# HG changeset patch
# User Steve Losh <steve@stevelosh.com>
# Date 1580486949 18000
# Node ID 2a7f613576bc5065e52a8684a50f87b7fa8cf019
# Parent  d3f648295e4f32c131f59d1d78ad31b3c113fc85# Parent  d4732eec7b9d696a5db1521506efba590a3f6b9a
Merge.

diff -r d3f648295e4f -r 2a7f613576bc bin/backup-local
--- 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
diff -r d3f648295e4f -r 2a7f613576bc bin/bootstrap.sh
--- 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"
diff -r d3f648295e4f -r 2a7f613576bc bin/disks
--- 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
diff -r d3f648295e4f -r 2a7f613576bc bin/mangle-signature
--- 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/^-- $/--  /'
diff -r d3f648295e4f -r 2a7f613576bc bin/rl
--- 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 \
        "$@"
diff -r d3f648295e4f -r 2a7f613576bc gnuplot
--- /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
diff -r d3f648295e4f -r 2a7f613576bc lisp/lines.lisp
--- /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"))
diff -r d3f648295e4f -r 2a7f613576bc vim/custom-dictionary.utf-8.add
--- 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