numapde-bibliography issueshttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues2020-01-17T13:48:54+01:00https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/1key structure2020-01-17T13:48:54+01:00Andreas Naumannkey structureBevor wir Repository füllen, schlage ich vor, einige Vorgaben zu diskutieren. Im Anschluss sollen die Vorgaben im Readme festgehalten werden.
1. Key struktur:
1) In dem alten Bibfile besitzen die Keys die Struktur:
````
...Bevor wir Repository füllen, schlage ich vor, einige Vorgaben zu diskutieren. Im Anschluss sollen die Vorgaben im Readme festgehalten werden.
1. Key struktur:
1) In dem alten Bibfile besitzen die Keys die Struktur:
````
AutornamenJahr[:rev][_preprint]
````
2) Wir wechseln auf die Struktur:
````
Autornamen:rev[_suffix]
````
Die erste Variante hat den Vorteil, dass wir anhand des Keys sofort das Jahr zuordnen können. Der Nachteil ist allerdings, dass sich das Jahr der Publikation ändert, wenn die Veröffentlichung des Journal verzögert ist. Infolgedessen würde sich der Key ändern. Dieses Problem wird Variante 2 gelöst.
2. Falls wir Struktur 1.1 verwenden, müssen wir das Jahr festlegen?
a) Das Jahr des ersten Preprints
b) Das Jahr der Veröffentlichung im Journal
https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/2biblatex types and fields2020-05-04T14:42:28+02:00Andreas Naumannbiblatex types and fieldsBiblatex and bibtex support different database types. In this issue we should clarify
- which **biblatex** entires will be supported in the bibliography
- which attributes are mandatory and optional.
After that, we can deside a tra...Biblatex and bibtex support different database types. In this issue we should clarify
- which **biblatex** entires will be supported in the bibliography
- which attributes are mandatory and optional.
After that, we can deside a transformation from biblatex to bibtex for the publications. Furthermore, we can extract some examples from the World.bib file and use them for the documentation in the README.md.
I used the field lists for [bibtex](https://ctan.kako-dev.de/biblio/bibtex/base/btxdoc.pdf) and [biblatex](http://tug.ctan.org/info/biblatex-cheatsheet/biblatex-cheatsheet.pdf)
common types are:
- article
- book
- inbook
- incollection
- inproceedings
- proceedings
- booklet
- manual
- misc
- unpublished
bibtex - only:
- conference
- techreport
- **mastersthesis**
- **phdthesis**
biblatex -only:
- periodical
- supperiodical
- suppbook
- bookinbook
- mvbook
- suppcollection
- collection
- mvcollection
- inreference
- reference
- mvreference
- report
- patent
- **thesis**
- online
- set
- xdata
As can be seen from the three lists. that biblatex combines the mastersthesis and phdthesis in one entry type thesis. Hence for bibtex, we have to specify the type in a field. I suggest the field __type__ .
Which biblatex-only types do we want to support and how do we want to transform them to bibtex?https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/3biblatex types - examples2020-02-04T23:05:15+01:00Andreas Naumannbiblatex types - examplesWe wanted to discuss the structure and rules of the biblatex entries. These rules include:
- We already use UTF-8 as encoding. Hence we do NOT use the bibtex-markup (ex. {L}agrangian), but write the word as is
- Titles in books are c...We wanted to discuss the structure and rules of the biblatex entries. These rules include:
- We already use UTF-8 as encoding. Hence we do NOT use the bibtex-markup (ex. {L}agrangian), but write the word as is
- Titles in books are capitalized. Do we enforce that also in the bibfile?
- Did we resolve the issue #1 already?
- How do we write the fields in CAPITAL, Mixed, or small ? The bibtex-cheatsheet writes everyting small.
- We had further topics, but I do not remember all of them.
