py2ls 0.1.10.12__py3-none-any.whl → 0.2.7.10__py3-none-any.whl

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Files changed (72) hide show
  1. py2ls/.DS_Store +0 -0
  2. py2ls/.git/.DS_Store +0 -0
  3. py2ls/.git/index +0 -0
  4. py2ls/.git/logs/refs/remotes/origin/HEAD +1 -0
  5. py2ls/.git/objects/.DS_Store +0 -0
  6. py2ls/.git/refs/.DS_Store +0 -0
  7. py2ls/ImageLoader.py +621 -0
  8. py2ls/__init__.py +7 -5
  9. py2ls/apptainer2ls.py +3940 -0
  10. py2ls/batman.py +164 -42
  11. py2ls/bio.py +2595 -0
  12. py2ls/cell_image_clf.py +1632 -0
  13. py2ls/container2ls.py +4635 -0
  14. py2ls/corr.py +475 -0
  15. py2ls/data/.DS_Store +0 -0
  16. py2ls/data/email/email_html_template.html +88 -0
  17. py2ls/data/hyper_param_autogluon_zeroshot2024.json +2383 -0
  18. py2ls/data/hyper_param_tabrepo_2024.py +1753 -0
  19. py2ls/data/mygenes_fields_241022.txt +355 -0
  20. py2ls/data/re_common_pattern.json +173 -0
  21. py2ls/data/sns_info.json +74 -0
  22. py2ls/data/styles/.DS_Store +0 -0
  23. py2ls/data/styles/example/.DS_Store +0 -0
  24. py2ls/data/styles/stylelib/.DS_Store +0 -0
  25. py2ls/data/styles/stylelib/grid.mplstyle +15 -0
  26. py2ls/data/styles/stylelib/high-contrast.mplstyle +6 -0
  27. py2ls/data/styles/stylelib/high-vis.mplstyle +4 -0
  28. py2ls/data/styles/stylelib/ieee.mplstyle +15 -0
  29. py2ls/data/styles/stylelib/light.mplstyl +6 -0
  30. py2ls/data/styles/stylelib/muted.mplstyle +6 -0
  31. py2ls/data/styles/stylelib/nature-reviews-latex.mplstyle +616 -0
  32. py2ls/data/styles/stylelib/nature-reviews.mplstyle +616 -0
  33. py2ls/data/styles/stylelib/nature.mplstyle +31 -0
  34. py2ls/data/styles/stylelib/no-latex.mplstyle +10 -0
  35. py2ls/data/styles/stylelib/notebook.mplstyle +36 -0
  36. py2ls/data/styles/stylelib/paper.mplstyle +290 -0
  37. py2ls/data/styles/stylelib/paper2.mplstyle +305 -0
  38. py2ls/data/styles/stylelib/retro.mplstyle +4 -0
  39. py2ls/data/styles/stylelib/sans.mplstyle +10 -0
  40. py2ls/data/styles/stylelib/scatter.mplstyle +7 -0
  41. py2ls/data/styles/stylelib/science.mplstyle +48 -0
  42. py2ls/data/styles/stylelib/std-colors.mplstyle +4 -0
  43. py2ls/data/styles/stylelib/vibrant.mplstyle +6 -0
  44. py2ls/data/tiles.csv +146 -0
  45. py2ls/data/usages_pd.json +1417 -0
  46. py2ls/data/usages_sns.json +31 -0
  47. py2ls/docker2ls.py +5446 -0
  48. py2ls/ec2ls.py +61 -0
  49. py2ls/fetch_update.py +145 -0
  50. py2ls/ich2ls.py +1955 -296
  51. py2ls/im2.py +8242 -0
  52. py2ls/image_ml2ls.py +2100 -0
  53. py2ls/ips.py +33909 -3418
  54. py2ls/ml2ls.py +7700 -0
  55. py2ls/mol.py +289 -0
  56. py2ls/mount2ls.py +1307 -0
  57. py2ls/netfinder.py +873 -351
  58. py2ls/nl2ls.py +283 -0
  59. py2ls/ocr.py +1581 -458
  60. py2ls/plot.py +10394 -314
  61. py2ls/rna2ls.py +311 -0
  62. py2ls/ssh2ls.md +456 -0
  63. py2ls/ssh2ls.py +5933 -0
  64. py2ls/ssh2ls_v01.py +2204 -0
  65. py2ls/stats.py +66 -172
  66. py2ls/temp20251124.py +509 -0
  67. py2ls/translator.py +2 -0
  68. py2ls/utils/decorators.py +3564 -0
  69. py2ls/utils_bio.py +3453 -0
  70. {py2ls-0.1.10.12.dist-info → py2ls-0.2.7.10.dist-info}/METADATA +113 -224
  71. {py2ls-0.1.10.12.dist-info → py2ls-0.2.7.10.dist-info}/RECORD +72 -16
  72. {py2ls-0.1.10.12.dist-info → py2ls-0.2.7.10.dist-info}/WHEEL +0 -0
@@ -0,0 +1,36 @@
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+ # Matplotlib style for Jupyter notebooks
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+
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+ # Set default figure size
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+ figure.figsize : 8, 6
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+
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+ # Set x axis
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+ xtick.major.size : 6
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+ xtick.major.width : 1
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+ xtick.minor.size : 3
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+ xtick.minor.width : 1
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+
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+ # Set y axis
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+ ytick.major.size : 6
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+ ytick.major.width : 1
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+ ytick.minor.size : 3
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+ ytick.minor.width : 1
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+
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+ # Fontsizes
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+ xtick.labelsize : 16
