Age | Commit message (Collapse) | Author |
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* wqflask/wqflask/templates/correlation_matrix.html - remove display:
none for short label div
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
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Run `2to3-3.8 -f idioms -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
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* wqflask/base/trait.py: See
<https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
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Run `2to3-3.8 -f reduce -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-reduce>
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Run `2to3-3.8 -f raw_input -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raw_input>
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Run `2to3-3.8 -f raise -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
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Run `2to3-3.8 -f next -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-next>
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Run `2to3-3.8 -f ne -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-ne>
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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>
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Run `2to3-3.8 -f has_key -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-has_key>
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Run `2to3-3.8 -f filter -w .`
See <https://docs.python.org/2/library/2to3.html#2to3fixer-filter>
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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>
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* 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 .`
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Run `2to3-3.8 -f map -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-map>
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* 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)
````
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* scripts/maintenance/readProbeSetMean_v7.py: Use "input". See
https://docs.python.org/3/whatsnew/3.0.html#builtins
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* wqflask/utility/svg.py: Use "!=". The operator, "<>" is removed in Python3
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* wqflask/utility/Plot.py: Update docstring.
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* scripts/maintenance/readProbeSetSE_v7.py: Run *dos2unix* against file
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* scripts/maintenance/readProbeSetSE_v7.py: Apply pep8 to file to replace tabs
with spaces and use correct indentation.
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Resolve merge conflicts from Pil Pillow conversion branch
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* 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.
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page
* wqflask/wqflask/templates/corr_scatterplot.html - reordered table and
X/Y trait info divs
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* wqflask/wqflask/marker_regression/display_mapping_results.py: replace piddle
method with PIL.ImageFont
* wqflask/wqflask/static/fonts: Add fonts in path
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* 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.
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* 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.
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Fix the
placement for the axes labels.
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* 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.
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Give the
rectangles black outlines to correspond to earlier drawings.
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Use the new
`draw_open_polygon()` utility to draw open polygons.
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* wqflask/utility/pillow_utils.py: New method.
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* wqflask/wqflask/marker_regression/display_mapping_results.py:
(DisplayMappingResults): Pillow uses 'fill' in place of 'color'.
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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().
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* 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.
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* wqflask/utility/Plot.py: Update font paths.
* wqflask/fonts/ttf: Update font files.
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* wqflask/wqflask/snp_browser/snp_browser.py: Use newer, and supported Pillow in
place of obsoleted Piddle library.
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* wqflask/fonts/ttf: Add ttf font files.
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* 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.
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Use Pillow's ImageColor module in place of the older Piddle colours.
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* wqflask/tests(api): Move all the files here to tests/wqflask. The test dir
should mirror the actual module structure
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* 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
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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
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summaries looking strange
* wqflask/wqflask/templates/show_trait_details.html - Set min-width of
table containing details to 1400px
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* 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"
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