Examples for the common types, listed in issue #2, are:
- article:
```
@ARTICLE{DHalluinForsythLabahn2005,
AUTHOR = {d'Halluin, Y. and Forsyth, Peter A. and Labahn, G.},
TITLE = {A semi-Lagrangian approach for American Asian options under jump diffusion},
JOURNAL = {SIAM Journal on Scientific Computing},
VOLUME = {27},
YEAR = {2005},
NUMBER = {1},
PAGES = {315--345},
ISSN = {1064-8275},
DOI = {10.1137/030602630},
}
```
- book:
```
@BOOK{Oettinger2004,
Title = {Beyond Equilibrium Thermodynamics},
Author = {Öttinger, H. C.},
Publisher = {Wiley},
Year = {2004},
Doi = {10.1002/0471727903}
}
- inbook:
```
@INBOOK{MERGEBookChapter8-2019,
author = {R. Dietze and N. Goldberg and R. Herzog and S. Hannusch and M. Hofmann and J. Ihlemann and L. Kroll and A. Meyer and F. Ospald and E. Peretzki and G. Rünger and H. Schmidt and N. Schramm and R. Springer and M. Stockmann and L. Ulke-Winter},
editor = {L. Kroll},
title = {Modellierung, integrative Simulation und Optimierung},
bookTitle = {Technologiefusion für multifunktionale Leichtbaustrukturen: Ressourceneffizienz durch die Schlüsseltechnologie ``Leichtbau''},
year = {2019},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
pages = {577--645},
isbn = {978-3-662-54734-2},
doi = {10.1007/978-3-662-54734-2_8}
}
```
- incollection
```
@INCOLLECTION{HerzogKneesMeyerSieversStoetznerThomas2019,
Title = {Rate-independent systems and their viscous regularizations: analysis, simulation and optimal control},
Author = {R. Herzog and D. Knees and C. Meyer and M. Sievers and A. Stötzner and S. Thomas},
Booktitle = {},
Publisher = {Springer},
Year = {2019},
Pages = {},
Series = {International Series of Numerical Mathematics},
Doi = {}
}
```
- proceedings
```
@PROCEEDINGS{SchulzSiebenbornWelker2015:3,
author = {Schulz, Volker H.and Siebenborn, Martin and Welker, Kathrin},
editor = {Nielsen, Frank and Barbaresco, Frédéric},
title = {PDE Constrained Shape Optimization as Optimization on Shape Manifolds},
booktitle = {Geometric Science of Information},
year = {2015},
publisher = {Springer International Publishing},
pages = {499--508},
isbn = {978-3-319-25040-3},
doi = {10.1007/978-3-319-25040-3_54}
}
```
- booklet
- manual
```
@MANUAL{AlnaesLangtangenLoggMardalSkavhaug2008:1_preprint,
Title = {UFC Specification and User Manual},
Author = {M. S. Aln\ae{}s and H.-P. Langtangen and A.Logg and K.-A. Mardal and O. Skavhaug},
Url = {http://www.fenicsproject.org/ufc/},
Year = {2008}
}
```
- misc
```
@MISC{PETSc,
Title = {PETSc web page},
Author = {Satish Balay and Kris Buschelman and William D. Gropp and Dinesh Kaushik and Matthew G. Knepley and Lois Curfman McInnes and Barry F. Smith and Hong Zhang},
Url = {http://www.mcs.anl.gov/petsc}
}
```
- unpublished
```
@UNPUBLISHED{DiscacciatiGriesse2007,
Title = {Numerical Solution of a Stationary Optimal Control Problem in Magnetohydrodynamics: Stokes Case},
Author = {M. Discacciati and R. Griesse},
Journal = {in preparation}
}
```https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/4Relation between journal and arXiv versions2020-06-11T17:57:54+02:00Roland HerzogRelation between journal and arXiv versionsTry out the `related` field of biblatex in order to have the journal version refer to an arXiv version. Do not set `relatedtype` nor `relatedstring`. Or use a new entry such as `numapdepreprint` which is not interpreted by biblatex.Try out the `related` field of biblatex in order to have the journal version refer to an arXiv version. Do not set `relatedtype` nor `relatedstring`. Or use a new entry such as `numapdepreprint` which is not interpreted by biblatex.