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Posted to commits@madlib.apache.org by ok...@apache.org on 2023/09/05 16:50:37 UTC
[madlib] branch madlib2-master updated (6d621d52 -> 70c548c1)
This is an automated email from the ASF dual-hosted git repository.
okislal pushed a change to branch madlib2-master
in repository https://gitbox.apache.org/repos/asf/madlib.git
from 6d621d52 Build: Add post- scripts for gppkg and gp7 version checks in madpack
new 845bcb5c Build: Use PG15 in jenkins build
new 40dfa0e3 DL: Update get_state_to_return to always return bytea
new b734a8f6 Build: Remove PyXB from cmake and use pyxb-x
new 395a8192 Fix anyarray -> anycompatiblearray change for PG14
new 70c548c1 Remove PyXB mentions from code, docs and licenses
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
README.md | 3 +-
ReadMe_Build.txt | 6 -
deploy/PGXN/ReadMe.txt | 1 -
licenses/third_party/PyXB_v1.2.6.txt | 268 ---------------------
src/CMakeLists.txt | 60 -----
src/madpack/madpack.py | 5 +-
src/patch/CMakeLists.txt | 2 -
src/patch/PyXB.sh | 223 -----------------
src/ports/postgres/modules/crf/crf.sql_in | 4 +-
.../modules/deep_learning/madlib_keras.py_in | 2 +-
.../test/unit_tests/test_madlib_keras.py_in | 4 +-
tool/docker/base/Dockerfile_postgres_15_Jenkins | 2 +-
tool/jenkins/jenkins_build.sh | 63 ++---
13 files changed, 42 insertions(+), 601 deletions(-)
delete mode 100644 licenses/third_party/PyXB_v1.2.6.txt
delete mode 100644 src/patch/CMakeLists.txt
delete mode 100755 src/patch/PyXB.sh
[madlib] 02/05: DL: Update get_state_to_return to always return bytea
Posted by ok...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
okislal pushed a commit to branch madlib2-master
in repository https://gitbox.apache.org/repos/asf/madlib.git
commit 40dfa0e3810b2f8d070941ba8053cc7b7886f169
Author: Orhan Kislal <ok...@apache.org>
AuthorDate: Fri Sep 1 20:34:48 2023 +0300
DL: Update get_state_to_return to always return bytea
get_state_to_return returned bytea in some cases and a single float in
others. The float value is not actually used so it did not break the
process. However, this still causes python instability and errors in
some cases. This commit fixes the issue by converting the float value to
bytea just like the rest of the options.
---
src/ports/postgres/modules/deep_learning/madlib_keras.py_in | 2 +-
.../modules/deep_learning/test/unit_tests/test_madlib_keras.py_in | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/ports/postgres/modules/deep_learning/madlib_keras.py_in b/src/ports/postgres/modules/deep_learning/madlib_keras.py_in
index 5a99f129..2bd98c4f 100644
--- a/src/ports/postgres/modules/deep_learning/madlib_keras.py_in
+++ b/src/ports/postgres/modules/deep_learning/madlib_keras.py_in
@@ -800,7 +800,7 @@ def get_state_to_return(segment_model, is_last_row, is_multiple_model, agg_image
new_state = serialize_state_with_nd_weights(
agg_image_count, updated_model_weights)
else:
- new_state = float(agg_image_count)
+ new_state = np.float32(agg_image_count).tostring()
return new_state
diff --git a/src/ports/postgres/modules/deep_learning/test/unit_tests/test_madlib_keras.py_in b/src/ports/postgres/modules/deep_learning/test/unit_tests/test_madlib_keras.py_in
index ab8dc383..3da8549d 100644
--- a/src/ports/postgres/modules/deep_learning/test/unit_tests/test_madlib_keras.py_in
+++ b/src/ports/postgres/modules/deep_learning/test/unit_tests/test_madlib_keras.py_in
@@ -127,7 +127,7 @@ class MadlibKerasFitEvalTransitionTestCase(unittest.TestCase):
image_count = kwargs['GD']['agg_image_count']
self.assertEqual(ending_image_count, image_count)
- image_count = new_state
+ image_count = np.fromstring(new_state,dtype=np.float32)[0]
self.assertEqual(ending_image_count, image_count)
def _test_fit_transition_multiple_model_no_cache_first_buffer_pass(self, **kwargs):
@@ -179,7 +179,7 @@ class MadlibKerasFitEvalTransitionTestCase(unittest.TestCase):
self.total_images_per_seg, self.accessible_gpus_for_seg,
self.dummy_prev_weights, **kwargs)
- image_count = new_state
+ image_count = np.fromstring(new_state,dtype=np.float32)[0]
self.assertEqual(ending_image_count, image_count)
def _test_fit_transition_multiple_model_no_cache_middle_buffer_pass(self,
[madlib] 01/05: Build: Use PG15 in jenkins build
Posted by ok...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
okislal pushed a commit to branch madlib2-master
in repository https://gitbox.apache.org/repos/asf/madlib.git
commit 845bcb5c8e6f0a71b609e50905683bd4d84ed70c
Author: Orhan Kislal <ok...@apache.org>
AuthorDate: Thu Aug 31 13:09:12 2023 +0300
Build: Use PG15 in jenkins build
---
tool/jenkins/jenkins_build.sh | 59 ++++++++++++++++++++++---------------------
1 file changed, 30 insertions(+), 29 deletions(-)
diff --git a/tool/jenkins/jenkins_build.sh b/tool/jenkins/jenkins_build.sh
index 72fb66ea..1a77b697 100755
--- a/tool/jenkins/jenkins_build.sh
+++ b/tool/jenkins/jenkins_build.sh
@@ -20,7 +20,7 @@
workdir=`pwd`
user_name=`whoami`
-# FIXME: Jenkins build is not working, even though PG13 compiles on local Mac.
