Commit 3c0b431e authored by Studer Gabriel's avatar Studer Gabriel
Browse files

Merge branch 'release-3.1.1'

parents 22760b42 de4ceb7a
......@@ -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
--------------------------------------------------------------------------------
......
......@@ -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)
......
ARG OPENSTRUCTURE_VERSION="2.0.0-bionic"
FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_VERSION}
ARG OPENSTRUCTURE_IMAGE_TAG="2.1.0-bionic"
FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
# ARGUMENTS
###########
ARG PROMOD_VERSION="3.1.0"
ARG PROMOD_VERSION="3.1.1"
ARG SRC_FOLDER="/usr/local/src"
......
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
......
......@@ -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/
......
......@@ -13,6 +13,7 @@
.. See the License for the specific language governing permissions and
.. limitations under the License.
.. _container:
|project| and Containers
========================
......
......@@ -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
--------------------
......
......@@ -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:
......
......@@ -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|
......
......@@ -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
--------------------------------------------------------------------------------
......
......@@ -13,6 +13,7 @@
.. See the License for the specific language governing permissions and
.. limitations under the License.
.. _container:
|project| and Containers
========================
......
......@@ -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
--------------------
......
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