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* feat: gui: File Picker

Squashed commit of the following:

commit f7600554889da2e2b12ad60b00debe596fb77d4c
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 18 07:47:20 2019 +0200

    test: fix getParentPathname test for backslash case

commit 1f3dafef0dd0785ab90c837d9fc32f6ad284cdbf
Merge: 086029a 5af99c6
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 17 14:16:15 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 086029a193568a0ee95f3cd17e015bca79588e55
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 17 14:10:32 2019 +0200

    test: getPathnameContent: adjust file size for Windows

commit 2f354b75cc1e8ed39a347e2ffbc28f5a6d7c6e67
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 17 14:09:39 2019 +0200

    test: review getParentPathname, Windows errors

commit f851674a17db95e66f12d4b76f5a85555a7c2673
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 21 11:46:39 2019 +0200

    style: rename applyPermutation to sortPairs

commit 271c2ea5cb1b0e86d1304ef3ccff13924e86ea39
Author: Douglas McCloskey <dmccloskey87@gmail.com>
Date:   Sun May 19 10:41:46 2019 +0200

    fix: implicit conversion from char to plog::util::nstring

commit 6c9d88305f45ba5fe24c5bbe02c183ea8cc563da
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 12:50:36 2019 +0200

    docs: Add docstrings for functions endsWith, getPathnameContent, getParentPathname, applyPermutation, is_less_than_icase, directorySize

commit 1dfc93df289ca71d80cf03f9dc602d40d77f54b9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:12:50 2019 +0200

    style: fix indentation in AppWindow::HelpMarker()

commit 07bdc05bef5538c0ad7891c52018c4046a49dc77
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:10:12 2019 +0200

    chore: remove dirent.h file

commit 64ad1c3bc60fd69384921a160663f74f0bc523bf
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:05:06 2019 +0200

    chore: remove Table.(h|cpp) files

commit bf944faccec33cbdb885ee350e6e1c79949e45de
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 13:09:12 2019 +0200

    style: make Widget class abstract, ::draw() is a pure virtual method

commit 9703cccaf880800cfb2188d3a5b2872de64f8954
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 11:24:22 2019 +0200

    style: FilePicker inherits from Widget

commit c46e70149da8e1bcef893aae705115e68dd3e9ec
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 10:35:44 2019 +0200

    style: rename Widget::show() (and derived classes') to ::draw()

commit a8076a06f2da0e09d6b5c8cceedad17ec0a1bd1d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 10:31:45 2019 +0200

    style: Widget's show() method is consistent in derived classes (no arguments)

commit 9e6811fbf8017e70b43b0735d4869bda5f0c7739
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 15:50:47 2019 +0200

    style: move FilePicker's widget title to class members, draw() has no arguments

commit 31a69d6cbd5df481cc8d94eef3267373e7fbe2e5
Merge: a2f7934 7ff25c1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 15:07:05 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit a2f79348b7713fe08ac590bb25f571c89f030e85
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 14:42:58 2019 +0200

    CI: install dependency libboost-filesystem-dev apt package

commit eaba243599da771cc77f2f37278c49305fb00fc4
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 14:25:42 2019 +0200

    refactor: remove class Table, use boost::filesystem

commit 61d879ac6c649a67cd9f37917fcf335fe2bf5178
Author: Douglas McCloskey <dmccloskey87@gmail.com>
Date:   Mon May 13 10:26:22 2019 +0200

    cmake: boost filesystem

commit b279d5e0a515bdec78bc9e9ef50284b22af867dc
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 9 12:55:19 2019 +0200

    fix: getParentPathname() does not fail on first-level path

    refactor: getParentPathname() uses new functions isRootPathname() and cleanupPathname()

    test: update getParentPathname() tests and add tests for new functions

commit c3cfc9730acd098edb086385968957f58c4805ff
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 15:20:48 2019 +0200

    feat: user can set a custom pathname (e.g. to change from C: to D:)

    closes #198

commit ae34abcb80ac86590bc2c620dfb71979e9ee261c
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 11:15:32 2019 +0200

    fix: Utilities_test folder's content updated

commit c5ae62b84a9bd2015711c5e2d7748b3ba4f42fd2
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 10:56:41 2019 +0200

    CI: debug Utilities_test failure, printing folder's content

commit 99088abf058277132b45da59145f3a59ad22ed74
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 10:56:15 2019 +0200

    test: add an output folder for tests' output data

commit 655346d6178fd4dfd57d5bbb95052827d20103b4
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 09:48:15 2019 +0200

    CI: ctest is verbose

commit 973ce6841f984444d76a56ee13d5a727da1ff8e8
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 09:46:18 2019 +0200

    fix: attempt to fix 'stat *' definition missing in Windows

commit 733fd121173f9ceb9fda44776b7981fe38263686
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 09:45:26 2019 +0200

    style: make Utilities::getPathnameContent() warning-free

commit a28f753ae6bacab5e51acf550e009ca60aa0a9f9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 16:43:33 2019 +0200

    test: Utilities::getParentPathname() (and fixes, accordingly)

commit eb82c815a20c0b1b1bed26ddf0c911927b4922f4
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 13:51:47 2019 +0200

    test: Utilities::getPathnameContent()

commit 4a8a04355112c21ee5074660f43835869f5df9f1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 12:41:50 2019 +0200

    fix: initialize ostringstream correctly in CastValue's operator std::string()

commit d2e60a981cd5309c2c526fbecb539a3f8b1b01b0
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 10:50:11 2019 +0200

    feat: CastValue can implicitly be cast to std::string (operator std::string())

commit 3b718d37b9b6e6a61ebfa8f1721b6864a22ef85f
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 10:48:56 2019 +0200

    refactor: move Column's methods up to Table, remove class Column, use typedef

commit 04bd167c86fa72f5db44407e3d39c2fa733db23a
Merge: 59dabd8 ff29218
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri May 3 11:05:11 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 59dabd8801067d01314f0aa070c5eba34aca4ef1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri May 3 11:04:43 2019 +0200

    fix: move dirent.h file from ui to core

commit 5b2ff8f14d6bef3fef44080bacdbb31a3b03b2c1
Merge: 99b5a1a 53b0abe
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 2 13:11:25 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 99b5a1a2752b17c14ed30510668a6f4d81b3be94
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 1 15:33:52 2019 +0200

    style: respect order of definition of data members in constructors

commit 0f844c95abffc554ac142bd945a0740899e27eb8
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 1 15:15:54 2019 +0200

    style: const_cast safe signed/unsigned comparison

commit 25ef79c49bb5195f042898de99be2288bc0d4c03
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 1 15:14:52 2019 +0200

    fix: Widget: polymorphic class' destructor is virtual

commit b65367fdfc9e377a146ea79664090465d0157501
Merge: 01bd972 9834d71
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 30 16:32:41 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 01bd97289a4a1b3a1dc9968315ea56c5bb4c6521
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 30 16:23:08 2019 +0200

    style: move getPathnameContent and getParentPathname to Utilities

    style: move CastValue implementation out of Utilities

    feat: move ui file picker code to class FilePicker

commit 27629c650b51b5fd48ea15156bf50736ba079572
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 29 15:11:06 2019 +0200

    feat: getPathnameContent uses class Table, and fetches name, size, type and date of entries

commit 35c7f1ee1d54a15d90eb3d5cbd09db8fe1b7a984
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 29 15:10:29 2019 +0200

    feat: implement class Table to manage column-oriented data

commit d72ae6e33b6af3e036aba330578898bcfbe6e00c
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 29 15:05:30 2019 +0200