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+ ytick.labelsize : 16
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+ legend.fontsize : 16
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+ legend.title_fontsize : 16
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+ axes.titlesize : 16
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+ axes.labelsize : 16
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+
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+ # Set line widths
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+ axes.linewidth : 1
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+ grid.linewidth : 1
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+ lines.linewidth : 2.
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+
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+ # Use sans-serif fonts
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+ font.family : sans-serif
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+ mathtext.fontset : dejavusans
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+
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+ # Use LaTeX for math formatting
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+ text.usetex : False
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+ _internal.classic_mode: false
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+ agg.path.chunksize: 0
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+ animation.bitrate: -1
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+ animation.codec: h264
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+ animation.convert_args: [[-layers, OptimizePlus]]
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+ animation.convert_path: convert
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+ animation.embed_limit: 20.0
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+ animation.ffmpeg_args: [[]]
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+ animation.ffmpeg_path: ffmpeg
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+ animation.frame_format: png
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+ animation.html: none
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+ animation.writer: ffmpeg
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+ axes.autolimit_mode: data
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+ axes.axisbelow: true
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+ axes.edgecolor: k
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+ axes.facecolor: white
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+ axes.formatter.limits: -5, 6
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+ axes.formatter.min_exponent: 0
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+ axes.formatter.offset_threshold: 4
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+ axes.formatter.use_locale: false
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+ axes.formatter.use_mathtext: false
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+ axes.formatter.useoffset: true
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+ axes.grid: false
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+ axes.grid.axis: both
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+ axes.grid.which: major
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+ axes.labelcolor: k
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+ axes.labelpad: 4.0
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+ axes.labelsize: 11.0
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+ axes.labelweight: normal
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+ axes.linewidth: 0.8
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+ axes.spines.bottom: true
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+ axes.spines.left: true
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+ axes.spines.right: true
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+ axes.spines.top: true
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+ axes.titlecolor: k
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+ axes.titlelocation: center
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+ axes.titlepad: 6.0
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+ axes.titlesize: 11.0
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+ axes.unicode_minus: false
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+ axes.xmargin: 0.05
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+ axes.ymargin: 0.05
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+ axes.zmargin: 0.05
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+ axes3d.automargin: false
