio.AlignIO.StockholmIO:module-Bio.AlignIO.StockholmIO' on page 1039 undefined on input line 109850
  Reference `api/Bio.AlignIO:module-Bio.AlignIO' on page 1039 undefined on input line 109840
  Reference `api/Bio.Blast.Applications:module-Bio.Blast.Applications' on page 1039 undefined on input line 109854
  Reference `api/Bio.Blast.NCBIWWW:module-Bio.Blast.NCBIWWW' on page 1039 undefined on input line 109855
  Reference `api/Bio.Blast.NCBIXML:module-Bio.Blast.NCBIXML' on page 1039 undefined on input line 109856
  Reference `api/Bio.Blast:module-Bio.Blast' on page 1039 undefined on input line 109853
  Reference `api/Bio.CAPS:module-Bio.CAPS' on page 1039 undefined on input line 109857
  Reference `api/Bio.PDB.binary_cif:module-Bio.PDB.binary_cif' on page 1040 undefined on input line 109947
  Reference `api/Bio.Phylo.Applications:module-Bio.Phylo.Applications' on page 1040 undefined on input line 109993
  Reference `api/Bio.Phylo.CDAO:module-Bio.Phylo.CDAO' on page 1040 undefined on input line 109995
  Reference `api/Bio.Phylo.CDAOIO:module-Bio.Phylo.CDAOIO' on page 1040 undefined on input line 109996
  Reference `api/Bio.Phylo.Consensus:module-Bio.Phylo.Consensus' on page 1040 undefined on input line 109997
  Reference `api/Bio.Phylo.PAML.baseml:module-Bio.Phylo.PAML.baseml' on page 1041 undefined on input line 110004
  Reference `api/Bio.Phylo.PAML.chi2:module-Bio.Phylo.PAML.chi2' on page 1041 undefined on input line 110005
  Reference `api/Bio.Phylo.PAML.codeml:module-Bio.Phylo.PAML.codeml' on page 1041 undefined on input line 110006
  Reference `api/Bio.Phylo.PAML.yn00:module-Bio.Phylo.PAML.yn00' on page 1041 undefined on input line 110007
  Reference `api/Bio.Phylo.PAML:module-Bio.Phylo.PAML' on page 1041 undefined on input line 110003
  Reference `api/Bio.Phylo.PhyloXML:module-Bio.Phylo.PhyloXML' on page 1041 undefined on input line 110008
  Reference `api/Bio.Phylo.PhyloXMLIO:module-Bio.Phylo.PhyloXMLIO' on page 1041 undefined on input line 110009
  Reference `api/Bio.Phylo.TreeConstruction:module-Bio.Phylo.TreeConstruction' on page 1041 undefined on input line 110010
  Reference `api/Bio.Phylo:module-Bio.Phylo' on page 1040 undefined on input line 109992
  Reference `api/Bio.SearchIO.BlastIO.blast_tab:module-Bio.SearchIO.BlastIO.blast_tab' on page 1041 undefined on input line 110029
  Reference `api/Bio.SearchIO.BlastIO.blast_xml:module-Bio.SearchIO.BlastIO.blast_xml' on page 1041 undefined on input line 110030
  Reference `api/Bio.SearchIO.BlastIO:module-Bio.SearchIO.BlastIO' on page 1041 undefined on input line 110028
  Reference `api/Bio.SearchIO.BlatIO:module-Bio.SearchIO.BlatIO' on page 1041 undefined on input line 110031
  Reference `api/Bio.SearchIO.ExonerateIO.exonerate_cigar:module-Bio.SearchIO.ExonerateIO.exonerate_cigar' on page 1041 undefined on input line 110033
  Reference `api/Bio.SearchIO.ExonerateIO.exonerate_text:module-Bio.SearchIO.ExonerateIO.exonerate_text' on page 1041 undefined on input line 110034
  Reference `api/Bio.SearchIO.ExonerateIO.exonerate_vulgar:module-Bio.SearchIO.ExonerateIO.exonerate_vulgar' on page 1041 undefined on input line 110035
  Reference `api/Bio.SearchIO.ExonerateIO:module-Bio.SearchIO.ExonerateIO' on page 1041 undefined on input line 110032
  Reference `api/Bio.SearchIO.FastaIO:module-Bio.SearchIO.FastaIO' on page 1041 undefined on input line 110036
  Reference `api/Bio.SearchIO.HHsuiteIO.hhsuite2_text:module-Bio.SearchIO.HHsuiteIO.hhsuite2_text' on page 1041 undefined on input line 110038