    feat: implement Utilities::CastValue::is_less_than()

    feat: implement operator<< for CastValue

commit 8c71e889f3a12d419334dac10a5886cad86813d9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Apr 25 13:41:50 2019 +0200

    feat: Utilities::CastValue supports long int

commit 81a1a15381f1e83320a25ec75929978acbd6973d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 23 11:27:35 2019 +0200

    chore: add dirent.h for Windows compatibility

commit 4abf6cfcf10b29b8f4e37b6d14ac52ae1182f147
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 16:18:08 2019 +0200

    style: move endsWith() to class Utilities

    test: Utilities::endsWith()

commit af0ddd9615e1147eb80be5a4508d50cd685ccd7a
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 15:58:46 2019 +0200

    feat: endsWith() supports case-insensitive

    feat: file picker's extensions-filter is case insensitive

commit cbdf4fd9b3b01e96fb04d54161272d5754667f25
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 15:38:02 2019 +0200

    feat: file picker shows content in columns / table

    fix: selected_pathname gets the pathname, not the filename

commit c379674f624ddeb34bb7965648c0cb97d3b39d82
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 14:24:37 2019 +0200

    feat: file type filter

    feat: implement endsWith() for strings

commit acfa6a5ff2f601ff8b5467558baba72e52faf91e
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 13:37:57 2019 +0200

    move AppWindow definition out of the main loop

commit 6d4b9af10dc165a2f90e92a0f5aa9ea6c48c3d60
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 13:26:53 2019 +0200

    style: Simplified one-liner Combo() for file type / extension selection

commit b29b1bcf0b64c42fe17164aed9dd4bf11498c519
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 13:09:18 2019 +0200

    feat: add filename input text, put "ok" and "cancel" buttons on same line

commit 6c6c6041be12589a77c4630e28ff2892660a1c9f
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 16 16:51:10 2019 +0200

    feat: getParentPathname()

    feat: use single-pane navigation

    feat: add "go up" directory button

    feat: do not insert "." and ".." to folder content

commit ba4b0f97a29eeb39c0118afa6277b92856b7ceac
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 15 16:52:45 2019 +0200

    feat: navigate directories, show their content

* refactor: SequenceProcessor, AppState, AppStateProcessor

Squashed commit of the following:

commit bb781fc4e0914f5f421221787996801bf73c25dd
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 17 10:21:29 2019 +0200

    style: move SequenceHandler* data member to base abstract class SequenceProcessor

commit a1841bee418686d783b41bab43a12b3678555fae
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri Jun 14 13:19:00 2019 +0200

    refactor: Improve AppStateProcessor hierarchy, remove unnecessary structs, make them private methods

commit 71872bea015debe1b88e26d9f6a33c6b5c1ef626
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 4 12:59:46 2019 +0200

    test: make test pass trivial check, constructor takes an argument

commit ad3322c4da19e6a5b16c4a3105b77f0ece16e490
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 4 12:38:35 2019 +0200

    fix: cmake config for UI tests

commit 0659dc31f07621c116724163ab9adfaa73dc7ce3
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 4 10:59:20 2019 +0200

    Revert "fix (not really): disable building ui tests"

    This reverts commit 4a31b86236fb0b4459efe7eca6719825c817550d.

commit 7756b56ebfbbdec9d8dae4d2e1078082b45b0616
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 3 14:16:33 2019 +0200

    feat: GUI can load a session from a sequence

    feat: implement processor LoadSessionFromSequence

    style: CLI uses LoadSessionFromSequence

    feat: add AppState to AppWindow

commit 561a21e80434a4b58c3548bcd6130dead9abf3a1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 3 14:08:59 2019 +0200

    feat: add AppStateProcessor logic to FilePicker

commit fe7c518d4747834d68dbde481f3ff0d4ad8602f0
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 28 15:11:04 2019 +0200

    refactor: AppStateProcessor's methods become structs/classes

commit 4a31b86236fb0b4459efe7eca6719825c817550d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 16:22:40 2019 +0200

    fix (not really): disable building ui tests

commit 380f13762659d61fee4adeae53e11eabe0363df7
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 15:40:16 2019 +0200

    Revert "TEST: see if it still can't link"

    This reverts commit 8e952b07fc2d9556a4a5217918aedbd7f1631eb0.

commit 8e952b07fc2d9556a4a5217918aedbd7f1631eb0
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 15:24:38 2019 +0200

    TEST: see if it still can't link

commit a7203bfe8280f544e6ffb792f8cd448d360a7d22
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 15:24:06 2019 +0200

    chore: explicit includes in Widget

commit bba1e3cbe905a47fadfe7276f9ac952bf5931663
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 14:56:30 2019 +0200

    refactor: make FilePicker instance a class member of AppWindow

commit 89c3856c9646b16f154b6875413c3afee86ce653
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 11:36:52 2019 +0200

    style: AppWindow's methods are not static, remove unnecessary includes

commit ba8489a9889b7880978ecb3d16afe060cd8805fb
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 11:13:11 2019 +0200

    Revert "CI: add --no-install-recommends to apt-get"

    This reverts commit ef0b964babf5603c0f11cdfc461cc0f34b3efd66.

commit ef0b964babf5603c0f11cdfc461cc0f34b3efd66
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 11:04:21 2019 +0200

    CI: add --no-install-recommends to apt-get

commit fd39238a98a81cf51f4357cea438c2c32bd39b2d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 10:59:33 2019 +0200

    Revert "CI: (temporary change) Build OpenMS in Release mode (to speedup CI)"

    This reverts commit 622cc4bddaca5c9ca134698fcd459ca7499094db.

commit 80636757b58399d2a90d553d9adea695a3054d7a
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:46:33 2019 +0200

    Revert "style: add a FilePicker instance to AppWindow's state, avoiding passing the instance between static methods"

    This reverts commit bd00640df0711489f31c4de844f3636c22eccaad.

commit 622cc4bddaca5c9ca134698fcd459ca7499094db
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:45:43 2019 +0200

    CI: (temporary change) Build OpenMS in Release mode (to speedup CI)

commit 352fb3bdccd19774e07552fc2004d321819e4fab
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:44:18 2019 +0200

    CI: Add "--depth 1" to git clone OpenMS command

commit ec6d651eeb248fa8d283616ff303b4423c8aef33
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:30:26 2019 +0200

    Revert "refactor: AppStateProcessor's methods become structs/classes"

    This reverts commit b59324aad8703a31bce01aa809e96141a0fda124.

commit b59324aad8703a31bce01aa809e96141a0fda124
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 28 15:11:04 2019 +0200

    refactor: AppStateProcessor's methods become structs/classes

commit bd00640df0711489f31c4de844f3636c22eccaad
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 27 16:50:21 2019 +0200

    style: add a FilePicker instance to AppWindow's state, avoiding passing the instance between static methods

    Methods are not static anymore, because they deal with AppWindow's state.

commit 74b3bf1347e7b70b02b9450a8cddbad45c56de41
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 27 15:18:28 2019 +0200

    refactor: separate CLI functionalities into AppState and AppStateProcessor

commit f04b5cd4d7e4d5c4d2ba1d13d6248a3765500215
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri May 24 12:26:58 2019 +0200

    fix: interface classes suppress copying

commit d0e8a44cfbe375ebe7e7f0f3622da5c7db72dce2
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 22 15:10:11 2019 +0200

    feat: implement mainMenuString

commit c5925ee99014fd302c474b9f4beca504205ffbe5
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 22 15:09:38 2019 +0200

    style: reduce/remove data from classes/struct RawDataProcessor and SequenceSegmentProcessor

commit 61ac71b6fe69c18e10f4dda459609ae340558d63
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 22 10:21:05 2019 +0200

    style: implement initializeDataDir() to simplify initializeDataDirs()

commit af04c7adb0a1055be34f9207531a15f57cf9bc38
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 21 15:58:32 2019 +0200

    refactor: SequenceProcessor is a base class

    Previous methods are now derived classes.

