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Merge with upstream #2

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a743705
Use Class.getSimpleName() instead of obsolete UtilMDE.unqualified_name()
mernst Mar 4, 2016
d94137d
remove unused and obsolete utilities
markro49 Mar 4, 2016
b5e3cf1
built with latest checker framework (1.9.12)
markro49 Mar 4, 2016
f512143
updates for release 5.2.24
markro49 Mar 4, 2016
cb8cb3c
Change version to 5.2.24
markro49 Mar 4, 2016
9d2bc2d
Bump version number for ongoing development.
markro49 Mar 4, 2016
9083965
update checker url
markro49 Mar 4, 2016
5293c7b
correct use of deprecated method name
markro49 Mar 5, 2016
e5f99c9
Suppress Signature Checker warning
mernst Mar 7, 2016
64c9813
Document removal of 32 bit support. Some corrections to making a dis…
markro49 Mar 8, 2016
ca2f3f7
Add debug_runtime flag to Chicory similar to DynComp.
markro49 Mar 8, 2016
651bf98
Merge branch 'master' of ssh://github.com/codespecs/daikon
markro49 Mar 8, 2016
e983062
Stop Chicory from adding UtilMDE info to data files.
markro49 Mar 10, 2016
cdfb027
Change version to 5.2.26
markro49 Mar 10, 2016
e065873
Bump version number for ongoing development.
markro49 Mar 10, 2016
c9575a8
Restore 32bit note after extra Daikon release.
markro49 Mar 10, 2016
656fa7d
add additional info to debug output
markro49 Mar 11, 2016
5460f46
Fix support for orig variables in splitters
markro49 Mar 11, 2016
3c271c5
update goal files for orig vars in splitters
markro49 Mar 11, 2016
80005f3
update goal files for orig vars in splitters
markro49 Mar 11, 2016
9e2869f
Merge branch 'master' of ssh://github.com/codespecs/daikon
markro49 Mar 11, 2016
514d21d
Add splitter support for a parameter and a member variable with the s…
markro49 Mar 16, 2016
318072b
correct checker framework error
markro49 Mar 16, 2016
2c40dc0
Update SplitterFactory test goal files.
markro49 Mar 16, 2016
c953b31
Fix bash syntax error
mernst Mar 17, 2016
73a4df9
Change printed format of isPointer invariant
mernst Mar 17, 2016
bc1665b
Set LC_ALL=C for deterministic POSIX sorting
mernst Mar 18, 2016
4fd1a76
Make output more deterministic
mernst Mar 19, 2016
465b59d
Adjust goals to account for deterministic output order
mernst Mar 19, 2016
00777b6
Upload build artifacts
mernst Mar 19, 2016
a8207a5
Fix incorrect commit (was diffs rather than results)
mernst Mar 19, 2016
e1022f1
Combine two "addons:" sections in .travis.yml
mernst Mar 19, 2016
15b89b6
Remove unneeded .goal.j8 files
mernst Mar 20, 2016
bcd8ac3
Disable uploading artifacts to Amazon S3
mernst Mar 20, 2016
74a929a
Put multi-line statement on one line
mernst Mar 20, 2016
37ae09b
Adapt to source code changes
mernst Mar 20, 2016
c2bacdb
Put multi-line return statement on one line
mernst Mar 20, 2016
8a94460
Java 8 goals
mernst Mar 20, 2016
0e7ac9d
Adapt to change in source code
mernst Mar 20, 2016
6bb8949
Explain differences between Java 7 and Java 8 behavior
mernst Mar 20, 2016
9b7c053
Add todo comment
mernst Mar 22, 2016
5ea1cc4
Chicory runs Daikon only if the subject program terminates successfully
mernst Mar 24, 2016
d73138a
Update CHANGES for upcoming release.
markro49 Mar 24, 2016
19af6f0
Add Javadoc links
mernst Mar 24, 2016
b5fc922
Merge branch 'master' of github.com:codespecs/daikon
mernst Mar 24, 2016
69591db
Tweak section 4.2 dataflow hierarchy
mernst Mar 25, 2016
c55454c
HTML fixes
mernst Mar 29, 2016
a026549
Use Travis default for build failure notifications
mernst Mar 29, 2016
a8117f3
Merge branch 'master' of github.com:codespecs/daikon
mernst Mar 29, 2016
