Merge branch 'master' into v5

CHANGELOG.md

@@ -2,6 +2,36 @@
 
 All notable changes to SeisComP are documented here.
 
+## 5.1.0
+
+-   scbulletin
+    -   Add option `--fdsn` for printing event parameters on just one line in
+        FDSN event format supporting to generate catalogs from event XML files.
+    -   Set output string of creation time of first origin time to event.
+-   scdbstrip
+    -   Fix reading `--days`.
+    -   Add options `-E` and `-Q` as well as module configuration for limiting
+        stripping to event parameters and waveforms quality control parameters,
+        respectively.
+-   scmssort
+    -   Report duplicate records whenever found.
+-   scquery
+    -   Do not require a database when using `--showqueries`.
+-   ql2sc
+    -   Add publicID prefix white- and blacklist configuration as alternative
+        to the already available agencyID filter.
+    -   Add option to ignore object removals during import.
+    -   Add more stable algorithm to synchronize the imported event with the
+        target system. This reduces the likelihood of infinite loops (re-imports)
+        on cross connected systems tremendously (note: it does not prevent that!).
+-   scinv
+    -   Add more tests to inventory check.
+    -   Add command-line options for tolerances: `max-elevation-difference` and
+        `max-sensor-depth` and corresponding module configuration parameters.
+    -   Add a test matrix to documentation reporting tests and consequences.
+-   FixedHypocenter
+    -   Set uncertainties in location to 0 km if entered manually.
+
 ## 5.0.1
 
 -   trunk
@@ -25,6 +55,9 @@ folder `rhel` instead of `centos`.
 The database schema receives an update and will increase the schema version
 to 0.12.
 
+-   VS(SC), Virtual Seismologist for SeisComP has been removed from the SeisComP
+    and is now available from a separate repository as an addon module. Read
+    the section "Addon Modules" of the seiscomp documentation for the details.
 -   fdsnws
     -   Fix broken unicode XML responses.
     -   Fix invalid request logging when HUP signal received.

README.md

@@ -120,6 +120,10 @@ the following global options are available:
 |SC_ENABLE_CONTRIB|ON|Enable inclusion of external contributions into the build. This includes all directories in `src/extras`.|
 |SC_GLOBAL_GUI|ON|Enables compilation of GUI components. This requires the Qt libraries to be installed. Either Qt4 or Qt5 are supported. The build will prefer Qt5 if found and will fallback to Qt4 if the Qt5 development libraries are not installed on the host system.|
 |SC_GLOBAL_GUI_QT5|ON|If SC_GLOBAL_GUI is enabled then Qt5 support will be enabled if this option is active. Otherwise only Qt4 will be supported.|
+|SC_DOC_GENERATE|OFF|Enable generation of documentation|
+|SC_DOC_GENERATE_HTML|ON|Enable generation of HTML documentation|
+|SC_DOC_GENERATE_MAN|ON|Enable generation of MAN pages|
+|SC_DOC_GENERATE_PDF|OFF|Enable generation of PDF documentation|
 
 ### Compilation
 

doc/base/addons/sed.rst

@@ -1,5 +1,15 @@
 .. _addons-sed:
 
+scdetect
+========
+
+Real-time earthquake detection based on waveform cross-correlation by ETHZ/SED.
+
+* Source code :
+  `GitHub <https://github.com/swiss-seismological-service/scdetect>`_.
+* Documentation: Included within the software package or
+  `online <https://scdetect.readthedocs.io/en/stable/>`_.
+
 scrtdd
 ======
 
@@ -16,6 +26,7 @@ sed-eew
 
 Modules for earthquake early warning by ETHZ/SED.
 
-* Source code for download:
+* Source code :
   `GitHub <https://github.com/SED-EEW/SED-EEW-SeisComP-contributions>`_.
-* Documentation: Included within the source code.
+* Documentation: Included within the software package or
+  `online <https://docs.gempa.de/sed-eew/current/seiscomp/share/doc/eew/html/>`_.

doc/base/concepts/messaging.rst

@@ -15,12 +15,12 @@ different :ref:`SeisComP modules <concepts_modules>` during runtime.
 Overview
 ========
 
-A typical real-time |scname| system consists of data processing and other modules (clients)
-and a messaging bus.
-The messaging bus connects all the clients letting them exchange information by messages
-through this bus.
-The messaging system is a fundamental concept of SeisComP following the publish-subscribe
-pattern [#wppubsub]_. It is provided by the |scname| module :ref:`scmaster`.
+A typical real-time |scname| system consists of data processing and other
+modules (clients) and a messaging bus. The messaging bus connects all the
+clients letting them exchange information by messages through this bus.
+The messaging system is a fundamental concept of SeisComP following the
+publish-subscribe pattern :cite:p:`wppubsub`. It is provided by the |scname|
+module :ref:`scmaster`.
 
