gets code from old repo

.dae-devops/Makefile

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+# ********** Please don't edit this file!
+# ********** It has been generated automatically by dae_devops version 0.4.1.dev0+g5d50877.d20230202.
+# ********** For repository_name soakdb3
+
+# ---------------------------------------------------------------------
+# These make targets are designed to be called from the command line and from .gitlab-ci.yml.
+# ---------------------------------------------------------------------
+
+# I put the package_pip artifacts int this place for now until I can use the corporate internal pipserver.
+# Maybe /dls_sw/work/python3/RHEL7-x86_64/distributions would be a better place?
+PIP_FIND_LINKS = /dls_sw/apps/bxflow/artifacts
+
+# I got these from https://gitlab.diamond.ac.uk/controls/reports/ci_templates/-/blob/master/defaults.yml.
+# Directory where docs are published.
+DOCS_PUBLISH_ROOT = /dls/cs-www/reports/gitlab-ci/soakdb3
+
+# ---------------------------------------------------------------------
+# These are called from the default before_script in the gitlab CI.
+# That meants it is normally called before any other job.
+# It installs things not covered by pyproject.toml.
+
+prepare_git_dependencies:
+	chmod a+x .dae-devops/prepare_git_dependencies.sh
+	.dae-devops/prepare_git_dependencies.sh
+
+# ---------------------------------------------------------------------
+# The validate stage makes sure code is ready to package and release.
+
+validate: \
+	validate_pre_commit \
+	validate_mypy \
+	validate_pytest
+	echo "validation complete"
+
+validate_pre_commit: 
+	tox -q -e pre-commit
+
+validate_mypy: 
+	tox -q -e mypy
+
+validate_pytest: 
+	tox -q -e pytest
+
+validate_docs: 
+	tox -q -e docs
+
+# ---------------------------------------------------------------------
+# The pip state packages and publishes for pip.
+
+package: \
+	package_pip
+
+package_pip:
+	pip install pipx twine
+	pipx run build
+
+# ---------------------------------------------------------------------
+# The publish stage publishes things which have already been built or packaged.
+
+publish: \
+	publish_pip \
+	publish_docs
+
+publish_pip:
+	cp -v -p dist/*.whl $(PIP_FIND_LINKS)
+
+publish_docs:
+	mkdir -p $(DOCS_PUBLISH_ROOT)
+	cp -r build/html/* $(DOCS_PUBLISH_ROOT)
+
+
+# dae_devops_fingerprint 34b29a58c90b39e1e1ed76b65f93ff7e

.dae-devops/docs/conventions.rst

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+.. # ********** Please don't edit this file!
+.. # ********** It has been generated automatically by dae_devops version 0.4.1.dev0+g5d50877.d20230202.
+.. # ********** For repository_name soakdb3
+
+Naming conventions
+=======================================================================
+
+Here are the naming conventions used within the source code.
+
+variables
+    lowercase, underscores
+
+constants
+    uppercase, underscores
+
+classes
+    camel case
+
+class methods
+    lowercase, underscores
+
+imports
+    require fully qualified package name (import <package> does nothing)
+
+    exception: top-level packages __init__.py will have __version__ defined in them
+
+python packages
+    lowercase, underscores
+
+repository
+    lowercase, hyphens
+
+
+.. # dae_devops_fingerprint 0445169078658533345b65f3aa83e741

.dae-devops/docs/developing.rst

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+.. # ********** Please don't edit this file!
+.. # ********** It has been generated automatically by dae_devops version 0.4.1.dev0+g5d50877.d20230202.
+.. # ********** For repository_name soakdb3
+
+Developing
+=======================================================================
+
+If you plan to make change to the code in this repository, you can use the steps below.
+
+Clone the repository::
+
+    $ git clone https://gitlab.diamond.ac.uk/xchem/soakdb3.git
+
+It is recommended that you install into a virtual environment so this
+installation will not interfere with any existing Python software.
+Make sure to have at least python version 3.8 then::
+
+    $ python3 -m venv /scratch/$USER/myvenv
+    $ source /scratch/$USER/myvenv/bin/activate
+    $ pip install --upgrade pip
+
+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.
+
+|
+
+If you plan to modify the docs, you will need to::
+
+    $ pip install -e .[docs]
+
+    
+
+
+.. # dae_devops_fingerprint 15edebaf385cab6a977170f7f93863d2

.dae-devops/docs/devops.rst

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+.. # ********** Please don't edit this file!
+.. # ********** It has been generated automatically by dae_devops version 0.4.1.dev0+g5d50877.d20230202.
+.. # ********** For repository_name soakdb3
+
+Devops
+=======================================================================
+
+There exists a 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
+- .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.
+
+Running these ops before pushing to the git server can make the turnaround quicker to fix things.
+
+Follow the steps in the Developing section.  Then you can run the following commands.
+
+Validation of the code::
+
+    $ make -f .dae-devops/Makefile validate_pre_commit
+    $ make -f .dae-devops/Makefile validate_mypy
+    $ make -f .dae-devops/Makefile validate_pytest
+    $ make -f .dae-devops/Makefile validate_docs
+
+Packaging:: 
+
+    $ make -f .dae-devops/Makefile package_pip
+
+Publishing::
+
+    $ make -f .dae-devops/Makefile publish_pip
+    $ make -f .dae-devops/Makefile publish_docs
+    
+
+
+.. # dae_devops_fingerprint 6c1e6805576b8da6554ec272ebab098b