61dc7f8
Remove comment
mernst Mar 29, 2016
c73c110
Clarify a sentence
mernst Mar 30, 2016
aaada5b
Improve validate target
mernst Apr 2, 2016
c45acf2
warn if java5 or earlier; also, no stackmap output in that case
markro49 Apr 4, 2016
77eb6c6
make debug code more robust
markro49 Apr 4, 2016
3e195e7
Merge branch 'master' of ssh://github.com/codespecs/daikon
markro49 Apr 4, 2016
2594e3d
texinfo fiddle to make spell-check happy
markro49 Apr 4, 2016
c0aab4d
updates for 5.3.0 release
markro49 Apr 4, 2016
d4ae43c
Fix typo
mernst Apr 5, 2016
152b687
Refactoring to account for Checker Framework bug
mernst Apr 5, 2016
d6e8ae9
Add final to formal parameters
mernst Apr 5, 2016
7461483
Update plume.jar
mernst Apr 5, 2016
ab083a1
don't include junit in daikon.jar
markro49 Apr 5, 2016
6d41880
Merge branch 'master' of ssh://github.com/codespecs/daikon
markro49 Apr 5, 2016
45da5e3
Change version to 5.3.0
markro49 Apr 5, 2016
c4c6db6
add junit.jar to test-staged-dist paths
markro49 Apr 5, 2016
20effc3
Bump version number for ongoing development.
markro49 Apr 5, 2016
58d6a5c
New command-line argument --user_defined_invariant
mernst Apr 5, 2016
a6ca289
Merge branch 'master' of github.com:codespecs/daikon
mernst Apr 5, 2016
c56da77
Tweak manual
mernst Apr 5, 2016
1e89a3c
Spell-check
mernst Apr 5, 2016
6fad7e5
Fix spelling errors
mernst Apr 5, 2016
d32a3fa
Move type annotation to more appropriate location in source code
mernst Apr 6, 2016
45857e2
Makefile tweaks
mernst Apr 6, 2016
bfdaabb
Call check_modified rather than add_modified
mernst Apr 6, 2016
46fa4e5
Punctuation fix
mernst Apr 6, 2016
1c858ed
Monster whitespace changes
mernst Apr 6, 2016
fc1f507
Changes for pluggable type-checking
mernst Apr 6, 2016
0537b1d
Merge branch 'master' of github.com:codespecs/daikon
mernst Apr 6, 2016
4d80184
Merge branch 'master' of github.com:codespecs/daikon
mernst Apr 6, 2016
0f5c9fd
More whitespace fixups
mernst Apr 6, 2016
4dddf01
Add target update-plume-jar to update plume.jar
mernst Apr 6, 2016
999a5cb
Don't unconditionally plume.jar
mernst Apr 6, 2016
5b819fc
BIBDIR environment variable is optional
mernst Apr 6, 2016
62fc634
Add annotations to show correct use of regexes
mernst Apr 6, 2016
9c0e933
Add missing parser-tests to nightly-test target
mernst Apr 7, 2016
0c5f0b7
Start of instructions that avoid long rebuild steps on release day
mernst Apr 7, 2016
8dcb47e
There is no Fjalar job on Jenkins. We should add one.
mernst Apr 7, 2016
40e01b9
Move spell-checking earlier in the release process
mernst Apr 7, 2016
8271118
Update Texinfo menu
mernst Apr 7, 2016
f4ca4dd
Explain why there is no Fjalar job on Jenkins
mernst Apr 7, 2016
ee8b22f
Script to test the Daikon distribution
mernst Apr 7, 2016
ddc5c8a
Echo commands
mernst Apr 7, 2016
06e4361
Test main distribution as well as staging one
mernst Apr 7, 2016
80b5510
Avoid the bashism "source"; use "." instead
mernst Apr 7, 2016
713f971
Expand a comment
mernst Apr 7, 2016
81ba62f
Shorten commands for testing the distribution
mernst Apr 7, 2016
5ffa1d9
The environment variable JAVA_HOME must be set
mernst Apr 7, 2016
58a2620
Shorten and automate release process
mernst Apr 7, 2016
c85eb9f
Automate another manual step
mernst Apr 7, 2016
7294d8c
Fix -path argument to find
mernst Apr 8, 2016
9725d9d
use parallel make for regression tests; clean up parser-tests
markro49 Apr 8, 2016
8a89b42
Merge branch 'master' of ssh://github.com/codespecs/daikon
markro49 Apr 8, 2016
bb38881
remove -Orecurse option on parallel make
markro49 Apr 8, 2016
4af7a4a
use -Orecures if make version 4.
