(#819) Add some unit tests

.github/workflows/pin_versions.py

@@ -7,7 +7,7 @@
 from functools import partial
 from sys import stderr, stdout
 
-SETUP_CFG_PATTERN = re.compile("(.*?)(@(.*))?\n")
+SETUP_CFG_PATTERN = re.compile("(.*?)\\s*(@(.*))?\n")
 PIP = "pip"
 
 
@@ -20,9 +20,7 @@ def normalize(package_name: str):
 
 
 def fetch_pin_versions() -> dict[str, str]:
-    process = subprocess.run(
-        [PIP, "freeze"], capture_output=True, encoding=locale.getpreferredencoding()
-    )
+    process = run_pip_freeze()
     if process.returncode == 0:
         output = process.stdout
         lines = output.split("\n")
@@ -40,21 +38,29 @@ def fetch_pin_versions() -> dict[str, str]:
         exit(1)
 
 
+def run_pip_freeze():
+    process = subprocess.run(
+        [PIP, "freeze"], capture_output=True, encoding=locale.getpreferredencoding()
+    )
+    return process
+
+
 def process_setup_cfg(input_fname, output_fname, dependency_processor):
     with open(input_fname) as input_file:
         with open(output_fname, "w") as output_file:
-            while line := input_file.readline():
-                output_file.write(line)
-                if line.startswith("install_requires"):
-                    break
-
-            while (line := input_file.readline()) and not line.isspace():
-                dependency_processor(line, output_file)
+            process_files(input_file, output_file, dependency_processor)
 
-            output_file.write(line)
 
-            while line := input_file.readline():
-                output_file.write(line)
+def process_files(input_file, output_file, dependency_processor):
+    while line := input_file.readline():
+        output_file.write(line)
+        if line.startswith("install_requires"):
+            break
+    while (line := input_file.readline()) and not line.isspace():
+        dependency_processor(line, output_file)
+    output_file.write(line)
+    while line := input_file.readline():
+        output_file.write(line)
 
 
 def strip_comment(line: str):