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+ axes3d.grid: true
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+ axes3d.mouserotationstyle: arcball
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+ axes3d.trackballborder: 0.2
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+ axes3d.trackballsize: 0.667
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+ boxplot.boxprops.color: black
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+ boxplot.boxprops.linestyle: -
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+ boxplot.boxprops.linewidth: 1.0
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+ boxplot.capprops.color: black
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+ boxplot.capprops.linestyle: -
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+ boxplot.flierprops.markerfacecolor: none
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+ boxplot.meanprops.color: C2
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+ boxplot.meanprops.linewidth: 1.0
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+ boxplot.meanprops.marker: ^
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+ boxplot.meanprops.markeredgecolor: C2
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+ boxplot.meanprops.markerfacecolor: C2
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+ boxplot.medianprops.color: C1
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+ boxplot.medianprops.linewidth: 1.0
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+ boxplot.notch: false
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+ boxplot.showcaps: true
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+ boxplot.showfliers: true
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+ boxplot.showmeans: false
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+ boxplot.vertical: true
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+ boxplot.whiskerprops.color: black
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+ boxplot.whiskerprops.linestyle: -
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+ boxplot.whiskerprops.linewidth: 1.0
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+ boxplot.whiskers: 1.5
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+ contour.corner_mask: true
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+ contour.negative_linestyle: dashed
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+ date.autoformatter.hour: %m-%d %H
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+ date.autoformatter.microsecond: %M:%S.%f
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+ date.autoformatter.minute: %d %H:%M
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+ date.autoformatter.month: %Y-%m
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+ date.autoformatter.second: %H:%M:%S
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+ date.autoformatter.year: %Y
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+ figure.autolayout: true
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+ figure.constrained_layout.hspace: 0.02
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+ figure.constrained_layout.use: false
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+ font.family: [sans-serif]
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+ font.fantasy: [[Chicago, Charcoal, Impact, Western, xkcd script, fantasy]]
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+ font.monospace: [[DejaVu Sans Mono, Bitstream Vera Sans Mono, Computer Modern Typewriter, Andale Mono, Nimbus Mono L, Courier New, Courier, Fixed, Terminal, monospace]]
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+ font.sans-serif: [Arial]
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+ font.serif: [Arial]
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+ font.stretch: normal
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+ font.style: normal
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+ font.variant: normal
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+ grid.linewidth: 0.75
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+ hatch.color: black
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+ hist.bins: 10
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+ image.aspect: equal
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+ image.cmap: Greys
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+ image.composite_image: true
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+ image.interpolation: antialiased
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+ image.interpolation_stage: auto
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+ image.lut: 256
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+ image.origin: upper