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/7rename the bibfile2020-02-02T01:30:36+01:00Andreas Naumannrename the bibfilerename the world.bib to numapde-general.bib, after all scripts are readyrename the world.bib to numapde-general.bib, after all scripts are readyhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/8Provide an integration test for the entire numapde.bib, sorted by entry type2020-04-28T22:51:34+02:00Roland HerzogProvide an integration test for the entire numapde.bib, sorted by entry typehttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/9Check what the betterbib tool can do for us2020-02-02T02:16:44+01:00Roland HerzogCheck what the betterbib tool can do for ushttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/10Manually add info of about 200 url entries from World.bib into numapde.bib2021-02-15T22:04:39+01:00Roland HerzogManually add info of about 200 url entries from World.bib into numapde.bibhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/12numapde-generate-citekeys.py should probably throw an error if DATE field is ...2020-06-10T18:07:35+02:00Roland Herzognumapde-generate-citekeys.py should probably throw an error if DATE field is emptyAndreas NaumannAndreas Naumannhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/13add new retrieval scripts2020-04-23T15:53:02+02:00Roland Herzogadd new retrieval scripts* mathscinet
* crossref
* scholar
* DBLP
see also https://www.doi2bib.org/* mathscinet
* crossref
* scholar
* DBLP
see also https://www.doi2bib.org/https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/14provide a documentation of the scripts, workflow2020-06-11T18:02:10+02:00Roland Herzogprovide a documentation of the scripts, workflowhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/15The letter æ does not seem to be supported by pdflatex (TeXLive 2017)2020-07-07T21:44:07+02:00Roland HerzogThe letter æ does not seem to be supported by pdflatex (TeXLive 2017)A document with `\cite{AlnaesLoggMardalSkavhaugLangtangen:2009:1}` does not correctly display æ while `cite{Oksendal:2000:1}` correctly shows the letter Ø.A document with `\cite{AlnaesLoggMardalSkavhaugLangtangen:2009:1}` does not correctly display æ while `cite{Oksendal:2000:1}` correctly shows the letter Ø.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/16biber --tool kills IDS fields in numapde.bib2021-02-15T23:31:18+01:00Roland Herzogbiber --tool kills IDS fields in numapde.bibA run of `numapde-canonicalize-bibliography.sh` (which uses `biber --tool`) kills the IDS (alias) fields.A run of `numapde-canonicalize-bibliography.sh` (which uses `biber --tool`) kills the IDS (alias) fields.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/17Make numapde-generate-citekeys.py work in a pipe (reading from stdin instead ...2020-03-03T15:05:39+01:00Roland HerzogMake numapde-generate-citekeys.py work in a pipe (reading from stdin instead from a file)Andreas NaumannAndreas Naumannhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/18Sometimes the title still has the (preliminary) key inside2020-02-04T23:02:04+01:00Ghost UserSometimes the title still has the (preliminary) key insideIn the current `numapde.bib` there is sometimes what seems to be a pre-key inside the title, see
[Line 4569](https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/blob/master/numapde.bib?expanded=true&viewer=simple#L4569)...In the current `numapde.bib` there is sometimes what seems to be a pre-key inside the title, see
[Line 4569](https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/blob/master/numapde.bib?expanded=true&viewer=simple#L4569) or 4563 directly above.
How does this happen?
