first commit

first commit


add IPAP processing script, scripts/proc-13Cm-ipap.com

#!/bin/csh

rm *.fid *.ft2

bruk2pipe -in ./ser \
  -bad 0.0 -ext -aswap -AMX -decim 1312 -dspfvs 21 -grpdly 76  \
  -xN              4096  -yN               1024  \
  -xT              2048  -yT                512  \
  -xMODE            DQD  -yMODE        Complex  \
  -xSW        15243.902  -ySW         7407.407  \
  -xOBS         950.454  -yOBS         238.996  \
  -xCAR           4.771  -yCAR          22.740  \
  -xLAB              1H  -yLAB             13C  \
  -ndim               2  -aq2D         Complex  \
  -out ./test.fid -verb -ov

# splits the original ser file (test.fid) of a ch13 ipap-ct-hsqc
# with four interleaved experimients
# into four separate data sets
# A(0), B(1/6J), C(1/3J), D(1/2J)
# Georg Kontaxis and Ad Bax, 22.Feb.2001

set matA = ( 1 0 \
             0 1 \
             0 0 \
             0 0 \
             0 0 \
             0 0 \
             0 0 \
             0 0 )

set matB = ( 0 0 \
             0 0 \
             1 0 \
             0 1 \
             0 0 \
             0 0 \
             0 0 \
             0 0 )

set matC = ( 0 0 \
             0 0 \
             0 0 \
             0 0 \
             1 0 \
             0 1 \
             0 0 \
             0 0 )

set matD = ( 0 0 \
             0 0 \
             0 0 \
             0 0 \
             0 0 \
             0 0 \
             1 0 \
             0 1 )

nmrPipe -in test.fid \
| nmrPipe -fn QMIX -ic 8 -oc 2 -cList $matA -time \
  -out ./A.fid -verb -ov

nmrPipe -in test.fid \
| nmrPipe -fn QMIX -ic 8 -oc 2 -cList $matB -time \
  -out ./B.fid -verb -ov

nmrPipe -in test.fid \
| nmrPipe -fn QMIX -ic 8 -oc 2 -cList $matC -time \
  -out ./C.fid -verb -ov

nmrPipe -in test.fid \
| nmrPipe -fn QMIX -ic 8 -oc 2 -cList $matD -time \
  -out ./D.fid -verb -ov

# lc.com
# Georg Kontaxis and Ad Bax, 26.Feb.2001
# script to generate linear combinations of ipap-ct-hsqc datasets
# for separation of ch3 multiplet into four subspectra
# note that the coefficients may need further adjustment by exp(2D/T2)
# to account for 13C T2 relaxation

addNMR -in1 A.fid -in2 D.fid -out A+D.fid -c1 1.0 -c2 1.14 -verb
addNMR -in1 A.fid -in2 D.fid -out A-D.fid -c1 1.0 -c2 1.14 -sub -verb

addNMR -in1 B.fid -in2 C.fid -out B+C.fid -c1 1.02 -c2 1.07 -verb
addNMR -in1 B.fid -in2 C.fid -out B-C.fid -c1 1.02 -c2 1.07 -sub -verb

# most downfield line
addNMR -in1 A+D.fid -in2 B+C.fid -out A+2B+2C+D.fid -c1 1.0 -c2 2.0 -verb

# center upfield line
addNMR -in1 A+D.fid -in2 B+C.fid -out A-B-C+D.fid -sub -c1 1.0 -c2 1.0 -verb

# center downfield line
addNMR -in1 A-D.fid -in2 B-C.fid -out A+B-C-D.fid -c1 1.0 -c2 1.0 -verb

# most upfield line
addNMR -in1 A-D.fid -in2 B-C.fid -out A-2B+2C-D.fid -sub -c1 1.0 -c2 2.0 -verb

#!/bin/csh

foreach spec (A-2B+2C-D  A+2B+2C+D  A-B-C+D  A+B-C-D)
   echo Processing Spectrum $spec

   nmrPipe -in $spec.fid \
   #| nmrPipe  -fn POLY -time                           \
   | nmrPipe  -fn SOL \
   | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
   | nmrPipe  -fn ZF -zf 2                             \
   | nmrPipe  -fn FT -verb                             \
   | nmrPipe  -fn PS -p0 91.0 -p1 0.0 -di             \
   | nmrPipe  -fn BASE -nw 100 -nl 8ppm -2ppm \
   | nmrPipe  -fn EXT -x1 2.2ppm -xn -0.5ppm -sw                       \
   | nmrPipe  -fn TP                                   \
   | nmrPipe  -fn LP -ps0-0 -fb \
   | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
   | nmrPipe  -fn ZF -zf 2                         \
   | nmrPipe  -fn FT -alt -verb                        \
   | nmrPipe  -fn PS -p0 0.0 -p1 0.0 -di               \
#   | nmrPipe  -fn TP                                   \
#   | nmrPipe  -fn POLY -auto                           \
      -ov -out $spec.ft2
end

rm *.fid

error: pathspec 'scripts/proc-13Cm-ipap.com' did not match any file(s) known to git