.github/workflows/test_data/pip_freeze.txt

@@ -0,0 +1,248 @@
+accessible-pygments==0.0.4
+aioca==1.7
+aiohttp==3.9.1
+aiosignal==1.3.1
+alabaster==0.7.16
+aniso8601==9.0.1
+anyio==4.2.0
+appdirs==1.4.4
+asciitree==0.3.3
+asttokens==2.4.1
+async-timeout==4.0.3
+attrs==23.2.0
+Babel==2.14.0
+beautifulsoup4==4.12.3
+bidict==0.22.1
+black==24.1.0
+blinker==1.7.0
+blueapi==0.3.15
+bluesky==1.12.0
+bluesky-kafka==0.10.0
+bluesky-live==0.0.8
+boltons==23.1.1
+build==1.0.3
+cachetools==5.3.2
+caproto==1.1.1
+certifi==2023.11.17
+cfgv==3.4.0
+chardet==5.2.0
+charset-normalizer==3.3.2
+click==8.1.3
+cloudpickle==3.0.0
+colorama==0.4.6
+comm==0.2.1
+confluent-kafka==2.3.0
+contourpy==1.2.0
+coverage==7.4.0
+cycler==0.12.1
+dask==2024.1.0
+databroker==1.2.5
+dataclasses-json==0.6.3
+decorator==5.1.1
+Deprecated==1.2.14
+diff_cover==8.0.3
+distlib==0.3.8
+dls-bluesky-core==0.0.3
+dls-dodal==1.13.1
+dnspython==2.5.0
+docopt==0.6.2
+doct==1.1.0
+docutils==0.20.1
+email-validator==2.1.0.post1
+entrypoints==0.4
+epicscorelibs==7.0.7.99.0.2
+event-model==1.19.9
+exceptiongroup==1.2.0
+executing==2.0.1
+fastapi==0.98.0
+fasteners==0.19
+filelock==3.13.1
+Flask==3.0.1
+Flask-RESTful==0.3.10
+fonttools==4.47.2
+freephil==0.2.1
+frozenlist==1.4.1
+fsspec==2023.12.2
+gitdb==4.0.11
+GitPython==3.1.41
+googleapis-common-protos==1.59.1
+graypy==2.1.0
+greenlet==3.0.3
+grpcio==1.60.0
+h11==0.14.0
+h5py==3.10.0
+hdf5plugin==4.3.0
+HeapDict==1.0.1
+historydict==1.2.6
+httpcore==1.0.2
+httptools==0.6.1
+httpx==0.26.0
+humanize==4.9.0
+-e git+ssh://[email protected]/DiamondLightSource/hyperion.git@5b88ce8b69483397adb66f78da5970a5186fcae2#egg=hyperion
+identify==2.5.33
+idna==3.6
+imageio==2.33.1
+imagesize==1.4.1
+importlib-metadata==6.11.0
+importlib-resources==6.1.1
+iniconfig==2.0.0
+intake==0.6.4
+ipython==8.20.0
+ipywidgets==8.1.1
+ispyb==10.0.0
+itsdangerous==2.1.2
+jedi==0.19.1
+Jinja2==3.1.3
+jsonschema==4.21.1
+jsonschema-specifications==2023.12.1
+jupyterlab-widgets==3.0.9
+kiwisolver==1.4.5
+livereload==2.6.3
+locket==1.0.0
+MarkupSafe==2.1.4
+marshmallow==3.20.2
+matplotlib==3.8.2
+matplotlib-inline==0.1.6
+mockito==1.4.0
+mongoquery==1.4.2
+msgpack==1.0.7
+msgpack-numpy==0.4.8
+multidict==6.0.4
+mypy==1.8.0
+mypy-extensions==1.0.0
+mysql-connector-python==8.3.0
+networkx==3.2.1
+nexgen==0.8.0
+nodeenv==1.8.0
+nose2==0.14.0
+nslsii==0.9.1
+numcodecs==0.12.1
+numpy==1.26.3
+opencv-python-headless==4.9.0.80
+opentelemetry-api==1.22.0
+opentelemetry-distro==0.43b0
+opentelemetry-exporter-jaeger==1.21.0
+opentelemetry-exporter-jaeger-proto-grpc==1.21.0
+opentelemetry-exporter-jaeger-thrift==1.21.0
+opentelemetry-instrumentation==0.43b0
+opentelemetry-sdk==1.22.0
+opentelemetry-semantic-conventions==0.43b0
+ophyd==1.9.0
+ophyd-async @ git+https://github.com/bluesky/ophyd-async@ec5729640041ee5b77b4614158793af3a34cf9d8
+orjson==3.9.12
+p4p==4.1.12
+packaging==23.2
+pandas==2.2.0
+parso==0.8.3
+partd==1.4.1
+pathlib2==2.3.7.post1
+pathspec==0.12.1
+pexpect==4.9.0
+pika==1.3.2
+pillow==10.2.0
+PIMS==0.6.1
+Pint==0.23
+pipdeptree==2.13.2
+platformdirs==4.1.0
+pluggy==1.4.0
+ply==3.11
+pre-commit==3.6.0
+prettytable==3.9.0
+prompt-toolkit==3.0.43
+protobuf==4.25.2
+psutil==5.9.8
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pvxslibs==1.3.1
+py==1.11.0
+pydantic==1.10.14
+pydata-sphinx-theme==0.15.2
+pyepics==3.5.2
+Pygments==2.17.2
+pymongo==4.6.1
+pyOlog==4.5.0
+pyparsing==3.1.1
+pyproject-api==1.6.1
+pyproject_hooks==1.0.0
+pyright==1.1.348
+pyright_diff_quality_plugin @ git+https://github.com/DiamondLightSource/pyright_diff_quality_plugin.git@77fc0819e708eb16ffdcaea06552a2804294b53e
+pytest==7.4.4
+pytest-asyncio==0.23.3
+pytest-cov==4.1.0
+pytest-random-order==1.1.1
+python-dateutil==2.8.2
+python-dotenv==1.0.1
+python-multipart==0.0.6
+pytz==2023.3.post1
+PyYAML==6.0.1
+pyzmq==25.1.2
+redis==5.0.1
+referencing==0.32.1
+requests==2.31.0
+rpds-py==0.17.1
+ruff==0.1.14
+scanspec==0.6.5
+scipy==1.12.0
+semver==3.0.2
+setuptools-dso==2.10
+six==1.16.0
+slicerator==1.1.0
+smmap==5.0.1
+sniffio==1.3.0
+snowballstemmer==2.2.0
+soupsieve==2.5
+Sphinx==7.2.6
+sphinx-autobuild==2021.3.14
+sphinx-copybutton==0.5.2
+sphinx_design==0.5.0
+sphinxcontrib-applehelp==1.0.8
+sphinxcontrib-devhelp==1.0.6
+sphinxcontrib-htmlhelp==2.0.5
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.7
+sphinxcontrib-serializinghtml==1.1.10
+SQLAlchemy==1.4.51
+stack-data==0.6.3
+starlette==0.27.0
+stomp.py==8.1.0
+suitcase-mongo==0.4.0
+suitcase-msgpack==0.3.0
+suitcase-utils==0.5.4
+super-state-machine==2.0.2
+tabulate==0.9.0
+thrift==0.16.0
+tifffile==2023.12.9
+tomli==2.0.1
+toolz==0.12.1
+tornado==6.4
+tox==3.28.0
+tox-direct==0.4
+tqdm==4.66.1
+traitlets==5.14.1
+types-mock==5.1.0.20240106
+types-PyYAML==6.0.12.12
+types-requests==2.31.0.20240125
+typing-inspect==0.9.0
+typing_extensions==4.5.0
+tzdata==2023.4
+tzlocal==5.2
+ujson==5.9.0
+urllib3==2.1.0
+uvicorn==0.27.0
+uvloop==0.19.0
+virtualenv==20.25.0
+watchfiles==0.21.0
+wcwidth==0.2.13
+websocket-client==1.7.0
+websockets==12.0
+Werkzeug==3.0.1
+widgetsnbextension==4.0.9
+workflows==2.26
+wrapt==1.16.0
+xarray==2024.1.1
+yarl==1.9.4
+zarr==2.16.1
+zict==2.2.0
+zipp==3.17.0
+zmq==0.0.0
+zocalo==0.30.2

