drop: support for unused databases

README.md

@@ -20,17 +20,12 @@ git clone --recurse-submodules https://github.com/rcsb/py-rcsb_db.git
 
 ```
 
-Optionally, run test suite (Python versions 3.9+) using
-[setuptools](https://setuptools.readthedocs.io/en/latest/) or
-[tox](http://tox.readthedocs.io/en/latest/example/platform.html):
+Optionally, run test suite (Python versions 3.9+) using either:
 
-```bash
-python setup.py test
-
-or simply run
-
-tox
-```
+- [setuptools](https://setuptools.readthedocs.io/en/latest/)
+  with `python setup.py test`
+- [tox](http://tox.readthedocs.io/en/latest/example/platform.html)
+  by running simply `tox`
 
 Installation is via the program [pip](https://pypi.python.org/pypi/pip).  To run tests
 from the source tree, the package must be installed in editable mode (i.e. -e):
@@ -44,9 +39,7 @@ pip install -e .
 You will need a few packages, before `pip install .` can work:
 
 ```bash
-
-sudo apt install default-libmysqlclient-dev flex bison
-
+sudo apt install flex bison
 ```
 
 ### Installing on macOS

azure-pipelines.yml

@@ -26,14 +26,14 @@ schedules:
 
 jobs:
   - template: azure-template-tox-job.yml
-    parameters: {tox: 'format_pep8', python: '3.10', os: 'linux', fixtures: 'mysql,mongodb'}
+    parameters: {tox: 'format_pep8', python: '3.10', os: 'linux', fixtures: 'mongodb'}
   - template: azure-template-tox-job.yml
-    parameters: {tox: 'lint_pylint', python: '3.10', os: 'linux', fixtures: 'mysql,mongodb'}
+    parameters: {tox: 'lint_pylint', python: '3.10', os: 'linux', fixtures: 'mongodb'}
   #- template: azure-template-tox-job.yml
-  #  parameters: {tox: 'test_coverage', python: '3.10', os: 'linux', fixtures: 'mysql,mongodb'}
+  #  parameters: {tox: 'test_coverage', python: '3.10', os: 'linux', fixtures: mongodb'}
   #
   - template: azure-template-tox-job.yml
-    parameters: {tox: 'py310', python: '3.10', os: 'linux', fixtures: 'mysql,mongodb'}
+    parameters: {tox: 'py310', python: '3.10', os: 'linux', fixtures: 'mongodb'}
   - template: azure-template-publish-job.yml
     parameters: {tox: 'py310', python: '3.10', os: 'linux'}
     #

azure-template-tox-job.yml

@@ -1,6 +1,6 @@
 # File: azure-template-tox-job.yml
 # Date: 8-Jul-2019 jdw split out from original pipeline
-# Supports: fixtures=mysql,mongodb (linux)
+# Supports: fixtures=mongodb (linux)
 #
 # Updates:
 #  6-Aug-2019  jdw build source and binary wheels by default.
@@ -63,7 +63,7 @@ jobs:
       # ----------------------------------------------
       - ${{ if startsWith(parameters.os, 'linux') }}:
           - script: lsb_release -a
-            displayName: "Ubuntu kernal version"
+            displayName: "Ubuntu kernel version"
           - script: which apt
             displayName: "Installing OS dependencies"
           - script: apt-cache policy | grep http | awk '{print $2 $3}' | sort -u
@@ -80,39 +80,6 @@ jobs:
           - script: sudo apt-get install bison
             displayName: "Install bison"
       #
-      - ? ${{ if and(contains(parameters.fixtures, 'mysql'), startsWith(parameters.os, 'linux')) }}
-        : - bash: |
-              sudo apt-get install python3-dev mysql-server
-              sudo apt-get install default-libmysqlclient-dev
-              sudo apt-get install python-mysqldb
-              sudo apt list --installed | grep -i mysql
-            displayName: "Install mysql development libraries"
-          - bash: |
-              echo "Retarting mysql service"
-              sudo systemctl restart mysql.service
-              mysql -V
-              mysql --user=root --password=root -e "use mysql; select * from user;"
-              #
-              echo "Try resetting password"
-              mysqladmin --user=root --password=root password 'ChangeMeSoon'
-              #
-              # mysql -u root  -p root -e "SET PASSWORD FOR root@'localhost' = PASSWORD(‘ChangeMeSoon’);"
-              # mysql -u root  -p root -e "FLUSH PRIVILEGES; update mysql.user set password=password('ChangeMeSoon') where user='root'; FLUSH PRIVILEGES;"
-              # UPDATE mysql.user SET Password=PASSWORD('ChangeMeSoon') WHERE User='root';
-
-              echo "Running preliminary mysql setup"
-              mysql --user=root --password=ChangeMeSoon <<_EOF_
-                DELETE FROM mysql.user WHERE User='';
-                DELETE FROM mysql.user WHERE User='root' AND Host NOT IN ('localhost', '127.0.0.1', '::1');
-                DROP DATABASE IF EXISTS test;
-                DELETE FROM mysql.db WHERE Db='test' OR Db='test\\_%';
-                FLUSH PRIVILEGES;
-              _EOF_
-              ps -ef | grep -i my
-              mysql --user=root --password=ChangeMeSoon -e "show databases;"
-              #
-            displayName: "Start and configure mysql ..."
-
         # -----
       - ? ${{ if and(contains(parameters.fixtures, 'mongodb'), startsWith(parameters.os, 'linux')) }}
         : # Mongo install
@@ -137,8 +104,11 @@ jobs:
       - script: 'python -c "import sys; print(sys.version); print(sys.executable)"'
         displayName: show python information
       #
-      - script: python -m pip install --upgrade pip tox
-        displayName: "Install tools"
+      - script: python -m pip install --upgrade pip
+        displayName: "Upgrade pip"
+      #
+      - script: pip install tox jsonschema 'rcsb.utils.chemref>=0.91' 'jsondiff>=1.2.0'
+        displayName: "Install test requirements"
         #
       - script: pip install -r requirements.txt
         displayName: "Install dependencies"

pylintrc

@@ -1,10 +1,5 @@
 [MASTER]
 
-# A comma-separated list of package or module names from where C extensions may
-# be loaded. Extensions are loading into the active Python interpreter and may
-# run arbitrary code.
-extension-pkg-whitelist=MySQLdb
-
 # Add files or directories to the blacklist. They should be base names, not
 # paths.
 ignore=CVS
@@ -302,11 +297,6 @@ ignored-argument-names=_.*|^ignored_|^unused_
 # Tells whether we should check for unused import in __init__ files.
 init-import=no
 
-# List of qualified module names which can have objects that can redefine
-# builtins.
-redefining-builtins-modules=six.moves,past.builtins,future.builtins,builtins,io
-
-
 [FORMAT]
 
 # Expected format of line ending, e.g. empty (any line ending), LF or CRLF.