Added recipe for dorkly

Added recipe for dorkly

a[contains(@data-ga-category,'Pagination') and text() = 'Next']

error: pathspec 'recipes/dorkly.com' did not match any file(s) known to git


Filter for nakedsecurity.sophos.com

Filter for nakedsecurity.sophos.com

Filter for security feed https://nakedsecurity.sophos.com/feed/

error: pathspec 'recipes/nakedsecurity.sophos.com' did not match any file(s) known to git


Script to create shareable images (shared libraries in Unixly terms) on VMS.

$! MKSHARED.COM -- script to created shareable images on VMS
$!
$! No command line parameters.  This should be run at the start of the source
$! tree (the same directory where one finds INSTALL.VMS).
$!
$! Input:	[.UTIL]LIBEAY.NUM,[.AXP.EXE.CRYPTO]LIBCRYPTO.OLB
$!		[.UTIL]SSLEAY.NUM,[.AXP.EXE.SSL]LIBSSL.OLB
$! Output:	[.AXP.EXE.CRYPTO]LIBCRYPTO.OPT,.MAP,.EXE
$!		[.AXP.EXE.SSL]LIBSSL.OPT,.MAP,.EXE
$!
$! So far, tests have only been made on VMS for Alpha.  VAX will come in time.
$! ===========================================================================
$
$! ----- Prepare info for processing: version number and file info
$ gosub read_version_info
$ if libver .eqs. ""
$ then
$   write sys$error "ERROR: Couldn't find any library version info..."
$   exit
$ endif
$
$ if f$getsyi("CPU") .ge. 128
$ then
$   libid  = "Crypto"
$   libnum = "[.UTIL]LIBEAY.NUM"
$   libdir = "[.AXP.EXE.CRYPTO]"
$   libolb = "''libdir'LIBCRYPTO.OLB"
$   libopt = "''libdir'LIBCRYPTO.OPT"
$   libmap = "''libdir'LIBCRYPTO.MAP"
$   libgoal= "''libdir'LIBCRYPTO.EXE"
$   libref = ""
$   gosub create_axp_shr
$   libid  = "SSL"
$   libnum = "[.UTIL]SSLEAY.NUM"
$   libdir = "[.AXP.EXE.SSL]"
$   libolb = "''libdir'LIBSSL.OLB"
$   libopt = "''libdir'LIBSSL.OPT"
$   libmap = "''libdir'LIBSSL.MAP"
$   libgoal= "''libdir'LIBSSL.EXE"
$   libref = "[.AXP.EXE.CRYPTO]LIBCRYPTO.EXE"
$   gosub create_axp_shr
$ else
$   libtit = "CRYPTO_TRANSFER_VECTOR"
$   libid  = "Crypto"
$   libnum = "[.UTIL]LIBEAY.NUM"
$   libdir = "[.VAX.EXE.CRYPTO]"
$   libmar = "''libdir'LIBCRYPTO.MAR"
$   libolb = "''libdir'LIBCRYPTO.OLB"
$   libopt = "''libdir'LIBCRYPTO.OPT"
$   libobj = "''libdir'LIBCRYPTO.OBJ"
$   libmap = "''libdir'LIBCRYPTO.MAP"
$   libgoal= "''libdir'LIBCRYPTO.EXE"
$   libref = ""
$   libvec = "LIBCRYPTO"
$   gosub create_vax_shr
$   libtit = "SSL_TRANSFER_VECTOR"
$   libid  = "SSL"
$   libnum = "[.UTIL]SSLEAY.NUM"
$   libdir = "[.VAX.EXE.SSL]"
$   libmar = "''libdir'LIBSSL.MAR"
$   libolb = "''libdir'LIBSSL.OLB"
$   libopt = "''libdir'LIBSSL.OPT"
$   libobj = "''libdir'LIBSSL.OBJ"
$   libmap = "''libdir'LIBSSL.MAP"
$   libgoal= "''libdir'LIBSSL.EXE"
$   libref = "[.VAX.EXE.CRYPTO]LIBCRYPTO.EXE"
$   libvec = "LIBSSL"
$   gosub create_vax_shr
$ endif
$ exit
$
$! ----- Soubroutines to actually build the shareable libraries
$! The way things work, there's a main shareable library creator for each
$! supported architecture, which is called from the main code above.
$! The creator will define a number of variables to tell the next levels of
$! subroutines what routines to use to write to the option files, call the
$! main processor, read_func_num, and when that is done, it will write version
$! data at the end of the .opt file, close it, and link the library.
$!
$! read_func_num reads through a .num file and calls the writer routine for
$! each line.  It's also responsible for checking that order is properly kept
$! in the .num file, check that each line applies to VMS and the architecture,
$! and to fill in "holes" with dummy entries.
$!
$! The creator routines depend on the following variables:
$! libnum	The name of the .num file to use as input
$! libolb	The name of the object library to build from
$! libid	The identification string of the shareable library
$! libopt	The name of the .opt file to write
$! libtit	The title of the assembler transfer vector file (VAX only)
$! libmar	The name of the assembler transfer vector file (VAX only)
$! libmap	The name of the map file to write