+# FIXME: Jenkins build is not working, even though PG15 compiles on local Mac.
# Need to find an efficient way to debug since it has a server crash.
echo "======================================================================"
@@ -30,8 +30,8 @@ echo "----------------------------------------------------------------------"
echo "ls -la"
ls -la
echo "-------------------------------"
-echo "rm -rf build"
-rm -rf build
+echo "rm -rf build_jenkins"
+rm -rf build_jenkins
echo "-------------------------------"
echo "rm -rf logs"
rm -rf logs
@@ -46,14 +46,14 @@ docker rm madlib
echo "Creating docker container"
# Pull down the base docker images
-echo "docker pull madlib/postgres_13:jenkins"
-docker pull madlib/postgres_13:jenkins
+echo "docker pull madlib/postgres_15:jenkins"
+docker pull madlib/postgres_15:jenkins
# Launch docker container with volume mounted from workdir
echo "-------------------------------"
cat <<EOF
-docker run -d -t -e POSTGRES_PASSWORD=postgres --name madlib --ulimit core=-1 --privileged -v "${workdir}":/madlib madlib/postgres_13:jenkins | tee logs/docker_setup.log
+docker run -d -t -e POSTGRES_PASSWORD=postgres --name madlib --ulimit core=-1 --privileged -v "${workdir}":/madlib madlib/postgres_15:jenkins | tee logs/docker_setup.log
EOF
-docker run -d -t -e POSTGRES_PASSWORD=postgres --name madlib --ulimit core=-1 --privileged -v "${workdir}":/madlib madlib/postgres_13:jenkins | tee logs/docker_setup.log
+docker run -d -t -e POSTGRES_PASSWORD=postgres --name madlib --ulimit core=-1 --privileged -v "${workdir}":/madlib madlib/postgres_15:jenkins | tee logs/docker_setup.log
echo "-------------------------------"
## This sleep is required since it takes a couple of seconds for the docker
@@ -61,9 +61,9 @@ echo "-------------------------------"
sleep 5
cat <<EOF
-docker exec madlib bash -c 'cp /madlib/tool/pg_hba.conf.postgres /var/lib/postgresql/data/pg_hba.conf; echo " * soft nproc unlimited" > /etc/security/limits.d/postgres-limits.conf ' | tee $workdir/logs/madlib_compile.log
+docker exec madlib bash -c 'cp /madlib/tool/pg_hba.conf.postgres /etc/postgresql/15/main/pg_hba.conf; echo " * soft nproc unlimited" > /etc/security/limits.d/postgres-limits.conf ' | tee $workdir/logs/madlib_compile.log
EOF
-docker exec madlib bash -c 'cp /madlib/tool/pg_hba.conf.postgres /var/lib/postgresql/data/pg_hba.conf; echo " * soft nproc unlimited" > /etc/security/limits.d/postgres-limits.conf ' | tee $workdir/logs/madlib_compile.log
+docker exec madlib bash -c 'cp /madlib/tool/pg_hba.conf.postgres /etc/postgresql/15/main/pg_hba.conf; echo " * soft nproc unlimited" > /etc/security/limits.d/postgres-limits.conf ' | tee $workdir/logs/madlib_compile.log
cat <<EOF
docker exec madlib bash -c 'service postgresql start' | tee $workdir/logs/madlib_compile.log
@@ -80,41 +80,42 @@ docker exec madlib bash -c 'apt-get update; apt-get install -y python3-pip; pip
echo "---------- Building package -----------"
# cmake, make, make install, and make package
cat <<EOF
-docker exec madlib bash -c 'rm -rf /build; mkdir /build; cd /build; cmake ../madlib; make clean; make -j$(nproc); make -j$(nproc); make install; make package; chown -R postgres:postgres /build ' | tee $workdir/logs/madlib_compile.log
+docker exec madlib bash -c 'rm -rf /build_jenkins; mkdir /build_jenkins; cd /build_jenkins; cmake ../madlib; make clean; make -j$(nproc); make -j$(nproc); make install; make package; chown -R postgres:postgres /build_jenkins ' | tee $workdir/logs/madlib_compile.log
EOF
-docker exec madlib bash -c 'rm -rf /build; mkdir /build; cd /build; cmake ../madlib; make clean; make -j$(nproc); make -j$(nproc); make install; make package; chown -R postgres:postgres /build ' | tee $workdir/logs/madlib_compile.log
+docker exec madlib bash -c 'rm -rf /build_jenkins; mkdir /build_jenkins; cd /build_jenkins; cmake ../madlib; make clean; make -j$(nproc); make -j$(nproc); make install; make package; chown -R postgres:postgres /build_jenkins ' | tee $workdir/logs/madlib_compile.log
echo "---------- Installing and running dev-check --------------------"
# Install MADlib and run dev check
+
cat <<EOF
-docker exec -u postgres madlib bash -c 'export PATH=$PATH:/usr/lib/postgresql/13/bin/; /build/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres install' | tee $workdir/logs/madlib_install.log
+docker exec -u postgres madlib bash -c 'export PATH=\$PATH:/usr/lib/postgresql/15/bin/; /build_jenkins/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres install' | tee $workdir/logs/madlib_install.log
EOF
-docker exec -u postgres madlib bash -c 'export PATH=$PATH:/usr/lib/postgresql/13/bin/; /build/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres install' | tee $workdir/logs/madlib_install.log
+docker exec -u postgres madlib bash -c 'export PATH=$PATH:/usr/lib/postgresql/15/bin/; /build_jenkins/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres install' | tee $workdir/logs/madlib_install.log
cat <<EOF
docker exec madlib bash -c 'mkdir -p /tmp'
