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2020-08-20Add backward support for urllibBonfaceKilz
* wqflask/base/trait.py: Remove unused imports * wqflask/db/call.py (Bench): Add urllib2 fallback for python2
2020-08-19Remove extra whitespace(or add it) from comma separated itemsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Make Python more idiomaticBonfaceKilz
Run `2to3-3.8 -f idioms -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
2020-08-19Rename xrange() to range() and wrap existing range() calls with listBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
2020-08-19Handle the rename of urllib and urllib2 to the urllib packageBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Replace backtick repr with the repr() functionBonfaceKilz
* wqflask/base/trait.py: See <https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
2020-08-19Handle the move of reduce() to functools.reduce()BonfaceKilz
Run `2to3-3.8 -f reduce -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-reduce>
2020-08-19Wrap `raise` statements in parenthesisBonfaceKilz
Run `2to3-3.8 -f raise -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
2020-08-19Convert the use of iterator’s next() methods to the next() functionBonfaceKilz
Run `2to3-3.8 -f next -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-next>
2020-08-19Convert the old not-equal syntax, <>, to !=BonfaceKilz
Run `2to3-3.8 -f ne -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-ne>
2020-08-19Replace `izip` with python's built-in equivalentBonfaceKilz
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>
2020-08-19Change `dict.has_key(key)` to `key in dict`BonfaceKilz
Run `2to3-3.8 -f has_key -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-has_key>
2020-08-19Fix dictionary iteration methodsBonfaceKilz
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>
2020-08-19Remove erroneous `if .. else` branchBonfaceKilz
* 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 .`
2020-08-19Wrap `map()` in a `list` callBonfaceKilz
Run `2to3-3.8 -f map -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-map>
2020-08-18Apply pep8BonfaceKilz
* 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) ````
2020-08-18Replace "<>" with "!="BonfaceKilz
* wqflask/utility/svg.py: Use "!=". The operator, "<>" is removed in Python3
2020-08-18Wrap print statements in parenthesesBonfaceKilz
2020-08-18Fix malformed docstringBonfaceKilz
* wqflask/utility/Plot.py: Update docstring.
2020-08-18Fix positioning for many instances of text in the mapping figurezsloan
* 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.
2020-08-10Add fonts for pillowPjotr Prins
* wqflask/wqflask/marker_regression/display_mapping_results.py: replace piddle method with PIL.ImageFont * wqflask/wqflask/static/fonts: Add fonts in path
2020-08-08Add a basic test for test_display_marking_results.pyBonfaceKilz
* 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.
2020-08-08Change Y Coodinate systemMuriithi Frederick Muriuki
* 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.
2020-08-08Fix placement for axes labelsMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: Fix the placement for the axes labels.
2020-08-08Use TEXT_Y_DISPLACEMENT instead of magic numbersMuriithi Frederick Muriuki
* 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.
2020-08-08Give rectangles black outlinesMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: Give the rectangles black outlines to correspond to earlier drawings.
2020-08-08Use new `draw_open_polygon()` utilityMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: Use the new `draw_open_polygon()` utility to draw open polygons.
2020-08-08Add draw_open_polygon() utilityMuriithi Frederick Muriuki
* wqflask/utility/pillow_utils.py: New method.
2020-08-08Replace "color" with "fill" keyword argumentMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: (DisplayMappingResults): Pillow uses 'fill' in place of 'color'.
2020-08-08Use draw_rotated_text()Muriithi Frederick Muriuki
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().
2020-08-08Create new utility module for drawingMuriithi Frederick Muriuki
* 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.
2020-08-08Fix font pathsMuriithi Frederick Muriuki
* wqflask/utility/Plot.py: Update font paths. * wqflask/fonts/ttf: Update font files.
2020-08-08Update SNP Browser to PillowMuriithi Frederick Muriuki
* wqflask/wqflask/snp_browser/snp_browser.py: Use newer, and supported Pillow in place of obsoleted Piddle library.
2020-08-08Add missing font filesMuriithi Frederick Muriuki
* wqflask/fonts/ttf: Add ttf font files.
2020-08-08Migrate code from Piddle to PillowMuriithi Frederick Muriuki
* 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.
2020-08-08Update the colours to use Pillow's ImageColorMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: Use Pillow's ImageColor module in place of the older Piddle colours.
2020-08-07Move wqflask/tests/api to wqflask/tests/wqflaskBonfaceKilz
* wqflask/tests(api): Move all the files here to tests/wqflask. The test dir should mirror the actual module structure
2020-08-05Set maximum width for trait page details in order to avoid longzsloan
summaries looking strange * wqflask/wqflask/templates/show_trait_details.html - Set min-width of table containing details to 1400px
2020-08-04Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-04Simplified logic in the @before_request that checks user permissionszsloan
* 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"
2020-08-04Reduced table cell margin a bit to make cell contents better align withzsloan
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
2020-08-04Merge pull request #415 from BonfaceKilz/tests/add-tests-for-gen-menuPjotr Prins
Tests/add tests for gen menu
2020-08-03Fixed table width issue when there's an N columnzsloan
* wqflask/wqflask/show_trait/show_trait.py - Just added more pixels in the function which determines the overall table width
2020-08-03Fixed issue where DataTables was initialized twice when selectingzsloan
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
2020-08-03Remove "+" when concatenating stringsBonfaceKilz
* wqflask/wqflask/api/gen_menu.py (build_types, build_datasets): Replace '+' when joining strings inside brackets
2020-08-03Fix some errors generated by running pylintBonfaceKilz
* wqflask/wqflask/api/gen_menu.py: Apply pylint. * wqflask/tests/api/test_gen_menu.py: Apply pylint.
2020-08-03Add extra test for "build_datasets"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Add test.
2020-08-03Move variable to setUpBonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Move variable
2020-08-03Add test for "gen_dropdown_json"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Add new test
2020-08-03Add tests for "get_datasets"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Add new tests
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 03:30:47 +0000