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minimal installation

CONFIG for PY4AMI A) everyone needs a config.ini file in their directory structure B) everyone needs environment variable $PYAMI_HOME

  • clone py4ami from github
  • verify it contains config.ini.master
  • make a subdirectory pyami under your home directory
  • cd ~ on Unix/MAC
  • mkdir pyami
  • copy the master config file to this directory
  • cp pyami/config.ini.master pyami/
  • set PYAMI_HOME to this directory
  • test with echo $PYAMI_HOME giving: /Users/pm286/pyami/

The rest of this file is for users who wish to change configuration

Config files and symbols

(** some of this may be out of date) Although pyami can be used with explict names

pyami -p /user/monty/python/myfiles/plants

it is easier and less error prone to use symbols such as

plants.p = /user/monty/python/myfiles/plants
pyami -p ${plants.p}

These symbols are defined in config files (normally *.ini) which are based on Python config files (see https://docs.python.org/3/library/configparser.html ). Python only uses a single file which defines symbols in sections and can be recursive. We extend this with multiple files to create a network of chained INI files, supporting projects and dictionaries. The extra rules are:

  • any *_ini symbol points to another config file which is then interpreted , thus building up a network (cyclic links are forbidden).
  • all variables are stored in the SymbolIni class and can be re-used on the commandline
  • pyami variables referenced inside config files (but not ouside) are referenced by the syntax $${...} to avoid clashing with python variables

predefined variables

The pyami system has a network of variables referencing standard dictiomaries and test/reference projects. These are rooted from:

pyami/pyami/config.ini

in the pyami distribution. Any user can rely on these variables.

They point to repository trees which must be separately checked out if they are to be used.

personal config.ini

The user needs a minimal config.ini file to tell the system where:

  • the downloaded pyami code is
  • the dictionary repositories are
  • any of the standard data/text repositories are.

She also needs to set the PYAMI_HOME environment variable to point to the directory containing her config.ini file

typical config.ini

# USER configuration file
#========================

# The symbols in DIRS and CODE point to communal resources, especially dictionaries, 
#   projects and parameters

; NOTE. All files use forward slash even on Windows
; use slash (/) to separate filename components, we will convert to file-separator automatically
; variables can be substituted using {}

[DIRS]
home              = ~
# where my projects are stored but yours may be different
project_dir       = ${home}/projects 
# my CEVOpen repo but yours may be different
cev_open =          ${DIRS:project_dir}/CEVOpen
# my dictionary repo but yours may be different
dict_dir =          ${DIRS:home}/dictionary
# my code directory but your may be different
code_dir =          ${home}/workspace

# PyAMI directories which are derived so don't alter them
pyami_package_dir = ${DIRS:code_dir}/pyami
pyami_src_dir     = ${DIRS:pyami_package_dir}/pyami

[SYMBOLS]
# my personal symbols
examples.p            = ${DIRS:pyami_src_dir}/tst/proj

[CODE]
# shared config INI file used by many of the tests - do not alter
code_config_ini =   ${DIRS:pyami_src_dir}/config.ini

The user will normally have a mixture od checked out repositories and these should be set in this file. (Later we will try to create a GUI to help).

central pyami config file

You need to check this out, but do not need to alter it.

# NOTE. All files use forward slash even on Windows
# use slash (/) to separate filename components, we will convert to file-separator automatically

# NOTE: PyAMI variables also use ${...} but to avoid being wrongly processed by ConfigParser
#       they are escaped as $${...} . They are then substituted in a PyAMI parse
#.      This ONLY happens in Config files

[SYMBOLS]
# symbols of general use

; # wikidata taxon name property
taxon_name.w = P225
; # italic content
all_italics.x = //p//italic/text()
; # species, e.g. Zea mays, T. rex, An. gambiae
species.r = [A-Z][a-z]?(\.|[a-z]{2,})\s+[a-z]{3,}

[URLS]
# alternatives to local filestore
petermr_url =     https://github.com/petermr
petermr_raw_url = https://raw.githubusercontent.com/petermr
tigr2ess.u =      https://github.com/petermr/tigr2ess/tree/master
# general dictionaries
dictionary_url = https://github.com/petermr/dictionary

[AMISEARCH]
# unused at present

[DICTIONARIES]
ov_ini       = $${dict_dir}/openvirus20210120/amidict.ini
cev_ini      = $${cev_open}/dictionary/amidict.ini

#docanal_ini  = ${dict_dir}/docanal/docanal.ini # not yet added


[PROJECTS]
# these are used in examples and tests but will probably be removed from here
open_battery =      $${project_dir}/open-battery
pr_liion =          ${open_battery}/liion
tigr2ess =          $${project_dir}/tigr2ess
open_diagram =      $${project_dir}/openDiagram
open_virus =        $${project_dir}/openVirus

minicorpora_ini =   $${cev_open}/minicorpora/config.ini
cev_searches_ini =  $${cev_open}/searches/config.ini
open_diag_ini =     $${project_dir}/openDiagram/physchem/resources/config.ini

You can see communal projects and symbols (e.g. Wikidata properties)