-docker exec madlib bash -c '/build/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres -d /tmp dev-check' | tee $workdir/logs/madlib_dev_check.log
-docker exec madlib bash -c '/build/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres -d /tmp unit-test' | tee -a $workdir/logs/madlib_dev_check.log
+docker exec madlib bash -c '/build_jenkins/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres -d /tmp dev-check' | tee $workdir/logs/madlib_dev_check.log
+docker exec madlib bash -c '/build_jenkins/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres -d /tmp unit-test' | tee -a $workdir/logs/madlib_dev_check.log
EOF
docker exec madlib bash -c 'mkdir -p /tmp'
-docker exec madlib bash -c 'rm -rf /build/src/ports/postgres/modules/deep_learning/test'
-docker exec madlib bash -c 'rm -rf /build/src/ports/postgres/13/modules/deep_learning/test'
+docker exec madlib bash -c 'rm -rf /build_jenkins/src/ports/postgres/modules/deep_learning/test'
+docker exec madlib bash -c 'rm -rf /build_jenkins/src/ports/postgres/15/modules/deep_learning/test'
# FIXME following tests fail on the docker
-docker exec madlib bash -c 'rm -rf /build/src/ports/postgres/modules/linalg/test/linalg.sql_in'
-docker exec madlib bash -c 'rm -rf /build/src/ports/postgres/modules/prob/test/prob.sql_in'
-docker exec madlib bash -c 'rm -rf /build/src/ports/postgres/modules/stats/test/cox_prop_hazards.sql_in'
-docker exec madlib bash -c 'rm -rf /build/src/ports/postgres/modules/utilities/test/path.sql_in'
-docker exec madlib bash -c 'rm -rf /build/src/ports/postgres/modules/mxgboost/test/madlib_xgboost.sql_in'
-docker exec madlib bash -c 'rm -rf /build/src/ports/postgres/modules/kmeans/test/kmeans.sql_in'
+docker exec madlib bash -c 'rm -rf /build_jenkins/src/ports/postgres/modules/linalg/test/linalg.sql_in'
+docker exec madlib bash -c 'rm -rf /build_jenkins/src/ports/postgres/modules/prob/test/prob.sql_in'
+docker exec madlib bash -c 'rm -rf /build_jenkins/src/ports/postgres/modules/stats/test/cox_prop_hazards.sql_in'
+docker exec madlib bash -c 'rm -rf /build_jenkins/src/ports/postgres/modules/utilities/test/path.sql_in'
+docker exec madlib bash -c 'rm -rf /build_jenkins/src/ports/postgres/modules/mxgboost/test/madlib_xgboost.sql_in'
+docker exec madlib bash -c 'rm -rf /build_jenkins/src/ports/postgres/modules/kmeans/test/kmeans.sql_in'
# Run dev check
-docker exec madlib bash -c '/build/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres -d /tmp dev-check' | tee $workdir/logs/madlib_dev_check.log
+docker exec madlib bash -c '/build_jenkins/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres -d /tmp dev-check' | tee $workdir/logs/madlib_dev_check.log
# Run unit tests, and append output to dev_check's log file
-docker exec madlib bash -c '/build/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres -d /tmp unit-test' | tee -a $workdir/logs/madlib_dev_check.log
+docker exec madlib bash -c '/build_jenkins/src/bin/madpack -s mad -p postgres -c postgres/postgres@localhost:5432/postgres -d /tmp unit-test' | tee -a $workdir/logs/madlib_dev_check.log
echo "--------- Copying packages -----------------"
-echo "docker cp madlib:build $workdir"
-docker cp madlib:build $workdir
+echo "docker cp madlib:build_jenkins $workdir"
+docker cp madlib:build_jenkins $workdir
echo "docker cp madlib:tmp $workdir"
docker cp madlib:tmp $workdir
@@ -122,8 +123,8 @@ echo "-------------------------------"
echo "ls -la"
ls -la
echo "-------------------------------"
-echo "ls -la build"
-ls -la build/
+echo "ls -la build_jenkins"
+ls -la build_jenkins/
echo "-------------------------------"
# convert dev-check test results to junit format for reporting
[madlib] 04/05: Fix anyarray -> anycompatiblearray change for PG14
Posted by ok...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
okislal pushed a commit to branch madlib2-master
in repository https://gitbox.apache.org/repos/asf/madlib.git
commit 395a81923864444c3a641187441bfdd0e022225f
Author: Orhan Kislal <ok...@apache.org>
AuthorDate: Sat Sep 2 09:02:58 2023 +0300
Fix anyarray -> anycompatiblearray change for PG14
---
src/madpack/madpack.py | 5 +++--
src/ports/postgres/modules/crf/crf.sql_in | 4 ++--
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/src/madpack/madpack.py b/src/madpack/madpack.py
index 87df1c06..fc4c6537 100755
--- a/src/madpack/madpack.py
+++ b/src/madpack/madpack.py
@@ -188,7 +188,8 @@ def _run_m4_and_append(schema, maddir_mod_py, module, sqlfile,
'-DMODULE_NAME=' + module,
'-I' + maddir_madpack,
sqlfile]
- if (((portid == 'postgres') & (dbver == '15'))):
+ if ( (portid == 'postgres') &
+ (is_rev_gte(get_rev_num(dbver), get_rev_num('14.0'))) ):
m4args = ['m4',
'-P',
'-DMADLIB_SCHEMA=' + schema,
@@ -197,7 +198,7 @@ def _run_m4_and_append(schema, maddir_mod_py, module, sqlfile,
'-DMODULE_PATHNAME=' + maddir_lib,
'-DMADLIB_LIBRARY_PATH=' + madlib_library_path,
'-DMODULE_NAME=' + module,
- '-DIS_PG_15=TRUE',
+ '-DUSE_COMPATIBLE_ARRAY=TRUE',
'-I' + maddir_madpack,
