ci: cleanup

Author: MRKonrad

.appveyor.yml

@@ -60,9 +60,11 @@ after_build:
   - mkdir deployment
   # change the name of the exe, zip it and copy the zip to the deployment folders
   - cd %APPVEYOR_BUILD_FOLDER%\install
-  - 7z a %EXE_EXTENDED_NAME%.zip bin\* -r # zip
+  - cd bin
+  - 7z a %EXE_EXTENDED_NAME%.zip *  # zip
+  - cd ..
   - 7z a %LIB_EXTENDED_NAME%.zip lib\* lib_static\* lib_shared\* include\* # zip
-  - copy %APPVEYOR_BUILD_FOLDER%\install\%EXE_EXTENDED_NAME%.zip %APPVEYOR_BUILD_FOLDER%\deployment\%EXE_EXTENDED_NAME%.zip
+  - copy %APPVEYOR_BUILD_FOLDER%\install\bin\%EXE_EXTENDED_NAME%.zip %APPVEYOR_BUILD_FOLDER%\deployment\%EXE_EXTENDED_NAME%.zip
   - copy %APPVEYOR_BUILD_FOLDER%\install\%LIB_EXTENDED_NAME%.zip %APPVEYOR_BUILD_FOLDER%\deployment\%LIB_EXTENDED_NAME%.zip
 
 test_script:

.travis.yml

@@ -149,9 +149,9 @@ deploy:
   provider: releases
   api_key:
     secure: ${GH_PERSONAL_ACCESS_TOKEN}
-  file_glob: ON
+  file_glob: true
   file: deployment/*
-  skip_cleanup: ON
+  skip_cleanup: true
   on:
     tags: ON
     condition: ${DEPLOY_BUILD} == "ON" # I guess I have to pick one compiler

CMakeLists.txt

@@ -135,6 +135,7 @@ MESSAGE("USE_VNL:              " ${USE_VNL})
 MESSAGE("USE_PRIVATE_NR2:      " ${USE_PRIVATE_NR2})
 #MESSAGE("USE_NR2:              " ${USE_NR2})
 #MESSAGE("USE_NR3:              " ${USE_NR3})
+MESSAGE("USE_LMFIT:            " ${USE_LMFIT})
 MESSAGE("USE_YAML:             " ${USE_YAML})
 MESSAGE("BUILD_SHARED_LIBS:    " ${BUILD_SHARED_LIBS})
 MESSAGE("CMAKE_INSTALL_PREFIX: " ${CMAKE_INSTALL_PREFIX})

README.md

@@ -1,8 +1,8 @@
 # Tomato
 
 A library to calculate parametric maps in MRI. It contains ShMOLLI implementation as in [this article](https://jcmr-online.biomedcentral.com/articles/10.1186/1532-429X-12-69).  
-**Github** repository can be found [here](https://github.com/MRKonrad/tomato).  
-**Documentation** in doxygen can be found [here](https://mrkonrad.github.io/tomato/html).
+*   **Github** repository can be found [here](https://github.com/MRKonrad/tomato).  
+*   **Documentation** in doxygen can be found [here](https://mrkonrad.github.io/tomato/html).
 
 | System                                    |     Status                                                         |
 |-------------------------------------------|:------------------------------------------------------------------:|
@@ -13,25 +13,26 @@ A library to calculate parametric maps in MRI. It contains ShMOLLI implementatio
 | [Test coverage - Codecov][codecov_link]   | [![codecov][codecov_badge]][codecov_link]                          |
 | [Downloads][downloads_link]               | [![GitHub Releases (by Release)][downloads_badge]][downloads_link] |
 
-
-# Usage
+## Usage
 
 *   App - download the latest version of `TomatoExe` from the [Releases][downloads_link] page and follow the youtube tutorial below
 [![Tomato tutorial](https://img.youtube.com/vi/0tzNZNiZh18/0.jpg)](https://www.youtube.com/watch?v=0tzNZNiZh18)
+
 *   Lib - download the latest version of `TomatoLib` from the [Releases][downloads_link] page
+
 *   Code - if you want to build the code please take a look at the scripts in the `scriptsBuild` and the continuous integrations scripts `.appveyor.yml` and `travis.yml`
 
 ## Tomato and Numerical Recipes
 
 **Important**  
 Original ShMOLLI (and based on it Tomato) uses code based on Numerical Recipes book. Due to Numerical Recipes licence I cannot share this part of the code online. Please contact me if you would like to use this part of the code. To make up for this limitation we provide a number of alternative fitting procedures.
 
-# Troubleshooting
+## Troubleshooting
 
 *   missing msvcp140.dll  
 Download <https://www.microsoft.com/en-us/download/details.aspx?id=48145> as suggested in <https://stackoverflow.com/questions/32998902/msvcp140-dll-missing>
 
-# Software Requirements Specification
+## Software Requirements Specification
 
 1.  Calculate ShMOLLI with exactly the same results as these from the previous implementation.
 2.  API for easily choosing
@@ -45,20 +46,21 @@ Download <https://www.microsoft.com/en-us/download/details.aspx?id=48145> as sug
 5.  Fast calculation.
 6.  Easily interfaced to calculation environments MATLAB, IDL and Python.  
 
