| Age | Commit message (Expand) | Author |
|---|
| 2020-08-19 | Replace backtick repr with the repr() function...* wqflask/base/trait.py: See
<https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
| BonfaceKilz |
| 2020-08-19 | Handle the move of reduce() to functools.reduce()...Run `2to3-3.8 -f reduce -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-reduce>
| BonfaceKilz |
| 2020-08-19 | Convert `raw_input` to `input`...Run `2to3-3.8 -f raw_input -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raw_input>
| BonfaceKilz |
| 2020-08-19 | Wrap `raise` statements in parenthesis...Run `2to3-3.8 -f raise -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
| BonfaceKilz |
| 2020-08-19 | Convert the use of iterator’s next() methods to the next() function...Run `2to3-3.8 -f next -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-next>
| BonfaceKilz |
| 2020-08-19 | Convert the old not-equal syntax, <>, to !=...Run `2to3-3.8 -f ne -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-ne>
| BonfaceKilz |
| 2020-08-19 | Replace `izip` with python's built-in equivalent...Run `2to3-3.8 -f itertools -w . && 2to3-3.8 -f itertools_imports -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools_imports>
and <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools>
| BonfaceKilz |
| 2020-08-19 | Change `dict.has_key(key)` to `key in dict`...Run `2to3-3.8 -f has_key -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-has_key>
| BonfaceKilz |
| 2020-08-19 | Wrap `filter()` usage in a `list` call...Run `2to3-3.8 -f filter -w .`
See <https://docs.python.org/2/library/2to3.html#2to3fixer-filter>
| BonfaceKilz |
| 2020-08-19 | Fix dictionary iteration methods...Run `2to3-3.8 -f dict -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and
<https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
| BonfaceKilz |
| 2020-08-19 | Remove erroneous `if .. else` branch...* wqflask/utility/svg.py [roct, ellipse, SVGelement]: Raise only a single value error
if either height or width is not defined. Fixes parsing error when running
`2to3-3.8 -f apply -w .`
| BonfaceKilz |
| 2020-08-19 | Wrap `map()` in a `list` call...Run `2to3-3.8 -f map -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-map>
| BonfaceKilz |
| 2020-08-18 | Apply pep8...* wqflask/utility/svg.py: Apply pep8 to fix indentation error when running
`2to3-3.8 -w .`:
````
RefactoringTool: Can't parse ./wqflask/utility/svg.py: IndentationError: unindent does not match any outer indentation level (<tokenize>, line 403)
````
| BonfaceKilz |
| 2020-08-18 | Replace "raw_input" with "input"...* scripts/maintenance/readProbeSetMean_v7.py: Use "input". See
https://docs.python.org/3/whatsnew/3.0.html#builtins
| BonfaceKilz |
| 2020-08-18 | Replace "<>" with "!="...* wqflask/utility/svg.py: Use "!=". The operator, "<>" is removed in Python3
| BonfaceKilz |
| 2020-08-18 | Wrap print statements in parentheses | BonfaceKilz |
| 2020-08-18 | Fix malformed docstring...* wqflask/utility/Plot.py: Update docstring.
| BonfaceKilz |
| 2020-08-18 | Replace DOS style line endings with UNIX style ones...* scripts/maintenance/readProbeSetSE_v7.py: Run *dos2unix* against file
| BonfaceKilz |
| 2020-08-18 | Apply pep8...* scripts/maintenance/readProbeSetSE_v7.py: Apply pep8 to file to replace tabs
with spaces and use correct indentation.
| BonfaceKilz |
| 2020-08-17 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2020-08-17 | Merge pull request #417 from BonfaceKilz/feature/pil-pillow-conversion...Resolve merge conflicts from Pil Pillow conversion branch | zsloan |
| 2020-08-18 | Fix positioning for many instances of text in the mapping figure...* wqflask/wqflask/marker_regression/display_mapping_results.py: Many text
instances had their positions changed by the switch from piddle to PIL. Change
various Y offsets and in some cases changing the logic of the way text is
positioned related to its length and font size.
* wqflask/wqflask/static/fonts/verdanab.ttf: Add bold Verdana, since there needs
to be a separate font file for bold text.
| zsloan |
| 2020-08-17 | Placed X/Y trait info before the table on the correlation scatterplot...page
* wqflask/wqflask/templates/corr_scatterplot.html - reordered table and
X/Y trait info divs
| zsloan |
| 2020-08-10 | Add fonts for pillow...* wqflask/wqflask/marker_regression/display_mapping_results.py: replace piddle
method with PIL.ImageFont
* wqflask/wqflask/static/fonts: Add fonts in path
| Pjotr Prins |
| 2020-08-08 | Add a basic test for test_display_marking_results.py...* wqflask/tests/wqflask/marker_regression/__init__.py: Add it
* wqflask/tests/wqflask/marker_regression/test_display_marking_results.py: Check
that PIL colors are being used instead of the deprecated Piddle colors.