.github/workflows/test_data/setup.cfg

@@ -0,0 +1,80 @@
+[metadata]
+name = hyperion
+description = Unattended MX data collection using BlueSky / Ophyd
+url = https://github.com/DiamondLightSource/hyperion
+license = BSD 3-Clause License
+long_description = file: README.rst
+long_description_content_type = text/x-rst
+classifiers =
+    Development Status :: 3 - Alpha
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+
+[options]
+python_requires = >=3.9
+packages = find:
+package_dir =
+    =src
+install_requires =
+    bluesky
+    pyepics
+    blueapi
+    flask-restful
+    ispyb
+    scanspec
+    numpy
+    nexgen @ git+https://github.com/dials/nexgen.git@db4858f6d91a3d07c6c0f815ef752849c0bf79d4
+    opentelemetry-distro
+    opentelemetry-exporter-jaeger
+    ophyd
+    semver
+    # For databroker
+    humanize
+    pandas
+    xarray
+    doct
+    databroker
+    dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@0aabdb389f65a30e629cec60a36c3b5298b7647f
+    pydantic<2.0 # See https://github.com/DiamondLightSource/hyperion/issues/774
+    scipy
+    pyzmq<25 # See https://github.com/DiamondLightSource/hyperion/issues/1103
+
+[options.entry_points]
+console_scripts =
+    hyperion = hyperion.__main__:main
+    hyperion-callbacks = hyperion.external_interaction.callbacks.__main__:main
+
+[options.extras_require]
+dev =
+    GitPython
+    black
+    pytest-cov
+    pytest-random-order
+    pytest-asyncio
+    ipython
+    mockito
+    pre-commit
+    mypy
+    matplotlib
+    tox
+    build
+    ruff
+    diff-cover
+    pyright
+    pyright_diff_quality_plugin @ git+https://github.com/DiamondLightSource/pyright_diff_quality_plugin.git
+
+
+[options.packages.find]
+where = src
+
+[options.package_data]
+hyperion = *.txt
+
+[mypy]
+# Ignore missing stubs for modules we use
+ignore_missing_imports = True
+#needed for opentelemetry
+namespace_packages = true
+[mypy-opentelemetry.sdk.*]
+implicit_reexport = True