fixes lint, adds dependency on xchembku

DiamondLightSource · Apr 24, 2023 · e6b95e6 · e6b95e6
1 parent b7d31b0
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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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 # ---------------------------------------------------------------------
@@ -69,4 +69,4 @@ publish_docs:
  cp -r build/html/* $(DOCS_PUBLISH_ROOT)
 
 
-# dae_devops_fingerprint fa91d06926a32d8ff4980e6c5026842a
+# dae_devops_fingerprint e508c365997a16fba9003f0e2c7345fc
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 0.5.1.
+.. # ********** It has been generated automatically by dae_devops version 0.5.2.
 .. # ********** For repository_name echolocator
 
 Naming conventions
@@ -31,4 +31,4 @@ repository
  lowercase, hyphens
 
 
-.. # dae_devops_fingerprint 7830c296da87a975c0ebe83db00c21a9
+.. # dae_devops_fingerprint f1b13dc77352fa3d7806ebc008156e6f
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 0.5.1.
+.. # ********** It has been generated automatically by dae_devops version 0.5.2.
 .. # ********** For repository_name echolocator
 
 Developing
@@ -36,4 +36,4 @@ If you plan to modify the docs, you will need to::
  
 
 
-.. # dae_devops_fingerprint c3acd7bd04d4c567174c7ba12f90efb0
+.. # dae_devops_fingerprint 8802592ab610cd9de3e657aeacb9c8c1
diff --git a/.dae-devops/docs/devops.rst b/.dae-devops/docs/devops.rst
@@ -1,5 +1,5 @@
 .. # ********** Please don't edit this file!
-.. # ********** It has been generated automatically by dae_devops version 0.5.1.
+.. # ********** It has been generated automatically by dae_devops version 0.5.2.
 .. # ********** For repository_name echolocator
 
 Devops
@@ -43,4 +43,4 @@ Publishing::
  
 
 
-.. # dae_devops_fingerprint 28cb19a7e59bd4e67a85edec626a491e
+.. # dae_devops_fingerprint 67a3e9939abb47f483bfd1180117473f
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 0.5.1.
+.. # ********** It has been generated automatically by dae_devops version 0.5.2.
 .. # ********** For repository_name echolocator
 
 About the documentation
@@ -21,4 +21,4 @@ improve most documentation - often immensely.
 
 `More information on this topic. <https://documentation.divio.com>`_
 
-.. # dae_devops_fingerprint 8ded9698d9d71eda17e2c49cd737a2e2
+.. # dae_devops_fingerprint 58611b915d52f7b59bbed09020e30356
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 0.5.1.
+.. # ********** It has been generated automatically by dae_devops version 0.5.2.
 .. # ********** For repository_name echolocator
 
 Installing
@@ -40,4 +40,4 @@ You can check the version that has been installed by typing::
  $ echolocator --version
  $ echolocator --version-json
 
-.. # dae_devops_fingerprint 3b5d52d009337767488822fafe22e1e7
+.. # dae_devops_fingerprint c6472f1053e4ee44f3e70cc67c9fbddd
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 0.5.1.
+.. # ********** It has been generated automatically by dae_devops version 0.5.2.
 .. # ********** For repository_name echolocator
 
 Testing
@@ -35,4 +35,4 @@ This allows peeking in there to see what's been written by the test.
 
 
 
-.. # dae_devops_fingerprint a5fefb92ded789eda5a2e4423a4e58e6
+.. # dae_devops_fingerprint 7daed3c9e65a523a0fbf7d347dfa6ebe
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 me=${BASH_SOURCE}
@@ -13,4 +13,4 @@ function __install {
 }
 
 
-# dae_devops_fingerprint 6a2693fd8a702bdea55e95346b54e455
+# dae_devops_fingerprint 5a8604ffa3b9c1409a994d31bcb9e1d4
diff --git a/.dae-devops/project.yaml b/.dae-devops/project.yaml
@@ -14,6 +14,7 @@ primary:
  dependencies:
  - type: pypi
  list:
+ - xchembku
  - dls_servbase
  - dls_mainiac
  - dls_utilpack

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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 # This file is for use as a devcontainer and a runtime container
@@ -40,4 +40,4 @@ ENV PATH=/venv/bin:$PATH
 ENTRYPOINT ["echolocator"]
 CMD ["--version"]
 
-# dae_devops_fingerprint b2386a8edacc7cf00dbcde0bcfe434a4
+# dae_devops_fingerprint 9302e007f97570a60d29bb25449a92bb
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 0.5.1.
+// ********** It has been generated automatically by dae_devops version 0.5.2.
 // ********** For repository_name echolocator
 
