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WIP changes to paper, plus some bug fixes #101

Merged
merged 61 commits into from
Sep 27, 2023
Merged

WIP changes to paper, plus some bug fixes #101

merged 61 commits into from
Sep 27, 2023

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paxtonfitzpatrick
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paxtonfitzpatrick and others added 30 commits September 8, 2023 19:11
@paxtonfitzpatrick
bump version string and URL for eventual resubmission release
dcce5a0
@paxtonfitzpatrick
Merge branch 'main' of https://github.com/ContextLab/davos into rev-1
82f9c02
@paxtonfitzpatrick
note support for IPython shells in metadata table
65aa0ad
@paxtonfitzpatrick
fix missing text in fig 2 caption
cb885a5
@paxtonfitzpatrick
remove unused import
9328489
@paxtonfitzpatrick
update comment text in snippet 1
4249f44
@paxtonfitzpatrick
update comment text in snippet 5
fd45bf4
@paxtonfitzpatrick
WIP rewriting projects section
0078780
@paxtonfitzpatrick
slightly tweak exception name
707cd46
@paxtonfitzpatrick
progress through tricky section of projects description
2a1c1b5
@paxtonfitzpatrick
more progress on projects section
9efd6c2
@paxtonfitzpatrick
fix typo in comment
dc704d8
@paxtonfitzpatrick
cleaned up tex file
ab2ffe6
@paxtonfitzpatrick
progress on projects section
9394022
@paxtonfitzpatrick
cleaned up tex file formatting
2c8f567
@paxtonfitzpatrick
additional text in projects section
c543b84
@paxtonfitzpatrick
finished projects section
b8d762e
@paxtonfitzpatrick
add subsection for top-level functions
17e2fbc
@paxtonfitzpatrick
add reference for MIND 2023
943c7ce
@paxtonfitzpatrick
add note on MIND to acknowledgements
01f3f69
@paxtonfitzpatrick
add reference to config section
494de95
@paxtonfitzpatrick
edits to section 2.2.4 up through writeable options
5e31af7
@paxtonfitzpatrick
edits through section 2.2.4
6b00371
@paxtonfitzpatrick
minor updates to projects section
761cd4a
@paxtonfitzpatrick
add AbstractProject description to all_projects bullet in sec 2.2.4
9529957
@paxtonfitzpatrick
working on section 2.2.5
1952751
@paxtonfitzpatrick
remove davos.require_pip() from section 2.2.5
bc254b6
@paxtonfitzpatrick
Fix ContextLab#97
8134b33 
- `davos.prune_projects()` now requires explicitly passing `yes=True` in non-interactive mode
- both `davos.prune_projects()` and `davos.Project.remove()` now respect `davos.suppress_stdout`
@paxtonfitzpatrick
addSmit17 (PEP 557) and HeimCann19 (PEP 594)
eef73ce
@jeremymanning
Merge pull request #3 from paxtonfitzpatrick/rev-1
6051bee 
merging paxton's changes into my fork
jeremymanning and others added 29 commits September 22, 2023 06:23
@jeremymanning
corrected gradient size mismatch
3ea4fa2
@paxtonfitzpatrick
add note about viewing all top-level attribute values via davos.config
ba6c113
@jeremymanning
shareable code 2d figure cleanup
2021835
@paxtonfitzpatrick
expanded start of top-level functions section slightly
bf4c3e3
@paxtonfitzpatrick
fix close-quotes character
cd9d2ab
@paxtonfitzpatrick
minor tweaks to section 2.2.4
cc067a4
@paxtonfitzpatrick
fix ContextLab#98: check juptyer notebook vs lab interface, store val…
88bc19f 
…ue in config, use value in command to get running servers
@paxtonfitzpatrick
edits through end of section 2
20b436a
@paxtonfitzpatrick
[no ci] fixed a typo in a comment
f8b071c
@paxtonfitzpatrick
added new paragraph to start of section 3
d15460c
@paxtonfitzpatrick
cleaned up source file from recent edits
9859b30
@paxtonfitzpatrick
Merge pull request #9 from jeremymanning/main
d53befc 
proposed new version of "shareable code" figure
@paxtonfitzpatrick
add ref for scikit-learn docs page
ca9e773
@paxtonfitzpatrick
fixed a typo in section 2.2.5
4591b25
@paxtonfitzpatrick
add info to require_python message, update line numbers accordingly
326dd18
@paxtonfitzpatrick
update fig 3 caption, other minor wording changes & typo fixes pre-se…
0527c20 
…ction 3
@paxtonfitzpatrick
update in-text example snippet fig numbers since there's now 8 instea…
9499d12 
…d of 7
@paxtonfitzpatrick
WIP updating illustrative example text
78e8db9
@paxtonfitzpatrick
rewrote section 3 intro paragraph
aaa9963
@paxtonfitzpatrick
refined first few illustrative example snippet descriptions:
bbacd55
@paxtonfitzpatrick
pop submodule names from top-level module namespace to deal with rela…
d6aa8ff 
…tive import issue
@paxtonfitzpatrick
restore subpackage/submodule objects to top-level namespace if reload…
c0ac228 
… fails
@paxtonfitzpatrick
issue warning about partial reload if user chooses to continue running
e2d0504
@paxtonfitzpatrick
increase stacklevel to show warning for relevent line in the notebook
643478f
@paxtonfitzpatrick
edits to section 3 up through example snippet 4
2d0c648
@paxtonfitzpatrick
update ipywidgets/widgetsnbextension example code lines, update indiv…
b504c7b 
…idual snippets to match
@paxtonfitzpatrick
progress on illustrative example walkthrough up to last snippet
2c75e75
@paxtonfitzpatrick
enforce caps in a way that won't Incur the Wrath of Codespell
e5a6967
@paxtonfitzpatrick
fixed a typo
f3f3195
@paxtonfitzpatrick paxtonfitzpatrick merged commit c305d41 into ContextLab:main Sep 27, 2023
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@paxtonfitzpatrick @jeremymanning