Can we perhaps store a pre-key in a field like `prekey` such that it in any case does not obstruse the title?https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/19Add eprint/eprinttype also to the publication2020-06-10T18:42:43+02:00Ghost UserAdd eprint/eprinttype also to the publicationOne thing I like to do with published papers is, to also add the `eprint`, `eprinttype` fields of the preprint. I know we currently have no way to link them directly but it would be nice if from the `World.bib` transferred these fields m...One thing I like to do with published papers is, to also add the `eprint`, `eprinttype` fields of the preprint. I know we currently have no way to link them directly but it would be nice if from the `World.bib` transferred these fields might survive.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/20Create a customized biblatex datamodel which can hold extra fields such as NU...2021-02-15T23:31:53+01:00Roland HerzogCreate a customized biblatex datamodel which can hold extra fields such as NUMAPDESTATUSA customized data model seems to be required in order for non-standard fields to survive a run of `biber --tool`.A customized data model seems to be required in order for non-standard fields to survive a run of `biber --tool`.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/21Introduce Merge2020-04-25T13:24:26+02:00Andreas NaumannIntroduce MergeWe propose a three step work flow:
1. download the bibliography, canonicalize and generate the cite keys
```
arxiv2bibtex 1812.00808 | bin/numapde-canonicalize-bibliography.sh - | bin/numapde-generate-citekeys.py | tee newEntry.bib
```
a...We propose a three step work flow:
1. download the bibliography, canonicalize and generate the cite keys
```
arxiv2bibtex 1812.00808 | bin/numapde-canonicalize-bibliography.sh - | bin/numapde-generate-citekeys.py | tee newEntry.bib
```
and check if they are correct (todo: use validate?)
2. append the entry:
```
cat newEntry.bib >> numapde.bib
```
3. finalize the keys:
```
numapde-finalize-keys.sh numapde.bib
```Andreas NaumannAndreas Naumannhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/22Frontent für Nutzer2020-04-25T15:06:00+02:00Andreas NaumannFrontent für Nutzer* Frontent `numapde-get-bib.sh`:
* Author, Title, schalter aus arxive2bib, msc usw
* Quellen Präferenz
* --raw (für rohdaten)
* Vereinheitlicht per canonalize
* Schalter für hinzufügen (--write-to)
* Bei --write-to Überprüfu...* Frontent `numapde-get-bib.sh`:
* Author, Title, schalter aus arxive2bib, msc usw
* Quellen Präferenz
* --raw (für rohdaten)
* Vereinheitlicht per canonalize
* Schalter für hinzufügen (--write-to)
* Bei --write-to Überprüfung für doppelte (nicht nur keys), sie issue #21
* Wechsel der Inputs je nach Anfragehttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/23Allow an editor in the pipe for numapde-get-bib.sh2020-05-09T20:23:42+02:00Roland HerzogAllow an editor in the pipe for numapde-get-bib.shImplement an `--edit` switch which will invoke `$EDITOR` in the pipe.
This will allow the user to edit retrieved entries on the fly.Implement an `--edit` switch which will invoke `$EDITOR` in the pipe.
This will allow the user to edit retrieved entries on the fly.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/24Implement an update mechanism for existing entries2020-12-04T13:17:06+01:00Roland HerzogImplement an update mechanism for existing entriesWhen
* a new version with an updated title is published on arXiv
* an existing article has updated information (e.g., when its print version has appeared)
it may be necessary to update existing entries (in <code>numapde.bib</code>).
I pr...When
* a new version with an updated title is published on arXiv
* an existing article has updated information (e.g., when its print version has appeared)
it may be necessary to update existing entries (in <code>numapde.bib</code>).
I propose to implement an '--update' switch to 'numapde-merge-bibliography.py' and 'numapde-get-doi.sh' which will
* go through the entries in <code>new.bib</code>
* and try to locate them in <code>old.bib</code>
* and replace them in <code>old.bib</code> (preserving the old citation key)https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/25Clean up numapde.bib2020-05-07T11:37:46+02:00Roland HerzogClean up numapde.bibThere are still some entries requiring work. Look for
* submitted
* (un)capitalization of `TITLE`There are still some entries requiring work. Look for
* submitted
* (un)capitalization of `TITLE`https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/26Add missing DOIs in numapde.bib2020-05-07T14:25:12+02:00Roland HerzogAdd missing DOIs in numapde.bibhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/27Check, convert all @MISC entries in numapde.bib2020-05-07T11:59:59+02:00Roland HerzogCheck, convert all @MISC entries in numapde.bibhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/28Error: XPath set is empty2020-05-07T11:45:09+02:00Roland HerzogError: XPath set is emptyExample:
`numapde-get-bib.sh 10.1109/ISBI.2009.5193034`Example:
`numapde-get-bib.sh 10.1109/ISBI.2009.5193034`https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/29dependency on mathbin2020-05-09T18:50:28+02:00Ghost Userdependency on mathbinCurrently we are depending on https://github.com/gerw/mathbin and that's nowhere mentioned.
