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[INFRA] Speedup CI #20

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merged 2 commits into from
Jan 31, 2024
Merged

[INFRA] Speedup CI #20

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dfc3362
[FIX] Code style
eseiler Jan 31, 2024
bb48e69
[INFRA] Use miniforge and pin packages
eseiler Jan 31, 2024
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28 changes: 8 additions & 20 deletions .github/workflows/lint.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,21 +29,15 @@ jobs:
ref: ${{ github.event.pull_request.head.ref }}
token: ${{ secrets.SEQAN_ACTIONS_PAT }}

- name: Cache conda
uses: actions/cache@v4
with:
path: ~/conda_pkgs_dir
save-always: true
key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}

- name: Setup conda
uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: false
activate-environment: snakemake
environment-file: environment.yml
auto-activate-base: false
use-only-tar-bz2: true
auto-update-conda: false
channel-priority: strict
environment-file: environment.yml
miniforge-version: latest

- name: Run isort
run: isort .
Expand Down Expand Up @@ -84,21 +78,15 @@ jobs:
repository: ${{ github.event.pull_request.head.repo.full_name }}
ref: ${{ github.event.pull_request.head.ref }}

- name: Cache conda
uses: actions/cache@v4
with:
path: ~/conda_pkgs_dir
save-always: true
key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}

- name: Setup conda
uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: false
activate-environment: snakemake
environment-file: environment.yml
auto-activate-base: false
use-only-tar-bz2: true
auto-update-conda: false
channel-priority: strict
environment-file: environment.yml
miniforge-version: latest

- name: Run pylint
run: pylint .
Expand Down
14 changes: 4 additions & 10 deletions .github/workflows/pages.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,21 +26,15 @@ jobs:
- name: Checkout
uses: actions/checkout@v4

- name: Cache conda
uses: actions/cache@v4
with:
path: ~/conda_pkgs_dir
save-always: true
key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}

- name: Setup conda
uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: false
activate-environment: snakemake
environment-file: environment.yml
auto-activate-base: false
use-only-tar-bz2: true
auto-update-conda: false
channel-priority: strict
environment-file: environment.yml
miniforge-version: latest

- name: Build HTML
run: python3 scripts/main.py
Expand Down
14 changes: 4 additions & 10 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,21 +23,15 @@ jobs:
- name: Checkout
uses: actions/checkout@v4

- name: Cache conda
uses: actions/cache@v4
with:
path: ~/conda_pkgs_dir
save-always: true
key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}

- name: Setup conda
uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: false
activate-environment: snakemake
environment-file: environment.yml
auto-activate-base: false
use-only-tar-bz2: true
auto-update-conda: false
channel-priority: strict
environment-file: environment.yml
miniforge-version: latest

- name: Build HTML
run: python3 scripts/main.py
13 changes: 6 additions & 7 deletions environment.yml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,11 @@
name: snakemake
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- black
- bokeh
- isort
- pylint
- snakemake
- snakefmt
- black=23.11.0
- bokeh=3.3.4
- isort=5.13.2
- pylint=3.0.3
- bioconda::snakemake=8.4.2
- bioconda::snakefmt=0.9.0
92 changes: 46 additions & 46 deletions scripts/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -126,59 +126,59 @@ def create_plot(interactive=False):
max_result_time, max_result_size = get_max_result(time_data_list[1:], 1.01), get_max_result(
size_data_list[1:], 1.01
)
p1 = figure(
plot1 = figure(
y_range=convert_list_to_string(size_data[time_structure[0]]),
x_range=(max_result_time, 0),
x_axis_label="time in minutes",
toolbar_location="left",
tools="",
)
renderers1 = p1.hbar_stack(
renderers1 = plot1.hbar_stack(
stackers=time_structure[1:], y=time_structure[0], height=0.4, source=(time_data), color=Set2_6
)
legend_items = []
for r in renderers1:
key, tag = r.name, r.name
legend_items.append((key, [r]))
for renderer in renderers1:
key, tag = renderer.name, renderer.name
legend_items.append((key, [renderer]))
if key == "wall_clock_time_in_seconds":
tag = "time_left"
p1.add_tools(
plot1.add_tools(
HoverTool(
tooltips=[
(f"{file_name}", "@value"),
("wall_clock_time_in_seconds", "@all_times{0.00} sek"),
(tag, "@$name{0.00} sek"),
("Percentage", f"@{key}_percentage{{0.00}}%"),
],
renderers=[r],
renderers=[renderer],
)
)
p1.toolbar_location = None
p1.toolbar.logo = None
p1.yaxis.visible = False
p1.extra_y_ranges = {
plot1.toolbar_location = None
plot1.toolbar.logo = None
plot1.yaxis.visible = False
plot1.extra_y_ranges = {
"zusätzliche_achse": FactorRange(factors=convert_list_to_string(size_data[time_structure[0]]))
}
zweite_y_achse = LinearAxis(y_range_name="zusätzliche_achse")
zweite_y_achse.major_label_text_font_size = "1pt"
zweite_y_achse.major_label_text_color = "#15191c"
p1.add_layout(zweite_y_achse, "right")
p1.xaxis.ticker = AdaptiveTicker(base=60, mantissas=[1, 2, 5], min_interval=60, max_interval=600)
p1.xaxis.formatter = CustomJSTickFormatter(
plot1.add_layout(zweite_y_achse, "right")
plot1.xaxis.ticker = AdaptiveTicker(base=60, mantissas=[1, 2, 5], min_interval=60, max_interval=600)
plot1.xaxis.formatter = CustomJSTickFormatter(
code="""
return (tick / 60);
"""
)
p1.y_range.range_padding = 0.1
p1.ygrid.grid_line_color = None
p1.axis.minor_tick_line_color = None
plot1.y_range.range_padding = 0.1
plot1.ygrid.grid_line_color = None
plot1.axis.minor_tick_line_color = None