markro49 Apr 8, 2016
b70224b
Use curly braces around one-statement for loop bodies
mernst Apr 9, 2016
31f1d1b
Improve text about "Could not find or load main class" error
mernst Apr 10, 2016
f1ff65f
Quote arguments that contain a space
mernst Apr 10, 2016
489ac66
Don't compile plume-lib .java files, which are not used
mernst Apr 12, 2016
61542af
Move comment
mernst Apr 12, 2016
d8647c1
Add comments and clean up distribution-check and test-staged-dist tar…
markro49 Apr 12, 2016
70b158e
Put comments in more logical order
mernst Apr 12, 2016
17ffb14
Explain how to install the travis program
mernst Apr 12, 2016
96dca7c
Merge branch 'master' of github.com:codespecs/daikon
mernst Apr 12, 2016
d40078b
Be more explicit about contents of ~/private/.travis-access-token
mernst Apr 12, 2016
8430a1e
Use more destriptive text in Travis job
mernst Apr 12, 2016
438c9a8
Quote curly braces
mernst Apr 12, 2016
ecc4f18
add support for -Werror
markro49 Apr 13, 2016
3cf5a35
minor updates to distribution chapter; spell check
markro49 Apr 13, 2016
0e79912
Add reformat and check-format Makefile targets
mernst Apr 20, 2016
39f944d
Improve Java code formatting
mernst Apr 20, 2016
e5bbfbd
Add braces
mernst Apr 20, 2016
9f10621
Check formatting on commit, not compile.
mernst Apr 20, 2016
c4c10a0
Fix problem with duplicate invariants caused by missing isSameFormula…
markro49 Apr 20, 2016
ade078e
Don't call "make reformat"
mernst Apr 21, 2016
a181b69
Tweak Javadoc
mernst Apr 23, 2016
e77fb25
Update list of .jar library files
mernst Apr 23, 2016
508df83
Put information about each license in its own section of the manual
mernst Apr 23, 2016
fbd755a
Update name of JUnit jar file
mernst Apr 23, 2016
25b13d2
Use "-Xlint:-options" with "-source 7 -target 7"
mernst Apr 23, 2016
0f9c954
Incomplete implementation of --disable-all-invariants switch
mernst Apr 23, 2016
a5d48ec
Organize imports according to Google Java style
mernst Apr 23, 2016
3b98486
Improve documentation of --user-defined-invariant
mernst Apr 23, 2016
eda1aa1
Introduce and use variable Invariant.invariantEnabledDefault
mernst Apr 23, 2016
3cd5506
Indicate error message when terminating Daikon
mernst Apr 23, 2016
e71734b
Make methods in Invariant abstract: enabled, instantiate_dyn, valid_t…
mernst Apr 23, 2016
f5a3718
Disable debugging output, turn a warning into an error
mernst Apr 23, 2016
0125a3d
Improve style in example code
mernst Apr 23, 2016
73eae9b
Link to Google Java Style
mernst Apr 23, 2016
e507dc1
Fix cut-and-paste error in receiver types
mernst Apr 23, 2016
c2d9d0e
Convey useful information even if exception message is null
mernst Apr 23, 2016
31bb428
Suppress a nullness warning
mernst Apr 23, 2016
6e67ad9
Remove spurious space
mernst Apr 23, 2016
722970b
Make Daikon typecheck under the Lock Checker
jthaine Apr 29, 2016
1ae22e6
Update plume.jar; fixes most but not all pluggable type-checking errors
mernst Apr 29, 2016
de6d0ca
Rename DCOMP_JAVA_FILES to INSTRUMENTATION_JAVA_FILES
mernst Apr 28, 2016
bbd3455
Merge branch 'master' of github.com:codespecs/daikon
mernst Apr 29, 2016
fed06d0
Add curly braces
mernst Apr 29, 2016
a5df643
Add JAVA_FILES_FOR_FORMAT variable; it's not yet correctly set
mernst Apr 29, 2016
34a4b21
Improve formatting
mernst Apr 29, 2016
54e4136
Merge branch 'master' of github.com:codespecs/daikon
mernst Apr 29, 2016
2b61188
New plume.jar
mernst Apr 29, 2016
d356b9a
Merge branch 'master' into typecheck-lock-new
jthaine Apr 29, 2016
2664ae0
Reformat
jthaine Apr 29, 2016
f299740
Merge branch 'master' into typecheck-lock-new
jthaine Apr 29, 2016