commit 271c2ea5cb1b0e86d1304ef3ccff13924e86ea39
Author: Douglas McCloskey <dmccloskey87@gmail.com>
Date:   Sun May 19 10:41:46 2019 +0200

    fix: implicit conversion from char to plog::util::nstring

commit 6c9d88305f45ba5fe24c5bbe02c183ea8cc563da
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 12:50:36 2019 +0200

    docs: Add docstrings for functions endsWith, getPathnameContent, getParentPathname, applyPermutation, is_less_than_icase, directorySize

commit 1dfc93df289ca71d80cf03f9dc602d40d77f54b9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:12:50 2019 +0200

    style: fix indentation in AppWindow::HelpMarker()

commit 07bdc05bef5538c0ad7891c52018c4046a49dc77
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:10:12 2019 +0200

    chore: remove dirent.h file

commit 64ad1c3bc60fd69384921a160663f74f0bc523bf
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:05:06 2019 +0200

    chore: remove Table.(h|cpp) files

commit bf944faccec33cbdb885ee350e6e1c79949e45de
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 13:09:12 2019 +0200

    style: make Widget class abstract, ::draw() is a pure virtual method

commit 9703cccaf880800cfb2188d3a5b2872de64f8954
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 11:24:22 2019 +0200

    style: FilePicker inherits from Widget

commit c46e70149da8e1bcef893aae705115e68dd3e9ec
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 10:35:44 2019 +0200

    style: rename Widget::show() (and derived classes') to ::draw()

commit a8076a06f2da0e09d6b5c8cceedad17ec0a1bd1d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 10:31:45 2019 +0200

    style: Widget's show() method is consistent in derived classes (no arguments)

commit 9e6811fbf8017e70b43b0735d4869bda5f0c7739
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 15:50:47 2019 +0200

    style: move FilePicker's widget title to class members, draw() has no arguments

commit 31a69d6cbd5df481cc8d94eef3267373e7fbe2e5
Merge: a2f7934 7ff25c1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 15:07:05 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit a2f79348b7713fe08ac590bb25f571c89f030e85
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 14:42:58 2019 +0200

    CI: install dependency libboost-filesystem-dev apt package

commit eaba243599da771cc77f2f37278c49305fb00fc4
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 14:25:42 2019 +0200

    refactor: remove class Table, use boost::filesystem

commit 61d879ac6c649a67cd9f37917fcf335fe2bf5178
Author: Douglas McCloskey <dmccloskey87@gmail.com>
Date:   Mon May 13 10:26:22 2019 +0200

    cmake: boost filesystem

commit b279d5e0a515bdec78bc9e9ef50284b22af867dc
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 9 12:55:19 2019 +0200

    fix: getParentPathname() does not fail on first-level path

    refactor: getParentPathname() uses new functions isRootPathname() and cleanupPathname()

    test: update getParentPathname() tests and add tests for new functions

commit c3cfc9730acd098edb086385968957f58c4805ff
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 15:20:48 2019 +0200

    feat: user can set a custom pathname (e.g. to change from C: to D:)

    closes #198

commit ae34abcb80ac86590bc2c620dfb71979e9ee261c
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 11:15:32 2019 +0200

    fix: Utilities_test folder's content updated

commit c5ae62b84a9bd2015711c5e2d7748b3ba4f42fd2
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 10:56:41 2019 +0200

    CI: debug Utilities_test failure, printing folder's content

commit 99088abf058277132b45da59145f3a59ad22ed74
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 10:56:15 2019 +0200

    test: add an output folder for tests' output data

commit 655346d6178fd4dfd57d5bbb95052827d20103b4
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 09:48:15 2019 +0200

    CI: ctest is verbose

commit 973ce6841f984444d76a56ee13d5a727da1ff8e8
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 09:46:18 2019 +0200

    fix: attempt to fix 'stat *' definition missing in Windows

commit 733fd121173f9ceb9fda44776b7981fe38263686
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 09:45:26 2019 +0200

    style: make Utilities::getPathnameContent() warning-free

commit a28f753ae6bacab5e51acf550e009ca60aa0a9f9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 16:43:33 2019 +0200

    test: Utilities::getParentPathname() (and fixes, accordingly)

commit eb82c815a20c0b1b1bed26ddf0c911927b4922f4
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 13:51:47 2019 +0200

    test: Utilities::getPathnameContent()

commit 4a8a04355112c21ee5074660f43835869f5df9f1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 12:41:50 2019 +0200

    fix: initialize ostringstream correctly in CastValue's operator std::string()

commit d2e60a981cd5309c2c526fbecb539a3f8b1b01b0
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 10:50:11 2019 +0200

    feat: CastValue can implicitly be cast to std::string (operator std::string())

commit 3b718d37b9b6e6a61ebfa8f1721b6864a22ef85f
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 10:48:56 2019 +0200

    refactor: move Column's methods up to Table, remove class Column, use typedef

commit 04bd167c86fa72f5db44407e3d39c2fa733db23a
Merge: 59dabd8 ff29218
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri May 3 11:05:11 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 59dabd8801067d01314f0aa070c5eba34aca4ef1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri May 3 11:04:43 2019 +0200

    fix: move dirent.h file from ui to core

commit 5b2ff8f14d6bef3fef44080bacdbb31a3b03b2c1
Merge: 99b5a1a 53b0abe
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 2 13:11:25 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 99b5a1a2752b17c14ed30510668a6f4d81b3be94
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 1 15:33:52 2019 +0200

    style: respect order of definition of data members in constructors

commit 0f844c95abffc554ac142bd945a0740899e27eb8
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 1 15:15:54 2019 +0200

    style: const_cast safe signed/unsigned comparison

commit 25ef79c49bb5195f042898de99be2288bc0d4c03
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 1 15:14:52 2019 +0200

    fix: Widget: polymorphic class' destructor is virtual

commit b65367fdfc9e377a146ea79664090465d0157501
Merge: 01bd972 9834d71
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 30 16:32:41 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 01bd97289a4a1b3a1dc9968315ea56c5bb4c6521
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 30 16:23:08 2019 +0200

    style: move getPathnameContent and getParentPathname to Utilities

    style: move CastValue implementation out of Utilities

    feat: move ui file picker code to class FilePicker

commit 27629c650b51b5fd48ea15156bf50736ba079572
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 29 15:11:06 2019 +0200

    feat: getPathnameContent uses class Table, and fetches name, size, type and date of entries

commit 35c7f1ee1d54a15d90eb3d5cbd09db8fe1b7a984
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 29 15:10:29 2019 +0200

    feat: implement class Table to manage column-oriented data

commit d72ae6e33b6af3e036aba330578898bcfbe6e00c
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 29 15:05:30 2019 +0200

    feat: implement Utilities::CastValue::is_less_than()

    feat: implement operator<< for CastValue

commit 8c71e889f3a12d419334dac10a5886cad86813d9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Apr 25 13:41:50 2019 +0200

    feat: Utilities::CastValue supports long int

commit 81a1a15381f1e83320a25ec75929978acbd6973d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 23 11:27:35 2019 +0200

    chore: add dirent.h for Windows compatibility

commit 4abf6cfcf10b29b8f4e37b6d14ac52ae1182f147
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 16:18:08 2019 +0200

