feat(plugins): Add Ag completion (#3534)

* Add Ag completion

A replacement for ack/grep https://github.com/ggreer/the_silver_searcher

* Create README.md

As requested in the PR: https://github.com/ohmyzsh/ohmyzsh/pull/3534

plugins/ag/README.md

@@ -0,0 +1,13 @@
+# The Silver Searcher
+
+This plugin provides completion support for [`ag`](https://github.com/ggreer/the_silver_searcher).
+
+To use it, add ag to the plugins array in your zshrc file.
+
+```zsh
+plugins=(... aws)
+```
+
+## INSTALLATION NOTES
+
+Besides oh-my-zsh, `ag` needs to be installed by following these steps: https://github.com/ggreer/the_silver_searcher#installing.

plugins/ag/_ag

@@ -0,0 +1,66 @@
+#compdef ag
+#autoload
+
+typeset -A opt_args
+
+# Took the liberty of not listing every option… specially aliases and -D
+_ag () {
+  local -a _1st_arguments
+  _1st_arguments=(
+    '--ackmate:Print results in AckMate-parseable format'
+    {'-A','--after'}':[LINES] Print lines after match (Default: 2)'
+    {'-B','--before'}':[LINES] Print lines before match (Default: 2)'
+    '--break:Print newlines between matches in different files'
+    '--nobreak:Do not print newlines between matches in different files'
+    {'-c','--count'}':Only print the number of matches in each file'
+    '--color:Print color codes in results (Default: On)'
+    '--nocolor:Do not print color codes in results'
+    '--color-line-number:Color codes for line numbers (Default: 1;33)'
+    '--color-match:Color codes for result match numbers (Default: 30;43)'
+    '--color-path:Color codes for path names (Default: 1;32)'
+    '--column:Print column numbers in results'
+    {'-H','--heading'}':Print file names (On unless searching a single file)'
+    '--noheading:Do not print file names (On unless searching a single file)'
+    '--line-numbers:Print line numbers even for streams'
+    {'-C','--context'}':[LINES] Print lines before and after matches (Default: 2)'
+    '-g:[PATTERN] Print filenames matching PATTERN'
+    {'-l','--files-with-matches'}':Only print filenames that contain matches'
+    {'-L','--files-without-matches'}':Only print filenames that do not contain matches'
+    '--no-numbers:Do not print line numbers'
+    {'-o','--only-matching'}':Prints only the matching part of the lines'
+    '--print-long-lines:Print matches on very long lines (Default: 2k characters)'
+    '--passthrough:When searching a stream, print all lines even if they do not match'
+    '--silent:Suppress all log messages, including errors'
+    '--stats:Print stats (files scanned, time taken, etc.)'
+    '--vimgrep:Print results like vim :vimgrep /pattern/g would'
+    {'-0','--null'}':Separate filenames with null (for "xargs -0")'
+
+    {'-a','--all-types'}':Search all files (does not include hidden files / .gitignore)'
+    '--depth:[NUM] Search up to NUM directories deep (Default: 25)'
+    {'-f','--follow'}':Follow symlinks'
+    {'-G','--file-search-regex'}':[PATTERN] Limit search to filenames matching PATTERN'
+    '--hidden:Search hidden files (obeys .*ignore files)'
+    {'-i','--ignore-case'}':Match case insensitively'
+    '--ignore:[PATTERN] Ignore files/directories matching PATTERN'
+    {'-m','--max-count'}':[NUM] Skip the rest of a file after NUM matches (Default: 10k)'
+    {'-p','--path-to-agignore'}':[PATH] Use .agignore file at PATH'
+    {'-Q','--literal'}':Do not parse PATTERN as a regular expression'
+    {'-s','--case-sensitive'}':Match case'
+    {'-S','--smart-case'}':Insensitive match unless PATTERN has uppercase (Default: On)'
+    '--search-binary:Search binary files for matches'
+    {'-t','--all-text'}':Search all text files (Hidden files not included)'
+    {'-u','--unrestricted'}':Search all files (ignore .agignore and _all_)'
+    {'-U','--skip-vcs-ignores'}':Ignore VCS files (stil obey .agignore)'
+    {'-v','--invert-match'}':Invert match'
+    {'-w','--word-regexp'}':Only match whole words'
+    {'-z','--search-zip'}':Search contents of compressed (e.g., gzip) files'
+
+    '--list-file-types:list of supported file types'
+  )
+
+  if [[ $words[-1] =~ "^-" ]]; then
+    _describe -t commands "ag options" _1st_arguments && ret=0
+  else
+    _files && ret=0
+  fi
+}

plugins/bedtools/README.md

@@ -0,0 +1,5 @@
+# Bedtools plugin
+
+This plugin adds support for the [bedtools suite](http://bedtools.readthedocs.org/en/latest/):
+
+* Adds autocomplete options for all bedtools sub commands.

