adds mysql support

DiamondLightSource · May 26, 2023 · 55decae · 55decae
2 parents 91ac055 + 48b658b
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diff --git a/.dae-devops/Makefile b/.dae-devops/Makefile
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 # ---------------------------------------------------------------------
@@ -69,4 +69,4 @@ publish_docs:
 	cp -r build/html/* $(DOCS_PUBLISH_ROOT)
 
 
-# dae_devops_fingerprint 3f13d455c444ad39930aabfc68547c2c
+# dae_devops_fingerprint 62bfff1938ace30f8cb33ab30b9c60d5
diff --git a/.dae-devops/docs/conventions.rst b/.dae-devops/docs/conventions.rst
@@ -1,5 +1,5 @@
 .. # ********** Please don't edit this file!
-.. # ********** It has been generated automatically by dae_devops version 0.5.2.
+.. # ********** It has been generated automatically by dae_devops version 0.5.3.
 .. # ********** For repository_name dls-normsql
 
 Naming conventions
@@ -31,4 +31,4 @@ repository
     lowercase, hyphens
 
 
-.. # dae_devops_fingerprint 81e582297295ea8d1145aeb4fb60ffef
+.. # dae_devops_fingerprint 8a72a4d0ee07d38513ef1273e9f9682e
diff --git a/.dae-devops/docs/developing.rst b/.dae-devops/docs/developing.rst
@@ -1,5 +1,5 @@
 .. # ********** Please don't edit this file!
-.. # ********** It has been generated automatically by dae_devops version 0.5.2.
+.. # ********** It has been generated automatically by dae_devops version 0.5.3.
 .. # ********** For repository_name dls-normsql
 
 Developing
@@ -22,7 +22,6 @@ Make sure to have at least python version 3.9 then::
 Install the package in edit mode which will also install all its dependencies::
 
     $ cd dls-normsql
-    $ export PIP_FIND_LINKS=/dls_sw/apps/bxflow/artifacts
     $ pip install -e .[dev]
 
 Now you may begin modifying the code.
@@ -36,4 +35,4 @@ If you plan to modify the docs, you will need to::
     
 
 
-.. # dae_devops_fingerprint 550d6069746935ee4e08d958dd046fa2
+.. # dae_devops_fingerprint 7b83e003f8bbbf54c27b4bd8141fb0e5
diff --git a/.dae-devops/docs/devops.rst b/.dae-devops/docs/devops.rst
@@ -1,23 +1,24 @@
 .. # ********** Please don't edit this file!
-.. # ********** It has been generated automatically by dae_devops version 0.5.2.
+.. # ********** It has been generated automatically by dae_devops version 0.5.3.
 .. # ********** For repository_name dls-normsql
 
 Devops
 =======================================================================
 
-There exists a a configuration file called ``.dae-devops/project.yaml``.
+In the top level of the repository there exists a configuration file called ``.dae-devops/project.yaml``.
 
 This file defines the project information needed for CI/CD.
 
 It is parsed by the ``dae_devops.force`` command which creates these files:
 
 - pyproject.toml
+- .githib/*
 - .gitlab-ci.yml
 - .dae-devops/Makefile
 - .dae-devops/docs/*
 
 Local CI/CD execution
------------------------------------------------------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 All the CI/CD ops which are run by the git server can be run at the command line.
 
@@ -32,15 +33,15 @@ Validation of the code::
     $ make -f .dae-devops/Makefile validate_pytest
     $ make -f .dae-devops/Makefile validate_docs
 
-Packaging:: 
+Packaging (for the Diamond intranet):: 
 
     $ make -f .dae-devops/Makefile package_pip
 
-Publishing::
+Publishing (for the Diamond intranet)::
 
     $ make -f .dae-devops/Makefile publish_pip
     $ make -f .dae-devops/Makefile publish_docs
     
+The Diamond intranet commands are not used for production. The production packaging and publishing are handled in the GitHub Actions workflows mechanism.
 