sqlfile]
diff --git a/src/ports/postgres/modules/crf/crf.sql_in b/src/ports/postgres/modules/crf/crf.sql_in
index 302de8a4..9354fdac 100644
--- a/src/ports/postgres/modules/crf/crf.sql_in
+++ b/src/ports/postgres/modules/crf/crf.sql_in
@@ -719,13 +719,13 @@ CREATE AGGREGATE MADLIB_SCHEMA.lincrf_lbfgs_step(
INITCOND='{0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}'
);
-m4_ifdef(`IS_PG_15',
+m4_ifdef(`USE_COMPATIBLE_ARRAY',
`DROP AGGREGATE IF EXISTS MADLIB_SCHEMA.array_union(anycompatiblearray) CASCADE;',
`DROP AGGREGATE IF EXISTS MADLIB_SCHEMA.array_union(anyarray) CASCADE;')
CREATE m4_ifdef(`__POSTGRESQL__', `',
m4_ifdef(`__HAS_ORDERED_AGGREGATES__', `ORDERED')) AGGREGATE
-m4_ifdef(`IS_PG_15',
+m4_ifdef(`USE_COMPATIBLE_ARRAY',
`MADLIB_SCHEMA.array_union(anycompatiblearray) (SFUNC = array_cat, STYPE = anycompatiblearray);',
`MADLIB_SCHEMA.array_union(anyarray) (SFUNC = array_cat, STYPE = anyarray);'
)
[madlib] 05/05: Remove PyXB mentions from code, docs and licenses
Posted by ok...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
okislal pushed a commit to branch madlib2-master
in repository https://gitbox.apache.org/repos/asf/madlib.git
commit 70c548c102b1e5d9013294284affcde00a6412fb
Author: Orhan Kislal <ok...@apache.org>
AuthorDate: Tue Sep 5 10:19:59 2023 +0300
Remove PyXB mentions from code, docs and licenses
---
README.md | 3 +-
ReadMe_Build.txt | 6 -
deploy/PGXN/ReadMe.txt | 1 -
licenses/third_party/PyXB_v1.2.6.txt | 268 -----------------------------------
src/CMakeLists.txt | 60 --------
src/patch/CMakeLists.txt | 2 -
src/patch/PyXB.sh | 223 -----------------------------
7 files changed, 1 insertion(+), 562 deletions(-)
diff --git a/README.md b/README.md
index a48a3b7c..1d988665 100644
--- a/README.md
+++ b/README.md
@@ -127,8 +127,7 @@ MADlib incorporates software from the following third-party components. Bundled
Downloaded at build time (or supplied as build dependencies):
6. [`Boost 1.61.0 (or newer)`](http://www.boost.org/) "provides peer-reviewed portable C++ source libraries"
-7. [`PyXB 1.2.6`](http://pyxb.sourceforge.net/) "Python library for XML Schema Bindings"
-8. [`Eigen 3.2.2`](http://eigen.tuxfamily.org/index.php?title=Main_Page) "C++ template library for linear algebra"
+7. [`Eigen 3.2.2`](http://eigen.tuxfamily.org/index.php?title=Main_Page) "C++ template library for linear algebra"
Licensing
==========
diff --git a/ReadMe_Build.txt b/ReadMe_Build.txt
index 583bd400..592d3a41 100644
--- a/ReadMe_Build.txt
+++ b/ReadMe_Build.txt
@@ -167,12 +167,6 @@ root directory) for more options, after having run `cmake` the first time.
with `-DEIGEN_TAR_SOURCE=/path/to/eigen_x.tar.gz`, in which case
this tarball is used.
-- `PYXB_TAR_SOURCE` (default: *empty*)
-
- PyXB is downloaded automatically, unless you call `./configure`
- with `-DPYXB_TAR_SOURCE=/path/to/pyxb_x.tar.gz`, in which case
- this tarball is used.
-
- `CREATE_RPM_FOR_UBUNTU` (default: *empty*)
By default, we create a .deb madlib installer on Ubuntu. If this
diff --git a/deploy/PGXN/ReadMe.txt b/deploy/PGXN/ReadMe.txt
index 3b1db376..78462bf4 100644
--- a/deploy/PGXN/ReadMe.txt
+++ b/deploy/PGXN/ReadMe.txt
@@ -39,7 +39,6 @@ Downloaded at build time:
http://www.boost.org/
- Eigen 3.2 "is a C++ template library for linear algebra"
http://eigen.tuxfamily.org/index.php?title=Main_Page
-- PyXB 1.2.4 "Python library for XML Schema Bindings"
License information regarding MADlib and included third-party libraries can be
found inside the 'licenses' directory.
diff --git a/licenses/third_party/PyXB_v1.2.6.txt b/licenses/third_party/PyXB_v1.2.6.txt
deleted file mode 100644
index 5c732c94..00000000
--- a/licenses/third_party/PyXB_v1.2.6.txt
+++ /dev/null
@@ -1,268 +0,0 @@
-From the PyXB licensing page
-(http://pyxb.sourceforge.net/legal.html)
-
-
- Apache License
- Version 2.0, January 2004
- http://www.apache.org/licenses/
-
- TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
- 1. Definitions.
-
- "License" shall mean the terms and conditions for use,
- reproduction,
- and distribution as defined by Sections 1 through 9 of this
- document.
-
- "Licensor" shall mean the copyright owner or entity authorized
- by
- the copyright owner that is granting the License.
-
- "Legal Entity" shall mean the union of the acting entity and all
- other entities that control, are controlled by, or are under
- common
- control with that entity. For the purposes of this definition,
- "control" means (i) the power, direct or indirect, to cause the
- direction or management of such entity, whether by contract or
- otherwise, or (ii) ownership of fifty percent (50%) or more of
- the
- outstanding shares, or (iii) beneficial ownership of such
- entity.
-
- "You" (or "Your") shall mean an individual or Legal Entity
- exercising permissions granted by this License.
-
- "Source" form shall mean the preferred form for making
- modifications,
- including but not limited to software source code, documentation
- source, and configuration files.
