A couple of projects (ZedGraph, MSGraph) were moved back to 4.0.

…new DLLS do not support reading MRM chromatograms)

* updated minimum .NET framework to 4.6.1
* added <assembly-dependency-ex> feature which allows specifying a subdirectory (<location-prefix>) for the DLL to be installed in (<assembly-dependency> always places the DLL next to the dependent target); I would have preferred to use the <assembly-dependency> feature, but because it is a 'dependency' feature, the value must be a file target, and it seems to strip subfeatures (e.g. <assembly-dependency>/path/to/some.DLL/<location-prefix>x64)

…k/20180518_MoveToNet452

* added Shimadzu TOF DLLs to WXS templates
* updated IDPicker project files to .NET 4.6.1

…u AnyCPU DLLs to tarball exclusion list

* fixed id attribute in IDPicker WIX template

* added TOF test file

…k/20180529_MoveToNet472

…to Skyline/work/20180529_MoveToNet472

… time zones

…to Skyline/work/20180529_MoveToNet472

Former-commit-id: b9c7a11e24be1444f50029d96221d08d9834ab1a

Former-commit-id: 3c678480f74904a62646f5c1fdea8e19a9424f72

Former-commit-id: 5bba2299bff7eec21cb34bf793f1ea4fe13964af

Former-commit-id: e629cdeb385f028abc5626d2f542dc55310f594b

Former-commit-id: 6c0afd83938c55b70023569189daa0c03ec3e0bc

- removed tss_pe.cpp from linking because it crashed with msvc-14.0
- disabled MassLynxRaw for msvc-14.0 (we don't yet have DLLs for that)

Former-commit-id: 25629c3445caaaf76c09d807258789d12c4e000d

- restore test library's source (accidentally deleted) back to boost tarball

Former-commit-id: 37d7c042f277d3f818fbe869577025f4590df25b

Former-commit-id: c166a3d11404fae9e999303f02b4d500c50e8941

…ide short form activationMethod values, as well as scan polarity and centroiding info. Code by user Parminder Kaur.

Former-commit-id: 9de69f0784f254a93943b85d02ffc8827ffdad72

* updated Boost to 1.67
* updated Boost-Build from latest master (this includes some warnings about coming lexer changes; the new lexer isn't turned on yet but it will be more lenient about whitespace in Jamfiles, e.g. requiring a space before semicolons)
* removed Boost.Filesystem jam logic about filesystem versions: v2 isn't in the code anymore
* removed MSVC version restrictions from Waters reader
* fixed some data dependencies copied around with common.copy (which seem to have broken somehow with Boost.Build changes) by using assembly-dependency instead, but this didn't work for doctests, so I moved Embedder's doctest into EmbedderTest
* removed `using namespace std;` from BlibFilter and BlibMaker, and fully specified the boost::log::aux::snprintf() calls to disambiguate them from ::snprintf() (which comes from including stdio.h in VC 2017 apparently, but not earlier VC)
* updated Agilent test tarball due to forcing fixed point Q1/Q3 masses

…mands for the latest VS version (i.e. the .NET projects)

* restored manifest dependencies to link action
* fixed warnings in UIMF reader

* reverted changes from make/copy to assembly-dependency (since it doesn't work on non-MSVC toolsets)

…t Parser; it was only being used vestigially anyway

…nto Skyline/work/20180529_MoveToNet472

…oWizard/pwiz into Skyline/work/20180529_MoveToNet472

… removed secure-scl=off since it's no longer relevant, and added unset-optimization flag so TeamCity can use optimization=speed and share many build artifacts with the core build

…oost 1.56 but not 1.62)

This reverts commit 71baca7.

* fixed make targets with new boost.build code by adding <dependency> on a build target, which makes all build features <relevant> (so <location> is calculated properly)
* fixed status detection in do_topograph_test action

…French

…tFrameworkVersion in Skyline.csproj (4.7.x or higher uses bjam toolset msvc-14.1, otherwise msvc-12.0)

…on TargetFrameworkVersion in Skyline.csproj (4.7.x or higher uses bjam toolset msvc-14.1, otherwise msvc-12.0)"

This reverts commit 2b0e29c - a couple of files got added by mistake.

* made Skyline build targets more granular
* fixed overzealous replace all in OptimizeTest (apparently I'm the only one with a '.' in their clone path!)