 Clients can be producers (sending messages) and/or consumers (receiving
 messages). The basic concept is really simple: A producer sends a message
@@ -129,9 +129,9 @@ the scheme parameter of the connection:
 * `scmp` (default): unencrypted,
 * `scmps`: encrypted.
 
-Scheme, host, port and :ref:`queue <messaging-scheme>` together form the connection URL of the messaging
-system which is configurable in :confval:`connection.server` or set by the
-command-line option ``-H``.
+Scheme, host, port and :ref:`queue <messaging-scheme>` together form the
+connection URL of the messaging system which is configurable in
+:confval:`connection.server` or set by the command-line option ``-H``.
 
 Examples:
 
@@ -204,19 +204,19 @@ while modules running on computer B use
 
    connection.server = computerA/production
 
-The database connection which is used by :ref:`scmaster` will be reported to the clients
-when they connect so no explicit database configuration is necessary.
+The database connection which is used by :ref:`scmaster` will be reported to the
+clients when they connect so no explicit database configuration is necessary.
 
-The messaging connection can be explicitly provided on the command line using the
-option ``-H`` considering the comments on the :ref:`scheme <messaging-scheme>` and
-:ref:`queue <messaging-queue>`, e.g.
+The messaging connection can be explicitly provided on the command line using
+the option ``-H`` considering the comments on the
+:ref:`scheme <messaging-scheme>` and :ref:`queue <messaging-queue>`, e.g.
 
 .. code-block:: sh
 
    scolv -H computerA/production
 
 
-Web frontend
+Web Frontend
 ============
 
 When running :ref:`scmaster` a web frontend is available which can be adjusted to
@@ -234,15 +234,9 @@ provide system information. The default port to access the web frontend is 18180
    scmaster: Web frontend
 
 
-Related modules
+Related Modules
 ===============
 
 * :ref:`scmaster`
 * :ref:`scm`
 * :ref:`scmm`
-
-
-References
-==========
-
-.. [#wppubsub] https://en.wikipedia.org/wiki/Publish-subscribe_pattern

doc/base/contributing-docs.rst

@@ -70,7 +70,7 @@ Images
 ======
 
 Any images should be placed in a suitable sub-directory of :file:`descriptions/media`.
-Read the :ref:`documentation on image styles <documentation_style_guide>` for more details.
+Read the :ref:`documentation on image styles <documentation_style_guide_image>` for more details.
 The images can then be referred to (in .rst) like::
 
     .. figure::  media/scolv/scolv-overview.png
@@ -572,10 +572,10 @@ References
 .. target-notes::
 
 .. _`SeisComP wiki` : https://www.seiscomp.de/
-.. _`reStructuredText` : https://docutils.sourceforge.net/rst.html
-.. _`Sphinx` : https://sphinx.pocoo.org/index.html
+.. _`reStructuredText` : https://docutils.sourceforge.io/rst.html
+.. _`Sphinx` : https://www.sphinx-doc.org/
 .. _`Python documentation` : https://docs.python.org/
-.. _`introduction to reST` : https://sphinx.pocoo.org/rest.html
-.. _`directives` : https://sphinx.pocoo.org/markup/index.html
+.. _`introduction to reST` : https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html
+.. _`directives` : https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html
 .. _`SeisComP on GitHub` : https://github.com/SeisComP
 .. _`discussion forum` : https://forum.seiscomp.de

doc/base/history.rst

@@ -7,23 +7,26 @@ Historical Information
 The first version of SeisComP was developed for the
 :term:`GEOFON` program operated by :term:`GFZ`.
 
-Originally, |scname| was designed as a high-standard, fully automatic data acquisition and (near-)real-time
-data processing tool including quality control, event detection and location as well as dissemination
-of event alerts.
+Originally, |scname| was designed as a high-standard, fully automatic data
+acquisition and (near-)real-time data processing tool including quality control,
+event detection and location as well as dissemination of event alerts.
 
