conda-forge / xeus-sqlite-feedstock

A conda-smithy repository for xeus-sqlite.

About xeus-sqlite-feedstock

Feedstock license: BSD-3-Clause

Home: https://github.com/jupyter-xeus/xeus-sqlite

Package license: BSD-3-Clause

Summary: Jupyter kernel for SQLite based on xeus

Documentation: https://xeus-sqlite.readthedocs.io

Current build status

Azure

Variant Status linux_64 linux_aarch64 linux_ppc64le osx_64

Current release info

Name	Downloads	Version	Platforms

Installing xeus-sqlite

Installing xeus-sqlite from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, xeus-sqlite can be installed with conda:

conda install xeus-sqlite

or with mamba:

mamba install xeus-sqlite

It is possible to list all of the versions of xeus-sqlite available on your platform with conda:

conda search xeus-sqlite --channel conda-forge

or with mamba:

mamba search xeus-sqlite --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search xeus-sqlite --channel conda-forge

# List packages depending on `xeus-sqlite`:
mamba repoquery whoneeds xeus-sqlite --channel conda-forge

# List dependencies of `xeus-sqlite`:
mamba repoquery depends xeus-sqlite --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating xeus-sqlite-feedstock

If you would like to improve the xeus-sqlite recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/xeus-sqlite-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

• If the version of a package is not being increased, please add or increase the build/number.
• If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

• @JohanMabille
• @SylvainCorlay
• @jtpio
• @marimeireles
• @martinRenou

xeus-sqlite-feedstock's Issues

xsqlite: symbol lookup error

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

The most recent xsqlite version that is currently installable from conda-forge seems to be broken,

(base) root@8cca2c0c3f67:/# conda create -n minimal -c conda-forge xeus-sqlite
(base) root@8cca2c0c3f67:/# conda activate minimal                                                                                                                                                            
(minimal) root@8cca2c0c3f67:/#  xsqlite                                                                                                                                                                       
xsqlite: symbol lookup error: /miniconda3/envs/minimal/bin/../lib/libxeus-sqlite.so.0: undefined symbol: _ZN4xeus12xinterpreter21internal_request_implERKN8nlohmann10basic_jsonISt3mapSt6vectorNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEblmdSaNS1_14adl_serializerES4_IhSaIhEEEE  

which also shows up in Jupyter server logs,

 # [I 2023-03-16 14:00:08.772 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (1/5), new random ports
 # /miniconda3/bin/xsqlite: symbol lookup error: /miniconda3/bin/../lib/libxeus-sqlite.so.0: undefined symbol: _ZN4xeus12xinterpreter21internal_request_implERKN8nlohmann10basic_jsonISt3mapSt6vectorNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEblmdSaNS1_14adl_serializerES4_IhSaIhEEEE
 # only install libspatialite and install xeus-sqlite from scratch

when attempting to start the corresponding Jupyter kernel (not installed in the above conda environment to keep things minimal).

Since I needed the package today for compatibility tests with a particular SQLite extension library, I ended up compiling xeus-sqlite myself (using this particular list as build environment) which unfortunately failed with,