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+ image.resample: true
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+ keymap.back: [[left, c, backspace, MouseButton.BACK]]
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+ keymap.copy: [[ctrl+c, cmd+c]]
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+ keymap.forward: [[right, v, MouseButton.FORWARD]]
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+ keymap.fullscreen: [[f, ctrl+f]]
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+ keymap.grid: [[g]]
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+ keymap.grid_minor: [[G]]
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+ keymap.help: [[f1]]
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+ keymap.home: [[h, r, home]]
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+ keymap.pan: [[p]]
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+ keymap.quit: [[ctrl+w, cmd+w, q]]
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+ keymap.quit_all: [[]]
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+ keymap.save: [[s, ctrl+s]]
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+ keymap.xscale: [[k, L]]
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+ keymap.yscale: [[l]]
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+ keymap.zoom: [[o]]
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+ legend.borderaxespad: 0.5
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+ legend.borderpad: 0.4
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+ legend.columnspacing: 2.0
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+ legend.facecolor: inherit
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+ legend.fancybox: true
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+ legend.frameon: false
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+ legend.markerscale: 1.0
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+ lines.antialiased: true
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+ lines.color: C0
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+ lines.dashdot_pattern: 6.4, 1.6, 1.0, 1.6
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+ lines.dotted_pattern: 1.0, 1.65
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+ xtick.labelsize: 11.0
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+ _internal.classic_mode: false
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+ backend: module://matplotlib_inline.backend_inline
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+ backend_fallback: true
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+ boxplot.meanprops.markeredgecolor: C2
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+ figure.dpi: 100.0
109
+ figure.edgecolor: white
110
+ figure.facecolor: white
111
+ figure.figsize: [6.0, 4.0]
112
+ figure.frameon: true
113
+ figure.labelsize: large
114
+ figure.labelweight: normal
115
+ figure.max_open_warning: 20
116
+ figure.raise_window: true
117
+ figure.subplot.bottom: 0.11
118
+ figure.subplot.hspace: 0.2
119
+ figure.subplot.left: 0.125
120
+ figure.subplot.right: 0.9
121
+ figure.subplot.top: 0.88
122
+ figure.subplot.wspace: 0.2
123
+ figure.titlesize: 11.0
124
+ figure.titleweight: normal
125
+ font.cursive: [[Apple Chancery, Textile, Zapf Chancery, Sand, Script MT, Felipa, Comic Neue, Comic Sans MS, cursive]]
126
+ font.family: [sans-serif]
127
+ font.fantasy: [[Chicago, Charcoal, Impact, Western, xkcd script, fantasy]]
128
+ font.monospace: [[DejaVu Sans Mono, Bitstream Vera Sans Mono, Computer Modern Typewriter, Andale Mono, Nimbus Mono L, Courier New, Courier, Fixed, Terminal, monospace]]
129
+ font.sans-serif: [Arial]
130
+ font.serif: [Arial]
131
+ font.size: 11.0
132
+ font.stretch: normal
133
+ font.style: normal
134
+ font.variant: normal
135
+ font.weight: normal
136
+ grid.alpha: 1.0
137
+ grid.color: .65
138
+ grid.linestyle: :
139
+ grid.linewidth: 0.75
140
+ hatch.color: black
141
+ hatch.linewidth: 1.0
142
+ hist.bins: 10
143
+ image.aspect: equal
144
+ image.cmap: Greys
145
+ image.composite_image: true
146
+ image.interpolation: antialiased
147
+ image.interpolation_stage: auto
148
+ image.lut: 256
149
+ image.origin: upper
150
+ image.resample: true
151
+ interactive: true
152
+ keymap.back: [[left, c, backspace, MouseButton.BACK]]
153
+ keymap.copy: [[ctrl+c, cmd+c]]
154
+ keymap.forward: [[right, v, MouseButton.FORWARD]]
155
+ keymap.fullscreen: [[f, ctrl+f]]
156
+ keymap.grid: [[g]]
157
+ keymap.grid_minor: [[G]]
158
+ keymap.help: [[f1]]
159
+ keymap.home: [[h, r, home]]
160
+ keymap.pan: [[p]]
161
+ keymap.quit: [[ctrl+w, cmd+w, q]]
162
+ keymap.quit_all: [[]]
163
