--- a/bin/backup-local Fri Jan 31 11:09:07 2020 -0500
+++ b/bin/backup-local Fri Jan 31 11:09:09 2020 -0500
@@ -2,7 +2,7 @@
set -euo pipefail
-restic --repo /backup/restic-repo \
+restic --repo /mnt/cryo/restic-ouroboros/repo \
--exclude-file=/home/sjl/src/dotfiles/restic/excludes.txt \
--password-file /home/sjl/.restic-password-local \
backup /home/sjl
--- a/bin/bootstrap.sh Fri Jan 31 11:09:07 2020 -0500
+++ b/bin/bootstrap.sh Fri Jan 31 11:09:09 2020 -0500
@@ -39,6 +39,7 @@
ensure_link "src/dotfiles/fish/functions" ".config/fish/functions"
ensure_link "src/dotfiles/gitconfig" ".gitconfig"
ensure_link "src/dotfiles/gitignore" ".gitignore"
+ensure_link "src/dotfiles/gnuplot" ".gnuplot"
ensure_link "src/dotfiles/hgignore" ".hgignore"
ensure_link "src/dotfiles/lisprc" ".lisprc"
ensure_link "src/dotfiles/lispwords" ".lispwords"
--- a/bin/disks Fri Jan 31 11:09:07 2020 -0500
+++ b/bin/disks Fri Jan 31 11:09:09 2020 -0500
@@ -2,7 +2,15 @@
set -euo pipefail
-lsblk -o name,mountpoint,model,label,size,fstype | egrep -v "^loop"
+lsblk -o name,mountpoint,model,label,size,fstype | grep -Pv "^loop" | awk '
+NR>1 && /^[a-zA-Z]/ { print "-----------------------------------------------------------------------------------------------------------------------" }
+ { print $0 }
+'
echo
echo
-df -h | egrep -v '^/dev/loop' | egrep -v tmpfs
+echo
+
+OUT=$(df -h)
+echo "$OUT" | head -1
+echo "$OUT" | head -1 | sed 's/./-/g'
+echo "$OUT" | tail +2 | grep -Pv '^/dev/loop' | grep -Pv tmpfs | sort -k6
--- a/bin/mangle-signature Fri Jan 31 11:09:07 2020 -0500
+++ b/bin/mangle-signature Fri Jan 31 11:09:09 2020 -0500
@@ -1,3 +1,3 @@
#!/usr/bin/env bash
-cat
+sed -Ee 's/^-- $/-- /'
--- a/bin/rl Fri Jan 31 11:09:07 2020 -0500
+++ b/bin/rl Fri Jan 31 11:09:09 2020 -0500
@@ -2,6 +2,6 @@
set -euo pipefail
-restic --repo /backup/restic-repo \
+restic --repo /mnt/cryo/restic-ouroboros/repo \
--password-file /home/sjl/.restic-password-local \
"$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gnuplot Fri Jan 31 11:09:09 2020 -0500
@@ -0,0 +1,9 @@
+set terminal qt noraise
+set samples 1000
+
+tau = 2 * pi
+e = 2.71828182845905
+r2 = sqrt(2.0)
+
+min(a, b) = (a<b) ? a : b
+max(a, b) = (a>b) ? a : b
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lisp/lines.lisp Fri Jan 31 11:09:09 2020 -0500
@@ -0,0 +1,351 @@
+(eval-when (:compile-toplevel :load-toplevel :execute)
+ (ql:quickload '(:adopt :cl-ppcre :with-user-abort) :silent t))
+
+(defpackage :lines
+ (:use :cl)
+ (:export :toplevel :*ui*))
+
+(in-package :lines)
+
+;; TODO: Optimize by eliminating collection when all matchers are in order.