-
- "Object" form shall mean any form resulting from mechanical
- transformation or translation of a Source form, including but
- not limited to compiled object code, generated documentation,
- and conversions to other media types.
-
- "Work" shall mean the work of authorship, whether in Source or
- Object form, made available under the License, as indicated by a
- copyright notice that is included in or attached to the work
- (an example is provided in the Appendix below).
-
- "Derivative Works" shall mean any work, whether in Source or
- Object
- form, that is based on (or derived from) the Work and for which
- the
- editorial revisions, annotations, elaborations, or other
- modifications
- represent, as a whole, an original work of authorship. For the
- purposes
- of this License, Derivative Works shall not include works that
- remain
- separable from, or merely link (or bind by name) to the
- interfaces of,
- the Work and Derivative Works thereof.
-
- "Contribution" shall mean any work of authorship, including
- the original version of the Work and any modifications or
- additions
- to that Work or Derivative Works thereof, that is intentionally
- submitted to Licensor for inclusion in the Work by the copyright
- owner
- or by an individual or Legal Entity authorized to submit on
- behalf of
- the copyright owner. For the purposes of this definition,
- "submitted"
- means any form of electronic, verbal, or written communication
- sent
- to the Licensor or its representatives, including but not
- limited to
- communication on electronic mailing lists, source code control
- systems,
- and issue tracking systems that are managed by, or on behalf of,
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- but
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- boilerplate notice, with the fields enclosed by brackets "[]"
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- you may not use this file except in compliance with the License.
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diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 247f6899..df12d6bd 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -75,30 +75,8 @@ if(NOT EIGEN_TAR_SOURCE)
set(EIGEN_TAR_SOURCE ${EIGEN_URL})
endif (NOT EIGEN_TAR_SOURCE)
-# We always download PyXB (unless it is already present in
-# ${CMAKE_CURRENT_BINARY_DIR}/third_party/downloads). It is also possible to
-# specify an alternative path to the PyXB tarball:
-# -DPYXB_TAR_SOURCE=/path/to/PyXB-x.x.x.tar.gz
-
-# set(PYXB_VERSION "1.2.6")
-# set(PYXB_TAR_MD5 5689c94a3c47419213b8872753a73c07)
-
-# set(PYXB_TAR "PyXB-${PYXB_VERSION}.tar.gz")
-# set(PYXB_URL "https://github.com/renalreg/PyXB-X/archive/refs/tags/v1.2.6.1.tar.gz")
-
-# if(NOT PYXB_TAR_SOURCE)
-# find_file(PYXB_TAR_SOURCE ${PYXB_TAR}
-# PATHS ${MAD_THIRD_PARTY}/downloads)
-# endif(NOT PYXB_TAR_SOURCE)
-
-# if(NOT PYXB_TAR_SOURCE)
-# set(PYXB_TAR_SOURCE ${PYXB_URL})
-# endif (NOT PYXB_TAR_SOURCE)
-
# -- Local definitions (filenames, paths, etc.) --------------------------------
-set(MAD_PATCH_DIR ${CMAKE_CURRENT_BINARY_DIR}/patch)
-
set(MAD_MODULE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/modules)
@@ -146,39 +124,6 @@ find_package(PythonInterp REQUIRED)
set(BUILD_PYTHON_LIBDIR "${CMAKE_BINARY_DIR}/src/lib/python")
-
-# if(IS_UBUNTU)
-# ExternalProject_Add(EP_pyxb
-# PREFIX ${MAD_THIRD_PARTY}
-# DOWNLOAD_DIR ${MAD_THIRD_PARTY}/downloads
-# URL ${PYXB_TAR_SOURCE}
-# URL_MD5 ${PYXB_TAR_MD5}
-# # PATCH_COMMAND "${CMAKE_CURRENT_SOURCE_DIR}/patch/PyXB.sh"
-# CONFIGURE_COMMAND ""
-# SOURCE_DIR ${MAD_THIRD_PARTY}/src/EP_pyxb
-# BUILD_COMMAND ""
-# BUILD_IN_SOURCE 1
-
-# INSTALL_COMMAND pip3 install .
-# )
-# endif(IS_UBUNTU)
-
-# if((NOT IS_UBUNTU))
-# ExternalProject_Add(EP_pyxb
-# PREFIX ${MAD_THIRD_PARTY}
-# DOWNLOAD_DIR ${MAD_THIRD_PARTY}/downloads
-# URL ${PYXB_TAR_SOURCE}
-# URL_MD5 ${PYXB_TAR_MD5}
-# # PATCH_COMMAND "${CMAKE_CURRENT_SOURCE_DIR}/patch/PyXB.sh"
-# CONFIGURE_COMMAND ""
-# SOURCE_DIR ${MAD_THIRD_PARTY}/src/EP_pyxb
-# BUILD_COMMAND ""
-# BUILD_IN_SOURCE 1
-
-# INSTALL_COMMAND ${PYTHON_EXECUTABLE} setup.py install --install-lib ${BUILD_PYTHON_LIBDIR} > /dev/null
-# )
-# endif((NOT IS_UBUNTU))
-
install(DIRECTORY ${BUILD_PYTHON_LIBDIR}
DESTINATION lib
COMPONENT core
@@ -379,14 +324,9 @@ add_sql_files(
)
add_custom_target(sqlFiles ALL DEPENDS ${SQL_TARGET_FILES})
-# -- Use all necessary patches directory ---------------------------------------
-
-include_directories(BEFORE "${MAD_PATCH_DIR}")
-
# -- Add subdirectories --------------------------------------------------------
-add_subdirectory(patch)
add_subdirectory(bin)
add_subdirectory(config)
add_subdirectory(madpack)
diff --git a/src/patch/CMakeLists.txt b/src/patch/CMakeLists.txt
deleted file mode 100644
index 12823887..00000000
--- a/src/patch/CMakeLists.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-add_custom_target(madlibPatches ALL DEPENDS ${MADLIB_TARGET_PATCH_FILES})
-add_dependencies(madlibPatches EP_eigen)
diff --git a/src/patch/PyXB.sh b/src/patch/PyXB.sh
deleted file mode 100755
index 39466809..00000000
--- a/src/patch/PyXB.sh
+++ /dev/null
@@ -1,223 +0,0 @@
-#!/bin/sh
-
-# Patch directly in the source tree. Ignore if the patch has already been
-# applied. (Probably there are situations where CMake isn't smart enough to
-# prevent that.)