+ keymap.save: [[s, ctrl+s]]
164
+ keymap.xscale: [[k, L]]
165
+ keymap.yscale: [[l]]
166
+ keymap.zoom: [[o]]
167
+ legend.borderaxespad: 0.5
168
+ legend.borderpad: 0.4
169
+ legend.columnspacing: 2.0
170
+ legend.edgecolor: none
171
+ legend.facecolor: inherit
172
+ legend.fancybox: true
173
+ legend.fontsize: 10.0
174
+ legend.framealpha: 0.8
175
+ legend.frameon: false
176
+ legend.handleheight: 0.7
177
+ legend.handlelength: 2.0
178
+ legend.handletextpad: 0.8
179
+ legend.labelcolor: k
180
+ legend.labelspacing: 0.5
181
+ legend.loc: best
182
+ legend.markerscale: 1.0
183
+ legend.numpoints: 1
184
+ legend.scatterpoints: 1
185
+ legend.shadow: false
186
+ legend.title_fontsize: 10.0
187
+ lines.antialiased: true
188
+ lines.color: C0
189
+ lines.dash_capstyle: CapStyle.round
190
+ lines.dash_joinstyle: JoinStyle.round
191
+ lines.dashdot_pattern: [6.4, 1.6, 1.0, 1.6]
192
+ lines.dashed_pattern: [3.7, 1.6]
193
+ lines.dotted_pattern: [1.0, 1.65]
194
+ lines.linestyle: -
195
+ lines.linewidth: 0.75
196
+ lines.marker: None
197
+ lines.markeredgecolor: auto
198
+ lines.markeredgewidth: 1.0
199
+ lines.markerfacecolor: auto
200
+ lines.markersize: 6.0
201
+ lines.scale_dashes: true
202
+ lines.solid_capstyle: CapStyle.round
203
+ lines.solid_joinstyle: JoinStyle.round
204
+ macosx.window_mode: system
205
+ markers.fillstyle: full
206
+ mathtext.bf: sans:bold
207
+ mathtext.bfit: sans:italic:bold
208
+ mathtext.cal: cursive
209
+ mathtext.default: it
210
+ mathtext.fallback: cm
211
+ mathtext.it: sans:italic
212
+ mathtext.rm: sans
213
+ mathtext.sf: sans
214
+ mathtext.tt: monospace
215
+ patch.antialiased: true
216
+ patch.edgecolor: white
217
+ patch.facecolor: C0
218
+ patch.force_edgecolor: false
219
+ patch.linewidth: 1.0
220
+ path.simplify: true
221
+ path.simplify_threshold: 0.111111111111
222
+ path.snap: true
223
+ pcolor.shading: auto
224
+ pcolormesh.snap: true
225
+ pdf.compression: 6
226
+ pdf.inheritcolor: false
227
+ pdf.use14corefonts: false
228
+ pgf.preamble:
229
+ pgf.rcfonts: true
230
+ pgf.texsystem: xelatex
231
+ polaraxes.grid: true
232
+ ps.distiller.res: 6000
233
+ ps.fonttype: 3
234
+ ps.papersize: letter
235
+ ps.useafm: false
236
+ savefig.directory: ~
237
+ savefig.dpi: figure
238
+ savefig.edgecolor: auto
239
+ savefig.facecolor: auto
240
+ savefig.format: png
241
+ savefig.orientation: portrait
242
+ savefig.pad_inches: 0.1
243
+ savefig.transparent: false
244
+ scatter.edgecolors: face
245
+ scatter.marker: o
246
+ svg.image_inline: true
247
+ text.antialiased: true
248
+ text.color: k
249
+ text.hinting: force_autohint
250
+ text.hinting_factor: 8
251
+ text.kerning_factor: 0
252
+ text.latex.preamble:
253
+ text.parse_math: true
254
+ text.usetex: false
255
+ timezone: UTC
256
+ tk.window_focus: false
257
+ toolbar: toolbar2
258
+ webagg.address: 127.0.0.1
259
+ webagg.open_in_browser: true
260
+ webagg.port: 8988
261
+ webagg.port_retries: 50
262
+ xaxis.labellocation: center
263
+ xtick.alignment: center
264
+ xtick.bottom: true
265
+ xtick.color: k
266
+ xtick.direction: out
267
+ xtick.labelbottom: true
268
+ xtick.labelcolor: inherit
269
+ xtick.labelsize: 11.0
270
+ xtick.labeltop: false
271
+ xtick.major.bottom: true
272
+ xtick.major.pad: 3.5
273
+ xtick.major.size: 2.0
274
+ xtick.major.top: true
275
+ xtick.major.width: 0.8
276
+ xtick.minor.bottom: true
277
+ xtick.minor.ndivs: auto
278
+ xtick.minor.pad: 3.4
279
+ xtick.minor.size: 2.0
280
+ xtick.minor.top: true
281
+ xtick.minor.visible: false
282
+ xtick.minor.width: 0.6
283
+ xtick.top: false
284
+ yaxis.labellocation: center
285
+ ytick.alignment: center_baseline
286
+ ytick.color: k
287
+ ytick.direction: out
288
+ ytick.labelcolor: inherit
289
+ ytick.labelleft: true
290
+ ytick.labelright: false
291
+ ytick.labelsize: 11.0
292
+ ytick.left: true
293
+ ytick.major.left: true
294
+ ytick.major.pad: 3.5
295
+ ytick.major.right: true
296
+ ytick.major.size: 3.5
297
+ ytick.major.width: 0.8
298
+ ytick.minor.left: true
299
+ ytick.minor.ndivs: auto
300
+ ytick.minor.pad: 3.4
301
+ ytick.minor.right: true
302
+ ytick.minor.size: 0.0
303
+ ytick.minor.visible: false
304
+ ytick.minor.width: 0.6
305
+ ytick.right: false
@@ -0,0 +1,4 @@
1
+ # Retro color style
2
+
3
+ # Set color cycle
4
+ axes.prop_cycle : cycler('color', ['4165c0', 'e770a2', '5ac3be', '696969', 'f79a1e', 'ba7dcd'])
@@ -0,0 +1,10 @@
1
+ # Sans-serif
2
+ font.family : sans-serif
3
+
4
+ # Latex with sans-serif fonts
5
+ mathtext.fontset : dejavusans
6
+
7
+ # In general, we need to be careful with the preamble. A common font for
8
+ # sans serif LaTeX is cmbright. However, it does not support bold fontweights
9
+ # so we use sfmath instead.
