mspire 0.2.0 → 0.2.1

data/INSTALL

@@ -20,11 +20,14 @@ or
 Development
 -----------
 
-prereq: [rant](http://make.rubyforge.org/) (with rubygems: 'gem install rant')
-
-    % rant -T
-    rant test       # Run all tests
-    rant doc        # Generate html documentation.
-    rant package    # Create packages.
-    rant reinstall  # uninstalls the package, packages a fresh one, and installs
-    rant clean      # Remove autogenerated and backup files.
+prereq: [rake](http://rake.rubyforge.org/) (with rubygems: 'gem install rake --remote')
+
+    % rake -T
+    rake clean              # Remove any temporary products.
+    rake html_docs          # creates docs in doc/html
+    rake package            # Build all the packages
+    rake test               # Run tests
+    rake test_ind           # Run unit tests individual on each test
+    rake upload_docs        # create and upload docs to server
+    ...etc...
+

data/Rakefile

@@ -58,7 +58,7 @@ end
 
 desc "create and upload docs to server"
 task :upload_docs => :html_docs do
-  sh "scp -i ~/.ssh/id_dsa_rubyforge -r doc/output/* jtprince@rubyforge.org:/var/www/gforge-projects/mspire/"
+  sh "scp -i ~/.ssh/rubyforge_key -r doc/output/* jtprince@rubyforge.org:/var/www/gforge-projects/mspire/"
 end
 
 desc "creates docs in doc/html"
@@ -140,7 +140,7 @@ tm = Time.now
 spec = Gem::Specification.new do |s|
   s.platform = Gem::Platform::RUBY
   s.name = NAME
-  s.version = "0.2.0"
+  s.version = "0.2.1"
   s.summary = "Mass Spectrometry Proteomics Objects, Scripts, and Executables"
   s.date = "#{tm.year}-#{tm.month}-#{tm.day}"
   s.email = "jprince@icmb.utexas.edu"
@@ -153,7 +153,7 @@ spec = Gem::Specification.new do |s|
   s.rdoc_options = rdoc_options
   s.extra_rdoc_files = rdoc_extra_includes
   s.executables = FL["bin/*"].map {|file| File.basename(file) }
-  s.add_dependency('libjtp', '~> 0.1.2')
+  s.add_dependency('libjtp', '~> 0.1.4')
   s.requirements << '"xmlparser" is the prefered xml parser right now.  REXML and regular expressions are used as fallback in some routines.'
   s.requirements << 'some plotting functions will not be available without the "gnuplot" gem (and underlying gnuplot binary)'
   s.requirements << 'the "t2x" binary (in archive) or readw.exe is required to convert .RAW files to mzXML in some applications'

data/changelog.txt

@@ -35,7 +35,8 @@ this in a future release.
 
 ## version 0.2.0
 
-** This is a definite code breaker **
-Revamped the way SpecID works (it is now subclassed).  Since I want to return
-the specific object that the file specifies, I use 'create' now instead of
-'new' (which forces one to return *that* class.
+Revamped the way SpecID works (it is now mixed-in).
+Added support for modifications to bioworks_to_pepxml.rb
+Can read .srf files (nearly interchangeable with bioworks files)
+Redid filter.rb
+

data/lib/spec_id/proph.rb

@@ -5,6 +5,11 @@ require 'instance_var_set_from_hash'
 require 'axml'
 require 'spec_id'
 
+
+module SpecID ; end
+module SpecID::Prot ; end
+module SpecID::Pep ; end
+
 class Proph
 
 

data/release_notes.txt

@@ -1,11 +1,2 @@
 
-Note two potentially significant bugs in the software corrected (see the
-changelog).  I haven't finished modifying the tests to reflect these changes,
-but I wanted to get the faulty software off the top of the stack.  A new
-release will shortly follow that passes all tests.  Use this release only as a
-correction to the previous.
 
