numapde-bibliography issueshttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues2021-05-10T09:29:23+02:00https://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 Herzoghttps://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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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?