MonetDB: json - Merge branch 'master' into branches/json

[Panagiotis Koutsourakis]

Changeset: 0b7d04a3aec4 for MonetDB
URL: https://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=0b7d04a3aec4
Added Files:
        clients/mapilib/mapi_prompt.h
        clients/mapilib/mapi_querytype.h
        documentation/Makefile
        documentation/make.bat
        documentation/source/conf.py
        documentation/source/index.rst
        documentation/source/input.rst
        gdk/gdk_tracer.c
        gdk/gdk_tracer.h
        monetdb5/mal/Tests/tracer00.malC
        monetdb5/mal/Tests/tracer00.stable.err
        monetdb5/mal/Tests/tracer00.stable.out
        monetdb5/mal/Tests/tst111.malC
        monetdb5/mal/Tests/tst111.stable.err
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        monetdb5/mal/Tests/tst112.malC
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        monetdb5/mal/Tests/tst113.malC
        monetdb5/mal/Tests/tst113.stable.err
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        monetdb5/mal/Tests/tst114.malC
        monetdb5/mal/Tests/tst114.stable.err
        monetdb5/mal/Tests/tst114.stable.out
        monetdb5/mal/Tests/tst117.malC
        monetdb5/mal/Tests/tst117.stable.err
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        monetdb5/mal/Tests/tst180.malC
        monetdb5/mal/Tests/tst180.stable.err
        monetdb5/mal/Tests/tst180.stable.out
        monetdb5/mal/Tests/tst190.malC
        monetdb5/mal/Tests/tst190.stable.err
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        monetdb5/mal/Tests/tst191.malC
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        monetdb5/mal/Tests/tst192.malC
        monetdb5/mal/Tests/tst192.stable.err
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        monetdb5/mal/Tests/tst193.malC
        monetdb5/mal/Tests/tst193.stable.err
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        monetdb5/mal/Tests/tst194.malC
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        monetdb5/mal/Tests/tst195.malC
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        monetdb5/mal/Tests/tst196.malC
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        monetdb5/mal/Tests/tst914.malC
        monetdb5/mal/Tests/tst914.stable.err
        monetdb5/mal/Tests/tst914.stable.out
        monetdb5/modules/mal/tracer.c
        monetdb5/modules/mal/tracer.h
        monetdb5/modules/mal/tracer.mal
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_00.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_01.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_02.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_03.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_04.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_05.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_06.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_07.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_09.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_10.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_11.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_12.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_13.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_16.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_17.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_18.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_19.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_20.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_21.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_23.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_24.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_25.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_26.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_27.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_28.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_29.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_30.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_32.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyloader3_01.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyloader3_02.sql
        sql/backends/monet5/UDF/pyapi3/Tests/pyloader3_05.sql
        sql/backends/monet5/UDF/pyapi3/connection.h
        sql/backends/monet5/UDF/pyapi3/conversion.h
        sql/backends/monet5/UDF/pyapi3/convert_loops.h
        sql/backends/monet5/UDF/pyapi3/emit.h
        sql/backends/monet5/UDF/pyapi3/formatinput.h
        sql/backends/monet5/UDF/pyapi3/pyapi.h
        sql/backends/monet5/UDF/pyapi3/pyheader.h
        sql/backends/monet5/UDF/pyapi3/pytypes.h
        sql/backends/monet5/UDF/pyapi3/type_conversion.h
        sql/backends/monet5/UDF/pyapi3/undef.h
        sql/backends/monet5/UDF/pyapi3/unicode.h
        sql/scripts/81_tracer.sql
        sql/test/BugTracker-2019/Tests/set-schema-mclient-msg.Bug-6754.sql
        