-tests currently failing:
-gi
-spec_id
-id_precision

metadata

@@ -3,8 +3,8 @@ rubygems_version: 0.9.2
 specification_version: 1
 name: mspire
 version: !ruby/object:Gem::Version 
-  version: 0.2.0
-date: 2007-04-25 00:00:00 -05:00
+  version: 0.2.1
+date: 2007-04-30 00:00:00 -05:00
 summary: Mass Spectrometry Proteomics Objects, Scripts, and Executables
 require_paths: 
 - lib
@@ -29,32 +29,32 @@ post_install_message:
 authors: 
 - John Prince
 files: 
-- lib/spec_id.rb
-- lib/align
-- lib/spec_id_xml.rb
 - lib/spec_id
-- lib/toppred.rb
-- lib/align.rb
+- lib/align
 - lib/spec
+- lib/spec_id.rb
 - lib/fasta.rb
+- lib/align.rb
+- lib/sample_enzyme.rb
 - lib/gi.rb
 - lib/roc.rb
-- lib/sample_enzyme.rb
-- lib/align/chams.rb
+- lib/spec_id_xml.rb
+- lib/toppred.rb
 - lib/spec_id/sequest.rb
-- lib/spec_id/filter.rb
 - lib/spec_id/bioworks.rb
-- lib/spec_id/srf.rb
+- lib/spec_id/proph.rb
 - lib/spec_id/precision.rb
-- lib/spec_id/protein_summary.rb
+- lib/spec_id/srf.rb
 - lib/spec_id/aa_freqs.rb
-- lib/spec_id/proph.rb
-- lib/spec/msrun.rb
-- lib/spec/scan.rb
+- lib/spec_id/protein_summary.rb
+- lib/spec_id/filter.rb
+- lib/align/chams.rb
 - lib/spec/mzxml
-- lib/spec/mzdata.rb
 - lib/spec/mzdata
+- lib/spec/msrun.rb
+- lib/spec/scan.rb
 - lib/spec/mzxml.rb
+- lib/spec/mzdata.rb
 - lib/spec/mzxml/parser.rb
 - lib/spec/mzdata/parser.rb
 - INSTALL
@@ -63,62 +63,62 @@ files:
 - LICENSE
 - changelog.txt
 - release_notes.txt
+- bin/gi2annot.rb
+- bin/protein_summary.rb
 - bin/bioworks2sequestXML_gui.rb
-- bin/srf_group.rb
+- bin/bioworks2excel.rb
 - bin/pepproph_filter.rb
-- bin/filter.rb
+- bin/fasta_shaker.rb
+- bin/bioworks_to_pepxml.rb
 - bin/protxml2prots_peps.rb
-- bin/raw_to_mzXML.rb
-- bin/gi2annot.rb
-- bin/id_class_anal.rb
-- bin/precision.rb
 - bin/id_precision.rb
-- bin/protein_summary.rb
-- bin/bioworks_to_pepxml.rb
-- bin/bioworks2excel.rb
+- bin/id_class_anal.rb
 - bin/mzxml_to_lmat.rb
-- bin/fasta_shaker.rb
 - bin/find_aa_freq.rb
-- script/prep_dir.rb
-- script/degenerate_peptides.rb
-- script/histogram_probs.rb
-- script/simple_protein_digestion.rb
-- script/top_hit_per_scan.rb
-- script/msvis.rb
+- bin/filter.rb
+- bin/srf_group.rb
+- bin/precision.rb
+- bin/raw_to_mzXML.rb
+- script/create_little_pepxml.rb
 - script/mzXML2timeIndex.rb
 - script/tpp_installer.rb
+- script/msvis.rb
+- script/histogram_probs.rb
+- script/prep_dir.rb
+- script/top_hit_per_scan.rb
 - script/filter-peps.rb
-- script/estimate_fpr_by_cysteine.rb
 - script/genuine_tps_and_probs.rb
-- script/create_little_pepxml.rb
+- script/simple_protein_digestion.rb
+- script/estimate_fpr_by_cysteine.rb
 - script/find_cysteine_background.rb
+- script/degenerate_peptides.rb
 test_files: 
-- test/tc_spec_id_xml.rb
-- test/tc_mzxml_to_lmat.rb
-- test/tc_id_class_anal.rb
+- test/tc_aa_freqs.rb
+- test/tc_proph.rb
 - test/tc_gi.rb
+- test/tc_align.rb
+- test/tc_sequest.rb
+- test/tc_spec.rb
+- test/tc_bioworks.rb
+- test/tc_protein_summary.rb
 - test/tc_fasta.rb
+- test/tc_msrun.rb
 - test/tc_peptide_parent_times.rb
 - test/tc_spec_id.rb
-- test/tc_roc.rb
 - test/tc_mzxml.rb
-- test/tc_sample_enzyme.rb
 - test/tc_srf.rb
-- test/tc_bioworks.rb
-- test/tc_spec.rb
-- test/tc_bioworks_to_pepxml.rb
-- test/tc_scan.rb
-- test/tc_sequest.rb
-- test/tc_fasta_shaker.rb
 - test/tc_id_precision.rb
-- test/tc_msrun.rb
-- test/tc_protein_summary.rb
+- test/tc_id_class_anal.rb
 - test/tc_filter_peps.rb
-- test/tc_filter.rb
-- test/tc_aa_freqs.rb
-- test/tc_proph.rb
-- test/tc_align.rb
 - test/tc_precision.rb
+- test/tc_filter.rb
+- test/tc_roc.rb
+- test/tc_scan.rb
+- test/tc_bioworks_to_pepxml.rb
+- test/tc_mzxml_to_lmat.rb
+- test/tc_fasta_shaker.rb
+- test/tc_sample_enzyme.rb
+- test/tc_spec_id_xml.rb
 rdoc_options: 
 - --main
 - README
@@ -129,22 +129,22 @@ extra_rdoc_files:
 - INSTALL
 - LICENSE
 executables: 
+- gi2annot.rb
+- protein_summary.rb
 - bioworks2sequestXML_gui.rb
-- srf_group.rb
+- bioworks2excel.rb
 - pepproph_filter.rb
-- filter.rb
+- fasta_shaker.rb
+- bioworks_to_pepxml.rb
 - protxml2prots_peps.rb
-- raw_to_mzXML.rb
-- gi2annot.rb
-- id_class_anal.rb
-- precision.rb
 - id_precision.rb
-- protein_summary.rb
-- bioworks_to_pepxml.rb
-- bioworks2excel.rb
+- id_class_anal.rb
 - mzxml_to_lmat.rb
-- fasta_shaker.rb
 - find_aa_freq.rb
+- filter.rb
+- srf_group.rb
+- precision.rb
+- raw_to_mzXML.rb
 extensions: []
 
 requirements: 
@@ -161,5 +161,5 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        version: 0.1.2
+        version: 0.1.4
     version: