mesa_cli 0.1.0

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data/README.md

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+mesa_cli
+========
+
+Command line tools for use with open source MESA stellar evolution code.
+
+I don't think this tool is done yet, but I wanted to get it out there. So far
+requires ruby, MesaScript, thor, and a working mesa directory accessed by
+`$MESA_DIR`.
+
+## Installation ##
+
+### Rubygems Installation
+
+Enter
+
+    gem install mesa_cli
+
+or if that doesn't work, enter
+
+    sudo gem install mesa_cli
+
+into your terminal. You should be done now!
+
+### Manual Installation
+
+If, for some reason, the rubygems installation doesn't work, you may clone this
+repository and install the single file `mesa` (located in `mesa_cli/bin/mesa`)
+as detailed below.
+
+1. Make sure you have Ruby 1.8.7 or higher (1.9.3 recommended)
+2. Install [mesascript](http://wmwolf.github.io/MesaScript/).
+3. Install the Thor gem via
+
+    sudo gem install thor
+
+4. Place `mesa` file in your path
+
+
+## Usage
+
+To get quick information, type `mesa help` to list the commands and see what
+they do. For detailed information on a particular command, type `mesa help
+command` to learn about an individual command (replacing the word "command" with the actual subcommand name). Brief summaries of commands are below.
+
+### default
+
+To use, just type
+
+    mesa default NAMELIST_NAME
+
+where namelist name is the name of a MESA star namelist, like `star_job`,
+`controls`, or `pgstar`.
+
+This command will open the proper defaults file for the corresponding namelist
+using whatever editor your system has set in the `EDITOR` variable. For
+instance,
+
+    mesa default star_job
+
+will open `$MESA_DIR/star/defaults/star_job.defaults` in vim or whatever default editor you've set up.
+
+### new
+
+To use, just type 
+
+    mesa new DIR_NAME
+
+where `DIR_NAME` is the name of a new MESA work directory.
+
+This makes a copy of `$MESA_DIR/star/work` into a directory with the name
+chosen. With no name (i.e. just typing `mesa new`), the directory will just be
+called work. The `inlist_project` will be renamed to `inlist_DIR_NAME`. If
+MesaScript is available, the main `inlist` file will be pointed to the newly-
+renamed `inlist_project`, and a MesaScript version of the new `inlist_project`
+will be made that compiles to `inlist_project`.
+
+The `-s` or `--simple` option will just copy the work directory and rename the
+directory only. No renaming of inlists or creation of MesaScript files will be
+done.
+
+The `-p` or `--pgstar` option will also point the main `inlist` file to the
+newly-named `inlist_project` file for the `pgstar` namelist instead of the
+default `inlist_pgstar`.
+
+### point
+
+To use, just type
+
+    mesa point INLIST_TO_POINT_TO
+
+where `INLIST_TO_POINT_TO` is the name of an inlist that you would like your local `inlist` file to point to. Currently this can only allow you to point to one inlist. By default, this will not point to the new inlist for the `pgstar` namelist, but it will for both of the `star_job` and `controls` namelists.
+
+The `-p` or `--pgstar` option will also point the main `inlist` file to the
+`INLIST_TO_POINT_TO` file for the `pgstar` namelist.
+
+### test
+
+To use, just type
+
+    mesa test TEST_CASE DIR_NAME
+
+where `TEST_CASE` is the name of a test case in `$MESA_DIR/star/test_suite` and `DIR_NAME` is the name of a directory to be created that will contain a copy of the proper test suite case.
+
+The second argument is optional, and if omitted, the new directory will have 
+the same name as the original test suite case. If neither argument is given, a
+list of every file in `$MESA_DIR/star/test_suite` is output. The listing
+behavior can also be forced by adding the `-l` or `--list` option to the call.
+
+Work directories made in this way are "de-test-suited" in that calls back to
+`inlist_test_suite` are deleted along with any other attempts to change the value of `mesa_dir`. All local path definitions (ones using `../../` or the
+like) will be made fully qualified. For example, `../../../` will be turned
+into `$MESA_DIR/`. Thus, references to other inlists, like 
+`inlist_massive_defaults` or models, like those found in
+`$MESA_DIR/data/star_data`, should remain intact. IF THESE EXTERNAL REFERENCES
+CONTAIN LOCAL PATHS, THINGS WILL BREAK. The only inlist that is strictly barred
+from this process is `inlist_test_suite` which currently only serves to set
+the `mesa_dir` via a local path, so references to this inlist are always 
+deleted.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