-SeisComP was further extended within the MEREDIAN project under the lead of GEOFON and `ORFEUS`_.
+SeisComP was further extended within the MEREDIAN project under the lead of
+GEOFON and :cite:t:`orfeus`.
 
-Following the devastating 2004 Indian Ocean earthquake and tsunami, the `GITEWS`_ (German Indian Ocean
-Tsunami Early Warning System) project led to additional functionality being implemented to fulfill the
-requirements of 24/7 early warning control centers. Major changes in the architecture of SeisComP
-were necessary and many new features resulted in the upgrade of SeisComP to version 3.
+Following the devastating 2004 Indian Ocean earthquake and tsunami, the
+:cite:t:`gitews` (German Indian Ocean Tsunami Early Warning System) project led
+to additional functionality being implemented to fulfill the requirements of
+24/7 early warning control centers. Major changes in the architecture of SeisComP
+were necessary and many new features resulted in the upgrade of SeisComP to 
+version 3.
 
-Since 2008 SeisComP has been jointly developed by :term:`gempa GmbH`, a spin-off company of GFZ and GFZ.
-Nowadays, gempa GmbH is the main SeisComP developing and service company.
-
-Major SeisComP releases are shown below. The important changes as of version 4.0 are documented in
-the :ref:`change log <sc-changelog>`.
+Since 2008 SeisComP has been jointly developed by :term:`gempa GmbH`, a spin-off
+company of GFZ and GFZ. Nowadays, gempa GmbH is the main SeisComP developing and
+service company.
 
+Major SeisComP releases are shown below. The important changes as of version 4.0
+are documented in the :ref:`changelog <sc-changelog>`.
 
 +---------+-----------+--------------------+-----------------------------------------------------+
 | Version | Name      |  Time              |                                                     |
@@ -66,11 +69,3 @@ the :ref:`change log <sc-changelog>`.
 | 4.0.0   |           | May 2020           | Adopts the GNU Affero General Public License v. 3.0,|
 |         |           |                    | (AGPL), support for Python3 and QT5                 |
 +---------+-----------+--------------------+-----------------------------------------------------+
-
-References
-==========
-
-.. target-notes::
-
-.. _`ORFEUS`: https://www.orfeus-eu.org
-.. _`GITEWS`: https://www.gitews.org

doc/base/installation.rst

@@ -8,7 +8,7 @@
 only under Linux. For production systems we recommend Linux distributions with
 long-term support (LTS). The Linux flavors under which |scname| has been tested
 are given along with the |scname| package names on the download sites of
-`SeisComP`_ and `gempa`_.
+:cite:t:`seiscomp` and :cite:t:`gempa`.
 
 The software can be obtained and installed from
 
@@ -25,7 +25,7 @@ Packages may include
 * Documentation,
 * Station configuration files (optional).
 
-Download these packages from `SeisComP`_ or `gempa`_.
+Download these packages from :cite:t:`seiscomp` or :cite:t:`gempa-download`.
 
 The next sections describe the installation of the binary packages of |scname|
 on
@@ -107,7 +107,8 @@ Simply follow a few steps to complete your installation of |scname|:
 
 #. Log in to your Linux system as user, e.g. sysop, the standard user in this
    documentation.
-#. Download the installation packages, e.g. from `SeisComP`_ or from `gempa`_:
+#. Download the installation packages, e.g. from :cite:t:`seiscomp` or
+   :cite:t:`gempa-download`:
 
    * :file:`seiscomp-[version]-[OS]-[arch].tar.gz`: main |scname| package with binaries, etc.
      Ensure to download the right package matching your operating system (OS) and
@@ -116,12 +117,12 @@ Simply follow a few steps to complete your installation of |scname|:
 
      .. note::
 
-        When receiving the packages from `gempa`_, the documentation is already
+        When receiving the packages from :cite:t:`gempa-download`, the documentation is already
         included in the main |scname| package to match the installed version. In this
         case, the documentation does not need to be downloaded and installed separately.
 
    * :file:`seiscomp-maps.tar.gz`: standard |scname| maps available on the
-     download site of `SeisComP`_.
+     download site of :cite:t:`seiscomp`.
 
 #. Copy the downloaded files to your $HOME directory.
 