I haven't understood all dependencies, but it sould either be mentioned or become a subrepo.
Even better would be to redo for example the `math...Currently we are depending on https://github.com/gerw/mathbin and that's nowhere mentioned.
I haven't understood all dependencies, but it sould either be mentioned or become a subrepo.
Even better would be to redo for example the `mathscinet`, either in python or in shell to eventually get rid of the dependency on perl, if possible. What are other scripts that depend on mathbin? Is it reasonable to reimplement them here (in python) or better to have the subrepo?https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/30Create a conversion file from BibLaTeX to BibTeX2020-05-11T00:26:42+02:00Roland HerzogCreate a conversion file from BibLaTeX to BibTeXThis conversion is necessary since most journals still use BibTeX rather than BibLaTeX.
However, `numapde.bib` uses the more modern BibLaTeX standard which is not downward compatible with BibTeX in all aspects.
I propose `numapde-prepar...This conversion is necessary since most journals still use BibTeX rather than BibLaTeX.
However, `numapde.bib` uses the more modern BibLaTeX standard which is not downward compatible with BibTeX in all aspects.
I propose `numapde-prepare-bibtex-file.sh` as the tentative name for the conversion script.
In order to come from `numapde.bib` (and possibly other `.bib` files such a `numapde-local.bib`) to a BibTeX file, I propose to let `numapade-prepare-manuscript.py` trigger `numapde-prepare-bib-file.sh`. In this way, we could hard code all command line switches for `numapde-prepare-bibtex-file.sh` which are necessary to come up with `manuscript-coap.bib` (for example) compatible for the `.bst` of the respective journal. In this way, the user does not need to know whether or not the `.bst` file a particular journal uses can cope with, e.g., `@ONLINE` entries or not.
Among the replacements that `numapde-prepare-bibtex-file.sh` will typically need to make are:
* conversion of `@THESIS`
* conversion of `@ONLINE`
* protection of uppercase characters, e.g., in the `TITLE` field
* conversion of `DATE` to `YEAR`
* possibly UTF8 transcription
There is one further issue. Since the preprint and journal version of a manuscript utilize the same `.yaml` file with meta data, they also normally use the same `.bib` file(s). I propose to override this behavior in the following manner. If an especially prepared `.bib` file exists, it will get preference and be the only `.bib` file used. The respective mechanism can be implemented into `numapade-prepare-manuscript.py`. If it does not exist, the file(s) specified in the `.yaml` file will be used. Our preprint class can be exempt from this rule.
Finally, the IntegrationTests should include a more thorough testing of all kinds of bibliography entries to ensure all types of entries to be treated correctly.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/31Correct some entries in numapde.bib2020-06-10T16:47:46+02:00Roland HerzogCorrect some entries in numapde.bib* HarderWachsmuth:2018:1
* PAMM as `@ARTICLE` or `@INPROCEEDINGS` ?
* HerrmannHerzogKroenerSchmidtVidalNunez:2017:1 is `@ONLINE` on arXiv?
* HerzogLegler:2018:1 and other `@REPORT` entries* HarderWachsmuth:2018:1
* PAMM as `@ARTICLE` or `@INPROCEEDINGS` ?
* HerrmannHerzogKroenerSchmidtVidalNunez:2017:1 is `@ONLINE` on arXiv?
