numapde-bibliography issueshttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues2021-07-14T10:19:16+02:00https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/58provide a docker toolchain2021-07-14T10:19:16+02:00Andreas Naumannprovide a docker toolchainThe scripts sometimes do not work directly on Mac.
One solution is the use of docker containers. Some scripts depend on the generated latex files. These files depend on the latex and biber version. These versions are often incompatible ...The scripts sometimes do not work directly on Mac.
One solution is the use of docker containers. Some scripts depend on the generated latex files. These files depend on the latex and biber version. These versions are often incompatible between host and docker container.
A solution to that would
1. recompile the manuscript with numapde-preprint in the container
2. clean the latex files (?)
3. copy the newly generated files from the new journal back to the data folder
How do we know in step 3, which files should be copied?https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/57make the shell scripts more comfortable for mac-users2021-06-21T18:53:02+02:00Andreas Naumannmake the shell scripts more comfortable for mac-usersin analogy to issue #56 we could also check for the shell and give better error messages for mac users.
According to [stackexchange](https://apple.stackexchange.com/questions/361870/what-are-the-practical-differences-between-bash-and-zs...in analogy to issue #56 we could also check for the shell and give better error messages for mac users.
According to [stackexchange](https://apple.stackexchange.com/questions/361870/what-are-the-practical-differences-between-bash-and-zsh) zsh is at some subtle points different to bash.
I would propose to:
* check the shells name. If it is not bash, print an error message and stop
* check the bash version at the very beginning and break if it is below 4.0https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/56Make scripts more failsafe and adhere to coding styles2021-06-21T10:56:02+02:00Roland HerzogMake scripts more failsafe and adhere to coding styleshttps://kvz.io/bash-best-practices.htmlhttps://kvz.io/bash-best-practices.htmlRoland 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 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/52Add a test for incomplete author given names to numapde-validate-bibliography.sh2021-02-26T10:13:57+01:00Roland HerzogAdd a test for incomplete author given names to numapde-validate-bibliography.shhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/51Add authors' given names to numapde.bib2021-02-26T10:13:13+01:00Roland HerzogAdd authors' given names to numapde.bibhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/50Explore possibilities of Crossref's API to send detailed queries2021-02-15T22:39:21+01:00Roland HerzogExplore possibilities of Crossref's API to send detailed queriesThe crossref API may serve as a replacement for mathscinet queries.The crossref API may serve as a replacement for mathscinet queries.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/48Look for titles segmented by period, which should be subtitles2021-01-29T15:58:01+01:00Roland HerzogLook for titles segmented by period, which should be subtitleshttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/47Include test for abbreviated publisher names in numapde-validate-bibliography.sh2021-01-10T16:50:58+01:00Roland HerzogInclude test for abbreviated publisher names in numapde-validate-bibliography.shRoland HerzogRoland Herzoghttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/46Misuse of docker build2021-01-08T10:48:54+01:00Ghost UserMisuse of docker buildhttps://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/blob/master/ci/Dockerfile
```
FROM gitlab/gitlab-runner
RUN apt-get update
RUN apt-get --no-install-recommends -y install texlive-full python3 recode python3-pip g...https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/blob/master/ci/Dockerfile
```
FROM gitlab/gitlab-runner
RUN apt-get update
RUN apt-get --no-install-recommends -y install texlive-full python3 recode python3-pip gawk biber coreutils grep perl diffutils moreutils wget libxml2-utils
RUN apt-get --no-install-recommends -y install python3-setuptools python3-wheel
RUN ["su", "-", "gitlab-runner", "-c", "pip3 install pybtex"]
```
The `gitlab/gitlab-runner` docker image must be used only to run the `gitlab-runner` software itself. This image will be rebuilt every time when `gitlab-runner` gets an update.
We could use something like `texlive/texlive` or `mfisherman/texlive-full` instead.https://gitlab.hrz.tu-chemnitz.de/numapde-public/numapde-bibliography/-/issues/45Check ranges of numbers and use of -- instead of -2021-01-01T15:15:43+01:00Roland HerzogCheck ranges of numbers and use of -- instead of -Number ranges occur in the `number`, `pages` fields, and possibly others.Number ranges occur in the `number`, `pages` fields, and possibly others.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/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/bf00933231