* commented out Topograph's MSTest:Clean since it doesn't seem to port well to VS 2017 and it may not be worth fixing
* fixed Skyline's test DLLs being deleted if build action fails

…isolate an issue that's been prematurely cutting off nightly tests

… termination, adding a catch for System.ComponentModel.InvalidAsynchronousStateException alongside the existing catch for InvalidOperationException on the hunch that it's the same condition but the OS now throws a different exception for it

* moved --incremental guard for generating version-ish files into generate-version.jam

* fixed --force-extract with libraries loaded via libraries/*.jam
* added no-clean option to tcbuild.bat

…o an attempt to include the unit test DLL more than once

…017-update

* updated project files to Visual Studio 2017 (msvc-14.1)
* updated Boost to 1.67
* updated Boost-Build from latest master (this includes some warnings about coming lexer changes; the new lexer isn't turned on yet but it will be more lenient about whitespace in Jamfiles, e.g. requiring a space before semicolons)
* added MSVC14 merge modules to installers
* added <assembly-dependency-ex> feature which allows specifying a subdirectory (<location-prefix>) for the DLL to be installed in (<assembly-dependency> always places the DLL next to the dependent target); I would have preferred to use the <assembly-dependency> feature, but because it is a 'dependency' feature, the value must be a file target, and it seems to strip subfeatures (e.g. <assembly-dependency>/path/to/some.DLL/<location-prefix>x64)
- added Shimadzu QTOF reader (still using old DataReader.dll because new DLLS do not support reading MRM chromatograms)
* cleaned up WXS templates by removing redundant Name and Id attributes
* updated Google.Protobuf.dll to version 3.5
* fixed getAnalysisDate() returning different time for different host time zones
* undefined "H5_HAVE_TIMEZONE" in order to fix VS2015 build.
* removed tss_pe.cpp from linking because it crashed with msvc-14.0
* fixed quickbuild not working with spaces in path
* updated pwiz RAMPAdapter to provide short form activationMethod values, as well as scan polarity and centroiding info.  Code by user Parminder Kaur.
* removed Boost.Filesystem jam logic about filesystem versions: v2 isn't in the code anymore
* removed MSVC version restrictions from Waters reader
* fixed some data dependencies copied around with common.copy (which seem to have broken somehow with Boost.Build changes) by using assembly-dependency instead, but this didn't work for doctests, so I moved Embedder's doctest into EmbedderTest
* removed `using namespace std;` from BlibFilter and BlibMaker, and fully specified the boost::log::aux::snprintf() calls to disambiguate them from ::snprintf() (which comes from including stdio.h in VC 2017 apparently, but not earlier VC)
* updated Agilent test tarball due to forcing fixed point Q1/Q3 masses
* added msvc_setup_script.bat for actions which need to access VS commands for the latest VS version (i.e. the .NET projects)
* fixed warnings in UIMF reader
* updated appveyor.yml
* removed boost.regex from Bumbershoot due to conflict with new Mascot Parser; it was only being used vestigially anyway
* replaced boost.regex with boost.xpressive in LibraryBabelFish
* changed build-apps.bat to use --abbreviate-paths instead of --hash, removed secure-scl=off since it's no longer relevant, and added unset-optimization flag so TeamCity can use optimization=speed and share many build artifacts with the core build
* fixed error trying to create directory '.' (apparently ignored in Boost 1.56 but not 1.62)
* fixed status detection in do_topograph_test action
* fixed Topograph and IDPicker tests for VS 2017
* made Skyline build targets more granular
* fixed overzealous replace all in OptimizeTest (apparently I'm the only one with a '.' in their clone path!)
* fixed 'libhdf5.settings: No such file or directory' error on Linux
* fixed BiblioSpec openswath/maxquant tests on Linux
* commented out Topograph's MSTest:Clean since it doesn't seem to port well to VS 2017 and it may not be worth fixing
* fixed Skyline's test DLLs being deleted if build action fails
* added --force-extract option for re-extracting tarballs
* added --force-generate-version to override --incremental
* moved --incremental guard for generating version-ish files into generate-version.jam
* added no-clean option to tcbuild.bat

…oWizard/pwiz into Skyline/work/20180529_MoveToNet472

…name and file copy messages ("1 file(s) copied")