data/bin/mesa

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+#! /usr/bin/env ruby
+require "thor"
+require "fileutils"
+begin
+  require "mesa_script"
+  $use_mesascript = true
+rescue LoadError
+  $use_mesascript = false
+end
+
+class MyCLI < Thor
+  option :simple, :type => :boolean, :aliases => :s,
+  :desc => "Just copy work directory and rename it. Nothing done with " +
+           "MesaScript."
+  option :pgstar, :type => :boolean, :aliases => [:p, :pgstar], 
+  :desc => "Point `inlist` to main inlist for pgstar in addition to star_job " +
+           "and controls (default points to `inlist_pgstar`)."
+
+  desc "new [NEW_DIR]", "Create MESA work dir called NEW_DIR (default 'work')."
+  long_desc <<-LONGDESC
+
+    `mesa new` will create a new work directory generated from your current
+    $MESA_DIR/star/work. The argument specifies the name of the new directory,
+    and the base name of the directory will be used to rename `inlist_project`
+    to `inlist_BASENAME_OF_ARGUMENT`. Finally, it uses MesaScript to point the
+    base `inlist` to the new one and converts the new inlist to MesaScript for
+    easy automation. This is only done if MesaScript is available.
+
+  LONGDESC
+  def new(new_dir="work")
+    return unless check_for_mesa_dir
+    work_dir = File.join(ENV['MESA_DIR'], 'star', 'work')
+    new_loc = new_dir
+    basename = File.basename(new_loc)
+    FileUtils.cp_r(work_dir, new_loc, :verbose => true)
+    unless options[:simple]
+      old_inlist_name = File.join(new_loc, "inlist_project")
+      short_name = "inlist_#{basename}"
+      new_inlist_name = File.join(new_loc, short_name)
+      File.rename(old_inlist_name, new_inlist_name)
+      if options[:pgstar]
+        create_control_inlist(new_loc, short_name, short_name, short_name)
+      else
+        create_control_inlist(new_loc, short_name, short_name)
+      end
+      create_ms_file(new_inlist_name, File.join(new_loc, basename + '.rb'))
+    end
+  end
+  
+  desc "point INLIST", "Point main `inlist` to INLIST."
+  option :pgstar, :type => :boolean, :aliases => [:p, :pgstar], 
+  :desc => "Point `inlist` to INLIST for pgstar in addition to star_job " +
+           "and controls (default points to `inlist_pgstar`)."
+  def point(inlist)
+    if options[:pgstar]
+      create_control_inlist(Dir.pwd, inlist, inlist, inlist)
+    else
+      create_control_inlist(Dir.pwd, inlist, inlist)
+    end
+  end
+  
+  desc "test [TEST_SUITE_CASE] [NEW_DIR]", "Copy test suite case work " +
+       "directory with name TEST_SUITE_CASE to location NEW_DIR."
+  long_desc <<-LONGDESC
+    `mesa test` will primarily create a new work directory based on an existing
+    test case located in $MESA_DIR/star/test_suite. Since the structure of
+    these directories varies wildly, no MesaScript or renaming niceties are 
+    done as in the standard `mesa new` command. The first argument is the name
+    of the test suite case to be copied. The second argument, if provided, will
+    be the name of the new directory. If this is omitted, the name remains the
+    same. If no arguments are given a list of available test suite cases are
+    printed out and no directories are copied.
+
+    The resulting directory will have all references to custom values of 
+    MESA_DIR removed and any local paths (like ../../inlist_massive_defaults)
+    will be converted to fully-qualified paths (like 
+    $MESA_DIR/star/inlist_massive_defaults). The resulting work directory should
+    be ready to make and run immediately as if it were in the test suite
+    directory.
+  LONGDESC
+  option :list, :type => :boolean, :aliases => :l, 
+  :desc => "lists available test suite cases"
+  
+  def test(test_case=nil, new_dir=nil)
+    return unless check_for_mesa_dir 
+
+    test_suite_dir = File.join(ENV['MESA_DIR'], 'star', 'test_suite')
+    if options[:list] or test_case.nil?
+      puts "test cases in #{test_suite_dir}:"
+      puts Dir.entries(test_suite_dir).select { |entry| entry[0] != '.' }
+      return
+    end
+    
+    work_dir = File.join(test_suite_dir, test_case)
+    unless File.directory?(work_dir)
+      puts "Unable to locate test suite case #{test_case} in directory " +
+      test_suite_dir + ". Exiting."
+      return
+    end
+    new_dir ||= File.join(FileUtils::pwd, test_case)
+    FileUtils.cp_r(work_dir, new_dir, :verbose => true)
+    inlist_files = Dir.glob(File.join(new_dir,"inlist*"))
+    inlist_files.each do |inlist_file|
+
+      # remove references to a new MESA_DIR
+      inlist_lines = IO.readlines(inlist_file).reject do |line|
+        line.downcase =~ /mesa_dir/
+      end
+
+      # remove references to inlist_test_suite
+      bad_numbers = []
+      bad_namelists = []
+      inlist_lines.each do |line|
+        if line =~ /inlist_test_suite/
+          line =~ /extra_(.+)_inlist(\d)/
+          bad_namelists << $1
+          bad_numbers << $2
+        end
+      end
+      bad_combos = bad_namelists.zip(bad_numbers)
+      bad_words = []
+      bad_combos.each do |namelist, number|
+        bad_words << "read_extra_#{namelist}_inlist#{number}"
+        bad_words << "extra_#{namelist}_inlist#{number}_name"
+      end
+      inlist_lines.reject! do |line|
+        any_found = false
+        bad_words.each do |bad_word|
+          if line.include?(bad_word)
+            any_found = true
+            break
+          end
+        end
+        any_found
+      end
+
+      # make local paths fully-qualified
+      new_inlist_lines = inlist_lines.map do |line|
+        if line =~ /((\.\.\/)+)/
+          line.sub(/((\.\.\/)+)/, File.expand_path(File.join(work_dir, $1))+'/')
+        else
+          line
+        end
+      end
+
+      # write out cleaned up inlist
+      IO.write(inlist_file, new_inlist_lines.join)
+    end
+
+    # Clean up makefule
+    makefile = File.join(new_dir, 'make', 'makefile')
+    make_lines = IO.readlines(makefile)
+
+    # Make sure MESA_DIR is not set in makefile
+    make_lines.reject! { |line| line =~ /\A\s*MESA_DIR/ }
+
+    # Make sure no local references to files in mesa tree are made
+    make_lines.reject! { |line| line =~ /\.\./ }
+    make_lines.reject! { |line| line.empty? }
+    IO.write(makefile, make_lines.join)
+  end
+
+  desc "default FILE_NAME", "Open defaults file for namelist FILE_NAME."
+  def default(filename)
+    return unless check_for_mesa_dir
+    defaults_dir = File.join(ENV['MESA_DIR'], 'star', 'defaults')
+    suffix = case
+    when %w{star_job controls pgstar}.include?(filename) then '.defaults'
+    when %w{profile_columns history_columns}.include?(filename) then '.list'
+    else
+      puts <<-BAD_NAME
+      Invalid file name: #{filename}. Must use 'star_job', 'controls', 'pgstar',
+      'profile_columns', or 'history_columns'.
+      BAD_NAME
+      return
+    end
+    editor = ENV['EDITOR'] || 'less'
+    system("#{editor} #{File.join(defaults_dir, filename)}#{suffix}")
+  end
+
+
+  private
+  def create_ms_file(inlist_name, ms_name)
+    ms_name += '.rb' unless ms_name[-3..-1] == '.rb'
+    source = File.join(inlist_name)
+    output = File.join(ms_name)
+    Inlist.inlist_to_mesascript(source, output) if $use_mesascript
+  end
+  
+  def check_for_mesa_dir
+    return true if ENV['MESA_DIR']
+
+    puts "WARNING: No environment variable $MESA_DIR found. Exiting."
+    return false
+  end
+
+  def create_control_inlist(dir, star_job, controls, pgstar = "inlist_pgstar")
+    Inlist.make_inlist(File.join(dir, 'inlist')) do
+          read_extra_star_job_inlist1 true
+          extra_star_job_inlist1_name star_job
+
+          read_extra_controls_inlist1 true
+          extra_controls_inlist1_name controls
+
+          read_extra_pgstar_inlist1 true
+          extra_pgstar_inlist1_name pgstar
+    end
+  end
+end
+
+MyCLI.start(ARGV)