    style: move endsWith() to class Utilities

    test: Utilities::endsWith()

commit af0ddd9615e1147eb80be5a4508d50cd685ccd7a
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 15:58:46 2019 +0200

    feat: endsWith() supports case-insensitive

    feat: file picker's extensions-filter is case insensitive

commit cbdf4fd9b3b01e96fb04d54161272d5754667f25
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 15:38:02 2019 +0200

    feat: file picker shows content in columns / table

    fix: selected_pathname gets the pathname, not the filename

commit c379674f624ddeb34bb7965648c0cb97d3b39d82
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 14:24:37 2019 +0200

    feat: file type filter

    feat: implement endsWith() for strings

commit acfa6a5ff2f601ff8b5467558baba72e52faf91e
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 13:37:57 2019 +0200

    move AppWindow definition out of the main loop

commit 6d4b9af10dc165a2f90e92a0f5aa9ea6c48c3d60
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 13:26:53 2019 +0200

    style: Simplified one-liner Combo() for file type / extension selection

commit b29b1bcf0b64c42fe17164aed9dd4bf11498c519
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 13:09:18 2019 +0200

    feat: add filename input text, put "ok" and "cancel" buttons on same line

commit 6c6c6041be12589a77c4630e28ff2892660a1c9f
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 16 16:51:10 2019 +0200

    feat: getParentPathname()

    feat: use single-pane navigation

    feat: add "go up" directory button

    feat: do not insert "." and ".." to folder content

commit ba4b0f97a29eeb39c0118afa6277b92856b7ceac
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 15 16:52:45 2019 +0200

    feat: navigate directories, show their content

* feat: gui: Workflow modal widget

Squashed commit of the following:

commit a74eeb308d7a019dc66312e776922d663464cd2a
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 13 14:54:32 2019 +0200

    test: AppStateProcessor::BuildCommandsFromIds

commit 472419ca9294703292ac4853cabcb5ecd70d1c45
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 13 14:54:03 2019 +0200

    feat: implement Appstate::Command::getID()

commit fb0900c836df438f15d4285111e5a94a99f3bfee
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 11 14:34:50 2019 +0200

    fix: avoid shadowing menu item with text below/under (level, z-index wise) it in workflow steps. Use Button instead of Text

commit 104fe2eb0d0eb7b74b77c2156ac65b235a06c7eb
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 6 15:10:33 2019 +0200

    feat: drag and drop steps

commit b44c19476c8972d46d89d5a403f3edce53437015
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 6 13:26:07 2019 +0200

    feat: add Workflow widget to the application

    The user can access this view from menu: Edit -> Workflows

commit 171488b3508d79f024be47879f5c35336a46fc16
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 6 13:25:32 2019 +0200

    feat: implement class Workflow, which helps with selecting the methods/steps to run

commit 28e4be4361bda2dd9b5bc79e9a4ac69f9bc620d9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 6 13:16:02 2019 +0200

    feat: Add processor class BuildCommandsFromIds to AppStateProcessor

    This code was present in CLI.cpp. It is now separated and implemented in AppStateProcessor so that also the GUI can make use of it

    style: replace unordered_map with map so that workflow's steps can be iterated in sorted order (by their IDs, here keys of the maps)

    feat: class Command implements getName(). This method returns the name of the workflow step, no matter the type of the processor (either raw data or sequence segment)

commit 71872bea015debe1b88e26d9f6a33c6b5c1ef626
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 4 12:59:46 2019 +0200

    test: make test pass trivial check, constructor takes an argument

commit ad3322c4da19e6a5b16c4a3105b77f0ece16e490
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 4 12:38:35 2019 +0200

    fix: cmake config for UI tests

commit 0659dc31f07621c116724163ab9adfaa73dc7ce3
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 4 10:59:20 2019 +0200

    Revert "fix (not really): disable building ui tests"

    This reverts commit 4a31b86236fb0b4459efe7eca6719825c817550d.

commit 7756b56ebfbbdec9d8dae4d2e1078082b45b0616
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 3 14:16:33 2019 +0200

    feat: GUI can load a session from a sequence

    feat: implement processor LoadSessionFromSequence

    style: CLI uses LoadSessionFromSequence

    feat: add AppState to AppWindow

commit 561a21e80434a4b58c3548bcd6130dead9abf3a1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 3 14:08:59 2019 +0200

    feat: add AppStateProcessor logic to FilePicker

commit fe7c518d4747834d68dbde481f3ff0d4ad8602f0
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 28 15:11:04 2019 +0200

    refactor: AppStateProcessor's methods become structs/classes

commit 4a31b86236fb0b4459efe7eca6719825c817550d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 16:22:40 2019 +0200

    fix (not really): disable building ui tests

commit 380f13762659d61fee4adeae53e11eabe0363df7
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 15:40:16 2019 +0200

    Revert "TEST: see if it still can't link"

    This reverts commit 8e952b07fc2d9556a4a5217918aedbd7f1631eb0.

commit 8e952b07fc2d9556a4a5217918aedbd7f1631eb0
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 15:24:38 2019 +0200

    TEST: see if it still can't link

commit a7203bfe8280f544e6ffb792f8cd448d360a7d22
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 15:24:06 2019 +0200

    chore: explicit includes in Widget

commit bba1e3cbe905a47fadfe7276f9ac952bf5931663
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 14:56:30 2019 +0200

    refactor: make FilePicker instance a class member of AppWindow

commit 89c3856c9646b16f154b6875413c3afee86ce653
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 11:36:52 2019 +0200

    style: AppWindow's methods are not static, remove unnecessary includes

commit ba8489a9889b7880978ecb3d16afe060cd8805fb
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 11:13:11 2019 +0200

    Revert "CI: add --no-install-recommends to apt-get"

    This reverts commit ef0b964babf5603c0f11cdfc461cc0f34b3efd66.

commit ef0b964babf5603c0f11cdfc461cc0f34b3efd66
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 11:04:21 2019 +0200

    CI: add --no-install-recommends to apt-get

commit fd39238a98a81cf51f4357cea438c2c32bd39b2d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 10:59:33 2019 +0200

    Revert "CI: (temporary change) Build OpenMS in Release mode (to speedup CI)"

    This reverts commit 622cc4bddaca5c9ca134698fcd459ca7499094db.

commit 80636757b58399d2a90d553d9adea695a3054d7a
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:46:33 2019 +0200

    Revert "style: add a FilePicker instance to AppWindow's state, avoiding passing the instance between static methods"

    This reverts commit bd00640df0711489f31c4de844f3636c22eccaad.

commit 622cc4bddaca5c9ca134698fcd459ca7499094db
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:45:43 2019 +0200

    CI: (temporary change) Build OpenMS in Release mode (to speedup CI)

commit 352fb3bdccd19774e07552fc2004d321819e4fab
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:44:18 2019 +0200

    CI: Add "--depth 1" to git clone OpenMS command

commit ec6d651eeb248fa8d283616ff303b4423c8aef33
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:30:26 2019 +0200

    Revert "refactor: AppStateProcessor's methods become structs/classes"

    This reverts commit b59324aad8703a31bce01aa809e96141a0fda124.

commit b59324aad8703a31bce01aa809e96141a0fda124
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 28 15:11:04 2019 +0200

    refactor: AppStateProcessor's methods become structs/classes

commit bd00640df0711489f31c4de844f3636c22eccaad
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 27 16:50:21 2019 +0200

    style: add a FilePicker instance to AppWindow's state, avoiding passing the instance between static methods

    Methods are not static anymore, because they deal with AppWindow's state.

commit 74b3bf1347e7b70b02b9450a8cddbad45c56de41
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 27 15:18:28 2019 +0200

    refactor: separate CLI functionalities into AppState and AppStateProcessor

commit f04b5cd4d7e4d5c4d2ba1d13d6248a3765500215
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri May 24 12:26:58 2019 +0200

    fix: interface classes suppress copying

commit d0e8a44cfbe375ebe7e7f0f3622da5c7db72dce2
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 22 15:10:11 2019 +0200

    feat: implement mainMenuString

commit c5925ee99014fd302c474b9f4beca504205ffbe5
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 22 15:09:38 2019 +0200

    style: reduce/remove data from classes/struct RawDataProcessor and SequenceSegmentProcessor

commit 61ac71b6fe69c18e10f4dda459609ae340558d63
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 22 10:21:05 2019 +0200

    style: implement initializeDataDir() to simplify initializeDataDirs()

commit af04c7adb0a1055be34f9207531a15f57cf9bc38
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 21 15:58:32 2019 +0200

    refactor: SequenceProcessor is a base class

    Previous methods are now derived classes.

commit 271c2ea5cb1b0e86d1304ef3ccff13924e86ea39
Author: Douglas McCloskey <dmccloskey87@gmail.com>
Date:   Sun May 19 10:41:46 2019 +0200

    fix: implicit conversion from char to plog::util::nstring

commit 6c9d88305f45ba5fe24c5bbe02c183ea8cc563da
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 12:50:36 2019 +0200

    docs: Add docstrings for functions endsWith, getPathnameContent, getParentPathname, applyPermutation, is_less_than_icase, directorySize

commit 1dfc93df289ca71d80cf03f9dc602d40d77f54b9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:12:50 2019 +0200

    style: fix indentation in AppWindow::HelpMarker()

commit 07bdc05bef5538c0ad7891c52018c4046a49dc77
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:10:12 2019 +0200

    chore: remove dirent.h file

commit 64ad1c3bc60fd69384921a160663f74f0bc523bf
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:05:06 2019 +0200

    chore: remove Table.(h|cpp) files

commit bf944faccec33cbdb885ee350e6e1c79949e45de
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 13:09:12 2019 +0200

    style: make Widget class abstract, ::draw() is a pure virtual method

commit 9703cccaf880800cfb2188d3a5b2872de64f8954
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 11:24:22 2019 +0200

    style: FilePicker inherits from Widget

commit c46e70149da8e1bcef893aae705115e68dd3e9ec
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 10:35:44 2019 +0200

    style: rename Widget::show() (and derived classes') to ::draw()

commit a8076a06f2da0e09d6b5c8cceedad17ec0a1bd1d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 10:31:45 2019 +0200

    style: Widget's show() method is consistent in derived classes (no arguments)

commit 9e6811fbf8017e70b43b0735d4869bda5f0c7739
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 15:50:47 2019 +0200

    style: move FilePicker's widget title to class members, draw() has no arguments

commit 31a69d6cbd5df481cc8d94eef3267373e7fbe2e5
Merge: a2f7934 7ff25c1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 15:07:05 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit a2f79348b7713fe08ac590bb25f571c89f030e85
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 14:42:58 2019 +0200

    CI: install dependency libboost-filesystem-dev apt package

commit eaba243599da771cc77f2f37278c49305fb00fc4
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 14:25:42 2019 +0200

    refactor: remove class Table, use boost::filesystem

commit 61d879ac6c649a67cd9f37917fcf335fe2bf5178
Author: Douglas McCloskey <dmccloskey87@gmail.com>
Date:   Mon May 13 10:26:22 2019 +0200

    cmake: boost filesystem

commit b279d5e0a515bdec78bc9e9ef50284b22af867dc
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 9 12:55:19 2019 +0200

    fix: getParentPathname() does not fail on first-level path

    refactor: getParentPathname() uses new functions isRootPathname() and cleanupPathname()

    test: update getParentPathname() tests and add tests for new functions

commit c3cfc9730acd098edb086385968957f58c4805ff
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 15:20:48 2019 +0200

    feat: user can set a custom pathname (e.g. to change from C: to D:)

    closes #198

commit ae34abcb80ac86590bc2c620dfb71979e9ee261c
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 11:15:32 2019 +0200

    fix: Utilities_test folder's content updated

commit c5ae62b84a9bd2015711c5e2d7748b3ba4f42fd2
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 10:56:41 2019 +0200

    CI: debug Utilities_test failure, printing folder's content

commit 99088abf058277132b45da59145f3a59ad22ed74
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 10:56:15 2019 +0200

    test: add an output folder for tests' output data

commit 655346d6178fd4dfd57d5bbb95052827d20103b4
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 09:48:15 2019 +0200

    CI: ctest is verbose

commit 973ce6841f984444d76a56ee13d5a727da1ff8e8
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 09:46:18 2019 +0200

    fix: attempt to fix 'stat *' definition missing in Windows

commit 733fd121173f9ceb9fda44776b7981fe38263686
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 8 09:45:26 2019 +0200

    style: make Utilities::getPathnameContent() warning-free

commit a28f753ae6bacab5e51acf550e009ca60aa0a9f9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 16:43:33 2019 +0200

    test: Utilities::getParentPathname() (and fixes, accordingly)

commit eb82c815a20c0b1b1bed26ddf0c911927b4922f4
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 13:51:47 2019 +0200

    test: Utilities::getPathnameContent()

commit 4a8a04355112c21ee5074660f43835869f5df9f1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 12:41:50 2019 +0200

    fix: initialize ostringstream correctly in CastValue's operator std::string()

commit d2e60a981cd5309c2c526fbecb539a3f8b1b01b0
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 10:50:11 2019 +0200

    feat: CastValue can implicitly be cast to std::string (operator std::string())

commit 3b718d37b9b6e6a61ebfa8f1721b6864a22ef85f
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 7 10:48:56 2019 +0200

    refactor: move Column's methods up to Table, remove class Column, use typedef

commit 04bd167c86fa72f5db44407e3d39c2fa733db23a
Merge: 59dabd8 ff29218
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri May 3 11:05:11 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 59dabd8801067d01314f0aa070c5eba34aca4ef1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri May 3 11:04:43 2019 +0200

    fix: move dirent.h file from ui to core

commit 5b2ff8f14d6bef3fef44080bacdbb31a3b03b2c1
Merge: 99b5a1a 53b0abe
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 2 13:11:25 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 99b5a1a2752b17c14ed30510668a6f4d81b3be94
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 1 15:33:52 2019 +0200

    style: respect order of definition of data members in constructors

commit 0f844c95abffc554ac142bd945a0740899e27eb8
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 1 15:15:54 2019 +0200

    style: const_cast safe signed/unsigned comparison

commit 25ef79c49bb5195f042898de99be2288bc0d4c03
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 1 15:14:52 2019 +0200

    fix: Widget: polymorphic class' destructor is virtual

commit b65367fdfc9e377a146ea79664090465d0157501
Merge: 01bd972 9834d71
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 30 16:32:41 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit 01bd97289a4a1b3a1dc9968315ea56c5bb4c6521
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 30 16:23:08 2019 +0200

    style: move getPathnameContent and getParentPathname to Utilities

    style: move CastValue implementation out of Utilities

    feat: move ui file picker code to class FilePicker

commit 27629c650b51b5fd48ea15156bf50736ba079572
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 29 15:11:06 2019 +0200

    feat: getPathnameContent uses class Table, and fetches name, size, type and date of entries

commit 35c7f1ee1d54a15d90eb3d5cbd09db8fe1b7a984
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 29 15:10:29 2019 +0200

    feat: implement class Table to manage column-oriented data

commit d72ae6e33b6af3e036aba330578898bcfbe6e00c
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 29 15:05:30 2019 +0200

    feat: implement Utilities::CastValue::is_less_than()

    feat: implement operator<< for CastValue

commit 8c71e889f3a12d419334dac10a5886cad86813d9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Apr 25 13:41:50 2019 +0200

    feat: Utilities::CastValue supports long int

commit 81a1a15381f1e83320a25ec75929978acbd6973d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 23 11:27:35 2019 +0200

    chore: add dirent.h for Windows compatibility

commit 4abf6cfcf10b29b8f4e37b6d14ac52ae1182f147
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 16:18:08 2019 +0200

    style: move endsWith() to class Utilities

    test: Utilities::endsWith()

commit af0ddd9615e1147eb80be5a4508d50cd685ccd7a
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 15:58:46 2019 +0200

    feat: endsWith() supports case-insensitive

    feat: file picker's extensions-filter is case insensitive

commit cbdf4fd9b3b01e96fb04d54161272d5754667f25
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 15:38:02 2019 +0200

    feat: file picker shows content in columns / table

    fix: selected_pathname gets the pathname, not the filename

commit c379674f624ddeb34bb7965648c0cb97d3b39d82
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 14:24:37 2019 +0200

    feat: file type filter

    feat: implement endsWith() for strings

commit acfa6a5ff2f601ff8b5467558baba72e52faf91e
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 13:37:57 2019 +0200

    move AppWindow definition out of the main loop

commit 6d4b9af10dc165a2f90e92a0f5aa9ea6c48c3d60
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 13:26:53 2019 +0200

    style: Simplified one-liner Combo() for file type / extension selection

commit b29b1bcf0b64c42fe17164aed9dd4bf11498c519
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed Apr 17 13:09:18 2019 +0200

    feat: add filename input text, put "ok" and "cancel" buttons on same line

commit 6c6c6041be12589a77c4630e28ff2892660a1c9f
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Apr 16 16:51:10 2019 +0200

    feat: getParentPathname()

    feat: use single-pane navigation

    feat: add "go up" directory button

    feat: do not insert "." and ".." to folder content

commit ba4b0f97a29eeb39c0118afa6277b92856b7ceac
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Apr 15 16:52:45 2019 +0200

    feat: navigate directories, show their content

* feat: gui: Report, Run workflow

Squashed commit of the following:

commit 2d8913ab7791487549344236ad6bb28f74d50d6a
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri Jun 14 14:13:49 2019 +0200

    style: rename SequenceSummary to PivotTable and FeatureSummary to FeatureDB

commit 06945d5212b901337148e8c121d938b4952f146e
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 13 13:59:00 2019 +0200

    todo: add TODO comments for multi-thread code

commit 483e0b9c387faf133041ca7175b2822e46e0f540
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 13 13:43:21 2019 +0200

    feat: add validation check on Report checkboxes. At least one of both column should be selected.

commit 0032c77f2cb7a4f653f91157800b56b0c87ec4a3
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 13 13:32:03 2019 +0200

    feat: use extern keyword to share global variables in FeatureMetadata.h and SampleType.h

    feat: define constexpr sizes in those headers

commit e042fa85a99c2a7b78cfca734fa400c80169a371
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 13 13:04:22 2019 +0200

    style: move Report constructor code to cpp file, initialize all checkboxes to false

commit 27d10b0fecabce40e9ae156eeb49141f9811ad2c
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 13 12:59:54 2019 +0200

    style: typo in method name, change to initializeMetadataAndSampleTypes()

commit 0df3301911569b81d32fe37e18c38981563f2dcb
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 13 12:56:36 2019 +0200

    style: add Sample types and Metadata headers to Report's lists

    style: put lower buttons on the same line

commit 75a70364cb61016f60aede496e9fa21950688995
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 13 10:13:27 2019 +0200

    style: rename Metadata to FeatureMetadata

commit ef2f817111c32502b963ab530a59b78d7a35d237
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 11 14:34:50 2019 +0200

    fix: avoid shadowing menu item with text below/under (level, z-index wise) it in workflow steps. Use Button instead of Text

commit af1f8b55ac3ff5fdbb51a38b3dc6b4dcd4740b78
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 11 14:30:01 2019 +0200

    style: do not close Report modal when a report is created

commit e6aecebf9332a5106fbabb33efad7968c28e17f5
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 10 17:34:50 2019 +0200

    feat: add Report widget to GUI

    fix: initialize data dirs (mzml, features in and out) when necessary

commit b113782267871b1d4c878d8869d86e7564e074e9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 10 17:33:18 2019 +0200

    feat: add widget Report to store a csv file with FeatureSummary or SequenceSummary

commit 5d3fddbcfe5a001d1777c783ee09c0eb504dd1c3
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 10 17:27:31 2019 +0200

    refactor: move SampleType out of MetaDataHandler to its own header file (SampleType.h), make it enum class

    refactor: create enum class Metadata, to avoid using strings

    refactor: AppState does not keep info about selected metadata and sample types

commit 104fe2eb0d0eb7b74b77c2156ac65b235a06c7eb
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 6 15:10:33 2019 +0200

    feat: drag and drop steps

commit b44c19476c8972d46d89d5a403f3edce53437015
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 6 13:26:07 2019 +0200

    feat: add Workflow widget to the application

    The user can access this view from menu: Edit -> Workflows

commit 171488b3508d79f024be47879f5c35336a46fc16
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 6 13:25:32 2019 +0200

    feat: implement class Workflow, which helps with selecting the methods/steps to run

commit 28e4be4361bda2dd9b5bc79e9a4ac69f9bc620d9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu Jun 6 13:16:02 2019 +0200

    feat: Add processor class BuildCommandsFromIds to AppStateProcessor

    This code was present in CLI.cpp. It is now separated and implemented in AppStateProcessor so that also the GUI can make use of it

    style: replace unordered_map with map so that workflow's steps can be iterated in sorted order (by their IDs, here keys of the maps)

    feat: class Command implements getName(). This method returns the name of the workflow step, no matter the type of the processor (either raw data or sequence segment)

commit 71872bea015debe1b88e26d9f6a33c6b5c1ef626
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 4 12:59:46 2019 +0200

    test: make test pass trivial check, constructor takes an argument

commit ad3322c4da19e6a5b16c4a3105b77f0ece16e490
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 4 12:38:35 2019 +0200

    fix: cmake config for UI tests

commit 0659dc31f07621c116724163ab9adfaa73dc7ce3
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue Jun 4 10:59:20 2019 +0200

    Revert "fix (not really): disable building ui tests"

    This reverts commit 4a31b86236fb0b4459efe7eca6719825c817550d.

commit 7756b56ebfbbdec9d8dae4d2e1078082b45b0616
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 3 14:16:33 2019 +0200

    feat: GUI can load a session from a sequence

    feat: implement processor LoadSessionFromSequence

    style: CLI uses LoadSessionFromSequence

    feat: add AppState to AppWindow

commit 561a21e80434a4b58c3548bcd6130dead9abf3a1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon Jun 3 14:08:59 2019 +0200

    feat: add AppStateProcessor logic to FilePicker

commit fe7c518d4747834d68dbde481f3ff0d4ad8602f0
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 28 15:11:04 2019 +0200

    refactor: AppStateProcessor's methods become structs/classes

commit 4a31b86236fb0b4459efe7eca6719825c817550d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 16:22:40 2019 +0200

    fix (not really): disable building ui tests

commit 380f13762659d61fee4adeae53e11eabe0363df7
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 15:40:16 2019 +0200