10
+ text.latex.preamble : \usepackage{amsmath} \usepackage{amssymb} \usepackage{sfmath}
@@ -0,0 +1,7 @@
1
+ # Matplotlib style for scatter plots
2
+
3
+ # Set markers (style, color, no lines)
4
+ axes.prop_cycle : (cycler('marker', ['o', 's', '^', 'v', '<', '>', 'd']) + cycler('color', ['0C5DA5', '00B945', 'FF9500', 'FF2C00', '845B97', '474747', '9e9e9e']) + cycler('ls', [' ', ' ', ' ', ' ', ' ', ' ', ' ']))
5
+
6
+ # Set marker size
7
+ lines.markersize : 3
@@ -0,0 +1,48 @@
1
+ # Matplotlib style for scientific plotting
2
+ # This is the base style for "SciencePlots"
3
+ # see: https://github.com/garrettj403/SciencePlots
4
+
5
+ # Set color cycle: blue, green, yellow, red, violet, gray
6
+ axes.prop_cycle : cycler('color', ['0C5DA5', '00B945', 'FF9500', 'FF2C00', '845B97', '474747', '9e9e9e'])
7
+
8
+ # Set default figure size
9
+ figure.figsize : 3.5, 2.625
10
+
11
+ # Set x axis
12
+ xtick.direction : in
13
+ xtick.major.size : 3
14
+ xtick.major.width : 0.5
15
+ xtick.minor.size : 1.5
16
+ xtick.minor.width : 0.5
17
+ xtick.minor.visible : True
18
+ xtick.top : True
19
+
20
+ # Set y axis
21
+ ytick.direction : in
22
+ ytick.major.size : 3
23
+ ytick.major.width : 0.5
24
+ ytick.minor.size : 1.5
25
+ ytick.minor.width : 0.5
26
+ ytick.minor.visible : True
27
+ ytick.right : True
28
+
29
+ # Set line widths
30
+ axes.linewidth : 0.5
31
+ grid.linewidth : 0.5
32
+ lines.linewidth : 1.
33
+
34
+ # Remove legend frame
35
+ legend.frameon : False
36
+
37
+ # Always save as 'tight'
38
+ savefig.bbox : tight
39
+ savefig.pad_inches : 0.05
40
+
41
+ # Use serif fonts
42
+ # font.serif : Times
43
+ font.family : serif
44
+ mathtext.fontset : dejavuserif
45
+
46
+ # Use LaTeX for math formatting
47
+ text.usetex : True
48
+ text.latex.preamble : \usepackage{amsmath} \usepackage{amssymb}
@@ -0,0 +1,4 @@
1
+ # Standard SciencePlots color cycle
2
+
3
+ # Set color cycle: blue, green, yellow, red, violet, gray
4
+ axes.prop_cycle : cycler('color', ['0C5DA5', '00B945', 'FF9500', 'FF2C00', '845B97', '474747', '9e9e9e'])
@@ -0,0 +1,6 @@
1
+ # Vibrant color scheme
2
+ # color-blind safe
3
+ # from Paul Tot's website: https://personal.sron.nl/~pault/
4
+
5
+ # Set color cycle
6
+ axes.prop_cycle : cycler('color', ['EE7733', '0077BB', '33BBEE', 'EE3377', 'CC3311', '009988', 'BBBBBB'])