Merge branch 'master' into develop

CHANGELOG

@@ -5,6 +5,13 @@
 Changelog
 ================================================================================
 
+Release 3.1.1
+--------------------------------------------------------------------------------
+
+* Bugfix release: reintroduces backwards compatibility in BuildRawModel.
+  See commit 0288eced23a9a541a88005a7ed30b8f019e06226 for details
+
+
 Release 3.1.0
 --------------------------------------------------------------------------------
 

CMakeLists.txt

@@ -25,7 +25,7 @@ include(PROMOD3)
 # versioning info
 set(PROMOD3_VERSION_MAJOR 3)
 set(PROMOD3_VERSION_MINOR 1)
-set(PROMOD3_VERSION_PATCH 0)
+set(PROMOD3_VERSION_PATCH 1)
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
 
@@ -101,7 +101,7 @@ if(NOT DISABLE_DOCUMENTATION)
   # this URL should always point to the latest version of OST
   set(OST_DOC_URL "https://www.openstructure.org/docs")
 endif()
-find_package(OPENSTRUCTURE 2.0.0 REQUIRED
+find_package(OPENSTRUCTURE 2.1.0 REQUIRED
              COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
 
 if(CMAKE_COMPILER_IS_GNUCXX)

container/Dockerfile

-ARG OPENSTRUCTURE_IMAGE_TAG="2.0.0-bionic"
+ARG OPENSTRUCTURE_IMAGE_TAG="2.1.0-bionic"
 FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
 
 # ARGUMENTS
 ###########
-ARG PROMOD_VERSION="3.1.0"
+ARG PROMOD_VERSION="3.1.1"
 ARG SRC_FOLDER="/usr/local/src"
 
 

container/Singularity

 BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/promod3:3.1.0-OST2.0.0-bionic
+From: registry.scicore.unibas.ch/schwede/promod3:3.1.1-OST2.1.0-bionic
 %post
 ##############################################################################
 # POST

doc/conf.py.in

@@ -286,7 +286,7 @@ rst_epilog = """
 .. |cmake| replace:: CMake
 .. |ost_l| replace:: OpenStructure
 .. |ost_s| replace:: OST
-.. |ost_version| replace:: 2.0.0
+.. |ost_version| replace:: 2.1.0
 .. |python| replace:: Python
 .. |sphinx| replace:: Sphinx
 .. _sphinx: http://sphinx-doc.org/

doc/container/index.rst

@@ -13,6 +13,7 @@
 ..  See the License for the specific language governing permissions and
 ..  limitations under the License.
 
+.. _container:
 
 |project| and Containers
 ========================

doc/container/singularity.rst

@@ -20,7 +20,8 @@ Singularity
 We do not provide a "standalone" Singularity image, but rather bootstrap from a 
 Docker image.
 
-Build the image with:
+Change to the directory containing the Singularity file
+(<PROMOD3_CHECKOUT>/container) and build the image with:
 
 .. code-block:: bash
 
@@ -56,6 +57,43 @@ To list all available |project| modelling actions:
 
     singularity run --app PM promod.img help
 
+So you can either run an action with:
+
+.. code-block:: bash
+
+    singularity run --app PM promod.img build-model [options]
+
+or an arbitrary Python script using OpenStructure / |project| with:
+
+.. code-block:: bash
+
+    singularity run --app PM promod.img my_script.py [options] 
+
+The Notebook app provides a jupyter notebook playground with OST, |project|, and
+nglview available. You can fire it up with:
+
+.. code-block:: bash
+
+    singularity run --app Notebook promod.img
+
+connect to the notebook, start a new OST kernel and test it with the following 
+code snippet:
+
+.. code-block:: python
+
+    from ost import io
+    from promod3 import loop
+    import nglview
+
+    # generate backbone with dihedrals of a helix and store it
+    sequence = "HELLYEAH"
+    bb_list = loop.BackboneList(sequence)
+    io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+    # display stored file
+    view = nglview.show_file("test.pdb")
+    view
+
 The Compound Library
 --------------------
 

doc/gettingstarted.rst

@@ -19,7 +19,7 @@ Getting Started
 
 Get and Run |project|
 --------------------------------------------------------------------------------
-First steps to get |project| up and running:
+Either utilize :ref:`containers <container>` or start from source code:
 
 #. Fetch the source code from https://git.scicore.unibas.ch/schwede/ProMod3.git.
    Or directly pull it with git:

doc/html/_sources/buildsystem.txt → doc/html/_sources/buildsystem.rst.txt

@@ -40,7 +40,7 @@ The currently preferred versions are:
 * |python|_ 3.6.0
 * |boost|_ 1.68.0
 * |eigen3|_ 3.3.1
-* |sphinx|_ 1.3.1
+* |sphinx|_ 1.4.9
 
 --------------------------------------------------------------------------------
  Using |cmake|

doc/html/_sources/changelog.txt → doc/html/_sources/changelog.rst.txt

@@ -5,6 +5,20 @@
 Changelog
 ================================================================================
 
+Release 3.1.1
+--------------------------------------------------------------------------------
+
+* Bugfix release: reintroduces backwards compatibility in BuildRawModel.
+  See commit 0288eced23a9a541a88005a7ed30b8f019e06226 for details
+
+
+Release 3.1.0
+--------------------------------------------------------------------------------
+
+* Introduce alignment processing steps in BuildRawModel
+* Several minor bug fixes, improvements, and speed-ups.
+
+
 Release 3.0.0
 --------------------------------------------------------------------------------
 

doc/html/_sources/container/index.txt → doc/html/_sources/container/index.rst.txt

@@ -13,6 +13,7 @@
 ..  See the License for the specific language governing permissions and
 ..  limitations under the License.
 
+.. _container:
 
 |project| and Containers
 ========================

doc/html/_sources/container/singularity.txt → doc/html/_sources/container/singularity.rst.txt

@@ -20,7 +20,8 @@ Singularity
 We do not provide a "standalone" Singularity image, but rather bootstrap from a 
 Docker image.
 
-Build the image with:
+Change to the directory containing the Singularity file
+(<PROMOD3_CHECKOUT>/container) and build the image with:
 
 .. code-block:: bash
 
@@ -56,6 +57,43 @@ To list all available |project| modelling actions:
 
     singularity run --app PM promod.img help
 
+So you can either run an action with:
+
+.. code-block:: bash
+
+    singularity run --app PM promod.img build-model [options]
+
+or an arbitrary Python script using OpenStructure / |project| with:
+
+.. code-block:: bash
+
+    singularity run --app PM promod.img my_script.py [options] 
+
+The Notebook app provides a jupyter notebook playground with OST, |project|, and
+nglview available. You can fire it up with:
+
+.. code-block:: bash
+
+    singularity run --app Notebook promod.img
+
+connect to the notebook, start a new OST kernel and test it with the following 
+code snippet:
+
+.. code-block:: python
+
+    from ost import io
+    from promod3 import loop
+    import nglview
+
+    # generate backbone with dihedrals of a helix and store it
+    sequence = "HELLYEAH"
+    bb_list = loop.BackboneList(sequence)
+    io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+    # display stored file
+    view = nglview.show_file("test.pdb")
+    view
+
 The Compound Library
 --------------------