-
-# generated by "diff -Naur old/setup.py new/setup.py"
-patch -N -p1 <<'EOF'
---- old/setup.py 2014-11-07 16:20:27.000000000 -0800
-+++ new/setup.py 2014-11-07 16:21:54.000000000 -0800
-@@ -21,152 +21,6 @@
-
- from distutils.core import setup, Command
-
--# Stupid little command to automatically update the version number
--# where it needs to be updated.
--class update_version (Command):
-- # Brief (40-50 characters) description of the command
-- description = "Substitute @VERSION@ in relevant files"
--
-- # List of option tuples: long name, short name (None if no short
-- # name), and help string.
-- user_options = [ ]
-- boolean_options = [ ]
--
-- # Files in the distribution that need to be rewritten when the
-- # version number changes
-- files = ( 'README.txt', 'pyxb/__init__.py', 'doc/conf.py' )
--
-- # The substitutions (key braced by @ signs)
-- substitutions = { 'VERSION' : version,
-- 'THIS_YEAR' : datetime.date.today().strftime('%Y'),
-- 'SHORTVERSION' : '.'.join(version.split('.')[:2]) }
--
-- def initialize_options (self):
-- pass
--
-- def finalize_options (self):
-- pass
--
-- def run (self):
-- for f in self.files:
-- text = open('%s.in' % (f,)).read()
-- for (k, v) in self.substitutions.items():
-- text = text.replace('@%s@' % (k,), v)
-- os.chmod(f, os.stat(f)[stat.ST_MODE] | stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH)
-- open(f,'w').write(text)
-- os.chmod(f, os.stat(f)[stat.ST_MODE] & ~(stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH))
--
--class test (Command):
--
-- # Brief (40-50 characters) description of the command
-- description = "Run all unit tests found in testdirs"
--
-- # List of option tuples: long name, short name (None if no short
-- # name), and help string.
-- user_options = [ ( 'testdirs=', None, 'colon separated list of directories to search for tests' ),
-- ( 'trace-tests', 'v', 'trace search for tests' ),
-- ( 'inhibit-output', 'q', 'inhibit test output' ),
-- ]
-- boolean_options = [ 'trace-tests', 'inhibit-output' ]
--
-- def initialize_options (self):
-- self.trace_tests = None
-- self.inhibit_output = None
-- self.testdirs = 'tests'
--
-- def finalize_options (self):
-- pass
--
-- # Regular expression that matches unittest sources
-- __TestFile_re = re.compile('^test.*\.py$')
--
-- def run (self):
-- # Make sure log messages are supported
-- logging.basicConfig()
--
-- # Walk the tests hierarchy looking for tests
-- dirs = self.testdirs.split(':')
-- tests = [ ]
-- while dirs:
-- dir = dirs.pop(0)
-- if self.trace_tests:
-- print('Searching for tests in %s' % (dir,))
-- for f in os.listdir(dir):
-- fn = os.path.join(dir, f)
-- statb = os.stat(fn)
-- if stat.S_ISDIR(statb[0]):
-- dirs.append(fn)
-- elif self.__TestFile_re.match(f):
-- tests.append(fn)
--
-- number = 0
-- import sys
-- import traceback
-- import unittest
-- import types
--
-- # Import each test into its own module, then add the test
-- # cases in it to a complete suite.
-- loader = unittest.defaultTestLoader
-- suite = unittest.TestSuite()
-- used_names = set()
-- for fn in tests:
-- stage = 'compile'
-- try:
-- # Assign a unique name for this test
-- test_name = os.path.basename(fn).split('.')[0]
-- test_name = test_name.replace('-', '_')
-- number = 2
-- base_name = test_name
-- while test_name in used_names:
-- test_name = '%s%d' % (base_name, number)
-- number += 1
--
-- # Read the test source in and compile it
-- rv = compile(open(fn).read(), test_name, 'exec')
-- state = 'evaluate'
--
-- # Make a copy of the globals array so we don't
-- # contaminate this environment.
-- g = globals().copy()
--
-- # The test cases use __file__ to determine the path to
-- # the schemas
-- g['__file__'] = fn
--
-- # Create a module into which the test will be evaluated.
-- module = types.ModuleType(test_name)
--
-- # The generated code uses __name__ to look up the
-- # containing module in sys.modules.
-- g['__name__'] = test_name
-- sys.modules[test_name] = module
--
-- # Import the test into the module, making sure the created globals look like they're in the module.
-- eval(rv, g)
-- module.__dict__.update(g)
--
-- # Find all subclasses of unittest.TestCase that were
-- # in the test source and add them to the suite.