-# Contributing and code of conduct
+## Contributing and code of conduct
 
 Please see [contributing.md](contributing.md) and [codeofconduct.md](codeofconduct.md).
 
-# Notes
+## Notes
 
 *   **Continuous integration** was tested [in this repo](https://github.com/MRKonrad/ContinousIntegrationPlayground).
 *   **Gitmodules**: after `git clone` run `git submodule update --init --recursive` to get the submodules code.
 *   It would be nice to follow [CppCoreGuidlines](https://github.com/isocpp/CppCoreGuidelines/blob/master/CppCoreGuidelines.md) as far as C++98 allows.
 *   Maybe I can write a script for github releases with [github releases REST api](https://developer.github.com/v3/repos/releases/#create-a-release) and [curl REST api](http://www.codingpedia.org/ama/how-to-test-a-rest-api-from-command-line-with-curl/#12_HEAD_requests)?
 *   LMFIT - somehow windows does not like the static library, so the dynamic is used
 
-# TODO:
+## TODO
 
+*   Deployment: exe and lib in one zip
 *   output SNR maps
 *   make sure SNR and nAmoebaCalls is the same as in Shmolli
 *   fix downloadITK_linux_osx

codeofconduct.md

@@ -22,12 +22,14 @@ include:
 
 Examples of unacceptable behavior by participants include:
 
-*   The use of sexualized language or imagery and unwelcome sexual attention or
-  advances
+*   The use of sexualized language or imagery and unwelcome sexual attention or advances
+
 *   Trolling, insulting/derogatory comments, and personal or political attacks
+
 *   Public or private harassment
-*   Publishing others' private information, such as a physical or electronic
-  address, without explicit permission
+
+*   Publishing others' private information, such as a physical or electronic address, without explicit permission
+
 *   Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
@@ -70,7 +72,7 @@ members of the project's leadership.
 This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
 available at <https://www.contributor-covenant.org/version/1/4/code-of-conduct.html>
 
-[homepage]: <https://www.contributor-covenant.org>
-
 For answers to common questions about this code of conduct, see
 <https://www.contributor-covenant.org/faq>
+
+[homepage]: <https://www.contributor-covenant.org>

CONTRIBUTING.md contributing.mdCONTRIBUTING.md renamed to contributing.md

@@ -1,20 +1,25 @@
 # Contributing to TOMATO
+
 We want to make contributing to this project as easy and transparent as
 possible.
 
 ## Our Development Process
+
 We use GitHub to sync code to and from our internal repository. We'll use GitHub
 to track issues and feature requests, as well as accept pull requests.
 
 ## Issues
+
 We use GitHub issues to track public bugs. Please ensure your description is
 clear and has sufficient instructions to be able to reproduce the issue.
 
 ## Report bugs using Github's [issues](https://github.com/MRKonrad/tomato/issues)
+
 We use GitHub issues to track public bugs. Report a bug by [opening a new issue](); it's that easy!
 
 
 ## Pull Requests
+
 We actively welcome your pull requests.
 
 1.  Fork the repo and create your branch from `master`.
@@ -25,26 +30,34 @@ We actively welcome your pull requests.
 6.  Issue that pull request!
 
 ## Any contributions you make will be under the MIT Software License
+
 In short, when you submit code changes, your submissions are understood to be under the same
 [MIT License](http://choosealicense.com/licenses/mit/) that covers the project.
 Feel free to contact the maintainers if that's a concern.
 
 ## Coding style
+
 *   Write code compatible with C++98
+
 *   Use underscore (`_variable`) in the name of a class member variable.
+
 *   C++98 does not allow me to use constructor delegation. Using methods like `setAllPointersToNull()` to make up for it.
+
 *   Order of methods in a class definition:
     *   functional (calculation, helpers etc)
     *   getters/setters
     *   disp()
     *   constructors/destructors
+    
 *   In **copy constructors** copy primitive types, set all pointers to zero.
 
 ## License
+
 By contributing to Draft.js, you agree that your contributions will be licensed
 under its BSD license.
 
 ## References
+
 This document was adapted from the open-source contribution guidelines for
 [Facebook's Draft](https://github.com/facebook/draft-js/blob/a9316a723f9e918afde44dea68b5f9f39b7d9b00/CONTRIBUTING.md)
 and [qMRLab](https://github.com/qMRLab/qMRLab/blob/master/CONTRIBUTING.md).

notepad.md

@@ -1,4 +1,6 @@
-# Different results from the configurations
+# NOTES
+
+## Different results from the configurations
 
 parameter_to_map: T1_SHMOLLI  
 functions_type: **FunctionsBasic/FunctionsShmolli**  
@@ -22,6 +24,6 @@ start_point_calc_method: **Default/StartPointSHMOLLI**
 Default: 2.2s and wrong results  
 StartPointSHMOLLI: 10s and seemingly correct results
 
-# 5 vs 7 samples
+## 5 vs 7 samples
 
 5 samples are calculated way slower. Maybe playing with fmax and maxIter would reduce the time?