.dae-devops/docs/docs_structure.rst

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+.. # ********** Please don't edit this file!
+.. # ********** It has been generated automatically by dae_devops version 0.4.1.dev0+g5d50877.d20230202.
+.. # ********** For repository_name soakdb3
+
+About the documentation
+-----------------------
+
+  :material-regular:`format_quote;2em`
+
+  The Grand Unified Theory of Documentation
+
+  -- David Laing
+
+There is a secret that needs to be understood in order to write good software
+documentation: there isn't one thing called *documentation*, there are four.
+
+They are: *tutorials*, *how-to guides*, *technical reference* and *explanation*.
+They represent four different purposes or functions, and require four different
+approaches to their creation. Understanding the implications of this will help
+improve most documentation - often immensely.
+
+`More information on this topic. <https://documentation.divio.com>`_
+
+.. # dae_devops_fingerprint 67609046712ef5d80210b74aafcf9f8f

.dae-devops/docs/installing.rst

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+.. # ********** Please don't edit this file!
+.. # ********** It has been generated automatically by dae_devops version 0.4.1.dev0+g5d50877.d20230202.
+.. # ********** For repository_name soakdb3
+
+Installing
+=======================================================================
+
+
+You will need python 3.8 or later. 
+
+On a Diamond Light Source internal computer, you can achieve Python 3.8 by::
+
+    $ module load python/3.8
+
+You can check your version of python by typing into a terminal::
+
+    $ python3 --version
+
+It is recommended that you install into a virtual environment so this
+installation will not interfere with any existing Python software::
+
+    $ python3 -m venv /scratch/$USER/myvenv
+    $ source /scratch/$USER/myvenv/bin/activate
+    $ pip install --upgrade pip
+
+
+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+https://gitlab.diamond.ac.uk/xchem/soakdb3.git
+
+The library should now be installed and the commandline interface on your path.
+You can check the version that has been installed by typing::
+
+    $ soakdb3 --version
+    $ soakdb3 --version-json
+
+.. # dae_devops_fingerprint 9711de96b7dee1be37a5adc08f134f01

.dae-devops/docs/testing.rst

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+.. # ********** Please don't edit this file!
+.. # ********** It has been generated automatically by dae_devops version 0.4.1.dev0+g5d50877.d20230202.
+.. # ********** For repository_name soakdb3
+
+Testing
+=======================================================================
+
+The package uses pytest for unit testing.
+
+If you want to run the tests, first get a copy of the code per the instructions in the Developing section.
+
+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
+
+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:
+
+    $ pytest -sv -ra --tb=line tests/the_test_you_want.py
+
+Each test will write files into its own directory::
+
+    /tmp/soakdb3/tests/....
+
+The tests clear their directory when they start, but not when they finish.
+This allows peeking in there to see what's been written by the test.
+
+
+
+
+.. # dae_devops_fingerprint ca6ebbe8dcda20b367a8cdec62584e82

.dae-devops/prepare_git_dependencies.sh

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+#!/usr/bin/env bash
+
+# ********** Please don't edit this file!
+# ********** It has been generated automatically by dae_devops version 0.4.1.dev0+g5d50877.d20230202.
+# ********** For repository_name soakdb3
+
+me=${BASH_SOURCE}
+echo "${me}: installing 0 dependencies for repository_name soakdb3"
+
+function __install {
+    echo ${me}: "$@"
+    "$@"
+}
+
+
+# dae_devops_fingerprint df8e2a901d15e29b023b2df0efd9f4b8

.dae-devops/project.yaml

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+# Primary information needed for devops.
+primary:
+    repository_name: soakdb3
+    package_name: soakdb3_lib
+    one_line_description: "Replacement for soakdb2, including a new database backend."
+    author:
+        name: David Erb
+        email: [email protected]
+    project_urls:
+        GitLab: https://gitlab.diamond.ac.uk/xchem
+    project_scripts:
+        soakdb3: "soakdb3_lib.__main__:main"
+        soakdb3.cli: "soakdb3_cli.main:main"
+    dependencies:
+        - type: pypi
+          list:
+              - dls_servbase
+              - dls_mainiac
+              - dls_utilpack

.devcontainer/Dockerfile

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+# ********** Please don't edit this file!
+# ********** It has been generated automatically by dae_devops version 0.4.1.dev0+g5d50877.d20230202.
+# ********** For repository_name soakdb3
+
+# This file is for use as a devcontainer and a runtime container
+#
+# The devcontainer should use the build target and run as root with podman
+# or docker with user namespaces.
+#
+FROM python:3.11 as build
+
+ARG PIP_OPTIONS
+
+# Add any system dependencies for the developer/build environment here e.g.
+# RUN apt-get update && apt-get upgrade -y && \
+#     apt-get install -y --no-install-recommends \
+#     desired-packages \
+#     && rm -rf /var/lib/apt/lists/*
+
+# set up a virtual environment and put it in PATH
+RUN python -m venv /venv
+ENV PATH=/venv/bin:$PATH
+
+# Copy any required context for the pip install over
+COPY . /context
+WORKDIR /context
+
+# install python package into /venv
+RUN pip install ${PIP_OPTIONS}
+
+FROM python:3.11-slim as runtime
+
+# Add apt-get system dependecies for runtime here if needed
+
+# copy the virtual environment from the build stage and put it in PATH
+COPY --from=build /venv/ /venv/
+ENV PATH=/venv/bin:$PATH
+
+# change this entrypoint if it is not the same as the repo
+ENTRYPOINT ["soakdb3"]
+CMD ["--version"]
+
+# dae_devops_fingerprint b0d69b5ce15a06bbb900d4671cb8311e