Dstara/fix mysql.c includes

.git_archival.txt

@@ -0,0 +1 @@
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.gitignore

@@ -11,4 +11,7 @@
 build/
 dist/
 MySQLdb/release.py
+tiledb/sql/release.py
 .coverage
+.idea
+tiledb/sql/version.py

.travis.yml

@@ -27,45 +27,49 @@ before_script:
   - "mysql --help"
   - "mysql --print-defaults"
   - "mysql -e 'create database mysqldb_test charset utf8mb4;'"
+  - "mysql -e 'create database test charset utf8mb4;'"
 
 script:
+  # Disable embedded for travis CI
+  - sed -i 's/embedded = True/embedded = False/g' site.cfg
   - pip install -e .
-  - pytest --cov ./MySQLdb
+  - pytest --cov ./tiledb/sql
 
 after_success:
   - codecov
 
 jobs:
   fast_finish: true
   include:
-    - &django_2_2
-      name: "Django 2.2 test"
-      env:
-        - DJANGO_VERSION=2.2.7
-      python: "3.5"
-      install:
-        - pip install -U pip
-        - wget https://github.com/django/django/archive/${DJANGO_VERSION}.tar.gz
-        - tar xf ${DJANGO_VERSION}.tar.gz
-        - pip install -e django-${DJANGO_VERSION}/
-        - cp ci/test_mysql.py django-${DJANGO_VERSION}/tests/
-        - pip install .
+    #- &django_2_2
+    #  name: "Django 2.2 test"
+    #  env:
+    #    - DJANGO_VERSION=2.2.7
+    #  python: "3.5"
+    #  install:
+    #    - pip install -U pip
+    #    - wget https://github.com/django/django/archive/${DJANGO_VERSION}.tar.gz
+    #    - tar xf ${DJANGO_VERSION}.tar.gz
+    #    - pip install -e django-${DJANGO_VERSION}/
+    #    - cp ci/test_mysql.py django-${DJANGO_VERSION}/tests/
+    #    - sed -i 's/embedded = True/embedded = False/g' site.cfg
+    #    - pip install .
 
-      before_script:
-        - mysql -e 'create user django identified by "secret"'
-        - mysql -e 'grant all on *.* to django'
-        - mysql_tzinfo_to_sql /usr/share/zoneinfo | mysql mysql
+    #  before_script:
+    #    - mysql -e 'create user django identified by "secret"'
+    #    - mysql -e 'grant all on *.* to django'
+    #    - mysql_tzinfo_to_sql /usr/share/zoneinfo | mysql mysql
 
-      script:
-        - cd django-${DJANGO_VERSION}/tests/
-        - ./runtests.py --parallel=1 --settings=test_mysql
+    #  script:
+    #    - cd django-${DJANGO_VERSION}/tests/
+    #    - ./runtests.py --parallel=1 --settings=test_mysql
     - name: flake8
       python: "3.8"
       install:
         - pip install -U pip
         - pip install flake8
       script:
-        - flake8 --ignore=E203,E501,W503 --max-line-length=88 .
+        - flake8 --ignore=E203,E501,W503,E402 --max-line-length=88 .
     - name: black
       python: "3.8"
       install:

Dockerfile

@@ -0,0 +1,139 @@
+FROM ubuntu:20.04
+LABEL maintainer="support@tiledb.io"
+
+ENV AWS_EC2_METADATA_DISABLED true
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=GMT
+
+RUN apt-get update && apt-get install -y \
+  gosu \
+  pwgen \
+  tzdata \
+  gcc \
+  g++ \
+  build-essential \
+  libasan5 \
+  bison \
+  chrpath \
+  cmake \
+  gdb \
+  gnutls-dev \
+  libaio-dev \
+  libboost-dev \
+  libdbd-mysql \
+  libjudy-dev \
+  libncurses5-dev \
+  libpam0g-dev \
+  libpcre3-dev \
+  libreadline-gplv2-dev \
+  libstemmer-dev \
+  libssl-dev \
+  libnuma-dev \
+  libxml2-dev \
+  lsb-release \
+  perl \
+  psmisc \
+  zlib1g-dev \
+  libcrack2-dev \
+  cracklib-runtime \
+  libjemalloc-dev \
+  libsnappy-dev \
+  liblzma-dev \
+  libzmq3-dev \
+  uuid-dev \
+  ccache \
+  git \
+  wget \
+  python3 \
+  python3-dev \
+  python3-pip \
+  && rm -rf /var/lib/apt/lists/*
+
+ENV MTR_MEM /tmp
+
+WORKDIR /tmp
+
+ENV TILEDB_VERSION="2.6.2"
+
+# Install tiledb using 2.6 release
+RUN mkdir build_deps && cd build_deps \
+ && git clone https://github.com/TileDB-Inc/TileDB.git -b ${TILEDB_VERSION} && cd TileDB \
+ && mkdir -p build && cd build \
+ && cmake -DTILEDB_VERBOSE=OFF -DTILEDB_S3=ON -DTILEDB_SERIALIZATION=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr .. \
+ && make -j$(nproc) \
+ && make install-tiledb \
+ && cd /tmp && rm -r build_deps
+
+ENV MARIADB_VERSION="mariadb-10.5.13"
+
+ARG MYTILE_VERSION="0.12.1"
+
+# Download mytile release
+RUN wget https://github.com/TileDB-Inc/TileDB-MariaDB/archive/${MYTILE_VERSION}.tar.gz -O /tmp/${MYTILE_VERSION}.tar.gz \
+  && tar xf /tmp/${MYTILE_VERSION}.tar.gz \
+  && mv TileDB-MariaDB-${MYTILE_VERSION} mytile
+
+# Copy example arrays to opt
+RUN cp -r /tmp/mytile/mysql-test/mytile/test_data/tiledb_arrays /opt/
+
+# Install curl after building tiledb
+RUN apt-get update && apt-get install -y \
+  libcurl4 \
+  libcurl4-openssl-dev \
+  && rm -rf /var/lib/apt/lists/*
+
+RUN wget https://downloads.mariadb.org/interstitial/${MARIADB_VERSION}/source/${MARIADB_VERSION}.tar.gz \
+  && tar xf ${MARIADB_VERSION}.tar.gz \
+  && mv /tmp/mytile ${MARIADB_VERSION}/storage/mytile \
+  && cd ${MARIADB_VERSION} \
+  && mkdir builddir \
+  && cd builddir \
+  && cmake -DPLUGIN_INNODB=NO \
+        -DPLUGIN_TOKUDB=NO \
+        -DPLUGIN_ROCKSDB=NO \
+        -DPLUGIN_MROONGA=NO \
+        -DPLUGIN_SPIDER=NO \
+        -DPLUGIN_SPHINX=NO \
+        -DPLUGIN_FEDERATED=NO \
+        -DPLUGIN_FEDERATEDX=NO \
+        -DPLUGIN_CONNECT=NO \
+        -DPLUGIN_PERFSCHEMA=NO \
+        -DCMAKE_BUILD_TYPE=Release \
+        -SWITH_DEBUG=0 \
+        -DWITH_EMBEDDED_SERVER=ON \
+        -DCMAKE_INSTALL_PREFIX=/opt/server .. \
+  && make -j$(nproc) \
+  && make install \
+  && cd ../../ \
+  && rm -r ${MARIADB_VERSION}
+
+# Add server binaries to path
+ENV PATH="${PATH}:/opt/server/bin"
+
+# Set ld library paths
+RUN echo "/usr/local/lib" >> /etc/ld.so.conf.d/usr-local.conf
+RUN echo "/usr/local/lib64" >> /etc/ld.so.conf.d/usr-local.conf
+RUN echo "/opt/server/lib" >> /etc/ld.so.conf.d/usr-local.conf
+RUN echo "/opt/server/lib64" >> /etc/ld.so.conf.d/usr-local.conf
+RUN echo "/opt/server/lib/plugin" >> /etc/ld.so.conf.d/usr-local.conf
+RUN echo "/opt/server/lib64/plugin" >> /etc/ld.so.conf.d/usr-local.conf
+
+RUN ldconfig /usr/local/lib
+
+ADD . /opt/tiledb-sql-py
+
+WORKDIR /opt/tiledb-sql-py
+
+# Newer setup tools needed for find_namespace_packages
+RUN pip3 install --upgrade setuptools
+
+RUN pip3 install -r requirements.txt
+
+RUN pip3 install .
+
+RUN pip3 install pandas numpy tiledb sqlalchemy
+
+WORKDIR /opt/
+
+CMD ["python3"]

MANIFEST.in

@@ -11,3 +11,4 @@ include site.cfg
 include setup_common.py
 include setup_posix.py
 include setup_windows.py
+include tiledb/sql/errmsg.sys

README.md

@@ -2,71 +2,77 @@
 
 [![Build Status](https://secure.travis-ci.org/PyMySQL/mysqlclient-python.png)](http://travis-ci.org/PyMySQL/mysqlclient-python)
 
-This is a fork of [MySQLdb1](https://github.com/farcepest/MySQLdb1).
+This is a fork of [mysqlclient-python](https://github.com/PyMySQL/mysqlclient-python).
 