173e721
Print helpful message if check-format fails
mernst Apr 29, 2016
fb0f87b
Remove misleading comment
jthaine Apr 30, 2016
6279847
Don't put curly braces on their own line
mernst May 1, 2016
82b0aa3
Use curly braces around if and for statement bodies
mernst May 1, 2016
b3d2e0c
Merge https://github.com/codespecs/daikon into typecheck-lock-new
mernst May 2, 2016
5456afd
minor changes to prepare for release
markro49 May 2, 2016
c9a2b63
Change version to 5.3.2
markro49 May 2, 2016
c9e5e85
Bump version number for ongoing development.
markro49 May 2, 2016
5ef9961
Avoid unnecessary line breaks in email
mernst May 2, 2016
7ba538a
Merge branch 'master' of github.com:codespecs/daikon
mernst May 2, 2016
b1fa9df
Improve debugging output
mernst May 4, 2016
c77ebd1
Improve debugging output
mernst May 4, 2016
58c7ec1
Edit section on troublesection slow execution
mernst May 4, 2016
87d35aa
Merge branch 'master' of github.com:codespecs/daikon
mernst May 4, 2016
a917681
Improve Javadoc style
mernst May 5, 2016
88de047
Improve Javadoc style
mernst May 6, 2016
f9bcaf2
Reduce git clone depth
mernst May 8, 2016
ff5185d
Fix check-format rule so it fails compilation
mernst May 8, 2016
8e1f92b
Remove spurious whitespace
mernst May 8, 2016
3e09138
Whitespace fixes
mernst May 8, 2016
2894293
Merge branch 'master' into typecheck-lock-new
mernst May 8, 2016
a7cc6b0
make -Werror the default for the daikon build
markro49 May 9, 2016
25f4b31
Trivial whitespace fix
mernst May 10, 2016
de50f64
Improve formatting
mernst May 10, 2016
456d6dc
Add curly braces
mernst May 10, 2016
beb25a4
Throw error even if assertions are not enabled
mernst May 10, 2016
7cd4957
Add curly braces around else clauses
mernst May 16, 2016
03c23ca
Remove needless parentheses in return statements
mernst May 16, 2016
1de8ae0
Add curly braces
mernst May 21, 2016
e27dba3
Don't send a message to multiple mailing lists
mernst May 23, 2016
f1d98f5
Fix indentation
mernst May 23, 2016
b9930f4
Merge branch 'master' into typecheck-lock-new
jthaine May 23, 2016
dfe60d3
Uncomment @SuppressWarnings annotations
mernst May 24, 2016
d4739dd
Improve formatting for annotations in comments with arguments
mernst May 24, 2016
1d2fd48
Add necessary synchronization
mernst May 24, 2016
520a433
Address review feedback
jthaine May 24, 2016
2a05ff8
Merge branch 'master' of github.com:codespecs/daikon
mernst May 24, 2016
f454743
Merge branch 'master' into typecheck-lock-new
jthaine May 24, 2016
4527737
Merge pull request #49 from codespecs/typecheck-lock-new
mernst May 24, 2016
90cff49
Add more italics in examples
mernst May 25, 2016
ea04f99
Hints about setting JAVA_HOME environment variable
mernst May 26, 2016
1409b8a
Put declaration annotations on their own line
mernst May 26, 2016
c8f07ae
Add curly braces
mernst May 26, 2016
4ab0fd8
num_samples may be called when its receiver is under initialization
mernst May 26, 2016
e4518d9
Merge branch 'master' of github.com:codespecs/daikon
mernst May 26, 2016
fbebf9a
Fix incorrect @UnknownInitialization annotations
mernst May 26, 2016
1581214
Add needless final modifiers
mernst May 26, 2016
3cc702c
Better guarding for not-yet-initialized slices
mernst May 26, 2016
e01f567
Put final modifier on correct formal parameter
mernst May 26, 2016
45d5318
Capture stderr of etags
mernst May 26, 2016
2cd32ad
No error if etags is not installed, unless it is used
mernst May 26, 2016
727a0ae
Suppress a warning until Checker Framework issue 752 is fixed
jthaine May 27, 2016
d6678a0
Work around typetools/checker-framework#755
smillst May 27, 2016
913cfea