$! libgoal	The name of the shareable library to write
$! libref	The name of a shareable library to link in
$!
$! read_func_num depends on the following variables from the creator:
$! libwriter	The name of the writer routine to call for each .num file line
$! -----
$
$! ----- Subroutines for AXP
$! -----
$! The creator routine
$ create_axp_shr:
$   open/write opt 'libopt'
$   write opt "identification=""",libid," ",libverstr,""""
$   write opt libolb,"/lib"
$   if libref .nes. "" then write opt libref,"/SHARE"
$   write opt "SYMBOL_VECTOR=(-"
$   libfirstentry := true
$   libwrch   := opt
$   libwriter := write_axp_transfer_entry
$   textcount = 0
$   gosub read_func_num
$   write opt ")"
$   write opt "GSMATCH=",libvmatch,",",libver
$   close opt
$   link/map='libmap'/full/share='libgoal' 'libopt'/option
$   return
$
$! The record writer routine
$ write_axp_transfer_entry:
$   if libentry .eqs. ".dummy" then return
$   if info_kind .eqs. "VARIABLE"
$   then
$     pr:=DATA
$   else
$     pr:=PROCEDURE
$   endif
$   textcount_this = f$length(pr) + f$length(libentry) + 5
$   if textcount + textcount_this .gt. 1024
$   then
$     write opt ")"
$     write opt "SYMBOL_VECTOR=(-"
$     textcount = 16
$     libfirstentry := true
$   endif
$   if libfirstentry
$   then
$     write 'libwrch' "    ",libentry,"=",pr," -"
$   else
$     write 'libwrch' "    ,",libentry,"=",pr," -"
$   endif
$   libfirstentry := false
$   textcount = textcount + textcount_this
$   return
$
$! ----- Subroutines for AXP
$! -----
$! The creator routine
$ create_vax_shr:
$   open/write mar 'libmar'
$   type sys$input:/out=mar:
;
; Transfer vector for VAX shareable image
;
$   write mar "	.TITLE ",libtit
$   write mar "	.IDENT /",libid,"/"
$   type sys$input:/out=mar:
;
; Define macro to assist in building transfer vector entries.  Each entry
; should take no more than 8 bytes.
;
	.MACRO FTRANSFER_ENTRY routine
	.ALIGN QUAD
	.TRANSFER routine
	.MASK	routine
	JMP	routine+2
	.ENDM TRANSFER_ENTRY
;
; Place entries in own program section.
;
$   write mar "	.PSECT $$",libvec,"QUAD,PIC,USR,CON,REL,LCL,SHR,EXE,RD,NOWRT"
$   write mar libvec,"_xfer:"
$   libwrch   := mar
$   libwriter := write_vax_ftransfer_entry
$   gosub read_func_num
$   type sys$input:/out=mar:
;
; Allocate extra storage at end of vector to allow for expansion.
;
$   write mar "	.BLKB 32768-<.-",libvec,"_xfer>	; 64 pages total."
$   libwriter := write_vax_vtransfer_entry
$   gosub read_func_num
$   write mar "	.END"
$   close mar
$   open/write opt 'libopt'
$   write opt "identification=""",libid," ",libverstr,""""
$   write opt libobj
$   write opt libolb,"/lib"
$   if libref .nes. "" then write opt libref,"/SHARE"
$   type sys$input:/out=opt:
!
! Ensure transfer vector is at beginning of image
!
CLUSTER=FIRST
$   write opt "COLLECT=FIRST,$$",libvec
$   write opt "GSMATCH=",libvmatch,",",libver
$   type sys$input:/out=opt:
!
! make psects nonshareable so image can be installed.
!
PSECT_ATTR=$CHAR_STRING_CONSTANTS,NOWRT
$   libwrch   := opt
$   libwriter := write_vax_psect_attr
$   gosub read_var_num
$   close opt
$   macro/obj='libobj' 'libmar'
$   link/map='libmap'/full/share='libgoal' 'libopt'/option
$   return
$
$! The record writer routine for VAX functions
$ write_vax_ftransfer_entry:
$   if info_kind .nes. "FUNCTION" then return
$   if libentry .eqs ".dummy"
$   then
$     write 'libwrch' "	.BLKB 8" ! Dummy is zeroes...
$   else
$     write 'libwrch' "	FTRANSFER_ENTRY ",libentry
$   endif
$   return
$! The record writer routine for VAX variables (should never happen!)
$ write_vax_psect_attr:
$   if info_kind .nes. "VARIABLE" then return
$   if libentry .eqs ".dummy" then return
$   write 'libwrch' "PSECT_ATTR=",libentry,",NOSHR"
$   return
$
$! ----- Common subroutines
$! -----
$! The .num file reader.  This one has great responsability.
$ read_func_num:
$   open libnum 'libnum'
$   goto read_nums
$
$ read_nums:
$   libentrynum=0
$   liblastentry:=false
$   entrycount=0
$   loop:
$     read/end=loop_end/err=loop_end libnum line
