Merge pull request #169 from I2PC/ds_changingDirStructure

changing the directory structure

.gitignore

@@ -46,14 +46,18 @@ gmon.out
 .directory
 .settings
 
-/config/*.conf
-/bin
-/lib
-/models/*
-/install/xmipp.conf
-/tests/data
+# ignore everything in src folder
+/build/*
+/src/*
+# except xmipp folder
+!/src/xmipp/*
+
+/src/xmipp/bin
+/src/xmipp/lib
+/src/xmipp/models/*
+/src/xmipp/tests/data
 
 # Ignore version file
 .devel_version
-/Debug/
-applications/programs/version
+/src/xmipp/Debug/
+/src/xmipp/applications/programs/version

.travis.yml

@@ -18,7 +18,6 @@ before_install:
  - source scripts/install_cuda_travis.sh
 script:
  - |
-     python ./scripts/travis_before_script.py && \
      build-wrapper-linux-x86-64 --out-dir bw-outputs ./xmipp && \
      sonar-scanner && \
      ccache -s

README.md

@@ -3,30 +3,30 @@
 [![Technical debt](https://sonarcloud.io/api/project_badges/measure?project=Xmipp&metric=sqale_index)](https://sonarcloud.io/component_measures?id=Xmipp&metric=sqale_index)
 [![Bugs](https://sonarcloud.io/api/project_badges/measure?project=Xmipp&metric=bugs)](https://sonarcloud.io/project/issues?id=Xmipp&resolved=false&types=BUG)
 --->
-# xmipp
+# Xmipp
 
-If you want to use it as a **Scipion package for production proposes**, please visit [this](https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#step-4-installing-xmipp3-and-other-em-plugins).
+Welcome to Xmipp. Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.
 
-If you want to use it as a **Scipion package for devel proposes**, please visit [this](https://github.com/I2PC/xmipp/wiki/Xmipp-bundle-installtion).
 
-To install Xmipp in a certain place (e.g. in the `xmipp-bundle` directory) follow this instructions:
+## Getting started
+**Xmipp as a Scipion package**
 
-```
-mkdir xmipp-bundle
-cd xmipp-bundle
-wget https://raw.githubusercontent.com/I2PC/xmipp/devel/xmipp -O xmipp
-chmod 755 xmipp
-./xmipp all N=4 br=devel
-ln -sf src/xmipp/xmipp xmipp  # optional, but VERY RECOMMENDED, to have always the last version of the xmipp script
-```
-where you can replace `N=4` for `N=#processors` and `br=master` for `br=devel` if you want the development version of Xmipp. You can see the whole usage of the xmipp script with `./xmipp --help`
+The recommended way to use Xmipp is via [Scipion](https://scipion-em.github.io/docs/index.html).
+It can be easily installed using the [Plugin manager](https://scipion-em.github.io/docs/docs/user/plugin-manager.html).
 
+**Xmipp as a standalone bundle (useful for developers)**
 
-### Using Scipion libraries
+Start by cloning the repository from GitHub.
 
-If you want xmipp to pick up SCIPION libraries define SCIPION_HOME=\<path to scipion\>
+In case you don't want to import settings from Scipion, set XMIPP_NOSCIPION flag to true (`export XMIPP_NOSCIPION=True`). Otherwise, define SCIPION_HOME=\<path to scipion\>
 
-**Note**: If some program (like `nvcc`) is not visible from your terminal (`which nvcc` returns nothing), but it is visible by Scipion (`$SCIPION_HOME/scipion run which nvcc` returns the nvcc path). Then, you can use Scipion as wrapper to install Xmipp:
-```
-$SCIPION_HOME/scipion run ./xmipp all N=8 br=devel
-```
+Next, run `xmipp` script in the root folder (it might be necessary to add execute permission via `chmod +x xmipp`). This will checkout additional repositories and build Xmipp for you.
+
+You can see the whole usage of the script with `./xmipp --help`. The most useful options are `br=branch_name` to select a specific branch to be checkout-ed, and `N=#processors` to use for the build.
+
+
+## FAQ
+
+If you want to use your specific version of Xmipp as a Scipion plugin, see following wiki [page](https://github.com/I2PC/xmipp/wiki/Migrating-branches-from-nonPluginized-Scipion-to-the-new-Scipion-Xmipp-structure#xmipp-plugin).
+
+Recently we have changed the directory structure. See this wiki [page](https://github.com/I2PC/xmipp/wiki/Transfer-to-new-directory-structure) for more information.