Fail script if any command it it fails
mernst May 31, 2016
55f08bc
Changelog for release 5.3.4
mernst May 31, 2016
579677a
Merge pull request #55 from smillst/master
markro49 May 31, 2016
5f07880
Change version to 5.3.4
markro49 Jun 1, 2016
d57fa0d
Bump version number for ongoing development.
markro49 Jun 1, 2016
4482b5a
Minor document corrections.
markro49 Jun 1, 2016
674d663
Use em-dash
mernst Jun 1, 2016
e1dbd6b
Merge branch 'master' of github.com:codespecs/daikon
mernst Jun 1, 2016
d6e2401
Add comment
mernst Jun 1, 2016
7263a18
Set pipefail option
mernst Jun 1, 2016
ae6662c
Merge branch 'master' of github.com:codespecs/daikon
mernst Jun 2, 2016
8969d50
Reference Simulink/Stateflow (SLSF) front end
mernst Jun 9, 2016
4483947
Update @menu that was missing the newest section
mernst Jun 9, 2016
43de106
Adapt to typetests organization
mernst Jun 10, 2016
92dd6fd
Change instances of the lock expression "itself" to "<self>"
jthaine Jun 15, 2016
76cfa18
Merge pull request #58 from codespecs/itself_to_self
jthaine Jun 15, 2016
3dd31dc
Add @RequiresNonNull annotation
mernst Jun 20, 2016
1830fed
Changes to goal files due to fixes in dyncomp_runtime.c.
markro49 Jun 20, 2016
0e929e3
Merge branch 'master' of ssh://github.com/codespecs/daikon
markro49 Jun 20, 2016
ec8d091
disable parallel make to debug problem on travis
markro49 Jun 21, 2016
ff17a27
remove rinjdael - it takes too long on Travis
markro49 Jun 21, 2016
54b3251
restore changes made for testing
markro49 Jun 21, 2016
4085dae
Don't run plume-lib tests, which use JUnit 4
mernst Jun 21, 2016
7cf523b
Include guava in plume.jar
mernst Jun 21, 2016
d92cf3d
Merge branch 'master' of github.com:codespecs/daikon
mernst Jun 21, 2016
916e9ab
Put class annotation and type annotation on different lines
mernst Jun 24, 2016
2cdee1d
new plume.jar with FileCompiler changes
markro49 Jun 24, 2016
def7c75
Merge branch 'master' of ssh://github.com/codespecs/daikon
markro49 Jun 24, 2016
471ceef
Update CHANGES file, fix spell check errors.
markro49 Jun 27, 2016
d0b1f54
Don't check format of generated files
mernst Jun 27, 2016
f14a2e8
Enforce formatting in file that creates .java files
mernst Jun 27, 2016
2f4f31e
Improve formatting
mernst Jun 27, 2016
cba5d81
Merge branch 'master' of github.com:codespecs/daikon
mernst Jun 27, 2016
f8d7ca5
temporary(?) turn off gtest - it takes too long
markro49 Jun 29, 2016
0e804ab
Merge branch 'master' of ssh://github.com/codespecs/daikon
markro49 Jun 29, 2016
f34d8a2
shorten rijndael running time via ppt-list-file
markro49 Jun 30, 2016
aa07de5
Turn gtest back on - rijndael was the problem.
markro49 Jul 5, 2016
8f24e37
set release date
markro49 Jul 5, 2016
a055d79
Change version to 5.3.6
markro49 Jul 5, 2016
99fab16
update microsoft research urls
markro49 Jul 5, 2016
f3eb662
Bump version number for ongoing development.
markro49 Jul 5, 2016
2383c9e
Fix typo
mernst Jul 6, 2016
ba5a5e7
Merge github.com:codespecs/daikon into xceptonHandle
mernst Jul 7, 2016
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17 changes: 3 additions & 14 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -104,20 +104,6 @@ doc/images/dfepl-flow.eps
doc/images/dfepl-flow.jpg
doc/images/dfepl-flow.pdf
doc/invariants-doc.texinfo
doc/valgrind-merge.aux
doc/valgrind-merge.cp
doc/valgrind-merge.cps
doc/valgrind-merge.fn
doc/valgrind-merge.fns
doc/valgrind-merge.html
doc/valgrind-merge.info
doc/valgrind-merge.ky
doc/valgrind-merge.log
doc/valgrind-merge.pdf
doc/valgrind-merge.pg
doc/valgrind-merge.toc
doc/valgrind-merge.tp
doc/valgrind-merge.vr
doc/www/pubs