+
+;;;; Configuration ------------------------------------------------------------
+(defparameter *version* "1.0.0")
+(defparameter *index-base* 0)
+(defparameter *include-numbers* nil)
+
+
+;;;; Functionality ------------------------------------------------------------
+(defclass matcher ()
+ ((designator :type string :initarg :designator :accessor designator)))
+
+(defmethod print-object ((o matcher) stream)
+ (print-unreadable-object (o stream :type t)
+ (format stream "~S" (designator o))))
+
+(defgeneric matches-line-p (matcher line-number))
+(defgeneric map-matching-lines (matcher function min max))
+(defgeneric maximum (matcher))
+
+
+(defclass single-line-matcher (matcher)
+ ((n :type (integer 0) :initarg :n :accessor n)))
+
+(defmethod matches-line-p ((matcher single-line-matcher) i)
+ (= (n matcher) i))
+
+(defmethod map-matching-lines ((matcher single-line-matcher) function min max)
+ (declare (ignore min max))
+ (funcall function (n matcher)))
+
+(defmethod maximum ((matcher single-line-matcher))
+ (n matcher))
+
+
+(defclass range-matcher (matcher)
+ ((m :type (or null (integer 0)) :initarg :m :accessor m)
+ (n :type (or null (integer 0)) :initarg :n :accessor n)))
+
+(defmethod matches-line-p ((matcher range-matcher) i)
+ (let ((m (m matcher))
+ (n (n matcher)))
+ (cond ((null m) (if (null n)
+ t
+ (<= i n)))
+ ((null n) (<= m i))
+ (t (<= m i n)))))
+
+(defmethod map-matching-lines ((matcher range-matcher) function min max)
+ (loop :with m = (or (m matcher) min)
+ :with n = (or (n matcher) max)
+ :for i :from (max m min) :to (min n max)
+ :do (funcall function i)))
+
+(defmethod maximum ((matcher range-matcher))
+ (n matcher))
+
+
+(defclass modulo-matcher (matcher)
+ ((n :type (integer 0) :initarg :n :accessor n)
+ (modulus :type (integer 1) :initarg :modulus :accessor modulus)))
+
+(defmethod matches-line-p ((matcher modulo-matcher) i)
+ (= (mod i (modulus matcher))
+ (n matcher)))
+
+(defmethod map-matching-lines ((matcher modulo-matcher) function min max)
+ (loop
+ :with n = (n matcher)
+ :with modulus = (modulus matcher)
+ :with start = (if (< n min)
+ (+ n modulus)
+ n)
+ :for i :from start :to max :by modulus
+ :do (funcall function i)))
+
+(defmethod maximum ((matcher modulo-matcher))
+ nil)
+
+
+(defun parse-single-line-designator (designator)
+ (ppcre:register-groups-bind
+ ((#'parse-integer n))
+ ("^(\\d+)$" designator)
+ (make-instance 'single-line-matcher :designator designator :n n)))
+
+(defun parse-range-designator (designator)
+ (ppcre:register-groups-bind
+ ((#'parse-integer m n))
+ ("^(\\d+)?-(\\d+)?$" designator)
+ (when (and m n)
+ (assert (<= m n) ()
+ "Bad line range designator ~S: start (~D) must not be greater than end (~D)."
+ designator m n))
+ (make-instance 'range-matcher :designator designator :m m :n n)))
+
+(defun parse-modulo-designator (designator)
+ (ppcre:register-groups-bind
+ ((#'parse-integer n modulus))
+ ("^(\\d+)?m(\\d+)$" designator)
+ (when (null n)
+ (setf n 0))
+ (assert (< n modulus) ()
+ "Bad modulo designator ~S: offset (~D) must be less than modulus (~D)."
+ designator n modulus)
+ (make-instance 'modulo-matcher :designator designator :n n :modulus modulus)))
+
+(defun parse-line-designator (designator)
+ (or (parse-single-line-designator designator)
+ (parse-range-designator designator)
+ (parse-modulo-designator designator)
+ (error "Could not parse line designator ~S" designator)))
+
+(defun parse-line-designators (designators)
+ (mapcar #'parse-line-designator (ppcre:split "," designators)))
+
+
+(defun dbg (&rest args)
+ (apply #'format *error-output* args)
+ (finish-output *error-output*))
+
+(defun compute-limit (matchers)
+ (let ((maxes (mapcar #'maximum matchers)))
+ (unless (some #'null maxes)
+ (reduce #'max maxes))))
+
+(defun collect-lines (matchers)
+ (loop
+ :with limit = (compute-limit matchers)
+ :with min = *index-base*
+ :with max = nil
+ :with lines = (make-hash-table)
+ :for i :from min
+ :for line = (read-line *standard-input* nil)
+ :while line
+ :while (or (null limit) (<= i limit))
+ :do (progn (setf max i)
+ (dolist (matcher matchers)
+ (when (matches-line-p matcher i)
+ (setf (gethash i lines) line))))
+ :finally (return (values lines min max))))
+
+(defun run (line-designators)
+ (let ((matchers (parse-line-designators line-designators))
+ (include-numbers *include-numbers*))
+ (multiple-value-bind (lines min max) (collect-lines matchers)
+ (dolist (matcher matchers)
+ (map-matching-lines matcher
+ (lambda (i)
+ (when include-numbers
+ (format *standard-output* "~D " i))
+ (write-line (gethash i lines)))
+ min max))))
+ (values))
+
+
+;;;; User Interface -----------------------------------------------------------
+(defmacro defparameters (parameters values-form)
+ `(progn
+ ,@(loop :for parameter :in parameters
+ :collect `(defparameter ,parameter nil))
+ (setf (values ,@parameters) ,values-form)
+ ',parameters))
+
+(defun make-boolean-options
+ (name &key
+ (name-no (intern (concatenate 'string (string 'no-) (string name))))
+ long
+ (long-no (when long (format nil "no-~A" long)))
+ short
+ (short-no (when short (char-upcase short)))
+ (result-key name)
+ help
+ help-no
+ manual
+ manual-no
+ initial-value)
+ (values (adopt:make-option name
+ :result-key result-key
+ :long long
+ :short short
+ :help help
+ :manual manual
+ :initial-value initial-value
+ :reduce (constantly t))
+ (adopt:make-option name-no
+ :result-key result-key
+ :long long-no
+ :short short-no
+ :help help-no
+ :manual manual-no
+ :reduce (constantly nil))))
+
+
+(defparameters (*option-debug* *option-no-debug*)
+ (make-boolean-options 'debug
+ :long "debug"
+ :short #\d
+ :help "Enable the Lisp debugger."
+ :help-no "Disable the Lisp debugger (default)."))
+
+(defparameter *option-help*
+ (adopt:make-option 'help
+ :help "Display help and exit."
+ :long "help"
+ :short #\h
+ :reduce (constantly t)))
+
+(defparameter *option-version*
+ (adopt:make-option 'version
+ :help "Display version information and exit."
+ :long "version"
+ :reduce (constantly t)))
+
+(defparameter *option-one-based*
+ (adopt:make-option 'one-based
+ :result-key 'index-base
+ :help "Start numbering lines at 1."
+ :short #\1
+ :long "one"
+ :reduce (constantly 1)))
+
+(defparameter *option-zero-based*
+ (adopt:make-option 'zero-based
+ :result-key 'index-base
+ :initial-value 0
+ :help "Start numbering lines at 0 (default)."
+ :short #\0
+ :long "zero"
+ :reduce (constantly 0)))
+
+(defparameter *option-other-base*
+ (adopt:make-option 'other-base
+ :result-key 'index-base
+ :help "Start numbering lines at N."
+ :parameter "N"
+ :short #\s
+ :long "start"
+ :key #'parse-integer
+ :reduce #'adopt:last))
+
+(defparameters (*option-include-numbers* *option-no-include-numbers*)
+ (make-boolean-options 'include-numbers
+ :long "number"
+ :short #\n
+ :help "Add line numbers to the output."
+ :help-no "Do not add line number to the output (default)."))
+
+
+(adopt:define-string *help-text*
+ "lines takes a string denoting which lines to print, and prints those lines ~
+ of standard input.")
+
+(defparameter *examples*
+ '(("Print line 1234:"
+ . "cat log.txt | lines 1234")
+ ("Print line 2, then line 1:"
+ . "cat log.txt | lines 2,1")
+ ("Print lines 6, 12, 100-200, and 999+ (1-indexed):"
+ . "cat log.txt | lines -1 6,12,100-200,999-")
+ ("Print lines 0, 2, 4, 6, …:"
+ . "cat log.txt | lines m2")
+ ("Print the third line of every set of four lines:"
+ . "cat foo.fastq | lines 3m4")))
+
+
+(defparameter *ui*
+ (adopt:make-interface
+ :name "lines"
+ :usage "[OPTIONS] LINE-DESIGNATORS"
+ :summary "print designated lines of standard input"
+ :help *help-text*
+ :examples *examples*
+ :contents (list
+ *option-help*
+ *option-version*
+ *option-debug*
+ *option-no-debug*
+ (adopt:make-group 'line-numbering
+ :title "Line Numbering"
+ :options (list
+ *option-one-based*
+ *option-zero-based*
+ *option-other-base*
+ *option-include-numbers*
+ *option-no-include-numbers*)))))
+
+
+(defmacro without-debugger (&body body)
+ `(multiple-value-prog1
+ (progn
+ #+sbcl (sb-ext:disable-debugger)
+ (progn ,@body))
+ (progn
+ #+sbcl (sb-ext:enable-debugger))))
+
+(defmacro exit-on-error (&body body)
+ `(without-debugger
+ (handler-case (progn ,@body)
+ (error (c) (adopt:print-error-and-exit c)))))
+
+(defmacro exit-on-error-unless (expr &body body)
+ `(if ,expr
+ (progn ,@body)
+ (exit-on-error ,@body)))
+
+(defmacro exit-on-ctrl-c (&body body)
+ `(handler-case
+ (with-user-abort:with-user-abort (progn ,@body))
+ (with-user-abort:user-abort () (adopt:exit 130))))
+
+
+(defun toplevel ()
+ (exit-on-ctrl-c
+ (multiple-value-bind (arguments options) (adopt:parse-options-or-exit *ui*)
+ (exit-on-error-unless (gethash 'debug options)
+ (cond
+ ((gethash 'help options) (adopt:print-help-and-exit *ui*))
+ ((gethash 'version options) (write-line *version*) (adopt:exit))
+ ((null arguments) (error "LINE-DESIGNATORS are required."))
+ (t (destructuring-bind (line-designators . more) arguments
+ (when more
+ (error "Unrecognized command line arguments: ~S" more))
+ (let ((*index-base* (gethash 'index-base options))
+ (*include-numbers* (gethash 'include-numbers options)))
+ (run line-designators)))))))))
+
+
+#; Scratch --------------------------------------------------------------------
+
+(let ((*standard-input* (make-string-input-stream
+"0 a foo
+1 b bar
+2 c baz
+3 d hello
+4 a world
+5 b yes
+6 c this
+7 d is
+8 a cat
+9 b meow")))
+ (run "4m4"))
--- a/vim/custom-dictionary.utf-8.add Fri Jan 31 11:09:07 2020 -0500
+++ b/vim/custom-dictionary.utf-8.add Fri Jan 31 11:09:09 2020 -0500
@@ -299,3 +299,7 @@
Phosphorylation
iterate's
memoization
+gnuplot
+Illumina
+Phred
+FastQC