| BonfaceKilz |
| 2020-08-08 | Change Y Coodinate system...* wqflask/wqflask/marker_regression/display_mapping_results.py: Piddle seemed to
centre text about the given Y coordinate, while Pillow requires specification to
top-left corner of the text. This slight change means text all over the image is
displaced somewhat, and this fixes the coordinate system for some of the text.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Fix placement for axes labels...* wqflask/wqflask/marker_regression/display_mapping_results.py: Fix the
placement for the axes labels.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Use TEXT_Y_DISPLACEMENT instead of magic numbers...* wqflask/wqflask/marker_regression/display_mapping_results.py: Use
TEXT_Y_DISPLACEMENT instead of magic numbers to help with making it clear that
the drawn text is displaced somewhat.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Give rectangles black outlines...* wqflask/wqflask/marker_regression/display_mapping_results.py: Give the
rectangles black outlines to correspond to earlier drawings.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Use new `draw_open_polygon()` utility...* wqflask/wqflask/marker_regression/display_mapping_results.py: Use the new
`draw_open_polygon()` utility to draw open polygons.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Add draw_open_polygon() utility...* wqflask/utility/pillow_utils.py: New method.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Replace "color" with "fill" keyword argument...* wqflask/wqflask/marker_regression/display_mapping_results.py:
(DisplayMappingResults): Pillow uses 'fill' in place of 'color'.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Use draw_rotated_text()...Use the new draw_rotated_text() function to draw the text rotated as was
formerly done.
* wqflask/utility/Plot.py (plotBar): Use draw_rotated_text().
* wqflask/wqflask/marker_regression/display_mapping_results.py:
(DisplayMappingResults) Use draw_rotated_text().
| Muriithi Frederick Muriuki |
| 2020-08-08 | Create new utility module for drawing...* wqflask/utility/pillow_utils.py: Create a module to hold some utility
functions for drawing with Pillow. Initialise the module with a function to draw
rotated text.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Fix font paths...* wqflask/utility/Plot.py: Update font paths.
* wqflask/fonts/ttf: Update font files.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Update SNP Browser to Pillow...* wqflask/wqflask/snp_browser/snp_browser.py: Use newer, and supported Pillow in
place of obsoleted Piddle library.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Add missing font files...* wqflask/fonts/ttf: Add ttf font files.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Migrate code from Piddle to Pillow...* wqflask/wqflask/marker_regression/display_mapping_results.py: Add font files
(DisplayMappingResults): Update the code from the Piddle way of things to the
Pillow way of things, for example, replace:
- pid.drawRect(...) with im_drawer.rectangle(...)
- pid.drawString(...) with im_drawer.text(...)
- pid.drawPolygon(...) with im_drawer.polygon(...) etc.
* wqflask/utility/Plot.py: Migrate code from the older, unsupported Piddle to
the newer Pillow library.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Update the colours to use Pillow's ImageColor...* wqflask/wqflask/marker_regression/display_mapping_results.py: Use Pillow's ImageColor module in place of the older Piddle colours.
| Muriithi Frederick Muriuki |
| 2020-08-07 | Move wqflask/tests/api to wqflask/tests/wqflask...* wqflask/tests(api): Move all the files here to tests/wqflask. The test dir
should mirror the actual module structure
| BonfaceKilz |
| 2020-08-06 | Added endpoint for changing some user details...* wqflask/wqflask/user_session.py - Added endpoint for /manage/user that
lets the user change their full_name or organization. Still need to add
something that lets them change their e-mail, since that will require a
confirmation
| zsloan |
| 2020-08-06 | Made a change that should fix the issue with the Y axis ticks extending...too high in mapping results
* wqflask/wqflask/marker_regression/display_mapping_results.py - When in
ful genome view, I changed it to subject the yTopOffset when drawing the
Y axis; single chromosome view seems to work okay so it's conditional on
that
| zsloan |
| 2020-08-05 | Set maximum width for trait page details in order to avoid long...summaries looking strange
* wqflask/wqflask/templates/show_trait_details.html - Set min-width of
table containing details to 1400px
| zsloan |
| 2020-08-04 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2020-08-04 | Simplified logic in the @before_request that checks user permissions...* wqflask/wqflask/views.py - Removed an if statement that was
unnecessary, because it already checks if dataset is either the string
"Temp" or of type "Temp"
| zsloan |
| 2020-08-04 | Reduced table cell margin a bit to make cell contents better align with...header
* wqflask/wqflask/static/new/css/show_trait.css - Changed right margin
from 20px to 15px to better account for the width of the sort arrows in
the header cell
| zsloan |
| 2020-08-04 | Merge pull request #415 from BonfaceKilz/tests/add-tests-for-gen-menu...Tests/add tests for gen menu | Pjotr Prins |
| 2020-08-03 | Fixed table width issue when there's an N column...* wqflask/wqflask/show_trait/show_trait.py - Just added more pixels in
the function which determines the overall table width
| zsloan |
| 2020-08-03 | Fixed issue where DataTables was initialized twice when selecting...cofactors, leading to an error in non-Chrome browsers
*
wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
- Added a line that checks if the table already exists before
initializing it; this issue is caused by a circular import issue, but
I'm not sure how to get around it yet
| zsloan |
| 2020-08-03 | Remove "+" when concatenating strings...* wqflask/wqflask/api/gen_menu.py (build_types, build_datasets): Replace '+'
when joining strings inside brackets
| BonfaceKilz |