 // For format details, see https://containers.dev/implementors/json_reference/
@@ -57,4 +57,4 @@
  "postCreateCommand": "pip install -e .[dev]"
 }
 
-// dae_devops_fingerprint 2507140a2722f4fa02e13592d5038e0e
+// dae_devops_fingerprint 529b4c792a9fdad91835e1a4b32e0138
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 0.5.1.
+.. # ********** It has been generated automatically by dae_devops version 0.5.2.
 .. # ********** For repository_name echolocator
 
 Contributing to the project
@@ -38,4 +38,4 @@ should follow.
 
 .. _Developer Guide: https://diamondlightsource.github.io/echolocator/main/developer/how-to/contribute.html
 
-.. # dae_devops_fingerprint aed6364e5eff2f9face6b54b84a417f7
+.. # dae_devops_fingerprint d17faed109d26c120150d4cad9b012bd
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 name: Install requirements
@@ -61,4 +61,4 @@ runs:
  shell: bash
 
 
-# dae_devops_fingerprint 6290682d4770755c7566572965cef561
+# dae_devops_fingerprint 1fae1b6e8b391bfca7aad4310624e6c4
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 # To get started with Dependabot version updates, you'll need to specify which
@@ -19,4 +19,4 @@ updates:
  schedule:
  interval: "weekly"
 
-# dae_devops_fingerprint 27e905899401fd7a982d82c6788a2760
+# dae_devops_fingerprint 6309098eb3479d1a200e487b05664e86
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 0.5.1. -->
+<!-- ********** It has been generated automatically by dae_devops version 0.5.2. -->
 <!-- ********** For repository_name echolocator -->
 
 <!DOCTYPE html>
@@ -14,4 +14,4 @@
 
 </html>
 
-<!-- dae_devops_fingerprint 3314813c65a9a431d1ca8363599c626a -->
+<!-- dae_devops_fingerprint ce6fecf5a9e91b53ee1d2d669fe82989 -->
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 import json
@@ -102,4 +102,4 @@ def main(args=None):
 if __name__ == "__main__":
  main()
 
-# dae_devops_fingerprint 5eddb1e43a2e9f5696fb135b3351e1e0
+# dae_devops_fingerprint e707603d7cbd385a51462ce91214bed6
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 name: Code CI
@@ -212,4 +212,4 @@ jobs:
  with:
  password: ${{ secrets.PYPI_TOKEN }}
 
-# dae_devops_fingerprint 3cd3d1b7aa3767bc7752d04d0cff1b98
+# dae_devops_fingerprint febe27315441a7232f0895dff16de450
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 name: Docs CI
@@ -56,4 +56,4 @@ jobs:
  publish_dir: .github/pages
  keep_files: true
 
-# dae_devops_fingerprint 516501c026fa1f7af1e7a6d88d046406
+# dae_devops_fingerprint 248b6927066389c57cb985f999015228
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 name: Docs Cleanup CI
@@ -46,4 +46,4 @@ jobs:
  git commit -am "Removing redundant docs version $DOCS_VERSION"
  git push
 
-# dae_devops_fingerprint 923700bb09fb043a8cdcb2b78e384f09
+# dae_devops_fingerprint 13b4db6f5b6317157d8d36b632434d2d
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 name: Link Check
@@ -27,4 +27,4 @@ jobs:
  - name: Check links
  run: tox -e docs build -- -b linkcheck
 
-# dae_devops_fingerprint d1ce8eee255cbe72206419b8b28d43df
+# dae_devops_fingerprint 75b08200910c30409c75d4d16a6e4d9a
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 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 32c6a111d128370b1daac92e1f2aecbe
+# dae_devops_fingerprint 14d3e80d54ae3da9497b0ce79d6fa611
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 0.5.1. */ 
+/* ********** It has been generated automatically by dae_devops version 0.5.2. */ 
 /* ********** For repository_name echolocator */ 
 
 /* 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 35feb33b9a913af2c9c4c41aaeba16f5 */ 
+/* dae_devops_fingerprint cfed7308662c39c7cab945fa6b416c7e */ 
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 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 from pathlib import Path
@@ -197,4 +197,4 @@ def setup(app):
  app.connect("source-read", ultimateReplace)
 