-- for (nm, obj) in g.items():
-- if (type == type(obj)) and issubclass(obj, unittest.TestCase):
-- suite.addTest(loader.loadTestsFromTestCase(obj))
-- if self.trace_tests:
-- print('%s imported' % (fn,))
-- except Exception as e:
-- print('%s failed in %s: %s' % (fn, stage, e))
-- raise
--
-- # Run everything
-- verbosity = 1
-- if self.trace_tests:
-- verbosity = 2
-- elif self.inhibit_output:
-- # Don't know how to do this for real
-- verbosity = 0
-- runner = unittest.TextTestRunner(verbosity=verbosity)
-- runner.run(suite)
--
- import glob
- import sys
- import pyxb.utils.utility
-@@ -177,44 +31,6 @@
- ]
- package_data = {}
-
--init_re = re.compile('^__init__\.py$')
--wxs_re = re.compile('^.*\.wxs$')
--
--setup_path = os.path.dirname(__file__)
--bundle_base = os.path.join(setup_path, 'pyxb', 'bundles')
--possible_bundles = []
--try:
-- possible_bundles.extend(os.listdir(bundle_base))
--except OSError as e:
-- print("Directory %s bundle search failed: %s" % (bundle_base, e))
--for possible_bundle in possible_bundles:
-- bundle_root = os.path.join(bundle_base, possible_bundle)
-- if not os.path.isdir(bundle_root):
-- continue
-- b_packages = []
-- b_data = { }
-- for fp in pyxb.utils.utility.GetMatchingFiles('%s//' % (bundle_root,), init_re):
-- bundle_path = os.path.dirname(os.path.normpath(fp))
-- try:
-- package_relpath = os.path.relpath(bundle_path, setup_path)
-- except AttributeError as e:
-- package_relpath = bundle_path
-- if setup_path and '.' != setup_path:
-- prefix_path = setup_path + os.path.sep
-- if not package_relpath.startswith(prefix_path):
-- print("Unable to determine relative path from %s to %s installation" % (setup_path, bundle_path))
-- sys.exit(1)
-- package_relpath = package_relpath[len(prefix_path):]
-- package = package_relpath.replace(os.path.sep, '.')
-- b_packages.append(package)
-- wxs_files = [os.path.basename(_f) for _f in pyxb.utils.utility.GetMatchingFiles(bundle_path, wxs_re) ]
-- if wxs_files:
-- b_data[package] = wxs_files
-- if 0 < len(b_data):
-- print('Found bundle in %s' % (bundle_root,))
-- packages.extend(b_packages)
-- package_data.update(b_data)
--
- setup(name='PyXB',
- description = 'PyXB ("pixbee") is a pure Python package that generates Python source code for classes that correspond to data structures defined by XMLSchema.',
- author='Peter A. Bigot',
-@@ -254,13 +70,9 @@
- ''',
- provides=[ 'PyXB' ],
- packages=packages,
-- package_data=package_data,
- # I normally keep these in $purelib, but distutils won't tell me where that is.
- # We don't need them in the installation anyway.
- #data_files= [ ('pyxb/standard/schemas', glob.glob(os.path.join(*'pyxb/standard/schemas/*.xsd'.split('/'))) ) ],
-- scripts=[ 'scripts/pyxbgen', 'scripts/pyxbwsdl', 'scripts/pyxbdump' ],
-- cmdclass = { 'test' : test,
-- 'update_version' : update_version },
- classifiers = [ 'Development Status :: 5 - Production/Stable'
- , 'Intended Audience :: Developers'
- , 'License :: OSI Approved :: Apache Software License'
-EOF
[madlib] 03/05: Build: Remove PyXB from cmake and use pyxb-x
Posted by ok...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
okislal pushed a commit to branch madlib2-master
in repository https://gitbox.apache.org/repos/asf/madlib.git
commit b734a8f672bef782d5415419934ae6adcb11d148
Author: Orhan Kislal <ok...@apache.org>
AuthorDate: Fri Sep 1 20:39:20 2023 +0300
Build: Remove PyXB from cmake and use pyxb-x
PyXB is abandoned and broken for py3.10+. pyxb-x is a patched version of
pyxb that still has backwards compatibility. Instead of trying to pack
pyxb with the MADlib, we just rely on yum like many other libraries.
---
src/CMakeLists.txt | 84 ++++++++++++-------------
tool/docker/base/Dockerfile_postgres_15_Jenkins | 2 +-
tool/jenkins/jenkins_build.sh | 4 +-
3 files changed, 45 insertions(+), 45 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9b02df8d..247f6899 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -80,20 +80,20 @@ endif (NOT EIGEN_TAR_SOURCE)
# specify an alternative path to the PyXB tarball:
# -DPYXB_TAR_SOURCE=/path/to/PyXB-x.x.x.tar.gz
-set(PYXB_VERSION "1.2.6")
-set(PYXB_TAR_MD5 4303573fc7094ce4664c5b71cd4bdb48)
+# set(PYXB_VERSION "1.2.6")
+# set(PYXB_TAR_MD5 5689c94a3c47419213b8872753a73c07)
-set(PYXB_TAR "PyXB-${PYXB_VERSION}.tar.gz")
-set(PYXB_URL "${SOURCEFORGE_BASE_URL}/pyxb/files/${PYXB_TAR}")
+# set(PYXB_TAR "PyXB-${PYXB_VERSION}.tar.gz")
+# set(PYXB_URL "https://github.com/renalreg/PyXB-X/archive/refs/tags/v1.2.6.1.tar.gz")
-if(NOT PYXB_TAR_SOURCE)
- find_file(PYXB_TAR_SOURCE ${PYXB_TAR}
- PATHS ${MAD_THIRD_PARTY}/downloads)
-endif(NOT PYXB_TAR_SOURCE)
+# if(NOT PYXB_TAR_SOURCE)
+# find_file(PYXB_TAR_SOURCE ${PYXB_TAR}
+# PATHS ${MAD_THIRD_PARTY}/downloads)
+# endif(NOT PYXB_TAR_SOURCE)
-if(NOT PYXB_TAR_SOURCE)
- set(PYXB_TAR_SOURCE ${PYXB_URL})
-endif (NOT PYXB_TAR_SOURCE)
+# if(NOT PYXB_TAR_SOURCE)
+# set(PYXB_TAR_SOURCE ${PYXB_URL})
+# endif (NOT PYXB_TAR_SOURCE)
# -- Local definitions (filenames, paths, etc.) --------------------------------
@@ -147,37 +147,37 @@ find_package(PythonInterp REQUIRED)
set(BUILD_PYTHON_LIBDIR "${CMAKE_BINARY_DIR}/src/lib/python")
-if(IS_UBUNTU)
-ExternalProject_Add(EP_pyxb
- PREFIX ${MAD_THIRD_PARTY}
- DOWNLOAD_DIR ${MAD_THIRD_PARTY}/downloads
- URL ${PYXB_TAR_SOURCE}
- URL_MD5 ${PYXB_TAR_MD5}
- PATCH_COMMAND "${CMAKE_CURRENT_SOURCE_DIR}/patch/PyXB.sh"
- CONFIGURE_COMMAND ""
- SOURCE_DIR ${MAD_THIRD_PARTY}/src/EP_pyxb
- BUILD_COMMAND ""
- BUILD_IN_SOURCE 1
-
- INSTALL_COMMAND pip3 install .