* HerzogLegler:2018:1 and other `@REPORT` entrieshttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/32Verify the bibliographies in numapde-journal-templates/IntegrationTest2020-07-02T13:30:19+02:00Roland HerzogVerify the bibliographies in numapde-journal-templates/IntegrationTestThings to look for:
* false lower case letters in titles
* URNs (EPRINT) falsely tagged as arXiv links
* DOIs which are not linked
As for issues with citations/references/links, consider test-aml.pdf
test-imanum.pdf
test-mma.pdf
test-nm...Things to look for:
* false lower case letters in titles
* URNs (EPRINT) falsely tagged as arXiv links
* DOIs which are not linked
As for issues with citations/references/links, consider test-aml.pdf
test-imanum.pdf
test-mma.pdf
test-nme.pdf
test-pamm.pdfhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/33terminal / stream issues2020-05-26T10:16:41+02:00Andreas Naumannterminal / stream issuesThere is an issue with the script bin/numapde-canonicalize.sh in combination with a non-interactive shell. The command
```
ssh localhost <PATH-TO-numapde-bibliography>/bin/numapde-canonicalize.sh --help
```
prints the help screen. But
`...There is an issue with the script bin/numapde-canonicalize.sh in combination with a non-interactive shell. The command
```
ssh localhost <PATH-TO-numapde-bibliography>/bin/numapde-canonicalize.sh --help
```
prints the help screen. But
```
ssh localhost <PATH-TO-numapde-bibliography>/bin/numapde-canonicalize.sh <PATH-TO-numapde-bibliography>/numapde.bib
```
stucks. Furthermore
```
ls -lhat /tmp/tmp.*
```
reveals several empty files with a similar naming scheme and recent timestamps.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/34bug in numapde-remove-extra-braces.awk2020-06-10T16:34:33+02:00Andreas Naumannbug in numapde-remove-extra-braces.awkThe script numapde-canonicalize-bibliography.sh removes a trailing brace. The sequence:
```
numapde-query-mathscinet.sh -m MR3984057 > MR3984057.bib
numapde-canonicalize-bibliography.sh MR3984057.bib
```
leads to the output
```
@ARTICLE{...The script numapde-canonicalize-bibliography.sh removes a trailing brace. The sequence:
```
numapde-query-mathscinet.sh -m MR3984057 > MR3984057.bib
numapde-canonicalize-bibliography.sh MR3984057.bib
```
leads to the output
```
@ARTICLE{MR3984057,
AUTHOR = {Adam, L. and Hintermüller, M. and Surowiec, T. M.},
DATE = {2019},
DOI = {10.1093/imanum/dry034},
ISSN = {0272-4979},
JOURNALTITLE = {IMA Journal of Numerical Analysis},
NUMBER = {3},
PAGES = {1276--1295},
TITLE = {A semismooth Newton method with analytical path-following for the $H^1$-projection onto the {Gibbs simplex},
VOLUME = {39},
}
```
with a missing closing brace for the TITLE. The brace exists in the original file. Please also note, that the title has a line break, which might lead to the error.Roland HerzogRoland Herzoghttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/35description and usage of numapde-prepare-bibtex-file.sh2020-06-12T13:10:34+02:00Andreas Naumanndescription and usage of numapde-prepare-bibtex-file.shHow is the script `numapde-prepare-bibtex-file.sh` supposed to be used? In the sandbox is a [test publication](https://gitlab.hrz.tu-chemnitz.de/numapde/Sandbox/Testpublication) which uses the style pamm, which in turn requires bibtex.
...How is the script `numapde-prepare-bibtex-file.sh` supposed to be used? In the sandbox is a [test publication](https://gitlab.hrz.tu-chemnitz.de/numapde/Sandbox/Testpublication) which uses the style pamm, which in turn requires bibtex.
Using bibtex, we do not get a bcf file, but bibtex creates a warning `Warning--empty <journal> in @article{Wu:2002:1}` in the file `manuscript-pamm.blg`.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/36biblatex's rendering of the letter æ is in conflict with the \ae command from...2020-07-02T14:00:44+02:00Roland Herzogbiblatex's rendering of the letter æ is in conflict with the \ae command from numapde-syntax.styIn `numapde-syntax.sty`, \ae introduces a convenient abbreviation for almost everywhere.
However, biblatex produces \ae{} as a transcription for the letter æ.