plugins/bedtools/_bedtools

@@ -0,0 +1,64 @@
+#compdef bedtools
+#autoload
+
+local curcontext="$curcontext" state line ret=1
+local -a _files
+
+_arguments -C \
+  '1: :->cmds' \
+  '2:: :->args' && ret=0
+
+case $state in
+  cmds)
+    _values "bedtools command" \
+        "--contact[Feature requests, bugs, mailing lists, etc.]" \
+        "--help[Print this help menu.]" \
+        "--version[What version of bedtools are you using?.]" \
+        "annotate[Annotate coverage of features from multiple files.]" \
+        "bamtobed[Convert BAM alignments to BED (& other) formats.]" \
+        "bamtofastq[Convert BAM records to FASTQ records.]" \
+        "bed12tobed6[Breaks BED12 intervals into discrete BED6 intervals.]" \
+        "bedpetobam[Convert BEDPE intervals to BAM records.]" \
+        "bedtobam[Convert intervals to BAM records.]" \
+        "closest[Find the closest, potentially non-overlapping interval.]" \
+        "cluster[Cluster (but don't merge) overlapping/nearby intervals.]" \
+        "complement[Extract intervals _not_ represented by an interval file.]" \
+        "coverage[Compute the coverage over defined intervals.]" \
+        "expand[Replicate lines based on lists of values in columns.]" \
+        "fisher[Calculate Fisher statistic b/w two feature files.]" \
+        "flank[Create new intervals from the flanks of existing intervals.]" \
+        "genomecov[Compute the coverage over an entire genome.]" \
+        "getfasta[Use intervals to extract sequences from a FASTA file.]" \
+        "groupby[Group by common cols. & summarize oth. cols. (~ SQL "groupBy")]" \
+        "igv[Create an IGV snapshot batch script.]" \
+        "intersect[Find overlapping intervals in various ways.]" \
+        "jaccard[Calculate the Jaccard statistic b/w two sets of intervals.]" \
+        "links[Create a HTML page of links to UCSC locations.]" \
+        "makewindows[Make interval "windows" across a genome.]" \
+        "map[Apply a function to a column for each overlapping interval.]" \
+        "maskfasta[Use intervals to mask sequences from a FASTA file.]" \
+        "merge[Combine overlapping/nearby intervals into a single interval.]" \
+        "multicov[Counts coverage from multiple BAMs at specific intervals.]" \
+        "multiinter[Identifies common intervals among multiple interval files.]" \
+        "nuc[Profile the nucleotide content of intervals in a FASTA file.]" \
+        "overlap[Computes the amount of overlap from two intervals.]" \
+        "pairtobed[Find pairs that overlap intervals in various ways.]" \
+        "pairtopair[Find pairs that overlap other pairs in various ways.]" \
+        "random[Generate random intervals in a genome.]" \
+        "reldist[Calculate the distribution of relative distances b/w two files.]" \
+        "sample[Sample random records from file using reservoir sampling.]" \
+        "shuffle[Randomly redistrubute intervals in a genome.]" \
+        "slop[Adjust the size of intervals.]" \
+        "sort[Order the intervals in a file.]" \
+        "subtract[Remove intervals based on overlaps b/w two files.]" \
+        "tag[Tag BAM alignments based on overlaps with interval files.]" \
+        "unionbedg[Combines coverage intervals from multiple BEDGRAPH files.]" \
+        "window[Find overlapping intervals within a window around an interval.]" \
+    ret=0
+    ;;
+  *)
+    _files
+    ;;
+esac
+
+return ret

plugins/debian/README.md

@@ -10,7 +10,7 @@ plugins=(... debian)
 
 ## Settings
 
-- `$apt_pref`: use apt or aptitude if installed, fallback is apt-get.
+- `$apt_pref`: use aptitude or apt if installed, fallback is apt-get.
 - `$apt_upgr`: use upgrade or safe-upgrade (for aptitude).
 
 Set `$apt_pref` and `$apt_upgr` to whatever command you want (before sourcing Oh My Zsh) to override this behavior.

plugins/debian/debian.plugin.zsh

@@ -1,13 +1,13 @@
-# Use apt or aptitude if installed, fallback is apt-get
+# Use aptitude or apt if installed, fallback is apt-get
 # You can just set apt_pref='apt-get' to override it.
 