-
-.. # dae_devops_fingerprint 35ea37a143cb4560425194afc2bad8ed
+.. # dae_devops_fingerprint d9ee7cc6b002b3508a4e55f96193c35e
diff --git a/.dae-devops/docs/docs_structure.rst b/.dae-devops/docs/docs_structure.rst
@@ -1,5 +1,5 @@
 .. # ********** Please don't edit this file!
-.. # ********** It has been generated automatically by dae_devops version 0.5.2.
+.. # ********** It has been generated automatically by dae_devops version 0.5.3.
 .. # ********** For repository_name dls-normsql
 
 About the documentation
@@ -21,4 +21,4 @@ improve most documentation - often immensely.
 
 `More information on this topic. <https://documentation.divio.com>`_
 
-.. # dae_devops_fingerprint 68095839584c6e3455c1bd06350312f4
+.. # dae_devops_fingerprint eda941e8a0c3d217a601fb11b90f639b
diff --git a/.dae-devops/docs/installing.rst b/.dae-devops/docs/installing.rst
@@ -1,5 +1,5 @@
 .. # ********** Please don't edit this file!
-.. # ********** It has been generated automatically by dae_devops version 0.5.2.
+.. # ********** It has been generated automatically by dae_devops version 0.5.3.
 .. # ********** For repository_name dls-normsql
 
 Installing
@@ -26,18 +26,17 @@ installation will not interfere with any existing Python software::
 
 You can now use ``pip`` to install the library and its dependencies::
 
-    $ export PIP_FIND_LINKS=/dls_sw/apps/bxflow/artifacts
     $ python3 -m pip install dls-normsql
 
 If you require a feature that is not currently released you can also install
 from git::
 
     $ python3 -m pip install git+https://gitlab.diamond.ac.uk/kbp43231/dls-normsql.git
 
-The library should now be installed and the commandline interface on your path.
+The library should now be installed and the commandline should be available.
 You can check the version that has been installed by typing::
 
     $ dls-normsql --version
     $ dls-normsql --version-json
 
-.. # dae_devops_fingerprint f0f3fa3bcf53a551add4ee39538eb44a
+.. # dae_devops_fingerprint a2fe8dfbc79c151a5b899b244a529aa6
diff --git a/.dae-devops/docs/testing.rst b/.dae-devops/docs/testing.rst
@@ -1,5 +1,5 @@
 .. # ********** Please don't edit this file!
-.. # ********** It has been generated automatically by dae_devops version 0.5.2.
+.. # ********** It has been generated automatically by dae_devops version 0.5.3.
 .. # ********** For repository_name dls-normsql
 
 Testing
@@ -11,17 +11,13 @@ If you want to run the tests, first get a copy of the code per the instructions
 
 Then you can run all tests by::
 
-    $ pytest
-
-Or this, which is the command used by the CI runner.
-
-    $ make -f .dae-devops/Makefile validate_pytest
+    $ tox -q -e pytest
 
 To run a single test you can do::
 
     $ pytest tests/the_test_you_want.py
 
-If you want to see more output of the test while it's running you can do:
+If you want to see more output of the test while it's running you can do::
 
     $ pytest -sv -ra --tb=line tests/the_test_you_want.py
 
@@ -35,4 +31,4 @@ This allows peeking in there to see what's been written by the test.
 
