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Ben Swift benswift Canberra https://benswift.me Ben is a scholar, hacker and livecoding artist. Currently a Senior Lecturer in CS at the Australian National University in Canberra, Australia.

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A modern LaTeX template for PhD/Masters/honours theses.

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My dotfiles. Emacs-centric, should work across OSX/Linux/Windows

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Jekyll blog source for my personal homepage

arrian/research-project 1

Australian National University thesis for Software Engineering (Honours) in 2014.

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Website for the 2020 Australasian Computer Music Conference

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Grade distribution analysis: are CS grades bimodal?

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website for the c/c/c studio group

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Mismatching MD5 for patched LLVM tarball

Cool, thanks. I am open to PRs on the CMake build process (I hacked it together, but I'm sure a real CMake expert could improve it) and now that we've got cross-platform automated tests (with GH actions) it should be comparatively easy to make such changes with confidence.

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Bump elliptic from 6.5.2 to 6.5.3 Bumps [elliptic](https://github.com/indutny/elliptic) from 6.5.2 to 6.5.3. - [Release notes](https://github.com/indutny/elliptic/releases) - [Commits](https://github.com/indutny/elliptic/compare/v6.5.2...v6.5.3) Signed-off-by: dependabot[bot] <support@github.com>

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Bump elliptic from 6.5.2 to 6.5.3 dependencies

Bumps elliptic from 6.5.2 to 6.5.3. <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/indutny/elliptic/commit/8647803dc3d90506aa03021737f7b061ba959ae1"><code>8647803</code></a> 6.5.3</li> <li><a href="https://github.com/indutny/elliptic/commit/856fe4d99fe7b6200556e6400b3bf585b1721bec"><code>856fe4d</code></a> signature: prevent malleability and overflows</li> <li>See full diff in <a href="https://github.com/indutny/elliptic/compare/v6.5.2...v6.5.3">compare view</a></li> </ul> </details> <br />

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issue closedanu-act-health-covid19-support/patientpaths

cannot reproduce GH Actions test results on local machine

Hey @Zac-HD

This might just be me failing the WOMM certification program, but I'm having trouble with the tests.

The backstory: I noticed that the build has been broken since eef0333, so I try to reproduce locally.

First, with HEAD at 89d0fa7a, I create a new venv and follow the installation instructions from the README:

smithy:patientpaths ben$ python --version
Python 3.7.7
smithy:patientpaths ben$ python -m venv .venv
smithy:patientpaths ben$ source .venv/bin/activate
(.venv) smithy:patientpaths ben$ pip install .

... SNIP ...

Successfully built patientpaths
Installing collected packages: zipp, importlib-metadata, pluggy, six, filelock, appdirs, distlib, virtualenv, pyparsing, packaging, py, toml, tox, patientpaths
Successfully installed appdirs-1.4.4 distlib-0.3.1 filelock-3.0.12 importlib-metadata-1.7.0 packaging-20.4 patientpaths-0.1.0 pluggy-0.13.1 py-1.9.0 pyparsing-2.4.7 six-1.15.0 toml-0.10.1 tox-3.17.0 virtualenv-20.0.26 zipp-3.1.0
WARNING: You are using pip version 19.2.3, however version 20.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Then, I run the tox check command (copied from the definition in .gitlab/workflows/ci.yml

(.venv) smithy:patientpaths ben$ python -m tox --recreate -e check
check recreate: /Users/ben/Documents/research/covid19-taskforce/patientpaths/.tox/check
check installdeps: --no-deps, --requirement=deps/check.txt
check installed: appdirs==1.4.4,attrs==19.3.0,autoflake==1.3.1,bandit==1.6.2,black==19.10b0,click==7.1.2,colorama==0.4.3,flake8==3.8.2,flake8-bandit==2.1.2,flake8-bugbear==20.1.4,flake8-builtins==1.5.3,flake8-comprehensions==3.2.2,flake8-docstrings==1.5.0,flake8-polyfill==1.0.2,gitdb==4.0.5,GitPython==3.1.2,importlib-metadata==1.6.0,isort==4.3.21,mccabe==0.6.1,mypy==0.770,mypy-extensions==0.4.3,pathspec==0.8.0,pbr==5.4.5,pycodestyle==2.6.0,pydocstyle==5.0.2,pyflakes==2.2.0,pyupgrade==2.4.4,PyYAML==5.3.1,regex==2020.5.14,shed==0.0.5,six==1.15.0,smmap==3.0.4,snowballstemmer==2.0.0,stevedore==1.32.0,tokenize-rt==4.0.0,toml==0.10.1,typed-ast==1.4.1,typing-extensions==3.7.4.2,zipp==3.1.0
check run-test-pre: PYTHONHASHSEED='3542416044'
check run-test: commands[0] | shed
check run-test: commands[1] | flake8
./list/lib/python3.7/site-packages/easy_install.py:1:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:60:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:60:1: D401 First line should be in imperative mood
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:112:1: D205 1 blank line required between summary line and description
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:112:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:141:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:142:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:145:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:146:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:149:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:194:1: S504 ssl.wrap_socket call with no SSL/TLS protocol version specified, the default SSLv23 could be insecure, possible security issue.
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:206:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:247:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/_deprecation_warning.py:2:1: D400 First line should end with a period

... SNIP: **LOTS** more similar output follows...

ERROR: InvocationError for command /Users/ben/Documents/research/covid19-taskforce/patientpaths/.tox/check/bin/flake8 (exited with code 1)
___________________________________ summary ____________________________________
ERROR:   check: commands failed

Ok, so just to make sure I'm not doing it wrong, I check out 01b23d8 (the last revision where the CI job passed) and repeat the process, and get the same error as described above.