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        sql/test/BugTracker-2020/Tests/All
        sql/test/BugTracker-2020/Tests/ifthenelse-crash.Bug-6815.sql
        sql/test/BugTracker-2020/Tests/ifthenelse-crash.Bug-6815.stable.err
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        sql/test/BugTracker-2020/Tests/median_avg-nulls.Bug-6807.sql
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        sql/test/analytics/Tests/analytics14.sql
        sql/test/analytics/Tests/analytics14.stable.err
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        sql/test/analytics/Tests/analytics15.sql
        sql/test/analytics/Tests/analytics15.stable.err
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        sql/test/analytics/Tests/analytics16.sql
        sql/test/analytics/Tests/analytics16.stable.err
        sql/test/analytics/Tests/analytics16.stable.out
        sql/test/analytics/Tests/analytics17.sql
        sql/test/analytics/Tests/analytics17.stable.err
        sql/test/analytics/Tests/analytics17.stable.out
        sql/test/wlcr/Tests/wlr110.py
        sql/test/wlcr/Tests/wlr110.stable.err
        sql/test/wlcr/Tests/wlr110.stable.out
        sql/test/wlcr/Tests/wlr35.py
        sql/test/wlcr/Tests/wlr35.stable.err
        sql/test/wlcr/Tests/wlr35.stable.out
Removed Files:
        clients/examples/python/mclient-python2.py
        clients/mapiclient/Tests/tachograph--help
        clients/mapiclient/Tests/tachograph--help.bat
        clients/mapiclient/Tests/tachograph--help.stable.err
        clients/mapiclient/Tests/tachograph--help.stable.out
        clients/mapiclient/Tests/tomograph--help
        clients/mapiclient/Tests/tomograph--help.bat
        clients/mapiclient/Tests/tomograph--help.stable.err
        clients/mapiclient/Tests/tomograph--help.stable.out
        clients/mapiclient/tachograph.c
        clients/mapiclient/tomograph.c
        debian/libmonetdb5-server-bam.install
        debian/monetdb-client-tools.docs
        debian/monetdb-client-tools.install
        debian/monetdb-python2.install
        sql/backends/monet5/Tests/createorreplace.sql
        sql/backends/monet5/Tests/createorreplace.stable.err
        sql/backends/monet5/Tests/createorreplace.stable.out
        sql/backends/monet5/Tests/pyapi00.sql
        sql/backends/monet5/Tests/pyapi00.stable.err
        sql/backends/monet5/Tests/pyapi00.stable.out
        sql/backends/monet5/Tests/pyapi01.sql
        sql/backends/monet5/Tests/pyapi01.stable.err
        sql/backends/monet5/Tests/pyapi01.stable.out
        sql/backends/monet5/Tests/pyapi02.sql
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        sql/backends/monet5/Tests/pyapi02.stable.out
        sql/backends/monet5/Tests/pyapi03.sql
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        sql/backends/monet5/Tests/pyapi04.sql
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        sql/backends/monet5/Tests/pyapi05.sql
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        sql/backends/monet5/Tests/pyapi06.sql
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        sql/backends/monet5/Tests/pyapi07.sql
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        sql/backends/monet5/Tests/pyapi07.stable.out
        sql/backends/monet5/Tests/pyapi08.sql
        sql/backends/monet5/Tests/pyapi08.stable.err
        sql/backends/monet5/Tests/pyapi08.stable.out
        sql/backends/monet5/Tests/pyapi09.sql
        sql/backends/monet5/Tests/pyapi09.stable.err
        sql/backends/monet5/Tests/pyapi09.stable.out
        sql/backends/monet5/Tests/pyapi10.sql
        sql/backends/monet5/Tests/pyapi10.stable.err
        sql/backends/monet5/Tests/pyapi10.stable.err.Windows
        sql/backends/monet5/Tests/pyapi10.stable.out
        sql/backends/monet5/Tests/pyapi11.sql
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        sql/backends/monet5/vaults/bam/default_schema.dia
        sql/backends/monet5/vaults/bam/default_schema.png
        sql/backends/monet5/vaults/bam/metadata.dia
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        sql/backends/monet5/vaults/bam/mykstring.h
        sql/backends/monet5/vaults/bam/paired_schema.dia
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        sql/include/sql_querytype.h
        
sql/test/BugTracker-2009/Tests/dumping_tables.SF-2776908--optimizers.options5
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        tools/mserver/tomographintro.docx
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Modified Files:
        .hgignore
        ChangeLog
        HowToStart.rst
        Makefile.ag
        MonetDB.spec
        NT/Makefile
        NT/mksqlwxs.py
        NT/monetdb_config.h.in
        NT/rules.msc
        NT/wincompile.py
        NT/winconfig.py
        README-Debian
        README-Fedora
        README.rst
        bootstrap
        buildtools/Makefile.ag
        buildtools/autogen/autogen.py
        buildtools/autogen/autogen/am.py
        buildtools/autogen/autogen/codegen.py
        buildtools/autogen/autogen/filesplit.py
        buildtools/autogen/autogen/msc.py
        buildtools/autogen/autogen/var.py
        buildtools/conf/Maddlog
        buildtools/conf/Makefile.ag
        buildtools/conf/fixlicense.py
        buildtools/conf/rules.mk
        buildtools/conf/website.html
        buildtools/doc/HowToRelease.rst
        buildtools/doc/windowsbuild.rst
        clients/Makefile.ag
        clients/NT/Makefile.ag
        clients/NT/mclient.bat
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        clients/NT/stethoscope.bat
        clients/Tests/All
        clients/Tests/MAL-signatures.stable.out
        clients/Tests/MAL-signatures.stable.out.int128
        clients/Tests/exports.stable.out
        clients/examples/C/Makefile.ag
        clients/examples/C/sample0.c
        clients/examples/C/sample1.c
        clients/examples/C/sample4.c
        clients/examples/C/smack00.c
        clients/examples/C/smack01.c
        clients/examples/Makefile.ag
        clients/examples/perl/Makefile.ag
        clients/examples/perl/malsample.pl
        clients/examples/perl/sqlsample.pl
        clients/examples/php/Makefile.ag
        clients/examples/php/sqlsample.php
        clients/examples/python/basics.py
        clients/examples/python/mclient-python3.py
        clients/examples/python/perf.py
        clients/examples/python/sqlsample.py
        clients/mapiclient/Makefile.ag
        clients/mapiclient/ReadlineTools.c
        clients/mapiclient/ReadlineTools.h
        clients/mapiclient/Tests/All
        clients/mapiclient/Tests/stethoscope--help.stable.err
        clients/mapiclient/dotfile.py
        clients/mapiclient/dotmonetdb.c
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        clients/mapiclient/dump.c
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        clients/mapiclient/eventparser.h
        clients/mapiclient/mclient.1
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        clients/mapiclient/mhelp.c
        clients/mapiclient/mhelp.h
        clients/mapiclient/msqldump.c
        clients/mapiclient/msqldump.h
        clients/mapiclient/stethoscope.c
        clients/mapilib/Makefile.ag
        clients/mapilib/mapi.c
        clients/mapilib/mapi.h
        clients/mapilib/mapi.rc
        clients/mapilib/monetdb-mapi.pc.in
        clients/odbc/Makefile.ag
        clients/odbc/doc/ExcelMonetDB.html
        clients/odbc/doc/unixODBC.html
        clients/odbc/driver/Makefile.ag
        clients/odbc/driver/ODBCConvert.c
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        clients/odbc/driver/ODBCDesc.c
        clients/odbc/driver/ODBCDesc.h
        clients/odbc/driver/ODBCEnv.c
        clients/odbc/driver/ODBCEnv.h
        clients/odbc/driver/ODBCError.c
        clients/odbc/driver/ODBCError.h
        clients/odbc/driver/ODBCGlobal.h
        clients/odbc/driver/ODBCQueries.h
        clients/odbc/driver/ODBCStmt.c
        clients/odbc/driver/ODBCStmt.h
        clients/odbc/driver/ODBCUtil.c
        clients/odbc/driver/ODBCUtil.h
        clients/odbc/driver/SQLAllocConnect.c
        clients/odbc/driver/SQLAllocEnv.c
        clients/odbc/driver/SQLAllocHandle.c
        clients/odbc/driver/SQLAllocStmt.c
        clients/odbc/driver/SQLBindCol.c
        clients/odbc/driver/SQLBindParameter.c
        clients/odbc/driver/SQLBrowseConnect.c
        clients/odbc/driver/SQLBulkOperations.c
        clients/odbc/driver/SQLCancel.c
        clients/odbc/driver/SQLCloseCursor.c
        clients/odbc/driver/SQLColAttribute.c
        clients/odbc/driver/SQLColAttributes.c
        clients/odbc/driver/SQLColumnPrivileges.c
        clients/odbc/driver/SQLColumns.c
        clients/odbc/driver/SQLConnect.c
        clients/odbc/driver/SQLCopyDesc.c
        clients/odbc/driver/SQLDataSources.c
        clients/odbc/driver/SQLDescribeCol.c
        clients/odbc/driver/SQLDescribeParam.c
        clients/odbc/driver/SQLDisconnect.c
        clients/odbc/driver/SQLDriverConnect.c
        clients/odbc/driver/SQLDrivers.c
        clients/odbc/driver/SQLEndTran.c
        clients/odbc/driver/SQLError.c
        clients/odbc/driver/SQLExecDirect.c
        clients/odbc/driver/SQLExecute.c
        clients/odbc/driver/SQLExtendedFetch.c
        clients/odbc/driver/SQLFetch.c
        clients/odbc/driver/SQLFetchScroll.c
        clients/odbc/driver/SQLForeignKeys.c
        clients/odbc/driver/SQLFreeConnect.c
        clients/odbc/driver/SQLFreeEnv.c
        clients/odbc/driver/SQLFreeHandle.c
        clients/odbc/driver/SQLFreeStmt.c
        clients/odbc/driver/SQLGetConnectAttr.c
        clients/odbc/driver/SQLGetConnectOption.c
        clients/odbc/driver/SQLGetCursorName.c
        clients/odbc/driver/SQLGetData.c
        clients/odbc/driver/SQLGetDescField.c
        clients/odbc/driver/SQLGetDescRec.c
        clients/odbc/driver/SQLGetDiagField.c
        clients/odbc/driver/SQLGetDiagRec.c
        clients/odbc/driver/SQLGetEnvAttr.c
        clients/odbc/driver/SQLGetFunctions.c
        clients/odbc/driver/SQLGetInfo.c
        clients/odbc/driver/SQLGetStmtAttr.c
        clients/odbc/driver/SQLGetStmtOption.c
        clients/odbc/driver/SQLGetTypeInfo.c
        clients/odbc/driver/SQLMoreResults.c
        clients/odbc/driver/SQLNativeSql.c
        clients/odbc/driver/SQLNumParams.c
        clients/odbc/driver/SQLNumResultCols.c
        clients/odbc/driver/SQLParamData.c
        clients/odbc/driver/SQLParamOptions.c
        clients/odbc/driver/SQLPrepare.c
        clients/odbc/driver/SQLPrimaryKeys.c
        clients/odbc/driver/SQLProcedureColumns.c
        clients/odbc/driver/SQLProcedures.c
        clients/odbc/driver/SQLPutData.c
        clients/odbc/driver/SQLRowCount.c
        clients/odbc/driver/SQLSetConnectAttr.c
        clients/odbc/driver/SQLSetConnectOption.c
        clients/odbc/driver/SQLSetCursorName.c
        clients/odbc/driver/SQLSetDescField.c
        clients/odbc/driver/SQLSetDescRec.c
        clients/odbc/driver/SQLSetEnvAttr.c
        clients/odbc/driver/SQLSetParam.c
        clients/odbc/driver/SQLSetPos.c
        clients/odbc/driver/SQLSetScrollOptions.c
        clients/odbc/driver/SQLSetStmtAttr.c
        clients/odbc/driver/SQLSetStmtOption.c
        clients/odbc/driver/SQLSpecialColumns.c
        clients/odbc/driver/SQLStatistics.c
        clients/odbc/driver/SQLTablePrivileges.c
        clients/odbc/driver/SQLTables.c
        clients/odbc/driver/SQLTransact.c
        clients/odbc/driver/driver.rc
        clients/odbc/samples/Makefile.ag
        clients/odbc/samples/arraytest.c
        clients/odbc/samples/odbcsample1.c
        clients/odbc/samples/testStmtAttr.c
        clients/odbc/samples/testgetinfo.c
        clients/odbc/setup/Makefile.ag
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        tools/Makefile.ag
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        tools/merovingian/client/Makefile.ag
        tools/merovingian/client/monetdb.c
        tools/merovingian/daemon/Makefile.ag
        tools/merovingian/daemon/argvcmds.c
        tools/merovingian/daemon/argvcmds.h
        tools/merovingian/daemon/client.c
        tools/merovingian/daemon/client.h
        tools/merovingian/daemon/config/.merovingian_properties.in
        tools/merovingian/daemon/config/Makefile.ag
        tools/merovingian/daemon/connections.c
        tools/merovingian/daemon/connections.h
        tools/merovingian/daemon/controlrunner.c
        tools/merovingian/daemon/controlrunner.h
        tools/merovingian/daemon/discoveryrunner.c
        tools/merovingian/daemon/discoveryrunner.h
        tools/merovingian/daemon/forkmserver.c
        tools/merovingian/daemon/forkmserver.h
        tools/merovingian/daemon/handlers.c
        tools/merovingian/daemon/handlers.h
        tools/merovingian/daemon/merovingian.c
        tools/merovingian/daemon/merovingian.h
        tools/merovingian/daemon/multiplex-funnel.c
        tools/merovingian/daemon/multiplex-funnel.h
        tools/merovingian/daemon/proxy.c
        tools/merovingian/daemon/proxy.h
        tools/merovingian/utils/Makefile.ag
        tools/merovingian/utils/control.c
        tools/merovingian/utils/control.h
        tools/merovingian/utils/database.c
        tools/merovingian/utils/database.h
        tools/merovingian/utils/glob.c
        tools/merovingian/utils/glob.h
        tools/merovingian/utils/properties.c
        tools/merovingian/utils/properties.h
        tools/merovingian/utils/utils.c
        tools/merovingian/utils/utils.h
        tools/monetdbbincopy
        tools/mserver/Makefile.ag
        tools/mserver/monet_version.c.in
        tools/mserver/monet_version.h
        tools/mserver/mserver5.1.in
        tools/mserver/mserver5.c
        tools/mserver/shutdowntest.c
Branch: json
Log Message:

Merge branch 'master' into branches/json


diffs (truncated from 346334 to 300 lines):

diff --git a/.hgignore b/.hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -91,3 +91,6 @@ NT/unistd.h
 # package building on Mac OS X
 MacOSX/build
 MacOSX/usr
+
+# Don't keep the result of the documentation compilation
+documentation/build
diff --git a/ChangeLog b/ChangeLog
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog file for devel
 # This file is updated with Maddlog
 
+* Thu Jan 30 2020 Sjoerd Mullender <sjo...@acm.org>
+- Removed support for bam and sam files.
+
 * Fri Dec  6 2019 Panagiotis Koutsourakis <kutsu...@monetdbsolutions.com>
 - Added mserver5 option (--set raw_strings=true|false) and monetdb
   database property (raw_strings=yes|no) to control interpretation
diff --git a/HowToStart.rst b/HowToStart.rst
--- a/HowToStart.rst
+++ b/HowToStart.rst
@@ -2,7 +2,7 @@
 .. License, v. 2.0.  If a copy of the MPL was not distributed with this
 .. file, You can obtain one at http://mozilla.org/MPL/2.0/.
 ..
-.. Copyright 1997 - July 2008 CWI, August 2008 - 2019 MonetDB B.V.
+.. Copyright 1997 - July 2008 CWI, August 2008 - 2020 MonetDB B.V.
 
 How To Start with MonetDB
 =========================
diff --git a/Makefile.ag b/Makefile.ag
--- a/Makefile.ag
+++ b/Makefile.ag
@@ -2,7 +2,7 @@
 # License, v. 2.0.  If a copy of the MPL was not distributed with this
 # file, You can obtain one at http://mozilla.org/MPL/2.0/.
 #
-# Copyright 1997 - July 2008 CWI, August 2008 - 2019 MonetDB B.V.
+# Copyright 1997 - July 2008 CWI, August 2008 - 2020 MonetDB B.V.
 
 SUBDIRS = buildtools common clients \
        gdk \
@@ -16,7 +16,7 @@ EXTRA_DIST = bootstrap configure configu
        MonetDB.spec rpm.mk.in COPYING README.rst license.txt HowToStart.rst \
        README-Fedora README-Debian
 
-EXTRA_DIST_DIR = NT debian MacOSX
+EXTRA_DIST_DIR = NT debian MacOSX documentation
 
 headers_config = {
        DIR = includedir/monetdb
diff --git a/MonetDB.spec b/MonetDB.spec
--- a/MonetDB.spec
+++ b/MonetDB.spec
@@ -66,16 +66,6 @@
 %endif
 %endif
 
-%if %{?rhel:0}%{!?rhel:1}
-# By default create the MonetDB-bam-MonetDB5 package.
-# Note that the samtools-devel RPM is not available on RedHat
-# Enterprise Linux and derivatives, even with EPEL availabe.
-# (Actually, at the moment of writing, samtools-devel is available in
-# EPEL for RHEL 6, but not for RHEL 7.  We don't make the distinction
-# here and just not build the MonetDB-bam-MonetDB5 RPM.)
-%bcond_without samtools
-%endif
-
 # By default use PCRE for the implementation of the SQL LIKE and ILIKE
 # operators.  Otherwise the POSIX regex functions are used.
 %bcond_without pcre
@@ -85,14 +75,9 @@
 %bcond_without rintegration
 %endif
 
-# On Fedora <= 30 and RHEL 7, create the MonetDB-python2 package.
-# On RHEL 6, numpy is too old.
-%if 0%{?rhel} == 7 || %{!?fedora:1000}%{?fedora} <= 30
-%bcond_without py2integration
-%endif
-%if %{?rhel:0}%{!?rhel:1}
-# On RHEL 6, Python 3 is too old, and on RHEL 7, the default Python 3
-# is too old (in both cases 3.4).
+%if 0%{?rhel} >= 7 || 0%{?fedora} > 0
+# On RHEL 6, Python 3 is too old.  On RHEL 7, Python 3 was too old
+# when RHEL 7 was released, but now it is ok.
 %bcond_without py3integration
 %endif
 
@@ -156,18 +141,6 @@ BuildRequires: readline-devel
 BuildRequires: unixODBC-devel
 # BuildRequires: uriparser-devel
 BuildRequires: pkgconfig(zlib)
-%if %{with samtools}
-BuildRequires: samtools-devel
-%endif
-%if %{with py2integration}
-BuildRequires: python-devel
-%if %{?rhel:1}%{!?rhel:0}
-# RedHat Enterprise Linux calls it simply numpy
-BuildRequires: numpy
-%else
-BuildRequires: python2-numpy
-%endif
-%endif
 %if %{with py3integration}
 BuildRequires: python3-devel >= 3.5
 BuildRequires: python3-numpy
@@ -293,34 +266,6 @@ MonetDB, you will very likely need this 
 %doc %{_mandir}/man1/mclient.1.gz
 %doc %{_mandir}/man1/msqldump.1.gz
 
