Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/paml/versions.
These checks were done:
- built on NixOS
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 -h’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 --help’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 help’ got 0 exit code
- found 4.9h with grep in /nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h
- directory tree listing: https://gist.github.com/b2a37e7cd2b4b41178f0698f3aac69e2
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/samtools/versions.
These checks were done:
- built on NixOS
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/novo2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl help’ got 0 exit code
- found 1.8 with grep in /nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8
- directory tree listing: https://gist.github.com/4673ea3645eb509035dcb386c4ad1da2
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/bcftools/versions.
These checks were done:
- built on NixOS
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/plot-vcfstats -h’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/plot-vcfstats --help’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/bcftools -h’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/bcftools --help’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/bcftools help’ got 0 exit code
- found 1.8 with grep in /nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8
- directory tree listing: https://gist.github.com/c9ddd760c0c740dabaabeb604fbb8a5a
Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:
- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.17.11 with grep in /nix/store/xmlvcz212yl8bij12jpqibhv8c8mqabs-picard-tools-2.17.11
- found 2.17.11 in filename of file in /nix/store/xmlvcz212yl8bij12jpqibhv8c8mqabs-picard-tools-2.17.11
Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:
- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.4.9 with grep in /nix/store/q5c9jyg6gc4v3ns7rw5lxj7v4v916a7f-igv-2.4.9
- found 2.4.9 in filename of file in /nix/store/q5c9jyg6gc4v3ns7rw5lxj7v4v916a7f-igv-2.4.9
Semi-automatic update. These checks were done:
- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 4.9g in filename of file in /nix/store/70p59yxnlzhbj8ig1ax8lrrsdbcf37zp-paml-4.9g
Semi-automatic update. These checks were performed:
- built on NixOS
- found 2.17.10 with grep in /nix/store/f74zildbrr99qmp5qkb579x9159n88c6-picard-tools-2.17.10
- found 2.17.10 in filename of file in /nix/store/f74zildbrr99qmp5qkb579x9159n88c6-picard-tools-2.17.10
cc "@jbedo"
Semi-automatic update. These checks were performed:
- built on NixOS
- found 2.4.8 with grep in /nix/store/3vwg5hpprkm3v345fy05gxdjicfakql7-igv-2.4.8
- found 2.4.8 in filename of file in /nix/store/3vwg5hpprkm3v345fy05gxdjicfakql7-igv-2.4.8
cc "@mimadrid"
Semi-automatic update. These checks were performed:
- built on NixOS
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -V` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -v` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -V` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -v` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --help` and found version 2.3.4.1
- found 2.3.4.1 with grep in /nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1
- found 2.3.4.1 in filename of file in /nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1
Semi-automatic update. These checks were performed:
- built on NixOS
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -h` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --help` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools help` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -v` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --version` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools version` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -h` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --help` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools help` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/plot-vcfstats -h` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/plot-vcfstats --help` got 0 exit code
- found 1.7 with grep in /nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7
* pkgs: refactor needless quoting of homepage meta attribute
A lot of packages are needlessly quoting the homepage meta attribute
(about 1400, 22%), this commit refactors all of those instances.
* pkgs: Fixing some links that were wrongfully unquoted in the previous
commit
* Fixed some instances
Meta attributes types are now enforce as of commit
90b9719f4f,
so ensure meta.priority is always set to an integer.
This fixes evaluation of `linuxPackages_latest.virtualbox`
(the impetus for this commit)
and other packages that use lowPrio or hiPrio.
- Add support for python bindings
- make neuron respect standard pythonpath prefix
- force exec_prefix == prefix to respect standard nix file hierarchy
- normalize indentation
- propagate dependencies necessary for nrniv_makefile usage
- Add support for darwin
(My OCD kicked in today...)
Remove repeated package names, capitalize first word, remove trailing
periods and move overlong descriptions to longDescription.
I also simplified some descriptions as well, when they were particularly
long or technical, often based on Arch Linux' package descriptions.
I've tried to stay away from generated expressions (and I think I
succeeded).
Some specifics worth mentioning:
* cron, has "Vixie Cron" in its description. The "Vixie" part is not
mentioned anywhere else. I kept it in a parenthesis at the end of the
description.
* ctags description started with "Exuberant Ctags ...", and the
"exuberant" part is not mentioned elsewhere. Kept it in a parenthesis
at the end of description.
* nix has the description "The Nix Deployment System". Since that
doesn't really say much what it is/does (especially after removing
the package name!), I changed that to "Powerful package manager that
makes package management reliable and reproducible" (borrowed from
nixos.org).
* Tons of "GNU Foo, Foo is a [the important bits]" descriptions
is changed to just [the important bits]. If the package name doesn't
contain GNU I don't think it's needed to say it in the description
either.
There are many more packages to fix, this is just a start.
Rules:
* Don't repeat the package name (not always that easy...)
* Start with capital letter
* Don't end with full stop
* Don't start with "The ..." or "A ..."
I've also added descriptions to some packages and rewritten others.
