update installation and upgrade instructions

docs/index.rst

@@ -2,7 +2,7 @@
 
 This is the official documentation of the `Deformability Cytometry Open
 Repository (DCOR) <https://dcor.mpl.mpg.de>`_, a public repository for
-real-time deformability cytometry (RT-DC) datasets hosted by the
+deformability cytometry datasets hosted by the
 `Max-Planck-Gesellschaft <https://www.mpg.de>`_.
 
 

docs/sec_develop.rst

@@ -26,73 +26,22 @@ Installation
 This part differs from the installation for production. We want to have the
 DCOR extensions installed in editable mode. 
 
-.. note::
-
-    If you are installing DCOR in a virtual machine, it makes sense to
-    access the extensions directories directly from the host system.
-    (without having to git or rsync data back and forth).
-
-    On the host machine, create a directory where all relevant repositories
-    will be cloned to (e.g. ``/home/paul/repos/DCOR``).
-
-
-    In Virtual Machine Manager, add a "Filesystem" hardware. Choose "Path" driver,
-    "Passthrough" mode, "Default" write policy and set the source path to where
-    the repositories are located on the host machine (``/home/paul/repos/DCOR``).
-    Set the target path to "/repos".
-
-    On the guest machine, add the following line to `/etc/fstab`:
-
-    .. code::
-    
-       /repos   /dcor-repos    9p  trans=virtio,version=9p2000.L,rw    0   0
-    
-    After ``mkdir /dcor-repos``, ``chmod a+rx /dcor-repos``,
-    and ``mount /dcor-repos``, you can then access
-    the repositories of the host machine directly from the guest machine.
-    In order for everything to work properly, libvirt needs access to
-    ``/home/paul/repos/DCOR``. The easiest way to achieve that
-    is to set the libvirt user to your user name, i.e. edit ``/etc/libvirt/qemu.conf``
-    and set ``user = "paul"`` (``systemctl restart libvirtd`` after doing so).
-
-
-Let's first choose a directory where all DCOR-related repositories will be
-located (e.g. `/dcor-repos`). Clone all relevant directories. If you are
-forking any of these repositories, you will wnat to run
-`git clone git@github.com:username/repository_name.git`` instead.
-
-.. code::
+Let's first set up our development environment. The ``dcor_control``
+package comes with a convenient ``dcor develop`` command. This command
+will create the ``/dcor-repos`` directory, clone all DCOR-related
+repositories into it and install each of them in editable mode.
 
-   mkdir -p /dcor-repos
-   cd /dcor-repos
-   git clone https://github.com/DCOR-dev/dcor_control.git
-   git clone https://github.com/DCOR-dev/dcor_shared.git
-   git clone https://github.com/DCOR-dev/ckanext-dc_log_view.git
-   git clone https://github.com/DCOR-dev/ckanext-dc_serve.git
-   git clone https://github.com/DCOR-dev/ckanext-dc_view.git
-   git clone https://github.com/DCOR-dev/ckanext-dcor_depot.git
-   git clone https://github.com/DCOR-dev/ckanext-dcor_schemas.git
-   git clone https://github.com/DCOR-dev/ckanext-dcor_theme.git
+.. note::
 
-Next, install each of those repositories in the CKAN virtual environment
-(in the exact same order).
+    If you have already installed all packages in editable mode from
+    GitHub repositories, a simple `dcor update` will only update those
+    (regardless of where they are located in the file system).
 
 .. code::
 
-    source /usr/lib/ckan/default/bin/activate
-    cd /dcor-repos
-    pip install --upgrade pip wheel
-    # shared extension dependency
-    pip install -e dcor_shared
-    # extensions
-    pip install -e ckanext-dc_log_view
-    pip install -e ckanext-dc_serve
-    pip install -e ckanext-dc_view
-    pip install -e ckanext-dcor_depot
-    pip install -e ckanext-dcor_schemas
-    pip install -e ckanext-dcor_theme
-    # dcor control (this must be installed at the very end)
-    pip install -e dcor_control
+   source /usr/lib/ckan/default/bin/activate
+   pip install dcor_control
+   dcor develop
 
 
 Initialization

docs/sec_self_hosting/upgrade.rst

@@ -55,13 +55,13 @@ steps to upgrade CKAN from the `CKAN docs
    Install the latest version of CKAN for your system::
 
      CKANMINOR=2.10
-     CKANPATCH=2.10.1
+     CKANPATCH=2.10.3
      UBUNTURELEASE=$(lsb_release -cs)
      DLNAMESERVR=python-ckan_${CKANMINOR}-${UBUNTURELEASE}_amd64.deb
      DLNAMELOCAL=python-ckan_${CKANPATCH}-${UBUNTURELEASE}_amd64.deb
      mkdir -p CKAN_updates
      wget https://packaging.ckan.org/${DLNAMESERVR} -O CKAN_updates/${DLNAMELOCAL}
-     apt remove python-ckan
+     apt-get -y remove python-ckan
      rm -rf /usr/lib/ckan/
      dpkg -i CKAN_updates/${DLNAMELOCAL}
 
@@ -71,7 +71,8 @@ steps to upgrade CKAN from the `CKAN docs
      source /usr/lib/ckan/default/bin/activate
      export CKAN_INI=/etc/ckan/default/ckan.ini
 
-8. Reinstall Solr. If already installed via apt, this will require you to first::
+8. For the upgrade from CKAN 2.0 to 2.10, Solr must be installed (previous versions of Solr were
+   installed via ``apt``)::
 
      apt purge tomcat9 solr-tomcat