(minimal) root@8cca2c0c3f67:/# mamba create -n compile1 -c conda-forge cxx-compiler cmake make 'xeus-zmq >=1.0.2,<2.0.0' cppzmq zeromq nlohmann_json xtl 'cpp-tabulate >=1.3,<2' sqlitecpp sqlite 'xvega >=0.0.10' 'xvega-bindings >=0.0.10' 'xproperty >=0.11.0,<0.12.0'
(minimal) root@8cca2c0c3f67:/# conda activate compile1
(compile1) root@8cca2c0c3f67:/
(compile1) root@8cca2c0c3f67:/# wget https://github.com/jupyter-xeus/xeus-sqlite/archive/refs/tags/0.6.0.zip
(compile1) root@8cca2c0c3f67:/# unzip 0.6.0.zip
(compile1) root@8cca2c0c3f67:/# cd xeus-sqlite-0.6.0/
(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# cmake -D CMAKE_INSTALL_PREFIX=$CONDA_PREFIX
CMake Warning:
  No source or binary directory provided.  Both will be assumed to be the
  same as the current working directory, but note that this warning will
  become a fatal error in future CMake releases.
-- The C compiler identification is GNU 11.3.0
-- The CXX compiler identification is GNU 11.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /miniconda3/envs/compile1/bin/x86_64-conda-linux-gnu-cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /miniconda3/envs/compile1/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Building xeus-sqlite v0.6.0
-- Found nlohmann_json: /miniconda3/envs/compile1/share/cmake/nlohmann_json/nlohmann_jsonConfig.cmake (found suitable version "3.11.2", minimum required is "3.2.0") 
-- Found LibUUID: /miniconda3/envs/compile1/lib/libuuid.so  
-- Found SQLite3: /miniconda3/envs/compile1/include (found version "3.40.0") 
-- Found xvega-bindings: /miniconda3/envs/compile1/lib/cmake/xvega-bindings/xvega-bindingsConfig.cmake (found suitable version "0.0.10", minimum required is "0.0.3") 
-- Found nlohmann_json: /miniconda3/envs/compile1/share/cmake/nlohmann_json/nlohmann_jsonConfig.cmake (found suitable version "3.11.2", minimum required is "3.7.3") 
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE  
-- Performing Test HAS_CPP17_FLAG
-- Performing Test HAS_CPP17_FLAG - Success
-- Found OpenSSL: /miniconda3/envs/compile1/lib/libcrypto.so (found version "3.1.0")  
-- Configuring done (0.7s)
-- Generating done (0.0s)
-- Build files have been written to: /xeus-sqlite-0.6.0
(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# make
[ 10%] Building CXX object CMakeFiles/xeus-sqlite.dir/src/xeus_sqlite_interpreter.cpp.o
/xeus-sqlite-0.6.0/src/xeus_sqlite_interpreter.cpp: In member function 'void xeus_sqlite::interpreter::process_SQLite_input(int, std::unique_ptr<SQLite::Database>&, const string&, xv::df_type&)':
/xeus-sqlite-0.6.0/src/xeus_sqlite_interpreter.cpp:323:33: error: cannot convert 'std::vector<std::variant<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, const char*, tabulate::Table> >' to 'const Row_t&' {aka 'const std::vector<std::variant<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, const char*, std::basic_string_view<char, std::char_traits<char> >, tabulate::Table> >&'}
  323 |             plain_table.add_row(col_names);
      |                                 ^~~~~~~~~
      |                                 |
      |                                 std::vector<std::variant<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, const char*, tabulate::Table> >
In file included from /xeus-sqlite-0.6.0/src/xeus_sqlite_interpreter.cpp:21:
/miniconda3/envs/compile1/include/tabulate/table.hpp:65:31: note:   initializing argument 1 of 'tabulate::Table& tabulate::Table::add_row(const Row_t&)'
   65 |   Table &add_row(const Row_t &cells) {
      |                  ~~~~~~~~~~~~~^~~~~
/xeus-sqlite-0.6.0/src/xeus_sqlite_interpreter.cpp:359:37: error: cannot convert 'std::vector<std::variant<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, const char*, tabulate::Table> >' to 'const Row_t&' {aka 'const std::vector<std::variant<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, const char*, std::basic_string_view<char, std::char_traits<char> >, tabulate::Table> >&'}
  359 |                 plain_table.add_row(row);
      |                                     ^~~
      |                                     |
      |                                     std::vector<std::variant<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, const char*, tabulate::Table> >
In file included from /xeus-sqlite-0.6.0/src/xeus_sqlite_interpreter.cpp:21:
/miniconda3/envs/compile1/include/tabulate/table.hpp:65:31: note:   initializing argument 1 of 'tabulate::Table& tabulate::Table::add_row(const Row_t&)'
   65 |   Table &add_row(const Row_t &cells) {
      |                  ~~~~~~~~~~~~~^~~~~
make[2]: *** [CMakeFiles/xeus-sqlite.dir/build.make:76: CMakeFiles/xeus-sqlite.dir/src/xeus_sqlite_interpreter.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:87: CMakeFiles/xeus-sqlite.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0#

Digging into details I found out that the problem seems to be caused by the cpp-tabulate package version (see potentially related problem here: p-ranav/tabulate#101). I was able to successfully compile xeus-sqlite by downgrading cpp-tabulate,