$     entrynum=f$int(f$element(1," ",f$edit(line,"COMPRESS,TRIM")))
$     entryinfo=f$element(2," ",f$edit(line,"COMPRESS,TRIM"))
$     curentry=f$element(0," ",f$edit(line,"COMPRESS,TRIM"))
$     info_exist=f$element(0,":",entryinfo)
$     info_platforms=","+f$element(1,":",entryinfo)+","
$     info_kind=f$element(2,":",entryinfo)
$     info_algorithms=","+f$element(3,":",entryinfo)+","
$     if info_exist .eqs. "NOEXIST" then goto loop
$     truesum = 0
$     falsesum = 0
$     negatives = 1
$     plat_i = 0
$     loop1:
$       plat_entry = f$element(plat_i,",",info_platforms)
$       plat_i = plat_i + 1
$       if plat_entry .eqs. "" then goto loop1
$       if plat_entry .nes. ","
$       then
$         if f$extract(0,1,plat_entry) .nes. "!" then negatives = 0
$         if f$getsyi("CPU") .lt. 128
$         then
$           if plat_entry .eqs. "EXPORT_VAR_AS_FUNCTION" then -
$             truesum = truesum + 1
$           if plat_entry .eqs. "!EXPORT_VAR_AS_FUNCTION" then -
$             falsesum = falsesum + 1
$         endif
$         if plat_entry .eqs. "VMS" then truesum = truesum + 1
$         if plat_entry .eqs. "!VMS" then falsesum = falsesum + 1
$       endif
$     endloop1:
$!DEBUG!$     if info_platforms - "EXPORT_VAR_AS_FUNCTION" .nes. info_platforms
$!DEBUG!$     then
$!DEBUG!$       write sys$output line
$!DEBUG!$       write sys$output "        truesum = ",truesum,-
$!DEBUG!		", negatives = ",negatives,", falsesum = ",falsesum
$!DEBUG!$     endif
$     if falsesum .ne. 0 then goto loop
$     if truesum+negatives .eq. 0 then goto loop
$     alg_i = 0
$     loop2:
$       alg_entry = f$element(alg_i,",",info_algorithms)
$	alg_i = alg_i + 1
$       if alg_entry .eqs. "" then goto loop2
$       if alg_entry .nes. ","
$       then
$         if alg_entry .eqs. "KRB5" then goto loop ! Special for now
$         if f$trnlnm("OPENSSL_NO_"+alg_entry) .nes. "" then goto loop
$       endif
$     endloop2:
$     if info_platforms - "EXPORT_VAR_AS_FUNCTION" .nes. info_platforms
$     then
$!DEBUG!$     write sys$output curentry," ; ",entrynum," ; ",entryinfo
$     endif
$   redo:
$     next:=loop
$     tolibentry=curentry
$     if libentrynum .ne. entrynum
$     then
$       entrycount=entrycount+1
$       if entrycount .lt. entrynum
$       then
$!DEBUG!$         write sys$output "Info: entrycount: ''entrycount', entrynum: ''entrynum' => 0"
$         tolibentry=".dummy"
$         next:=redo
$       endif
$       if entrycount .gt. entrynum
$       then
$         write sys$error "Decreasing library entry numbers!  Can't continue"
$         write sys$error """",line,""""
$         close libnum
$         return
$       endif
$       libentry=tolibentry
$!DEBUG!$       write sys$output entrycount," ",libentry," ",entryinfo
$       if libentry .nes. "" .and. libwriter .nes. "" then gosub 'libwriter'
$     else
$       write sys$error "Info: ""''curentry'"" is an alias for ""''libentry'"".  Overriding..."
$     endif
$     libentrynum=entrycount
$     goto 'next'
$   loop_end:
$   close libnum
$   return
$
$! The version number reader
$ read_version_info:
$   libver = ""
$   open/read vf [.CRYPTO]OPENSSLV.H
$   loop_rvi:
$     read/err=endloop_rvi/end=endloop_rvi vf rvi_line
$     if rvi_line - "SHLIB_VERSION_NUMBER """ .eqs. rvi_line then -
	goto loop_rvi
$     libverstr = f$element(1,"""",rvi_line)
$     libvmajor = f$element(0,".",libverstr)
$     libvminor = f$element(1,".",libverstr)
$     libvedit = f$element(2,".",libverstr)
$     libvpatch = f$cvui(0,8,f$extract(1,1,libvedit)+"@")-f$cvui(0,8,"@")
$     libvedit = f$extract(0,1,libvedit)
$     libver = f$string(f$int(libvmajor)*100)+","+-
	f$string(f$int(libvminor)*100+f$int(libvedit)*10+f$int(libvpatch))
$     if libvmajor .eqs. "0"
$     then
$       libvmatch = "EQUAL"
$     else
$       ! Starting with the 1.0 release, backward compatibility should be
$       ! kept, so switch over to the following
$       libvmatch = "LEQUAL"
$     endif
$   endloop_rvi:
$   close vf
$   return