    Revert "TEST: see if it still can't link"

    This reverts commit 8e952b07fc2d9556a4a5217918aedbd7f1631eb0.

commit 8e952b07fc2d9556a4a5217918aedbd7f1631eb0
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 15:24:38 2019 +0200

    TEST: see if it still can't link

commit a7203bfe8280f544e6ffb792f8cd448d360a7d22
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 15:24:06 2019 +0200

    chore: explicit includes in Widget

commit bba1e3cbe905a47fadfe7276f9ac952bf5931663
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 14:56:30 2019 +0200

    refactor: make FilePicker instance a class member of AppWindow

commit 89c3856c9646b16f154b6875413c3afee86ce653
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 11:36:52 2019 +0200

    style: AppWindow's methods are not static, remove unnecessary includes

commit ba8489a9889b7880978ecb3d16afe060cd8805fb
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 11:13:11 2019 +0200

    Revert "CI: add --no-install-recommends to apt-get"

    This reverts commit ef0b964babf5603c0f11cdfc461cc0f34b3efd66.

commit ef0b964babf5603c0f11cdfc461cc0f34b3efd66
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 11:04:21 2019 +0200

    CI: add --no-install-recommends to apt-get

commit fd39238a98a81cf51f4357cea438c2c32bd39b2d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 10:59:33 2019 +0200

    Revert "CI: (temporary change) Build OpenMS in Release mode (to speedup CI)"

    This reverts commit 622cc4bddaca5c9ca134698fcd459ca7499094db.

commit 80636757b58399d2a90d553d9adea695a3054d7a
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:46:33 2019 +0200

    Revert "style: add a FilePicker instance to AppWindow's state, avoiding passing the instance between static methods"

    This reverts commit bd00640df0711489f31c4de844f3636c22eccaad.

commit 622cc4bddaca5c9ca134698fcd459ca7499094db
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:45:43 2019 +0200

    CI: (temporary change) Build OpenMS in Release mode (to speedup CI)

commit 352fb3bdccd19774e07552fc2004d321819e4fab
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:44:18 2019 +0200

    CI: Add "--depth 1" to git clone OpenMS command

commit ec6d651eeb248fa8d283616ff303b4423c8aef33
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 29 09:30:26 2019 +0200

    Revert "refactor: AppStateProcessor's methods become structs/classes"

    This reverts commit b59324aad8703a31bce01aa809e96141a0fda124.

commit b59324aad8703a31bce01aa809e96141a0fda124
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 28 15:11:04 2019 +0200

    refactor: AppStateProcessor's methods become structs/classes

commit bd00640df0711489f31c4de844f3636c22eccaad
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 27 16:50:21 2019 +0200

    style: add a FilePicker instance to AppWindow's state, avoiding passing the instance between static methods

    Methods are not static anymore, because they deal with AppWindow's state.

commit 74b3bf1347e7b70b02b9450a8cddbad45c56de41
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 27 15:18:28 2019 +0200

    refactor: separate CLI functionalities into AppState and AppStateProcessor

commit f04b5cd4d7e4d5c4d2ba1d13d6248a3765500215
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Fri May 24 12:26:58 2019 +0200

    fix: interface classes suppress copying

commit d0e8a44cfbe375ebe7e7f0f3622da5c7db72dce2
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 22 15:10:11 2019 +0200

    feat: implement mainMenuString

commit c5925ee99014fd302c474b9f4beca504205ffbe5
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 22 15:09:38 2019 +0200

    style: reduce/remove data from classes/struct RawDataProcessor and SequenceSegmentProcessor

commit 61ac71b6fe69c18e10f4dda459609ae340558d63
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 22 10:21:05 2019 +0200

    style: implement initializeDataDir() to simplify initializeDataDirs()

commit af04c7adb0a1055be34f9207531a15f57cf9bc38
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Tue May 21 15:58:32 2019 +0200

    refactor: SequenceProcessor is a base class

    Previous methods are now derived classes.

commit 271c2ea5cb1b0e86d1304ef3ccff13924e86ea39
Author: Douglas McCloskey <dmccloskey87@gmail.com>
Date:   Sun May 19 10:41:46 2019 +0200

    fix: implicit conversion from char to plog::util::nstring

commit 6c9d88305f45ba5fe24c5bbe02c183ea8cc563da
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 12:50:36 2019 +0200

    docs: Add docstrings for functions endsWith, getPathnameContent, getParentPathname, applyPermutation, is_less_than_icase, directorySize

commit 1dfc93df289ca71d80cf03f9dc602d40d77f54b9
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:12:50 2019 +0200

    style: fix indentation in AppWindow::HelpMarker()

commit 07bdc05bef5538c0ad7891c52018c4046a49dc77
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:10:12 2019 +0200

    chore: remove dirent.h file

commit 64ad1c3bc60fd69384921a160663f74f0bc523bf
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Mon May 20 10:05:06 2019 +0200

    chore: remove Table.(h|cpp) files

commit bf944faccec33cbdb885ee350e6e1c79949e45de
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 13:09:12 2019 +0200

    style: make Widget class abstract, ::draw() is a pure virtual method

commit 9703cccaf880800cfb2188d3a5b2872de64f8954
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 11:24:22 2019 +0200

    style: FilePicker inherits from Widget

commit c46e70149da8e1bcef893aae705115e68dd3e9ec
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 10:35:44 2019 +0200

    style: rename Widget::show() (and derived classes') to ::draw()

commit a8076a06f2da0e09d6b5c8cceedad17ec0a1bd1d
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Thu May 16 10:31:45 2019 +0200

    style: Widget's show() method is consistent in derived classes (no arguments)

commit 9e6811fbf8017e70b43b0735d4869bda5f0c7739
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 15:50:47 2019 +0200

    style: move FilePicker's widget title to class members, draw() has no arguments

commit 31a69d6cbd5df481cc8d94eef3267373e7fbe2e5
Merge: a2f7934 7ff25c1
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   Wed May 15 15:07:05 2019 +0200

    Merge branch 'develop' into gui/file_picker

commit a2f79348b7713fe08ac590bb25f571c89f030e85
Author: Pasquale Domenico Colaianni <pasdom@biosustain.dtu.dk>
Date:   …
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@dmccloskey @pcolaianni
@sgalkina @m00dy @ahmedskhalil
8 people authored Jul 16, 2020
1 parent 5af99c6 commit 59b7959
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21 changes: 14 additions & 7 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,16 +8,21 @@ jobs:

working_directory: ~/SmartPeak2

resource_class: large

steps:
- checkout
- run: |
apt-get update
- run: |
apt-get install -y git cmake qt5-default libboost-dev libeigen3-dev libxerces-c-dev coinor-libcbc-dev libsvm-dev libboost-iostreams-dev libboost-date-time-dev libboost-math-dev libwildmagic-dev libsqlite3-dev libglpk-dev seqan-dev libsdl2-dev libhdf5-dev
- run: >
apt-get install -y git cmake qt5-default libboost-dev libeigen3-dev
libxerces-c-dev coinor-libcbc-dev libsvm-dev libboost-iostreams-dev
libboost-date-time-dev libboost-math-dev libwildmagic-dev libsqlite3-dev
libglpk-dev seqan-dev libsdl2-dev libhdf5-dev libboost-filesystem-dev
- run: |
cd ~ &&
git clone --branch chore/replace_boost_regex https://github.com/biosustain/OpenMS.git &&
cd OpenMS &&
git clone --branch develop --depth 1 https://github.com/OpenMS/OpenMS.git &&
cd OpenMS && git submodule update --init THIRDPARTY &&
cmake -DBOOST_USE_STATIC=OFF -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Debug -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF ~/OpenMS &&
make -j4 OpenMS
- run:
Expand All @@ -30,15 +35,17 @@ jobs:
command: |
mkdir ~/SmartPeak2_build
cd ~/SmartPeak2_build
cmake -DEIGEN_USE_GPU=OFF -DUSE_SUPERBUILD=OFF -DBOOST_USE_STATIC=OFF -G "Unix Makefiles" -DCMAKE_PREFIX_PATH=$HOME/OpenMS-build/ -DPLOG_INCLUDE_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/plog/include -DIMGUI_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/imgui -DImGui_INCLUDE_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/imgui -DCMAKE_BUILD_TYPE=Debug ~/SmartPeak2
cmake -DEIGEN_USE_GPU=OFF -DUSE_SUPERBUILD=OFF -DBOOST_USE_STATIC=OFF -G "Unix Makefiles" -DCMAKE_PREFIX_PATH=$HOME/OpenMS-build/ -DPLOG_INCLUDE_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/plog/include -DIMGUI_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/imgui -DImGui_INCLUDE_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/imgui -DIMPLOT_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/implot -DCMAKE_BUILD_TYPE=Debug ~/SmartPeak2
make -j4
- run:
command: |
cd ~/SmartPeak2_build || exit 1
ctest -j4
ls -l ~/SmartPeak2/src/tests/class_tests/smartpeak/data
ctest -V
ls -l ~/SmartPeak2/src/tests/class_tests/smartpeak/data
- run:
command: |
~/SmartPeak2/.circleci/run_examples.sh
~/SmartPeak2/.circleci/run_examples.sh ~/SmartPeak2_build/bin
workflows:
version: 2
Expand Down
28 changes: 23 additions & 5 deletions .circleci/run_examples.sh
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Original file line number Diff line number Diff line change
@@ -1,5 +1,21 @@
#!/usr/bin/env bash

if [ $# -eq 0 ]
then
echo "Error: please provide the path to the binaries"
echo "Example: ./run_example.sh ~/SmartPeak2_build/bin"
exit 1
fi

# workaround for cygwin error in appveyor:
# https://github.com/appveyor/ci/issues/1956#issuecomment-492008640
command_prefix=""

if [ $# -eq 2 ]
then
command_prefix=$2
fi

run_example()
{
filename=$1
Expand All @@ -16,18 +32,20 @@ run_example()
return $RET_VALUE
}

# Assumption: SmartPeak2 build folder
cd ~/SmartPeak2_build/bin || return 1
cd $1 || return 1

echo "build directory: $1"
echo "unix binaries: $command_prefix"

{
(run_example GCMS_SIM_Unknown_test)&
(run_example HPLC_UV_Standards_test)&
(run_example HPLC_UV_Unknown_test)&
(run_example LCMS_MRM_QCs_test)&
(run_example LCMS_MRM_Standards_test)&
# (run_example LCMS_MRM_Standards_test)&
(run_example LCMS_MRM_Unknown_test)&
} |
tee examples_log.txt
${command_prefix}tee examples_log.txt

# When adding a new example, update the comparison n==NUMBER_OF_EXAMPLES
grep -c "PASS" examples_log.txt | ( read n && (( n==6 )) )
${command_prefix}grep -c "PASS" examples_log.txt | ( read n && (( n==5 )) )
10 changes: 5 additions & 5 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -40,15 +40,15 @@ build*/

cmake-build-debug/

src/examples/data/*/FeatureSummary.csv
src/examples/data/*/SequenceSummary.csv
src/examples/data/*/FeatureDB.csv
src/examples/data/*/PivotTable.csv
src/examples/data/HPLC_UV_Standards/features/
src/examples/data/HPLC_UV_Unknowns/features/
src/examples/data/LCMS_MRM_Standards/features/
src/examples/data/LCMS_MRM_Unknowns/features/
src/examples/data/LCMS_MRM_QCs/features/
src/examples/data/GCMS_SIM_Unknowns/features/
src/examples/data/GCMS_FullScan_Unknowns/
src/tests/class_tests/smartpeak/data/SequenceParser_writeDataMatrixFromMetaValue.csv
src/tests/class_tests/smartpeak/data/SequenceParser_writeDataTableFromMetaValue.csv
src/tests/class_tests/smartpeak/data/CSVWriterTest.csv

# MacOS
*.DS_Store
78 changes: 0 additions & 78 deletions .travis.yml
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This file was deleted.

26 changes: 15 additions & 11 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ if (USE_SUPERBUILD)
project ("SuperBuild" NONE)
include(external/plog.cmake)
include(external/imgui.cmake)
include(external/implot.cmake)
if (MSVC)
include(external/eigen.cmake)
include(external/boost.cmake)
Expand Down Expand Up @@ -77,9 +78,9 @@ list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake/Windows")
#------------------------------------------------------------------------------
# SmartPeak Version Information
#------------------------------------------------------------------------------
set (smartPeak_VERSION_MAJOR 1)
set (smartPeak_VERSION_MINOR 0)
set (smartPeak_VERSION_PATCH 0)
set (SMARTPEAK_PACKAGE_VERSION_MAJOR 1)
set (SMARTPEAK_PACKAGE_VERSION_MINOR 0)
set (SMARTPEAK_PACKAGE_VERSION_PATCH 0)

#------------------------------------------------------------------------------
# retrieve detailed informations on the working copy (git)
Expand Down Expand Up @@ -153,11 +154,19 @@ endif()
set(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)

if (CMAKE_BUILD_TYPE STREQUAL "Debug")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -Wextra -Wpedantic -Wconversion -g")
if (MSVC)
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /W3 /Z7")
elseif (CMAKE_COMPILER_IS_GNUCXX)
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -Wextra -Wpedantic -Wconversion -g")
endif()
set(CMAKE_EXE_LINKER_FLAGS_DEBUG "${CMAKE_EXE_LINKER_FLAGS_DEBUG}")
set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS}")
elseif (CMAKE_BUILD_TYPE STREQUAL "Release")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -Wall -Wextra -Wpedantic -Wconversion")
if (MSVC)
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} /W3")
elseif (CMAKE_COMPILER_IS_GNUCXX)
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -Wall -Wextra -Wpedantic -Wconversion")
endif()
endif()

# Windows/Linux specific issues
Expand Down Expand Up @@ -265,6 +274,7 @@ install_export_targets()
# Installation and packaging:
#------------------------------------------------------------------------------
# packaging routines:

if(NOT "${PACKAGE_TYPE}" STREQUAL "none")
include(cmake/package_general.cmake)
if("${PACKAGE_TYPE}" STREQUAL "dmg") # .. MacOSX
Expand All @@ -274,13 +284,7 @@ if(NOT "${PACKAGE_TYPE}" STREQUAL "none")
elseif("${PACKAGE_TYPE}" STREQUAL "deb") # .. debs
include(cmake/package_deb.cmake)
elseif("${PACKAGE_TYPE}" STREQUAL "nsis") # .. Windows nsis
# For now we use the old NSIS script AS IS
# i.e. although CMake runs make install etc. NSIS
# will use everything from the usual build folder like before.
# TODO automate more and let CMake generate install commands
# in the script. Unfortunately we have a lot of specific code in the script.
include(cmake/package_nsis.cmake)
endif()
include(CPack)
include(cmake/package_components.cmake)
endif()
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