 if [[ -z $apt_pref || -z $apt_upgr ]]; then
-    if [[ -e $commands[apt] ]]; then
-        apt_pref='apt'
-        apt_upgr='upgrade'
-    elif [[ -e $commands[aptitude] ]]; then
+    if [[ -e $commands[aptitude] ]]; then
         apt_pref='aptitude'
         apt_upgr='safe-upgrade'
+    elif [[ -e $commands[apt] ]]; then
+        apt_pref='apt'
+        apt_upgr='upgrade'
     else
         apt_pref='apt-get'
         apt_upgr='upgrade'

plugins/git/README.md

@@ -116,6 +116,7 @@ plugins=(... git)
 | gpf                  | git push --force-with-lease                                                                                                      |
 | gpf!                 | git push --force                                                                                                                 |
 | gpoat                | git push origin --all && git push origin --tags                                                                                  |
+| gpr                  | git pull --rebase                                                                                                                |
 | gpu                  | git push upstream                                                                                                                |
 | gpv                  | git push -v                                                                                                                      |
 | gr                   | git remote                                                                                                                       |

plugins/git/git.plugin.zsh

@@ -215,6 +215,7 @@ alias gpd='git push --dry-run'
 alias gpf='git push --force-with-lease'
 alias gpf!='git push --force'
 alias gpoat='git push origin --all && git push origin --tags'
+alias gpr='git pull --rebase'
 alias gpu='git push upstream'
 alias gpv='git push -v'
 

plugins/isodate/README.md

@@ -0,0 +1,22 @@
+# Isodate plugin
+
+**Maintainer:** [@Frani](https://github.com/frani)
+
+This plugin adds completion for the [ISO 8601](https://en.wikipedia.org/wiki/ISO_8601),
+as well as some aliases for common Date commands.
+
+To use it, add `isodate` to the plugins array in your zshrc file:
+
+```zsh
+plugins=(... isodate)
+```
+
+## Aliases
+
+| Alias         | Command                              | Description                                                                |
+|---------------|--------------------------------------|----------------------------------------------------------------------------|
+| isodate       | `date +%Y-%m-%dT%H:%M:%S%z`          | Display the current date with UTC offset and ISO 8601-2 extended format    |
+| isodate_utc   | `date -u +%Y-%m-%dT%H:%M:%SZ`        | Display the current date in UTC and ISO 8601-2 extended format             |
+| isodate_basic | `date -u +%Y%m%dT%H%M%SZ`            | Display the current date in UTC and ISO 8601 basic format                  |
+| unixstamp     | `date +%s`                           | Display the current date as a Unix timestamp (seconds since the Unix epoch)|
+| date_locale   | `date +"%c"`                         | Display the current date using the default locale's format                 |

plugins/isodate/isodate.plugin.zsh

@@ -0,0 +1,7 @@
+# work with date ISO 8601 easy
+
+alias isodate="date +%Y-%m-%dT%H:%M:%S%z"
+alias isodate_utc="date -u +%Y-%m-%dT%H:%M:%SZ"
+alias isodate_basic="date -u +%Y%m%dT%H%M%SZ"
+alias unixstamp="date +%s"
+alias date_locale="date +"%c""

plugins/mercurial/mercurial.plugin.zsh

@@ -63,3 +63,9 @@ function hgic() {
 function hgoc() {
     hg outgoing "$@" | grep "changeset" | wc -l
 }
+
+function hg_get_bookmark_name() {
+  if [ $(in_hg) ]; then
+    echo $(hg id -B)
+  fi
+}

plugins/samtools/README.md

@@ -0,0 +1,5 @@
+# Samtools plugin
+
+This plugin adds support for [samtools](http://www.htslib.org/):
+
+* Adds autocomplete options for all samtools sub commands.

plugins/samtools/_samtools

@@ -0,0 +1,40 @@
+#compdef samtools
+#autoload
+
+local curcontext="$curcontext" state line ret=1
+local -a _files
+
+_arguments -C \
+  '1: :->cmds' \
+  '2:: :->args' && ret=0
+
+case $state in
+  cmds)
+    _values "samtools command" \
+        "view[SAM<->BAM conversion]" \
+        "sort[sort alignment file]" \
+        "mpileup[multi-way pileup]" \
+        "depth[compute the depth]" \
+        "faidx[index/extract FASTA]" \
+        "tview[text alignment viewer]" \
+        "index[index alignment]" \
+        "idxstats[BAM index stats (r595 or later)]" \
+        "fixmate[fix mate information]" \
+        "flagstat[simple stats]" \
+        "calmd[recalculate MD/NM tags and '=' bases]" \
+        "merge[merge sorted alignments]" \
+        "rmdup[remove PCR duplicates]" \
+        "reheader[replace BAM header]" \
+        "cat[concatenate BAMs]" \
+        "bedcov[read depth per BED region]" \
+        "targetcut[cut fosmid regions (for fosmid pool only)]" \
+        "phase[phase heterozygotes]" \
+        "bamshuf[shuffle and group alignments by name]"
+    ret=0
+    ;;
+  *)
+    _files
+    ;;
+esac
+
+return ret

plugins/ubuntu/ubuntu.plugin.zsh

@@ -15,6 +15,9 @@ alias agli='apt list --installed'
 # List available updates only
 alias aglu='apt list --upgradable'
 
+alias acsp='apt-cache showpkg'
+compdef _acsp acsp='apt-cache showpkg'
+
 # superuser operations ######################################################
 
 alias afu='sudo apt-file update'