…nto Skyline/work/20180529_MoveToNet472

- added instrument config to Shimadzu reader
* added Skyline test for basic reading of Shimadzu data

* updated project files to Visual Studio 2017 (msvc-14.1)
* updated Boost to 1.67
* updated Boost-Build from latest master (this includes some warnings about coming lexer changes; the new lexer isn't turned on yet but it will be more lenient about whitespace in Jamfiles, e.g. requiring a space before semicolons)
* added MSVC14 merge modules to installers
* added <assembly-dependency-ex> feature which allows specifying a subdirectory (<location-prefix>) for the DLL to be installed in (<assembly-dependency> always places the DLL next to the dependent target); I would have preferred to use the <assembly-dependency> feature, but because it is a 'dependency' feature, the value must be a file target, and it seems to strip subfeatures (e.g. <assembly-dependency>/path/to/some.DLL/<location-prefix>x64)
- added Shimadzu QTOF reader (still using old DataReader.dll because new DLLS do not support reading MRM chromatograms)
* cleaned up WXS templates by removing redundant Name and Id attributes
* updated Google.Protobuf.dll to version 3.5
* fixed getAnalysisDate() returning different time for different host time zones
* undefined "H5_HAVE_TIMEZONE" in order to fix VS2015 build.
* removed tss_pe.cpp from linking because it crashed with msvc-14.0
* fixed quickbuild not working with spaces in path
* updated pwiz RAMPAdapter to provide short form activationMethod values, as well as scan polarity and centroiding info.  Code by user Parminder Kaur.
* removed Boost.Filesystem jam logic about filesystem versions: v2 isn't in the code anymore
* removed MSVC version restrictions from Waters reader
* fixed some data dependencies copied around with common.copy (which seem to have broken somehow with Boost.Build changes) by using assembly-dependency instead, but this didn't work for doctests, so I moved Embedder's doctest into EmbedderTest
* removed `using namespace std;` from BlibFilter and BlibMaker, and fully specified the boost::log::aux::snprintf() calls to disambiguate them from ::snprintf() (which comes from including stdio.h in VC 2017 apparently, but not earlier VC)
* updated Agilent test tarball due to forcing fixed point Q1/Q3 masses
* added msvc_setup_script.bat for actions which need to access VS commands for the latest VS version (i.e. the .NET projects)
* fixed warnings in UIMF reader
* updated appveyor.yml
* removed boost.regex from Bumbershoot due to conflict with new Mascot Parser; it was only being used vestigially anyway
* replaced boost.regex with boost.xpressive in LibraryBabelFish
* changed build-apps.bat to use --abbreviate-paths instead of --hash, removed secure-scl=off since it's no longer relevant, and added unset-optimization flag so TeamCity can use optimization=speed and share many build artifacts with the core build
* fixed error trying to create directory '.' (apparently ignored in Boost 1.56 but not 1.62)
* fixed status detection in do_topograph_test action
* fixed Topograph and IDPicker tests for VS 2017
* made Skyline build targets more granular
* fixed overzealous replace all in OptimizeTest (apparently I'm the only one with a '.' in their clone path!)
* fixed 'libhdf5.settings: No such file or directory' error on Linux
* fixed BiblioSpec openswath/maxquant tests on Linux
* commented out Topograph's MSTest:Clean since it doesn't seem to port well to VS 2017 and it may not be worth fixing
* fixed Skyline's test DLLs being deleted if build action fails
* added --force-extract option for re-extracting tarballs
* added --force-generate-version to override --incremental
* moved --incremental guard for generating version-ish files into generate-version.jam
* added no-clean option to tcbuild.bat

- added instrument config to Shimadzu reader
* added Skyline test for basic reading of Shimadzu data

* fixed SkylineTester to return non-zero exit code when it fails to create zip file
* changed SkylineTester to use AttachConsole() instead of AllocConsole() so that it uses the current console instead of creating new windows when building from command-line

…oWizard/pwiz into Skyline/work/20180529_MoveToNet472

…g a file, there's no point in putting up a retry dialog as it's an unattended script

…om/ProteoWizard/pwiz into Skyline/work/20180529_MoveToNet472

…ng with unedeletable files

…e source tree can't be removed before updating (maybe a race condition due to asynch call?). Simplify the situation by replacing use of UI element DeleteWIndow with a simple synchronous call to Directory.Delete