@@ -426,17 +427,8 @@ PostgreSQL
      :file:`/var/lib/pgsql/data/postgresql.conf`
 
 
-Next steps
+Next Steps
 ==========
 
-Now everything is installed and the system can be configured. The :ref:`next chapter<getting-started>`
-chapter explains the first steps.
-
-References
-==========
-
-.. target-notes::
-
-.. _`gempa` : https://data.gempa.de/packages/Public/seiscomp/
-.. _`SeisComP` : https://www.seiscomp.de
-.. _`GitHub` : https://github.com/SeisComP
+Now everything is installed and the system can be configured. The
+:ref:`next chapter<getting-started>` chapter explains the first steps.

doc/base/introduction.rst

@@ -14,7 +14,8 @@ research centers, companies and governmental agencies world-wide by:
 
 * Powerful and reliable automatic data processing in real time or during post-processing
 * User-friendly and comprehensive graphical interfaces
-* Modern and well-maintained OpenSource software on `GitHub`_ welcoming community contributions.
+* Modern and well-maintained OpenSource software on GitHub
+  :cite:p:`seiscomp-github` welcoming community contributions.
 
 The first work on what became |scname| today began nearly two decades ago
 with developments at :term:`GFZ` of plugins for digitizers.
@@ -64,7 +65,8 @@ The guidelines for the design of |scname| are:
 
 These design principles have given |scname| much robustness and flexibility
 to respond to new developments. The |scname| community is encouraged to contribute
-their |scname| source code on `GitHub`_. Examples and guidelines for generating
+their |scname| source code on GitHub :cite:p:`seiscomp-github`. Examples and
+guidelines for generating
 code are given in the :ref:`developer section <sec_index_developers>`.
 
 
@@ -75,13 +77,15 @@ This documentation begins with an :ref:`overview` and a :ref:`concepts` section
 necessary for understanding and using |scname| successfully.
 The :ref:`Glossary section <glossary>` introduces technical terms.
 All important code changes are listed in the :ref:`change log <sc-changelog>`.
-When using |scname| or contributing source code, you should understand the :ref:`license terms <license>`.
+When using |scname| or contributing source code, you should understand the
+:ref:`license terms <license>`.
 If you actually make use of |scname| and publish the results, we ask you to give
 appropriate reference as set out on the :ref:`Citation section <citation>`.
 
 In the following section the documentation covers the :ref:`installation <installation>`
 and how to configure and operate a working |scname| system.
-A few :ref:`tutorials` will guide you through a first example set up and further operations.
+A few :ref:`tutorials` will guide you through a first example set up and further
+operations.
 
 The tutorials are followed by :ref:`detailed technical descriptions <sec_index_modules>`
 of each individual |scname| module, grouped by their general functionality:
@@ -93,26 +97,18 @@ of each individual |scname| module, grouped by their general functionality:
 * Utilities
 
 and many more :ref:`extensions <sec_index_extensions>` like descriptions of the
-:term:`RecordStream`, magnitude types, locators, GUI customizations, waveform filters or plugins.
+:term:`RecordStream`, magnitude types, locators, GUI customizations, waveform
+filters or plugins.
 
 The final part of the documentation relates to
 :ref:`contributing your own source code <sec_index_developers>` to |scname|.
 This requires a deeper knowledge of the |scname| :ref:`data model<api-datamodel-python>`
 and other details.
 This part also includes guidelines for developers such as
-:ref:`coding conventions <coding_conventions>`, :ref:`unit tests <unittests>` and a
-:ref:`guide for contributing documentation <contributing_documentation>`.
-:ref:`Some Python examples <sdk-python-examples>` help you to get started quickly
-with programming for |scname|.
+:ref:`coding conventions <coding_conventions>`, :ref:`unit tests <unittests>`
+and a :ref:`guide for contributing documentation <contributing_documentation>`.
+:ref:`Some Python examples <sdk-python-examples>` help you to get started
+quickly with programming for |scname|.
 
 |scname| is developed and distributed under the terms of the GNU
-`Affero General Public License`_, as set out in the :ref:`license` section.
-
-
-References
-==========
-
-.. target-notes::
-
-.. _`GitHub` : https://github.com/SeisComP
-.. _`Affero General Public License` : https://www.gnu.org/licenses/agpl-3.0.html
+:cite:t:`agpl`, as set out in the :ref:`license` section.