-This project adds Python 3 support and bug fixes.
-I hope this fork is merged back to MySQLdb1 like distribute was merged back to setuptools.
+This project is designed to be used with TileDB-SQL which is a reduced build of MariaDB with support for using
+the [MyTile](https://github.com/TileDB-Inc/TileDB-MariaDB) storage engine for accessing TileDB Arrays.
 
+This is not meant to be used a general purpose MariaDB Client, it is only meant to be used with linking against
+the embedded version of MariaDB. This has been tested only with MariaDB 10.4 and the MyTile storage engine.
 
-## Support
+# Install
 
-**Do Not use Github Issue Tracker to ask help.  OSS Maintainer is not free tech support**
+## Docker
 
-When your question looks relating to Python rather than MySQL:
+A docker image is available on dockerhub under [tiledb/tiledb-sql-py](https://hub.docker.com/r/tiledb/tiledb-sql-py/).
+This docker image will drop you into a python shell and has tiledb, tiledb-sql-py, pandas and numpy preinstalled.
 
-* Python mailing list [python-list](https://mail.python.org/mailman/listinfo/python-list)
-* Slack [pythondev.slack.com](https://pyslackers.com/web/slack)
+```
+docker run -it --rm tiledb/tiledb-sql-py
+```
 
-Or when you have question about MySQL:
+## Conda
 
-* [MySQL Community on Slack](https://lefred.be/mysql-community-on-slack/)
+Conda packages will be available on conda forge soon.
 
+```
+conda install -c conda-forge tiledb-sql
+```
 
-## Install
+## Pypi
 
-### Windows
+A pypi package will be build from conda using conda-press
 
-Building mysqlclient on Windows is very hard.
-But there are some binary wheels you can install easily.
+```
+pip install tiledb-sql
+```
 
-### macOS (Homebrew)
+## Compiling From Source
 
-Install MySQL and mysqlclient:
+### Prerequisites
 
-```
-# Assume you are activating Python 3 venv
-$ brew install mysql
-$ pip install mysqlclient
-```
+You may need to install the Python development headers and compile MariaDB from source
 
-If you don't want to install MySQL server, you can use mysql-client instead:
+#### Python development headers
 
-```
-# Assume you are activating Python 3 venv
-$ brew install mysql-client
-$ echo 'export PATH="/usr/local/opt/mysql-client/bin:$PATH"' >> ~/.bash_profile
-$ export PATH="/usr/local/opt/mysql-client/bin:$PATH"
-$ pip install mysqlclient
-```
+* `sudo apt-get install python-dev default-libmysqlclient-dev`  # Debian / Ubuntu
+* `sudo yum install python-devel mysql-devel`  # Red Hat / CentOS
+* `brew install mysql-connector-c`  # macOS (Homebrew)  (Currently, it has bug. See below)
+
+On Windows, there are binary wheels you can install without MySQLConnector/C or MSVC.
 
-### Linux
+#### Compiling MyTile
 
-**Note that this is a basic step.  I can not support complete step for build for all
-environment.  If you can see some error, you should fix it by yourself, or ask for
-support in some user forum.  Don't file a issue on the issue tracker.**
+Please follow the [MyTile compilation instructions](https://docs.tiledb.com/developer/mariadb/installation)
 
-You may need to install the Python 3 and MySQL development headers and libraries like so:
+### Building TileDB-SQL-Py package
 
-* `$ sudo apt-get install python3-dev default-libmysqlclient-dev build-essential`  # Debian / Ubuntu
-* `% sudo yum install python3-devel mysql-devel`  # Red Hat / CentOS
+If you've installed mytile into `$HOME/mytile_server` simply build the python package with:
+
+```
+PATH="$HOME/mytile_server/bin:${PATH}" python setup.py build_ext --inplace
+```
 
-Then you can install mysqlclient via pip now:
+Now you can use it with
 
 ```
-$ pip install mysqlclient
+import tiledb.sql
+import pandas
+db = tiledb.sql.connect(db="test")
+pd.read_sql(sql="select * from `s3://my_bucket/my_array`, con=db)
 ```
 
-### Documentation
+# Documentation
 
-Documentation is hosted on [Read The Docs](https://mysqlclient.readthedocs.io/)
+Documentation is hosted on [TileDB Developer Docs](https://docs.tiledb.com/developer/api-usage/running-sql)