(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# mamba install -c conda-forge 'cpp-tabulate >=1.3,<1.5'
(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# cmake -D CMAKE_INSTALL_PREFIX=$CONDA_PREFIX
CMake Warning:
  No source or binary directory provided.  Both will be assumed to be the
  same as the current working directory, but note that this warning will
  become a fatal error in future CMake releases.
-- Building xeus-sqlite v0.6.0
-- Found nlohmann_json: /miniconda3/envs/compile1/share/cmake/nlohmann_json/nlohmann_jsonConfig.cmake (found suitable version "3.11.2", minimum required is "3.2.0") 
-- Found nlohmann_json: /miniconda3/envs/compile1/share/cmake/nlohmann_json/nlohmann_jsonConfig.cmake (found suitable version "3.11.2", minimum required is "3.7.3") 
-- Configuring done (0.0s)
-- Generating done (0.0s)
-- Build files have been written to: /xeus-sqlite-0.6.0
(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# make
[ 10%] Building CXX object CMakeFiles/xeus-sqlite.dir/src/xeus_sqlite_interpreter.cpp.o
[ 20%] Building CXX object CMakeFiles/xeus-sqlite.dir/src/xvega_sqlite.cpp.o
[ 30%] Building CXX object CMakeFiles/xeus-sqlite.dir/src/xlite.cpp.o
[ 40%] Linking CXX shared library libxeus-sqlite.so
[ 40%] Built target xeus-sqlite
[ 50%] Building CXX object CMakeFiles/xeus-sqlite-static.dir/src/xeus_sqlite_interpreter.cpp.o
[ 60%] Building CXX object CMakeFiles/xeus-sqlite-static.dir/src/xvega_sqlite.cpp.o
[ 70%] Building CXX object CMakeFiles/xeus-sqlite-static.dir/src/xlite.cpp.o
[ 80%] Linking CXX static library libxeus-sqlite.a
[ 80%] Built target xeus-sqlite-static
[ 90%] Building CXX object CMakeFiles/xsqlite.dir/src/main.cpp.o
[100%] Linking CXX executable xsqlite
[100%] Built target xsqlite
(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# make install
[ 40%] Built target xeus-sqlite
[ 80%] Built target xeus-sqlite-static
[100%] Built target xsqlite
Install the project...
-- Install configuration: "RELEASE"
-- Installing: /miniconda3/envs/compile1/lib/libxeus-sqlite.so.0.6.0
-- Installing: /miniconda3/envs/compile1/lib/libxeus-sqlite.so.0
-- Installing: /miniconda3/envs/compile1/lib/libxeus-sqlite.so
-- Installing: /miniconda3/envs/compile1/include/xeus-sqlite/xeus_sqlite_config.hpp
-- Installing: /miniconda3/envs/compile1/include/xeus-sqlite/xeus_sqlite_interpreter.hpp
-- Installing: /miniconda3/envs/compile1/include/xeus-sqlite/xvega_sqlite.hpp
-- Installing: /miniconda3/envs/compile1/lib/libxeus-sqlite.a
-- Up-to-date: /miniconda3/envs/compile1/include/xeus-sqlite/xeus_sqlite_config.hpp
-- Up-to-date: /miniconda3/envs/compile1/include/xeus-sqlite/xeus_sqlite_interpreter.hpp
-- Up-to-date: /miniconda3/envs/compile1/include/xeus-sqlite/xvega_sqlite.hpp
-- Installing: /miniconda3/envs/compile1/bin/xsqlite
-- Installing: /miniconda3/envs/compile1/share/jupyter/kernels
-- Installing: /miniconda3/envs/compile1/share/jupyter/kernels/xsqlite
-- Installing: /miniconda3/envs/compile1/share/jupyter/kernels/xsqlite/logo-32x32.png
-- Installing: /miniconda3/envs/compile1/share/jupyter/kernels/xsqlite/logo-64x64.png
-- Installing: /miniconda3/envs/compile1/share/jupyter/kernels/xsqlite/kernel.json
-- Installing: /miniconda3/envs/compile1/lib/cmake/xeus-sqlite/xeus-sqliteConfig.cmake
-- Installing: /miniconda3/envs/compile1/lib/cmake/xeus-sqlite/xeus-sqliteConfigVersion.cmake
-- Installing: /miniconda3/envs/compile1/lib/cmake/xeus-sqlite/xeus-sqliteTargets.cmake
-- Installing: /miniconda3/envs/compile1/lib/cmake/xeus-sqlite/xeus-sqliteTargets-release.cmake
(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# 

The xsqlite command then works as expected,

(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# which xsqlite
/miniconda3/envs/compile1/bin/xsqlite
(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# xsqlite
registering handler for SIGSEGV
Starting xeus-sqlite kernel...

If you want to connect to this kernel from an other client, just copy and paste the following content inside of a `kernel.json` file. And then run for example:

# jupyter console --existing kernel.json

kernel.json

{
    "transport": "tcp",
    "ip": "127.0.0.1",
    "control_port": 59160,
    "shell_port": 58035,
    "stdin_port": 57773,
    "iopub_port": 64823,
    "hb_port": 49944,
    "signature_scheme": "hmac-sha256",
    "key": "93cee6f5c9e34383947a8b7e720880ed"
}

Run with XEUS 3.0.5

^C(compile1) root@8cca2c0c3f67:/xeus-sqlite-0.6.0# 

both from the command line and from JupyterLab directly.

Installed packages

# packages in environment at /miniconda3/envs/minimal:                                                                                                                                                        
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.40.0               h753d276_0    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
openssl                   3.1.0                h0b41bf4_0    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
sqlite                    3.40.0               h4ff8645_0    conda-forge
sqlitecpp                 3.1.1                h0251d09_0    conda-forge
xeus                      3.0.5                hac2b420_1    conda-forge
xeus-sqlite               0.6.0                hdd8d261_0    conda-forge
xeus-zmq                  1.0.2                h0541b36_2    conda-forge
xvega                     0.0.10               hf52228f_1    conda-forge
xvega-bindings            0.0.10               hf52228f_1    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge

Environment info

active environment : minimal
    active env location : /miniconda3/envs/minimal
            shell level : 2
       user config file : /root/.condarc
 populated config files : 
          conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.9.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.35=0
                          __linux=5.4.0=0
                          __unix=0=0
       base environment : /miniconda3  (writable)
      conda av data dir : /miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /miniconda3/pkgs
                          /root/.conda/pkgs
       envs directories : /miniconda3/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/23.1.0 requests/2.28.1 CPython/3.10.9 Linux/5.4.0-144-generic ubuntu/22.04.2 glibc/2.35
                UID:GID : 0:0
             netrc file : None
           offline mode : False