Merge branch 'mysql-compat' into main

DiamondLightSource · May 26, 2023 · c585b37 · c585b37
2 parents 27b88f9 + 072b5ed
commit c585b37
Show file tree

Hide file tree

Showing 37 changed files with 120 additions and 204 deletions.
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 soakdb3
 
 # ---------------------------------------------------------------------
@@ -69,4 +69,4 @@ publish_docs:
 	cp -r build/html/* $(DOCS_PUBLISH_ROOT)
 
 
-# dae_devops_fingerprint 17444c38bc0036a20fb9a2d8c598b25b
+# dae_devops_fingerprint aa3527f5e00cc362a1553a0469ebd9c9
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 soakdb3
 
 Naming conventions
@@ -31,4 +31,4 @@ repository
     lowercase, hyphens
 
 
-.. # dae_devops_fingerprint 1e0adc6d888883afb554f2a9ce26c63a
+.. # dae_devops_fingerprint de902f373135c81a658a17ca32158297
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 soakdb3
 
 Developing
@@ -9,7 +9,7 @@ If you plan to make change to the code in this repository, you can use the steps
 
 Clone the repository::
 
-    $ git clone None/soakdb3.git
+    $ git clone https://github.com/DiamondLightSource/soakdb3.git
 
 It is recommended that you install into a virtual environment so this
 installation will not interfere with any existing Python software.
@@ -22,7 +22,6 @@ Make sure to have at least python version 3.1 then::
 Install the package in edit mode which will also install all its dependencies::
 
     $ cd soakdb3
-    $ 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 f01a1063bf5a9d381914e10c67393683
+.. # dae_devops_fingerprint ee39ac128183f0afe7cce3adcab8dd2a
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 soakdb3
 
 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 f77696d690fbd428333796c0bf2f67df
+.. # dae_devops_fingerprint 643e7f13e98318c4428bcec7cbb50a96
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 soakdb3
 
 About the documentation
@@ -21,4 +21,4 @@ improve most documentation - often immensely.
 
 `More information on this topic. <https://documentation.divio.com>`_
 
-.. # dae_devops_fingerprint 70cac733177dd5256bdaf910bc955cb7
+.. # dae_devops_fingerprint f7cd26a8269dc852910966084289b296
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 soakdb3
 
 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 soakdb3
 
 If you require a feature that is not currently released you can also install
 from git::
 
-    $ python3 -m pip install git+None/soakdb3.git
+    $ python3 -m pip install git+https://github.com/DiamondLightSource/soakdb3.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::
 
     $ soakdb3 --version
     $ soakdb3 --version-json
 
-.. # dae_devops_fingerprint d1f5270520ca9bb0a9330cba69440cef
+.. # dae_devops_fingerprint c122d062e225aa06bbb8e80da0553fd7
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 soakdb3
 
 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 ad42b32e9ade79a4dd31dda7541e07f0
+.. # dae_devops_fingerprint 588faee19542e87356f922601b113be3
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 soakdb3
 
 me=${BASH_SOURCE}
@@ -13,4 +13,4 @@ function __install {
 }
 
 
-# dae_devops_fingerprint af7f370578b9e81ef22fb808092418e9
+# dae_devops_fingerprint b5d67b78d8b53f60536200e8bfa6d4d6
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 soakdb3
 
 # This file is for use as a devcontainer and a runtime container
@@ -40,4 +40,4 @@ ENV PATH=/venv/bin:$PATH
 ENTRYPOINT ["soakdb3"]
 CMD ["--version"]
 
-# dae_devops_fingerprint 9ff8e9331ec715bc6a58b17884119f6e
+# dae_devops_fingerprint b47bdd9a358105e4dd26f540f42bbf7b
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 soakdb3
 
 // For format details, see https://containers.dev/implementors/json_reference/
@@ -57,4 +57,4 @@
     "postCreateCommand": "pip install -e .[dev]"
 }
 
-// dae_devops_fingerprint b7efe3515fabdbef051883e85a7dbc63
+// dae_devops_fingerprint 9524218bef5e86a01794006032ad7fcb
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 soakdb3
 
 Contributing to the project
@@ -38,4 +38,4 @@ should follow.
 