 
 
-.. # dae_devops_fingerprint 16abfa1d4f582c07e1ea9281771b8f4f
+.. # dae_devops_fingerprint 1801aaf6bd998d192c9fb4cdd6c3e79f
diff --git a/.dae-devops/prepare_git_dependencies.sh b/.dae-devops/prepare_git_dependencies.sh
@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 me=${BASH_SOURCE}
@@ -13,4 +13,4 @@ function __install {
 }
 
 
-# dae_devops_fingerprint d2a7e27cfad2e9f2547dc2b0da58fdd1
+# dae_devops_fingerprint b7ad9765b7da993eecef6a4ce23802c2
diff --git a/.dae-devops/project.yaml b/.dae-devops/project.yaml
@@ -13,5 +13,8 @@ primary:
   dependencies:
     - type: pypi
       list:
-        - aiosqlite
         - dls-utilpack
+        - aiosqlite
+        - aiomysql
+        # cryptography package is required for aiomysql sha256_password or caching_sha2_password auth methods
+        - cryptography
diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 # This file is for use as a devcontainer and a runtime container
@@ -40,4 +40,4 @@ ENV PATH=/venv/bin:$PATH
 ENTRYPOINT ["dls-normsql"]
 CMD ["--version"]
 
-# dae_devops_fingerprint 41ae7527130d2727aa06cd91ff8e5702
+# dae_devops_fingerprint a5c05253a7982ce4ee2e60abd1a254f0
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,5 +1,5 @@
 // ********** Please don't edit this file!
-// ********** It has been generated automatically by dae_devops version 0.5.2.
+// ********** It has been generated automatically by dae_devops version 0.5.3.
 // ********** For repository_name dls-normsql
 
 // For format details, see https://containers.dev/implementors/json_reference/
@@ -57,4 +57,4 @@
     "postCreateCommand": "pip install -e .[dev]"
 }
 
-// dae_devops_fingerprint bf6676a0739eeb0e671f3518d7739877
+// dae_devops_fingerprint 1c59c18009b5b4578be9201b399a2b6c
diff --git a/.github/CONTRIBUTING.rst b/.github/CONTRIBUTING.rst
@@ -1,5 +1,5 @@
 .. # ********** Please don't edit this file!
-.. # ********** It has been generated automatically by dae_devops version 0.5.2.
+.. # ********** It has been generated automatically by dae_devops version 0.5.3.
 .. # ********** For repository_name dls-normsql
 
 Contributing to the project
@@ -38,4 +38,4 @@ should follow.
 
 .. _Developer Guide: https://diamondlightsource.github.io/dls-normsql/main/developer/how-to/contribute.html
 
-.. # dae_devops_fingerprint e4fc983b36dd78a7c7fefcb6ac9fdd13
+.. # dae_devops_fingerprint 1e4da81da23bd1f1ea6d675517d6f9c5
diff --git a/.github/actions/install_requirements/action.yml b/.github/actions/install_requirements/action.yml
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 name: Install requirements
@@ -61,4 +61,4 @@ runs:
       shell: bash
 
 
-# dae_devops_fingerprint 8d7ad9a9e4bbb3b504abc3a0f33579ee
+# dae_devops_fingerprint 66e539b4856f80b66acfd95402e76d05
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 # To get started with Dependabot version updates, you'll need to specify which
@@ -19,4 +19,4 @@ updates:
     schedule:
       interval: "weekly"
 
-# dae_devops_fingerprint b8759630d6502121150bac83a60ac05d
+# dae_devops_fingerprint 61dd9f51dc2d4a0486ac8a76be91051f
diff --git a/.github/pages/index.html b/.github/pages/index.html
@@ -1,5 +1,5 @@
 <!-- ********** Please don't edit this file! -->
-<!-- ********** It has been generated automatically by dae_devops version 0.5.2. -->
+<!-- ********** It has been generated automatically by dae_devops version 0.5.3. -->
 <!-- ********** For repository_name dls-normsql -->
 
 <!DOCTYPE html>
@@ -14,4 +14,4 @@
 
 </html>
 
-<!-- dae_devops_fingerprint d1650ec0d6d7791f6b665a22c9b8c4ff -->
+<!-- dae_devops_fingerprint 4f2d286affbfbe691ff33fdbac641eb5 -->
diff --git a/.github/pages/make_switcher.py b/.github/pages/make_switcher.py
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 import json
@@ -102,4 +102,4 @@ def main(args=None):
 if __name__ == "__main__":
     main()
 