An example is the entry `Newton:1686:1` in `numapde.bib`, as cited, for instan...In `numapde-syntax.sty`, \ae introduces a convenient abbreviation for almost everywhere.
However, biblatex produces \ae{} as a transcription for the letter æ.
An example is the entry `Newton:1686:1` in `numapde.bib`, as cited, for instance, in `numapde-bibliography/IntegrationTest/numapde-bibliography-dump-nonarticles.tex`.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/37Citations with æ are still incorrectly cited2020-07-17T10:32:17+02:00Roland HerzogCitations with æ are still incorrectly citedIt is not enough to reset \ae in the bibliography environment. When author names are spelled out by \cite, \ae still appears as "a.e.".It is not enough to reset \ae in the bibliography environment. When author names are spelled out by \cite, \ae still appears as "a.e.".Roland HerzogRoland Herzoghttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/38Make numapde-validate-bibliography.sh recognize all upper cases2021-02-15T23:08:50+01:00Roland HerzogMake numapde-validate-bibliography.sh recognize all upper casesExamples:
* 10.1142/s0218202511500230 in the TITLE field
* 10.1142/s0218202511500230 in the AUTHOR fieldExamples:
* 10.1142/s0218202511500230 in the TITLE field
* 10.1142/s0218202511500230 in the AUTHOR fieldRoland HerzogRoland Herzoghttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/39Duplicate DOIs will not be found by numapde-merge-bibliogphy.py if they diffe...2020-09-01T14:25:51+02:00Roland HerzogDuplicate DOIs will not be found by numapde-merge-bibliogphy.py if they differ by caseExample:
* 10.1007/BF00933231
* 10.1007/bf00933231Example:
* 10.1007/BF00933231
* 10.1007/bf00933231https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/40numapde-get-bib.sh 1910.08892 --merge numapde.bib fails2020-09-07T09:04:14+02:00Roland Herzognumapde-get-bib.sh 1910.08892 --merge numapde.bib failsIt fails with
```
File "/home/roland/Work/public/numapde-bibliography/bin/numapde-merge-bibliography.py", line 47, in <module>
curDOI = entry.fields.get('DOI').upper()
AttributeError: 'NoneType' object has no attribute 'upper'
```It fails with
```
File "/home/roland/Work/public/numapde-bibliography/bin/numapde-merge-bibliography.py", line 47, in <module>
curDOI = entry.fields.get('DOI').upper()
AttributeError: 'NoneType' object has no attribute 'upper'
```Andreas NaumannAndreas Naumannhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/41numapde-get-bib.sh --merge fails when several entries share the same temporar...2020-11-20T13:17:57+01:00Roland Herzognumapde-get-bib.sh --merge fails when several entries share the same temporary cite key`numapde-get-bib.sh -a yousept -y 2012 --merge numapde.bib`
Happy to discuss possible fixes. Since the format of temporary cite keys is currently used in many places, a good solution may require some thought.`numapde-get-bib.sh -a yousept -y 2012 --merge numapde.bib`
Happy to discuss possible fixes. Since the format of temporary cite keys is currently used in many places, a good solution may require some thought.Andreas NaumannAndreas Naumannhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/42Implement --update switch into numapde-get-bib.sh2020-12-04T15:17:45+01:00Roland HerzogImplement --update switch into numapde-get-bib.shRoland HerzogRoland Herzoghttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/43Incorrect transcription of umlauts from arXiv2021-01-22T12:26:04+01:00Roland HerzogIncorrect transcription of umlauts from arXivAuthor name transcriptions from arXiv for BibLaTeX are incorrect, see for instance, `numapde-get-bib.sh 2012.11478`. Consequently, the generated cite key is also incorrect.Author name transcriptions from arXiv for BibLaTeX are incorrect, see for instance, `numapde-get-bib.sh 2012.11478`. Consequently, the generated cite key is also incorrect.Roland HerzogRoland Herzoghttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/44Incorrect key suffix2021-01-22T12:37:04+01:00Roland HerzogIncorrect key suffix`numapde-get-bib.sh 10.1007/s11228-016-0380-9 --merge numapde.bib` (from commit f72e1b7093312d1437f97220f557718170d3072e) generates the citation key `Hosseini:2016:2` instead of `Hosseini:2016:1`. A possible reason is an incorrect detect...