p1.yaxis.major_tick_line_color = None
p1.yaxis.minor_tick_line_color = None
p1.outline_line_color = None
p1.sizing_mode = "scale_both"
p1.title.text = "Double click on legend/plot to hide/show the legend"
p1.title.align = "right"
plot1.yaxis.major_tick_line_color = None
plot1.yaxis.minor_tick_line_color = None
plot1.outline_line_color = None
plot1.sizing_mode = "scale_both"
plot1.title.text = "Double click on legend/plot to hide/show the legend"
plot1.title.align = "right"

legend = Legend(items=legend_items)
legend.location = "center"
Expand All @@ -189,30 +189,30 @@ def create_plot(interactive=False):
# legend.nrows = 3
legend.title = "Default parameters:\n\t\t\tt_max = 192\n\t\tunion estimation (U) = yes\n\t\t\trearrangement (R) = yes\n\t\t\tk-mer size (k) = 32\n\t\t\tnumber of hash function (hash) = 2\n\t\t\talpha = 1.2\n\t\t\trelaxed false positive rate (r-fpr) = 0.5\n\t\t\tmaximum false positive rate (fpr) = 0.05"
legend.title_text_color = "#e0e0e0"
p1.add_layout(legend, "left")
plot1.add_layout(legend, "left")
toggle_legend_js = CustomJS(
args={"legend": legend},
code="""
legend.visible = !legend.visible
""",
)
p1.js_on_event(events.DoubleTap, toggle_legend_js)
plot1.js_on_event(events.DoubleTap, toggle_legend_js)

p2 = figure(
plot2 = figure(
y_range=convert_list_to_string(size_data[size_structure[0]]),
x_range=(0, max_result_size),
x_axis_label="size in GB",
toolbar_location="right",
tools="",
)
legend_items = []
renderers2 = p2.hbar_stack(
renderers2 = plot2.hbar_stack(
size_structure[1:], y=size_structure[0], height=0.4, source=(size_data), color=Set2_4
)
for r in renderers2:
key = r.name
legend_items.append((key, [r]))
p2.add_tools(
for renderer in renderers2:
key = renderer.name
legend_items.append((key, [renderer]))
plot2.add_tools(
HoverTool(
tooltips=[
(f"{file_name}", "@value"),
Expand All @@ -221,36 +221,36 @@ def create_plot(interactive=False):
("Percentage", f"@{key}_percentage{{0.00}}%"),
("avg_load_factor", f"@{key}_avg_load_factor{{0.00}}"),
],
renderers=[r],
renderers=[renderer],
)
)
p2.toolbar.logo = None
p2.toolbar_location = None
p2.y_range.range_padding = 0.1
p2.ygrid.grid_line_color = None
p2.axis.minor_tick_line_color = None
p2.outline_line_color = None
p2.title.text = "Click on legend entries to mute the corresponding bars"
plot2.toolbar.logo = None
plot2.toolbar_location = None
plot2.y_range.range_padding = 0.1
plot2.ygrid.grid_line_color = None
plot2.axis.minor_tick_line_color = None
plot2.outline_line_color = None
plot2.title.text = "Click on legend entries to mute the corresponding bars"

legend = Legend(items=legend_items)
legend.location = "center"
legend.glyph_height = 12
legend.glyph_width = 12
legend.click_policy = "mute"
p2.add_layout(legend, "right")
plot2.add_layout(legend, "right")
toggle_legend_js = CustomJS(
args={"legend": legend},
code="""
legend.visible = !legend.visible
""",
)
p2.js_on_event(events.DoubleTap, toggle_legend_js)
plot2.js_on_event(events.DoubleTap, toggle_legend_js)

p2.yaxis.major_tick_line_color = None
p2.yaxis.minor_tick_line_color = None
p2.yaxis.major_label_standoff = 15
p2.sizing_mode = "scale_both"
both_plots = row(p1, p2)
plot2.yaxis.major_tick_line_color = None
plot2.yaxis.minor_tick_line_color = None
plot2.yaxis.major_label_standoff = 15
plot2.sizing_mode = "scale_both"
both_plots = row(plot1, plot2)
both_plots.sizing_mode = "scale_both"
vercel_logo = """
<svg width="209" height="40" viewBox="0 0 209 40" fill="none" xmlns="http://www.w3.org/2000/svg">
Expand Down
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