metadata

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+--- !ruby/object:Gem::Specification
+name: mesa_cli
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- William Wolf
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-01-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.19'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.19'
+- !ruby/object:Gem::Dependency
+  name: mesa_script
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.1.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.1.2
+description: "    MESA CLI is a command-line interface for doing several tasks with
+  Modules\n    for Experiments in Stellar Astrophysics (MESA; mesa.sourceforge.net).
+  This\n    package includes one executable, `mesa`. Actions are performed by entering\n
+  \   `mesa` followed by various subcommands. A list of available subcommands can\n
+  \   be displayed by entering\n\n    mesa help\n\n    Any individual subcommand is
+  documented by typing `mesa help` followed by\n    the name of the subcommand, for
+  instance,\n\n    mesa help new\n\n    will give information about what the `new`
+  command does. For detailed\n    instructions, see the readme on the github page
+  at \n\n    https://github.com/wmwolf/mesa_cli\n"
+email: wmwolf@physics.ucsb.edu
+executables:
+- mesa
+extensions: []
+extra_rdoc_files: []
+files:
+- README.md
+- bin/mesa
+homepage: https://wmwolf.github.io
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.3
+signing_key: 
+specification_version: 4
+summary: Mesa CLI - a command line interface for simple MESA tasks.
+test_files: []