-)
-endif(IS_UBUNTU)
-
-if((NOT IS_UBUNTU))
-ExternalProject_Add(EP_pyxb
- PREFIX ${MAD_THIRD_PARTY}
- DOWNLOAD_DIR ${MAD_THIRD_PARTY}/downloads
- URL ${PYXB_TAR_SOURCE}
- URL_MD5 ${PYXB_TAR_MD5}
- PATCH_COMMAND "${CMAKE_CURRENT_SOURCE_DIR}/patch/PyXB.sh"
- CONFIGURE_COMMAND ""
- SOURCE_DIR ${MAD_THIRD_PARTY}/src/EP_pyxb
- BUILD_COMMAND ""
- BUILD_IN_SOURCE 1
-
- INSTALL_COMMAND ${PYTHON_EXECUTABLE} setup.py install --install-lib ${BUILD_PYTHON_LIBDIR} > /dev/null
-)
-endif((NOT IS_UBUNTU))
+# if(IS_UBUNTU)
+# ExternalProject_Add(EP_pyxb
+# PREFIX ${MAD_THIRD_PARTY}
+# DOWNLOAD_DIR ${MAD_THIRD_PARTY}/downloads
+# URL ${PYXB_TAR_SOURCE}
+# URL_MD5 ${PYXB_TAR_MD5}
+# # PATCH_COMMAND "${CMAKE_CURRENT_SOURCE_DIR}/patch/PyXB.sh"
+# CONFIGURE_COMMAND ""
+# SOURCE_DIR ${MAD_THIRD_PARTY}/src/EP_pyxb
+# BUILD_COMMAND ""
+# BUILD_IN_SOURCE 1
+
+# INSTALL_COMMAND pip3 install .
+# )
+# endif(IS_UBUNTU)
+
+# if((NOT IS_UBUNTU))
+# ExternalProject_Add(EP_pyxb
+# PREFIX ${MAD_THIRD_PARTY}
+# DOWNLOAD_DIR ${MAD_THIRD_PARTY}/downloads
+# URL ${PYXB_TAR_SOURCE}
+# URL_MD5 ${PYXB_TAR_MD5}
+# # PATCH_COMMAND "${CMAKE_CURRENT_SOURCE_DIR}/patch/PyXB.sh"
+# CONFIGURE_COMMAND ""
+# SOURCE_DIR ${MAD_THIRD_PARTY}/src/EP_pyxb
+# BUILD_COMMAND ""
+# BUILD_IN_SOURCE 1
+
+# INSTALL_COMMAND ${PYTHON_EXECUTABLE} setup.py install --install-lib ${BUILD_PYTHON_LIBDIR} > /dev/null
+# )
+# endif((NOT IS_UBUNTU))
install(DIRECTORY ${BUILD_PYTHON_LIBDIR}
DESTINATION lib
diff --git a/tool/docker/base/Dockerfile_postgres_15_Jenkins b/tool/docker/base/Dockerfile_postgres_15_Jenkins
index 37798616..760a6787 100644
--- a/tool/docker/base/Dockerfile_postgres_15_Jenkins
+++ b/tool/docker/base/Dockerfile_postgres_15_Jenkins
@@ -55,7 +55,7 @@ RUN apt-get update && apt-get install -y \
postgresql-client-15 \
libpq-dev
-RUN python3 -m pip install dill rtree xgboost mock pandas numpy scikit-learn
+RUN python3 -m pip install dill rtree xgboost mock pandas numpy scikit-learn pyxb-x
## To build an image from this docker file, from madlib folder, run:
# docker build -t madlib/postgres_15:jenkins -f tool/docker/base/Dockerfile_postgres_15_Jenkins .
diff --git a/tool/jenkins/jenkins_build.sh b/tool/jenkins/jenkins_build.sh
index 1a77b697..fb6df8f7 100755
--- a/tool/jenkins/jenkins_build.sh
+++ b/tool/jenkins/jenkins_build.sh
@@ -73,9 +73,9 @@ docker exec madlib bash -c 'service postgresql start' | tee $workdir/logs/madlib
echo "---------- Install pip, and mock -----------"
# cmake, make, make install, and make package
cat <<EOF
-docker exec madlib bash -c 'apt-get update; apt-get install -y python3-pip; pip install mock pandas numpy xgboost scikit-learn pyyaml' | tee $workdir/logs/madlib_compile.log
+docker exec madlib bash -c 'apt-get update; apt-get install -y python3-pip; pip install mock pandas numpy xgboost scikit-learn pyyaml pyxb-x' | tee $workdir/logs/madlib_compile.log
EOF
-docker exec madlib bash -c 'apt-get update; apt-get install -y python3-pip; pip install mock pandas numpy xgboost scikit-learn pyyaml' | tee $workdir/logs/madlib_compile.log
+docker exec madlib bash -c 'apt-get update; apt-get install -y python3-pip; pip install mock pandas numpy xgboost scikit-learn pyyaml pyxb-x' | tee $workdir/logs/madlib_compile.log
echo "---------- Building package -----------"
# cmake, make, make install, and make package