Open kjappelbaum opened 2 years ago
Copied to Shweata (owner) and Ayush, We are currently working on the installation in PyPI. There seems to be a dependency of ScispaCy which needs a venv.
Would you be interested in having a demo on Wed in the Lightning BYOC 5-minutes talks? Or maybe you are full?
On Tue, Feb 8, 2022 at 1:18 PM Kevin Jablonka @.***> wrote:
Hi, completely fine if you do not want to merge any of this - it is probably mostly my own preference (except for the things in the setup.py).
Still WIP.
You can view, comment on, or merge this pull request online at:
https://github.com/petermr/docanalysis/pull/4 Commit Summary
- 0605240 https://github.com/petermr/docanalysis/pull/4/commits/0605240643bed4a6d09a34772e9689534915563d chore: did some basic linting
- 38dd3d6 https://github.com/petermr/docanalysis/pull/4/commits/38dd3d65ca6d1e5a6d2ee6d3b53e1e00e40d961b chore: also format setup.py
File Changes
(10 files https://github.com/petermr/docanalysis/pull/4/files)
- M README.md https://github.com/petermr/docanalysis/pull/4/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5 (14)
- D init.py https://github.com/petermr/docanalysis/pull/4/files#diff-8e2c1f727276d30ced72fa67cb848772a9802162bec39b42a8df5359fd063a4c (0)
- M docanalysis/init.py https://github.com/petermr/docanalysis/pull/4/files#diff-c221b7cf74738970404d481f8254483887aed6aacc524b85cecd7f75b61c69c1 (2)
- M docanalysis/docanalysis.py https://github.com/petermr/docanalysis/pull/4/files#diff-4222cefd227947770ab989b9e06fd323536439d23e346cb30f439a3c9d61e226 (36)
- M docanalysis/entity_extraction.py https://github.com/petermr/docanalysis/pull/4/files#diff-27a01fdec5695ed46b7bb4645d615be3215be409a6be0c74aae6bc4a31142237 (155)
- M docanalysis/extract_entities.py https://github.com/petermr/docanalysis/pull/4/files#diff-84f2eccc935b03d44560a7714f99ba13800c57fa2dc8161c45c36a7403f5f160 (291)
- M docanalysis/frequency_analysis.py https://github.com/petermr/docanalysis/pull/4/files#diff-a2ad57b2bc2f5c60c36b55938996cc3d52ca64efeba91067e5e4741cb314ebe2 (16)
- R examples/demo.py https://github.com/petermr/docanalysis/pull/4/files#diff-6f304341f18bda556d58ef6369e3ac2c981331f3f1ae107e36b5da8b991b56ec (0)
- R examples/pmr_demo.py https://github.com/petermr/docanalysis/pull/4/files#diff-9e6b752ef36451af51bac2307d7754ae4cdb021761f4062228729a6f3946eebd (0)
- M setup.py https://github.com/petermr/docanalysis/pull/4/files#diff-60f61ab7a8d1910d86d9fda2261620314edcae5894d5aaa236b821c7256badd7 (59)
Patch Links:
- https://github.com/petermr/docanalysis/pull/4.patch
- https://github.com/petermr/docanalysis/pull/4.diff
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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
We certainly have time for a demo! I will also respond to your email.
I thin Ayush has fixed the problems that I mentioned. Shweata is up for the demo (and she has had experience in virtual meetings). Ayush and Shweata will deal with the PR
Will continue working on the PR later / or we can discuss how much you want to adapt some linting/style/code layout "semi"-standards.
One very useful set of tools that @kjappelbaum could share our expertise on would be employing continuous integration (via GitHub actions, for example). I was speaking about this earlier on Gather
We are delighted to have your experience. We believe in testing, linting, PEP-8 and all the other Knights of the Python Table.
At the moment we are concentrated on getting a good demo for Shweata tomorrow, but after that we would be delighted to have your suggestions.
All codes have some, but not enough, docstrings; some but not enough tests; some but not enough examples/tutorials.
All the code is aiming towards argparsing - docanalysis + pygetpapers has the main framework; py4ami has a lot but is probably bloated; pyamiimage has many tests, some examples but not yet CLI.
P.
On Tue, Feb 8, 2022 at 4:56 PM Kevin Jablonka @.***> wrote:
Will continue working on the PR later / or we can discuss how much you want to adapt some linting/style/code layout "semi"-standards.
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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
We are delighted to have your experience.
Happy to give a demo tomorrow in one of the breaks. I can make a draft PR to whichever repo you think would be most useful, the test harness could then be used across each of these related packages
In fact, I see pygetpapers already uses this, so perhaps just a demo will suffice :)
one can maybe just use one of the cookiecutters ;) https://github.com/kjappelbaum/cookiecutter-snekpack (a broken fork of charlie's)
Yes, I think Ayush introduced this for pygetpapers a few months back. We haven't done it for all the code yet.
P.
On Tue, Feb 8, 2022 at 5:41 PM Matthew Evans @.***> wrote:
In fact, I see pygetpapers already uses this, so perhaps just a demo will suffice :)
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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
Would be happy to see cookiecutters in action. I tried this some months back to try to structure my projects but I didn't know enough Python then.
On Tue, Feb 8, 2022 at 6:09 PM Kevin Jablonka @.***> wrote:
one can maybe just use one of the cookiecutters ;) https://github.com/kjappelbaum/cookiecutter-snekpack (a broken fork of charlie's)
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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
Happy to show once (i love https://timothycrosley.com/project-6-cruft for this) - unfortunately was too busy with the breakout rooms and other orga things to join the hacking room today :(
Hi, completely fine if you do not want to merge any of this - it is probably mostly my own preference (except for the things in the
setup.py
).Still WIP.