-%package client-tools
-Summary: MonetDB - Monet Database Management System Client Programs
-Group: Applications/Databases
-Requires: %{name}-client%{?_isa} = %{version}-%{release}
-%if (0%{?fedora} >= 22)
-# tomograph executes these two:
-Recommends: /usr/bin/gs
-Recommends: /usr/bin/gnuplot
-%endif
-
-%description client-tools
-MonetDB is a database management system that is developed from a
-main-memory perspective with use of a fully decomposed storage model,
-automatic index management, extensibility of data types and search
-accelerators.  It also has an SQL front end.
-
-This package contains stethoscope, tomograph, and tachograph.  These
-tools can be used to monitor the MonetDB database server.
-
-%files client-tools
-%defattr(-,root,root)
-%{_bindir}/stethoscope
-%{_bindir}/tachograph
-%{_bindir}/tomograph
-%dir %{_datadir}/doc/MonetDB-client-tools
-%docdir %{_datadir}/doc/MonetDB-client-tools
-%{_datadir}/doc/MonetDB-client-tools/*
-
 %package client-devel
 Summary: MonetDB - Monet Database Management System Client Programs
 Group: Applications/Databases
@@ -341,7 +286,7 @@ This package contains the files needed t
 %defattr(-,root,root)
 %dir %{_includedir}/monetdb
 %{_libdir}/libmapi.so
-%{_includedir}/monetdb/mapi.h
+%{_includedir}/monetdb/mapi*.h
 %{_libdir}/pkgconfig/monetdb-mapi.pc
 
 %package client-odbc
@@ -467,29 +412,6 @@ This package contains support for readin
 %{_libdir}/monetdb5/lib_lidar.so
 %endif
 
-%if %{with samtools}
-%package bam-MonetDB5
-Summary: MonetDB5 SQL interface to the bam library
-Group: Applications/Databases
-Requires: MonetDB5-server%{?_isa} = %{version}-%{release}
-
-%description bam-MonetDB5
-MonetDB is a database management system that is developed from a
-main-memory perspective with use of a fully decomposed storage model,
-automatic index management, extensibility of data types and search
-accelerators.  It also has an SQL front end.
-
-This package contains the interface to load and query BAM (binary
-version of Sequence Alignment/Map) data.
-
-%files bam-MonetDB5
-%defattr(-,root,root)
-%{_libdir}/monetdb5/autoload/*_bam.mal
-%{_libdir}/monetdb5/createdb/*_bam.sql
-%{_libdir}/monetdb5/bam.mal
-%{_libdir}/monetdb5/lib_bam.so
-%endif
-
 %if %{with rintegration}
 %package R
 Summary: Integration of MonetDB and R, allowing use of R from within SQL
@@ -516,32 +438,6 @@ install it.
 %{_libdir}/monetdb5/lib_rapi.so
 %endif
 