 .. _Developer Guide: https://diamondlightsource.github.io/soakdb3/main/developer/how-to/contribute.html
 
-.. # dae_devops_fingerprint 0b06b2cb53ea0279a6a2a8c8515122a1
+.. # dae_devops_fingerprint 9f9b8d29e13fc36a91cb18e92de3c255
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 soakdb3
 
 name: Install requirements
@@ -61,4 +61,4 @@ runs:
       shell: bash
 
 
-# dae_devops_fingerprint 3711ce9b640be2b9a9910ce11917caab
+# dae_devops_fingerprint 4bec23778f08376d659e5f9a364d8090
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 soakdb3
 
 # To get started with Dependabot version updates, you'll need to specify which
@@ -19,4 +19,4 @@ updates:
     schedule:
       interval: "weekly"
 
-# dae_devops_fingerprint 1b0b6977928285597c9445dd3bdfdc4f
+# dae_devops_fingerprint 0f56118bd55142e0710b36f4ac80c196
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 soakdb3 -->
 
 <!DOCTYPE html>
@@ -14,4 +14,4 @@
 
 </html>
 
-<!-- dae_devops_fingerprint a9b7e91437b814a6673514c65cb04fd1 -->
+<!-- dae_devops_fingerprint 928af9be6608752e095084f282661a42 -->
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 soakdb3
 
 import json
@@ -102,4 +102,4 @@ def main(args=None):
 if __name__ == "__main__":
     main()
 
-# dae_devops_fingerprint 3a0cb26bb487b84867ea34a995083006
+# dae_devops_fingerprint ab3ccbd5659d924b435fbf16b8432c57
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 soakdb3
 
 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 9d63584e1f4dbf1aade23a343c04004c
+# dae_devops_fingerprint adf2b49cc576a9c060e1d3257841b202
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 soakdb3
 
 name: Docs CI
@@ -56,4 +56,4 @@ jobs:
           publish_dir: .github/pages
           keep_files: true
 
-# dae_devops_fingerprint d09a79a9137e0fcb2c0c252f79e1b14a
+# dae_devops_fingerprint b7a223c7e424fa87fa8a411a885477e5
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 soakdb3
 
 name: Docs Cleanup CI
@@ -46,4 +46,4 @@ jobs:
           git commit -am "Removing redundant docs version $DOCS_VERSION"
           git push
 
-# dae_devops_fingerprint 53695740e43f166fa79c006dec2ce042
+# dae_devops_fingerprint ea9d13b83d6931e7a1f8beb23393a10d
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 soakdb3
 
 name: Link Check
@@ -27,4 +27,4 @@ jobs:
       - name: Check links
         run: tox -e docs build -- -b linkcheck
 
-# dae_devops_fingerprint 3f831adefea459ca44abcabff90bae1a
+# dae_devops_fingerprint 577e29e04eaace429f3b265715dd1db0
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 soakdb3
 
 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 4565f44d5a1e853692f58b6ae3a96c61
+# dae_devops_fingerprint 7738035675008c0815875d47c0aab949
diff --git a/configurations/development.yaml b/configurations/development.yaml
@@ -33,7 +33,7 @@ dataface_specification:
                       pattern: "^[Yy][:]"
                       replace: "/dls/labxchem/"
                 database:
-                    type: "soakdb3_lib.databases.aiosqlite"
+                    type: "dls_normsql.aiosqlite"
                     filename: "set by code"
                     backup_directory: "set by code"
                     log_level: "WARNING"
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 soakdb3 */ 
 
 /* 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 7587ab332856ef902636e87b51f8b664 */ 
+/* dae_devops_fingerprint 18b364be4830ff06599c595e92feab70 */