 
-# dae_devops_fingerprint 20b12f1e3c3fe99e0b1b302ef56d79fc
+# dae_devops_fingerprint 522695c29baed7676543987e99fc61dd
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,5 +1,5 @@
 # ********** Please don't edit this file!
-# ********** It has been generated automatically by dae_devops version 0.5.1.
+# ********** It has been generated automatically by dae_devops version 0.5.2.
 # ********** For repository_name echolocator
 
 [build-system]
@@ -16,7 +16,7 @@ classifiers = [
  "Programming Language :: Python :: 3.11",
 ]
 description = "XChem GUI for manually targeting drop points for the Echo dispenser."
-dependencies = ["dls_servbase", "dls_mainiac", "dls_utilpack"]
+dependencies = ["xchembku", "dls_servbase", "dls_mainiac", "dls_utilpack", "beautifulsoup4"]
 dynamic = ["version"]
 license.file = "LICENSE"
 readme = "README.rst"
@@ -34,6 +34,7 @@ dev = [
  "pydocstyle[toml]",
  "tox-direct",
  "types-mock",
+ "types-PyYAML",
 ]
 docs = [
  "pydata-sphinx-theme>=0.12",
@@ -84,7 +85,7 @@ exclude = [".tox", "venv"]
 
 [tool.pytest.ini_options]
 # Run pytest with all our checkers, and don't spam us with massive tracebacks on error
-addopts = " --tb=native -vv --doctest-modules --doctest-glob=\"*.rst\"\n "
+addopts = " --tb=native -vv --doctest-modules --doctest-glob=\"*.rst\"\n --cov=echolocator_lib --cov-report term --cov-report xml:cov.xml\n "
 # https://iscinumpy.gitlab.io/post/bound-version-constraints/#watch-for-warnings
 filterwarnings = "error"
 # Doctest python code in docs, python code in src docstrings, test functions in tests
@@ -102,4 +103,4 @@ source = ["src", "**/site-packages/"]
 [tool.tox]
 legacy_tox_ini = "[tox]\nskipsdist=True\n\n[testenv:{pre-commit,mypy,pytest,docs}]\n# Don't create a virtualenv for the command, requires tox-direct plugin\ndirect = True\npassenv = *\nallowlist_externals = \n pytest \n pre-commit\n mypy\n sphinx-build\n sphinx-autobuild\ncommands =\n pytest: pytest {posargs}\n mypy: mypy src tests {posargs}\n pre-commit: pre-commit run --all-files {posargs}\n docs: sphinx-{posargs:build -EW --keep-going} -T docs build/html\n"
 
-# dae_devops_fingerprint 69fbb150408506fd907682cb5b2f8e24
+# dae_devops_fingerprint 8d6ec2f437b47d4156e639a67957fdc1
diff --git a/src/echolocator_lib/composers/html.py b/src/echolocator_lib/composers/html.py
@@ -1,20 +1,18 @@
 import html
 import logging
-import re
 from pathlib import Path
-from typing import Optional, Sequence, Union
+from typing import List, Optional, Sequence, Union
 
 import numpy as np
 
 # Base class for generic things.
 from dls_utilpack.thing import Thing
+
+# Models which we can compose.
 from xchembku_api.models.crystal_well_needing_droplocation_model import (
  CrystalWellNeedingDroplocationModel,
 )
 
-# Database record field names coming from database fields.
-from echolocator_api.databases.constants import ImageFieldnames
-
 # Class to do the work using prettytable.
 from echolocator_lib.composers.prettyhelper import PrettyHelper
 
@@ -41,7 +39,7 @@ def __init__(self, specification=None):
  self.__indent = 0
 
  # ----------------------------------------------------------------------------------------
- def compose_image_list(self, models: [CrystalWellNeedingDroplocationModel]):
+ def compose_image_list(self, models: List[CrystalWellNeedingDroplocationModel]):
  """
  Compose the image list as an html table.
  """

diff --git a/src/echolocator_lib/guis/aiohttp.py b/src/echolocator_lib/guis/aiohttp.py
@@ -179,15 +179,15 @@ async def direct_shutdown(self):
  async def dispatch(self, request_dict, opaque):
  """"""
 
+ command = require("request json", request_dict, Keywords.COMMAND)
+
  # Having no xchembku client reference means we must be shutting down.
  if self.__xchembku is None:
  raise RuntimeError(
  "refusing to execute command %s because server is shutting down"
  % (command)
  )
 
- command = require("request json", request_dict, Keywords.COMMAND)
-
  if command == Commands.LOAD_TABS:
  return await self._load_tabs(opaque, request_dict)