-%if %{with py2integration}
-%package python2
-Summary: Integration of MonetDB and Python, allowing use of Python from within 
SQL
-Group: Applications/Databases
-Requires: MonetDB-SQL-server5%{?_isa} = %{version}-%{release}
-
-%description python2
-MonetDB is a database management system that is developed from a
-main-memory perspective with use of a fully decomposed storage model,
-automatic index management, extensibility of data types and search
-accelerators.  It also has an SQL front end.
-
-This package contains the interface to use the Python language from
-within SQL queries.  This package is for Python 2.
-
-NOTE: INSTALLING THIS PACKAGE OPENS UP SECURITY ISSUES.  If you don't
-know how this package affects the security of your system, do not
-install it.
-
-%files python2
-%defattr(-,root,root)
-%{_libdir}/monetdb5/pyapi.*
-%{_libdir}/monetdb5/autoload/*_pyapi.mal
-%{_libdir}/monetdb5/lib_pyapi.so
-%endif
-
 %if %{with py3integration}
 %package python3
 Summary: Integration of MonetDB and Python, allowing use of Python from within 
SQL
@@ -629,6 +525,7 @@ exit 0
 %attr(2770,monetdb,monetdb) %dir %{_localstatedir}/monetdb5
 %attr(2770,monetdb,monetdb) %dir %{_localstatedir}/monetdb5/dbfarm
 %{_bindir}/mserver5
+%exclude %{_bindir}/stethoscope
 %{_libdir}/libmonetdb5.so.*
 %dir %{_libdir}/monetdb5
 %dir %{_libdir}/monetdb5/autoload
@@ -642,9 +539,6 @@ exit 0
 %if %{with lidar}
 %exclude %{_libdir}/monetdb5/lidar.mal
 %endif
-%if %{with py2integration}
-%exclude %{_libdir}/monetdb5/pyapi.mal
-%endif
 %if %{with py3integration}
 %exclude %{_libdir}/monetdb5/pyapi3.mal
 %endif
@@ -663,9 +557,6 @@ exit 0
 %if %{with lidar}
 %exclude %{_libdir}/monetdb5/autoload/*_lidar.mal
 %endif
-%if %{with py2integration}
-%exclude %{_libdir}/monetdb5/autoload/*_pyapi.mal
-%endif
 %if %{with py3integration}
 %exclude %{_libdir}/monetdb5/autoload/*_pyapi3.mal
 %endif
@@ -674,13 +565,8 @@ exit 0
 %endif
 %exclude %{_libdir}/monetdb5/autoload/??_sql*.mal
 %{_libdir}/monetdb5/autoload/*.mal
-%if %{with samtools}
-%exclude %{_libdir}/monetdb5/bam.mal
-%exclude %{_libdir}/monetdb5/autoload/*_bam.mal
-%endif
 %{_libdir}/monetdb5/lib_capi.so
 %{_libdir}/monetdb5/lib_generator.so
-%{_libdir}/monetdb5/lib_opt_sql_append.so
 %{_libdir}/monetdb5/lib_udf.so
 %doc %{_mandir}/man1/mserver5.1.gz
 %dir %{_datadir}/doc/MonetDB
@@ -782,9 +668,6 @@ use SQL with MonetDB, you will need to i
 %if %{with lidar}
 %exclude %{_libdir}/monetdb5/createdb/*_lidar.sql
 %endif
-%if %{with samtools}
-%exclude %{_libdir}/monetdb5/createdb/*_bam.sql
-%endif
 %{_libdir}/monetdb5/createdb/*.sql
 %{_libdir}/monetdb5/sql*.mal
 %if %{with hugeint}
@@ -967,7 +850,7 @@ export CFLAGS
        --enable-mapi=yes \
        --enable-netcdf=no \
        --enable-odbc=yes \
-       
--enable-py2integration=%{?with_py2integration:yes}%{!?with_py2integration:no} \
+       --enable-profiler=no \
        
--enable-py3integration=%{?with_py3integration:yes}%{!?with_py3integration:no} \
        
--enable-rintegration=%{?with_rintegration:yes}%{!?with_rintegration:no} \
        --enable-sanitizer=no \
@@ -986,11 +869,9 @@ export CFLAGS
        --with-openssl=yes \
        --with-proj=no \
        --with-pthread=yes \
-       --with-python2=%{?with_py2integration:yes}%{!?with_py2integration:no} \
        --with-python3=yes \
        --with-readline=yes \
        --with-regex=%{?with_pcre:PCRE}%{!?with_pcre:POSIX} \
-       --with-samtools=%{?with_samtools:yes}%{!?with_samtools:no} \
        --with-snappy=no \
        --with-unixodbc=yes \
        --with-uuid=yes \
@@ -1040,6 +921,9 @@ install -d -m 0775 %{buildroot}%{_locals
 # .la files
 rm -f %{buildroot}%{_libdir}/*.la
 rm -f %{buildroot}%{_libdir}/monetdb5/*.la
+rm -f %{buildroot}%{_libdir}/monetdb5/opt_sql_append.mal
+rm -f %{buildroot}%{_libdir}/monetdb5/lib_opt_sql_append.so
+rm -f %{buildroot}%{_libdir}/monetdb5/autoload/??_opt_sql_append.mal
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