-# dae_devops_fingerprint 321882bf975a37cedc9e7def02e120fa
+# dae_devops_fingerprint dd357c9cfe8e116f70c977b7d94d62db
diff --git a/.github/workflows/code.yml b/.github/workflows/code.yml
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 name: Code CI
@@ -39,7 +39,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"] # can add windows-latest, macos-latest
-        python: ["3.10", "3.11"]
+        python: ["3.10"]
         install: ["-e .[dev,docs]"]
         # Make one version be non-editable to test both paths of version code
         include:
@@ -69,6 +69,10 @@ jobs:
       - name: List dependency tree
         run: pipdeptree
 
+      # TODO: Make startup of MySQL able to be configured.
+      - name: Start up the MySQL that comes with Unbuntu
+        run: sudo /etc/init.d/mysql start
+
       - name: Run tests
         run: |
           sudo apt install environment-modules
@@ -212,4 +216,4 @@ jobs:
         with:
           password: ${{ secrets.PYPI_TOKEN }}
 
-# dae_devops_fingerprint 0eca35d77828ef5ba3c51d0d68628f12
+# dae_devops_fingerprint d13e8289ca6252679ab7d9ae8db75617
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 name: Docs CI
@@ -56,4 +56,4 @@ jobs:
           publish_dir: .github/pages
           keep_files: true
 
-# dae_devops_fingerprint ea6935f4eb0060233fc35dcccd2a0a36
+# dae_devops_fingerprint 0c3ce8bebad77dab099617eae89e2247
diff --git a/.github/workflows/docs_clean.yml b/.github/workflows/docs_clean.yml
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 name: Docs Cleanup CI
@@ -46,4 +46,4 @@ jobs:
           git commit -am "Removing redundant docs version $DOCS_VERSION"
           git push
 
-# dae_devops_fingerprint 53d885e9033e0abb28bcc63d8252ca03
+# dae_devops_fingerprint b47d6e45e6ea9f929b8afe4f238d9473
diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 name: Link Check
@@ -27,4 +27,4 @@ jobs:
       - name: Check links
         run: tox -e docs build -- -b linkcheck
 
-# dae_devops_fingerprint f31df44c662aa0a356bb2a62fe64eade
+# dae_devops_fingerprint 674bb9fc122cc739ba92fe18045f0f1f
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 variables:
@@ -87,4 +87,4 @@ package_pip:
 #     # The validate_docs artifacts are in the build/html folder.
 #     - make -f .dae-devops/Makefile publish_docs
 
-# dae_devops_fingerprint 19ac89e7287f70ae7f5f96292102fde8
+# dae_devops_fingerprint f4eece0911ee4d3dbab40d858bc4962d
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
@@ -1,5 +1,5 @@
 /* ********** Please don't edit this file! */ 
-/* ********** It has been generated automatically by dae_devops version 0.5.2. */ 
+/* ********** It has been generated automatically by dae_devops version 0.5.3. */ 
 /* ********** For repository_name dls-normsql */ 
 
 /* The theme normally has this, but I think it's ok to use the full width of the window in all @media sizes.
@@ -15,4 +15,4 @@
     max-width: 100%;
 }
 
-/* dae_devops_fingerprint b13b064702739049faa6ce9119be9039 */ 
+/* dae_devops_fingerprint cadc619d1b64a206ac3a5e05c7b9d498 */ 
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.2.
+# ********** It has been generated automatically by dae_devops version 0.5.3.
 # ********** For repository_name dls-normsql
 
 from pathlib import Path
@@ -197,4 +197,4 @@ def setup(app):
     app.connect("source-read", ultimateReplace)
 
 
-# dae_devops_fingerprint 404e6b95750b57333b0799fcd1a2c408
+# dae_devops_fingerprint cd8b8b6c6077d960c9ed6af1579909b3