# Files generated by java-cpp
Expand Down Expand Up @@ -452,6 +438,7 @@ tools/kmeans/*.o

examples/**/*.class
examples/**/*.dtrace.gz
examples/**/*.inv.gz

tests/**/*.class
tests/**/*.comp
Expand Down Expand Up @@ -512,3 +499,5 @@ tests/diff-tests/schedule2/schedule2*.txt
tests/chicory-tests/option-tests/*.txt
tests/**/merged/

# Coverity intermediate files
java/cov-int/
11 changes: 11 additions & 0 deletions .travis-build.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
#!/bin/bash -v

# Fail the whole script if any command fails
set -e

export SHELLOPTS

# TODO: The tests ought to work even if $DAIKONDIR is not set.
export DAIKONDIR=`pwd`

make nightly-test
52 changes: 52 additions & 0 deletions .travis.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
language: java

## Version for Ubuntu 14.04 Trusty.
## Problem: The job times out on travis-ci.org, but the container-based version
## does not.
# script: make DAIKONDIR=`pwd` nightly-test
# sudo: required
# dist: trusty
# before_install:
# - sudo apt-get update -qq
# - sudo apt-get install -qq graphviz texinfo texlive

## Version for container-based infrastructure.
## Skip generating the manual because the version of makeinfo installed
## on Ubuntu 12.04 Precise doesn't take the --pdf command-line option.
script: make DAIKONDIR=`pwd` nightly-test-except-doc-pdf
sudo: false
addons:
apt:
packages:
- graphviz
- texi2html
- texinfo
## Enable this when you wish to see JUnit reports.
## Disable to minimize use of Amazon S3.
# artifacts:
# paths:
# # "find tests -print" produces too long a command line
# - $(find tests -name '*txt*' -print | tr "\n" ":")
# - $(find tests -name '*decls*' -print | tr "\n" ":")
# s3_region: "us-west-2"
# debug: true
# On Travis-CI's Ubuntu 12.04 infrastructure, makeinfo does not take the
# --split=chapter command-line argument but texi2html does.
env: TEXI2HTML=texi2html

jdk:
- oraclejdk8
# - oraclejdk7
- openjdk7

after_success:
- |
if [[ ($TRAVIS_BRANCH == master) &&
($TRAVIS_PULL_REQUEST == false) &&
( (! $TRAVIS_JOB_NUMBER == *.*) || ($TRAVIS_JOB_NUMBER == *.1) ) ]] ; then
curl -LO https://raw.github.com/mernst/plume-lib/master/bin/trigger-travis.sh
sh trigger-travis.sh typetests daikon-typecheck $TRAVISTOKEN
fi

git:
depth: 3
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