`numapde-get-bib.sh 10.1007/s11228-016-0380-9 --merge numapde.bib` (from commit f72e1b7093312d1437f97220f557718170d3072e) generates the citation key `Hosseini:2016:2` instead of `Hosseini:2016:1`. A possible reason is an incorrect detection of the (non-existent) `Hosseini:2016:1` in `GrohsHosseini:2016:1`.Roland HerzogRoland Herzoghttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/49Make numapde-prepare-bibtex-file.sh append SUBTITLE to TITLE field2021-02-15T17:49:21+01:00Roland HerzogMake numapde-prepare-bibtex-file.sh append SUBTITLE to TITLE fieldhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/53abbreviate non-last names2021-02-27T18:12:21+01:00Andreas Naumannabbreviate non-last names```
awk '{ if (match($0, /^[ ]*AUTHOR = {(.*)}/, array)) nNames=split(array[1], names, " and "); for(nameNr in names) { split(names[nameNr], lastOthers, ","); nParts=split(lastOthers[2], parts, " "); printf "%s,",lastOthers[1] ; for(pN...```
awk '{ if (match($0, /^[ ]*AUTHOR = {(.*)}/, array)) nNames=split(array[1], names, " and "); for(nameNr in names) { split(names[nameNr], lastOthers, ","); nParts=split(lastOthers[2], parts, " "); printf "%s,",lastOthers[1] ; for(pNr=1 ; pNr <=nParts; pNr++) {printf " %s.",substr(parts[pNr],1,1) ; } if(nameNr < nNames) printf " and "; } printf "\n" }'
```https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/54numapde-get-bib.sh introduces incorrect protection marks2021-04-23T11:01:34+02:00Roland Herzognumapde-get-bib.sh introduces incorrect protection marks`numapde-get-bib.sh 10.1007/978-3-030-50450-2_8` is OK but `numapde-get-bib.sh 10.1007/978-3-030-50450-2_8 --merge new.bib` introduces a stray backslash into the DOI:
```@INCOLLECTION{AlbiCristianiPareschiPeri:2020:1,
AUTHOR = {Albi, G...`numapde-get-bib.sh 10.1007/978-3-030-50450-2_8` is OK but `numapde-get-bib.sh 10.1007/978-3-030-50450-2_8 --merge new.bib` introduces a stray backslash into the DOI:
```@INCOLLECTION{AlbiCristianiPareschiPeri:2020:1,
AUTHOR = {Albi, Giacomo and Cristiani, Emiliano and Pareschi, Lorenzo and Peri, Daniele},
PUBLISHER = {Springer International Publishing},
BOOKTITLE = {Crowd Dynamics, Volume 2},
DATE = {2020},
DOI = {10.1007/978-3-030-50450-2\_8},
PAGES = {159--197},
TITLE = {Mathematical Models and Methods for Crowd Dynamics Control},
}
```
A similar issues occurs with existing backslashes, as in `numapde-get-bib.sh 10.1137/17m1117872`, where the publisher entry contains `\\&` instead of the original and correct `\&`.Roland HerzogRoland Herzoghttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/55Correctly handle compound given names2021-05-10T09:29:23+02:00Roland HerzogCorrectly handle compound given names`numapde-abbreviate-given-names.awk` does not handle compound given names correctly, such as *Karl-Heinz*. A possible solution is to split given names not only at " ", but also at "-", and to remember the matches and insert them in betwe...`numapde-abbreviate-given-names.awk` does not handle compound given names correctly, such as *Karl-Heinz*. A possible solution is to split given names not only at " ", but also at "-", and to remember the matches and insert them in between the abbreviated given names parts.Roland HerzogRoland Herzog