error: pathspec 'VMS/mkshared.com' did not match any file(s) known to git


update

update


adding cname

adding cname

remote: Support for password authentication was removed on August 13, 2021.
remote: Please see https://docs.github.com/en/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
fatal: Authentication failed for 'https://github.com/anthonyrhook/hookedonus.git/'


adding an example nginx config with gunicorn

# config for a flask app

upstream zulu {
    # proxying to gunicorn running on localhost
	server 127.0.0.1:5000;
}

server {
	server_name zulu.example.com;
	root /path/to/www/zulu;
	index index.html;

        try_files  $uri/index.html $uri.html $uri @zulu;

        location @zulu {
	      proxy_set_header  X-Real-IP        $remote_addr;
	      proxy_set_header  X-Forwarded-For  $proxy_add_x_forwarded_for;
	      proxy_set_header  Host             $http_host;
	      proxy_redirect    off;
	      proxy_intercept_errors on;

	      # proxy cache config
	      client_max_body_size       10m;
	      client_body_buffer_size    256k;

	      proxy_buffer_size          32k;
	      proxy_buffers              8 64k;
	      proxy_busy_buffers_size    128k;
	      proxy_temp_file_write_size 128k;

	      proxy_cache zulu-cache;
              proxy_cache_valid  200 302  10s;
              proxy_cache_valid  404      10s;
	      proxy_cache_key         "$scheme$host$request_uri";

	      # the line below will bypass and cache requests with the header
	      # X-Whattup-Yo
	      # See http://wiki.nginx.org/HttpProxyModule#proxy_cache_bypass
	      # and http://wiki.nginx.org/HttpCoreModule#.24http_HEADER
	      proxy_cache_bypass $http_something_secret;

	      # next line should keep us from having stampeding herd problems
	      proxy_cache_use_stale updating error timeout;

	      proxy_pass        http://zulu;
        }
        error_page   500 502 503 504  /500.html;
        location = /500.html {
                 root /path/to/www/zulu;
        }
        error_page   404  /404.html;
        location = /404.html {
                 root /path/to/www/zulu;
        }

        # rewrites can go here
        # rewrite ^/old.html /new/file.html permanent;
}

error: pathspec 'nginx/zulu.example.com' did not match any file(s) known to git


initial upload

initial upload

remote: Support for password authentication was removed on August 13, 2021.
remote: Please see https://docs.github.com/en/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
fatal: Authentication failed for 'https://github.com/lexologics/angular-webpack-project-setup.git/'