  Reference `api/Bio.SearchIO.HHsuiteIO:module-Bio.SearchIO.HHsuiteIO' on page 1041 undefined on input line 110037
  Reference `api/Bio.SearchIO.HmmerIO.hmmer2_text:module-Bio.SearchIO.HmmerIO.hmmer2_text' on page 1041 undefined on input line 110040
  Reference `api/Bio.SearchIO.HmmerIO.hmmer3_domtab:module-Bio.SearchIO.HmmerIO.hmmer3_domtab' on page 1041 undefined on input line 110041
  Reference `api/Bio.SearchIO.HmmerIO.hmmer3_tab:module-Bio.SearchIO.HmmerIO.hmmer3_tab' on page 1041 undefined on input line 110042
  Reference `api/Bio.SearchIO.HmmerIO.hmmer3_text:module-Bio.SearchIO.HmmerIO.hmmer3_text' on page 1041 undefined on input line 110043
  Reference `api/Bio.SearchIO.HmmerIO:module-Bio.SearchIO.HmmerIO' on page 1041 undefined on input line 110039
  Reference `api/Bio.SearchIO.InterproscanIO.interproscan_xml:module-Bio.SearchIO.InterproscanIO.interproscan_xml' on page 1041 undefined on input line 110045
  Reference `api/Bio.SearchIO.InterproscanIO:module-Bio.SearchIO.InterproscanIO' on page 1041 undefined on input line 110044
  Reference `api/Bio.SearchIO:module-Bio.SearchIO' on page 1041 undefined on input line 110027
  Reference `api/Bio.codonalign.codonalignment:module-Bio.codonalign.codonalignment' on page 1039 undefined on input line 109860
  Reference `api/Bio.codonalign.codonseq:module-Bio.codonalign.codonseq' on page 1039 undefined on input line 109861
  Reference `api/Bio.codonalign:module-Bio.codonalign' on page 1039 undefined on input line 109859
  Reference `api/Bio.motifs.alignace:module-Bio.motifs.alignace' on page 1040 undefined on input line 109915
  Reference `api/Bio.motifs.applications:module-Bio.motifs.applications' on page 1040 undefined on input line 109916
  Reference `api/Bio.motifs.clusterbuster:module-Bio.motifs.clusterbuster' on page 1040 undefined on input line 109917
  Reference `api/Bio.motifs.jaspar.db:module-Bio.motifs.jaspar.db' on page 1040 undefined on input line 109919
  Reference `api/Bio.motifs.jaspar:module-Bio.motifs.jaspar' on page 1040 undefined on input line 109918
  Reference `api/Bio.motifs.mast:module-Bio.motifs.mast' on page 1040 undefined on input line 109920
  Reference `api/Bio.motifs.matrix:module-Bio.motifs.matrix' on page 1040 undefined on input line 109921
  Reference `api/Bio.motifs.meme:module-Bio.motifs.meme' on page 1040 undefined on input line 109922
  Reference `api/Bio.motifs.minimal:module-Bio.motifs.minimal' on page 1040 undefined on input line 109923
  Reference `api/Bio.motifs.pfm:module-Bio.motifs.pfm' on page 1040 undefined on input line 109924
  Reference `api/Bio.motifs.thresholds:module-Bio.motifs.thresholds' on page 1040 undefined on input line 109925
  Reference `api/Bio.motifs.transfac:module-Bio.motifs.transfac' on page 1040 undefined on input line 109926
  Reference `api/Bio.motifs.xms:module-Bio.motifs.xms' on page 1040 undefined on input line 109927
  Reference `api/Bio.motifs:module-Bio.motifs' on page 1040 undefined on input line 109914
  Reference `api/Bio.pairwise2:module-Bio.pairwise2' on page 1040 undefined on input line 109938
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 93 reference(s)
Latexmk: All targets (Biopython_doc.pdf) are up-to-date
make[1]: Leaving directory '/home/pcock/repositories/biopython/Doc/_build/latex'

Page 1039 in the PDF is the bibliography, but going by the labels on the pages themselves, page 1039 is the start of the Python module index (where most links seem to work):

image

There seems to be a pattern to this, perhaps where code is defined vs exposed via __all__?
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@peterjc