So, I seem to be doing something wrong. Maybe my venv-fu is a bit rusty, usually I use Poetry these days and it takes care of all that stuff for me. Still, the fact that it's erroring out on linting-type stuff for site-packages seems weird---can you tell me how to fix it?

And either way, any tips on how to un-break the build in master would be much appreciated :)

closed time in 25 days

benswift

issue commentanu-act-health-covid19-support/patientpaths

cannot reproduce GH Actions test results on local machine

Ah, ok - thanks. So I should have tox installed as a 'system' module, and then it'll manage the venvs for the various versions that it tests?

benswift

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issue commentanu-act-health-covid19-support/patientpaths

tests

@Zac-HD are you able to add in the basic tests you mention for (1)?

benswift

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issue commentanu-act-health-covid19-support/patientpaths

tests

Hey @Zac-HD yep, agree that testing invariants like "conservation of people", etc. are probably good ones to test for now.

Re: (2) yep, I realise that direct equality checks aren't what we're after. I guess the reason I said "compare" results from old vs new was thinking about whether there were some sorts of consistency checks we could do. For example, comparing the differences in the output statistics under various scenarios---e.g. what's the (average) difference in total number of excess capacity required under a specific set of R_0, rho, etc.

Partially because I haven't actually seen any confirmation yet that the new model gives results that are in the ballpark of the old one. @Markopolo141 may have done this? Either way, I think it's important to run the old vs new and see what some of the differences are (even if it doesn't make sense to turn it into a test).

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issue openedanu-act-health-covid19-support/patientpaths

cannot reproduce GH Actions test results on local machine

Hey @Zac-HD

This might just be me failing the WOMM certification program, but I'm having trouble with the tests.

The backstory: I noticed that the build has been broken since eef0333, so I try to reproduce locally.

First, with HEAD at 89d0fa7a, I create a new venv and follow the installation instructions from the README:

smithy:patientpaths ben$ python --version
Python 3.7.7
smithy:patientpaths ben$ python -m venv .venv
smithy:patientpaths ben$ source .venv/bin/activate
(.venv) smithy:patientpaths ben$ pip install .

... SNIP ...

Successfully built patientpaths
Installing collected packages: zipp, importlib-metadata, pluggy, six, filelock, appdirs, distlib, virtualenv, pyparsing, packaging, py, toml, tox, patientpaths
Successfully installed appdirs-1.4.4 distlib-0.3.1 filelock-3.0.12 importlib-metadata-1.7.0 packaging-20.4 patientpaths-0.1.0 pluggy-0.13.1 py-1.9.0 pyparsing-2.4.7 six-1.15.0 toml-0.10.1 tox-3.17.0 virtualenv-20.0.26 zipp-3.1.0
WARNING: You are using pip version 19.2.3, however version 20.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Then, I run the tox check command (copied from the definition in .gitlab/workflows/ci.yml

(.venv) smithy:patientpaths ben$ python -m tox --recreate -e check
check recreate: /Users/ben/Documents/research/covid19-taskforce/patientpaths/.tox/check
check installdeps: --no-deps, --requirement=deps/check.txt
check installed: appdirs==1.4.4,attrs==19.3.0,autoflake==1.3.1,bandit==1.6.2,black==19.10b0,click==7.1.2,colorama==0.4.3,flake8==3.8.2,flake8-bandit==2.1.2,flake8-bugbear==20.1.4,flake8-builtins==1.5.3,flake8-comprehensions==3.2.2,flake8-docstrings==1.5.0,flake8-polyfill==1.0.2,gitdb==4.0.5,GitPython==3.1.2,importlib-metadata==1.6.0,isort==4.3.21,mccabe==0.6.1,mypy==0.770,mypy-extensions==0.4.3,pathspec==0.8.0,pbr==5.4.5,pycodestyle==2.6.0,pydocstyle==5.0.2,pyflakes==2.2.0,pyupgrade==2.4.4,PyYAML==5.3.1,regex==2020.5.14,shed==0.0.5,six==1.15.0,smmap==3.0.4,snowballstemmer==2.0.0,stevedore==1.32.0,tokenize-rt==4.0.0,toml==0.10.1,typed-ast==1.4.1,typing-extensions==3.7.4.2,zipp==3.1.0
check run-test-pre: PYTHONHASHSEED='3542416044'
check run-test: commands[0] | shed
check run-test: commands[1] | flake8
./list/lib/python3.7/site-packages/easy_install.py:1:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:60:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:60:1: D401 First line should be in imperative mood
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:112:1: D205 1 blank line required between summary line and description
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:112:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:141:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:142:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:145:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:146:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:149:17: E128 continuation line under-indented for visual indent
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:194:1: S504 ssl.wrap_socket call with no SSL/TLS protocol version specified, the default SSLv23 could be insecure, possible security issue.
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:206:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/ssl_support.py:247:1: D400 First line should end with a period
./list/lib/python3.7/site-packages/setuptools/_deprecation_warning.py:2:1: D400 First line should end with a period

... SNIP: **LOTS** more similar output follows...

ERROR: InvocationError for command /Users/ben/Documents/research/covid19-taskforce/patientpaths/.tox/check/bin/flake8 (exited with code 1)
___________________________________ summary ____________________________________
ERROR:   check: commands failed

Ok, so just to make sure I'm not doing it wrong, I check out 01b23d8 (the last revision where the CI job passed) and repeat the process, and get the same error as described above.

So, I seem to be doing something wrong. Maybe my venv-fu is a bit rusty, usually I use Poetry these days and it takes care of all that stuff for me. Still, the fact that it's erroring out on linting-type stuff for site-packages seems weird---can you tell me how to fix it?

And either way, any tips on how to un-break the build in master would be much appreciated :)

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