Merge branch 'mysql' into main

DiamondLightSource · May 26, 2023 · e76a4e8 · e76a4e8
2 parents 3d8afdd + 830a30e
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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-servbase
 
 # ---------------------------------------------------------------------
@@ -69,4 +69,4 @@ publish_docs:
 	cp -r build/html/* $(DOCS_PUBLISH_ROOT)
 
 
-# dae_devops_fingerprint dc970803af5fac409092e34299b9fa8a
+# dae_devops_fingerprint 7a40fdc6afce4991715aeda7ae70c444
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-servbase
 
 Naming conventions
@@ -31,4 +31,4 @@ repository
     lowercase, hyphens
 
 
-.. # dae_devops_fingerprint de2f9c8adee74d13de393fe798054c9a
+.. # dae_devops_fingerprint cbd0a78343b6577aa4ddb9d59a242b04
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-servbase
 
 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-servbase
-    $ 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 85a9a86c29f573bd408647f7092b6fbe
+.. # dae_devops_fingerprint ac891cf352ef89b3b20d2c601dd9ddc4
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-servbase
 
 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 d203976f0fb58a25033c89155e85466e
+.. # dae_devops_fingerprint 84e8a32100211cbba64804a3e5c5b337
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-servbase
 
 About the documentation
@@ -21,4 +21,4 @@ improve most documentation - often immensely.
 
 `More information on this topic. <https://documentation.divio.com>`_
 
-.. # dae_devops_fingerprint 4c487ab610c69b04a69e018d6726347d
+.. # dae_devops_fingerprint 6ef08be920f12050c1c579cf6e9d4253
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-servbase
 
 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-servbase
 
 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-servbase.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-servbase --version
     $ dls-servbase --version-json
 
-.. # dae_devops_fingerprint 4595ce95067039bcca5e2ff516cd03af
+.. # dae_devops_fingerprint 64d7ae0dde8939e479b9c793df928d15
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-servbase
 
 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 6b049b05d346f33c50ff7c08811e9754
+.. # dae_devops_fingerprint 3bd80bbd88306473a1ee98b988b17986
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-servbase
 
 me=${BASH_SOURCE}
@@ -13,4 +13,4 @@ function __install {
 }
 
 
-# dae_devops_fingerprint 903ed54702867ede6f0174cc61d4b713
+# dae_devops_fingerprint 663e11dbca4cdd5f84a218a64398a688
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-servbase
 
 # This file is for use as a devcontainer and a runtime container
@@ -40,4 +40,4 @@ ENV PATH=/venv/bin:$PATH
 ENTRYPOINT ["dls-servbase"]
 CMD ["--version"]
 
-# dae_devops_fingerprint d98578ac4f9faec948660e9198138f35
+# dae_devops_fingerprint 80986671f8602f6e4666f78f98141826
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-servbase
 
 // For format details, see https://containers.dev/implementors/json_reference/
@@ -57,4 +57,4 @@
     "postCreateCommand": "pip install -e .[dev]"
 }
 
-// dae_devops_fingerprint a69fcd5d4332da3e6af3b97a7f171509
+// dae_devops_fingerprint 35358278c2556f05447815a0833301dc
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-servbase
 
 Contributing to the project
@@ -38,4 +38,4 @@ should follow.
 
 .. _Developer Guide: https://diamondlightsource.github.io/dls-servbase/main/developer/how-to/contribute.html
 
-.. # dae_devops_fingerprint 65b30b94836cca6d96fc062a2f20730a
+.. # dae_devops_fingerprint 0f4cbc1f77b787f03a9a4d268ed08055
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-servbase
 
 name: Install requirements
@@ -61,4 +61,4 @@ runs:
       shell: bash
 
 
-# dae_devops_fingerprint c59b1a1b3a2300f4ab9f3fc9274b213c
+# dae_devops_fingerprint 492458ca501cde9a298a80a102ff22a4
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-servbase
 
 # To get started with Dependabot version updates, you'll need to specify which
@@ -19,4 +19,4 @@ updates:
     schedule:
       interval: "weekly"
 
-# dae_devops_fingerprint 122e34b2a7528692f5975e2fb7cc167d
+# dae_devops_fingerprint b5838c5e0d9b5041500c5cb701fb5e5b
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-servbase -->
 
 <!DOCTYPE html>
@@ -14,4 +14,4 @@
 
 </html>
 
-<!-- dae_devops_fingerprint 33224c1113136243f88379d0197f501e -->
+<!-- dae_devops_fingerprint f42d18d6994629b2878c5e7336501264 -->
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-servbase
 
 import json
@@ -102,4 +102,4 @@ def main(args=None):
 if __name__ == "__main__":
     main()
 
-# dae_devops_fingerprint fe647176edcb02077a904f8e42cf4367
+# dae_devops_fingerprint 7a1b58b851c5198d7d380e4ab78d0b49
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-servbase
 
 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 f06ae327848fe3cd45de89312a6cfadf
+# dae_devops_fingerprint 480a147d8af93a934e6ad0fd272e60e5
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-servbase
 
 name: Docs CI
@@ -56,4 +56,4 @@ jobs:
           publish_dir: .github/pages
           keep_files: true
 
-# dae_devops_fingerprint 7eb227aeb2a5da22835482ebc7fe11dd
+# dae_devops_fingerprint fb2dde86086783119d0b0b805151bf09
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-servbase
 
 name: Docs Cleanup CI
@@ -46,4 +46,4 @@ jobs:
           git commit -am "Removing redundant docs version $DOCS_VERSION"
           git push
 
-# dae_devops_fingerprint cd9ac693f5bf252fbaf5c9585cb1dd76
+# dae_devops_fingerprint d46d59a6f5197bd11b1cece615feb4df
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-servbase
 
 name: Link Check
@@ -27,4 +27,4 @@ jobs:
       - name: Check links
         run: tox -e docs build -- -b linkcheck
 
-# dae_devops_fingerprint dddcd5c3991c4a5f1f8ae8a99b66fbcb
+# dae_devops_fingerprint 0198bfb9fadda488379138f6b2e7f5e3
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-servbase
 
 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 e156b7559726d32f77aea7cfd628aee8
+# dae_devops_fingerprint 814043c19b1379f7f1d7b188546a7734
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-servbase */ 
 
 /* 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 18ea0db9563c9bb76b88d1451e9cb254 */ 
+/* dae_devops_fingerprint b94b4f0075614442e536fdd79bcf79f7 */ 
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-servbase
 
 from pathlib import Path
@@ -197,4 +197,4 @@ def setup(app):
     app.connect("source-read", ultimateReplace)
 
 
-# dae_devops_fingerprint 9cd088d2151788486c59b6e240be074b
+# dae_devops_fingerprint 529445ac120d879ddd71245754e51ecb