Merge branch 'fix-failing-docs' into 'master' (38fdff89) · Commits · Utopia / utopia

.gitlab-ci.yml

+9 −5

Original line number	Diff line number	Diff line
		@@ -56,6 +56,7 @@ variables:
		UPDATE_UTOPIA_BASE_IMAGE: "false"
		DEPLOY_DOCKER_IMAGE: "false"
		DEPLOY_DOCS: "false"
		FORCE_DEPLOY_DOCS: "false"


		# Run pipelines:
		@@ -513,12 +514,12 @@ test:link_install_tree:
		# Build the documentation and expose it as a review environment
		docs:build:
		stage: docs
		allow_failure: true
		when: always
		extends:
		- .use_multicore_group_runners
		needs:
		- build:models
		when: always
		allow_failure: false
		before_script:
		- cd build
		- cmake ..
		@@ -553,7 +554,8 @@ docs:build:
		# - a documentation review environment, which is meant to always be created
		# even if the build:docs job failed with allow_failure set.
		# - the production-level documentation by running a GitLab Pages job, which
		# ends up being served under docs.utopia-project.org
		# ends up being served under docs.utopia-project.org — this will only be
		# deployed if the docs:build was successful
		# - the latest Utopia docker image to Docker Hub: ccees/utopia:latest


		@@ -577,10 +579,12 @@ pages:
		image: alpine
		stage: deploy
		rules:
		- if: '$DEPLOY_DOCS == "true"'
		- if: '$FORCE_DEPLOY_DOCS == "true"'
		when: always
		- if: '$DEPLOY_DOCS == "true"'
		when: on_success
		- if: '$CI_COMMIT_BRANCH == "master"'
		when: always
		when: on_success
		- when: never
		needs:
		- docs:build

doc/_cfg/SEIRD/multiverse_plots/eval.yml

+42 −15

Original line number	Diff line number	Diff line
		@@ -21,6 +21,9 @@ _default_style: &default_style
		mathtext.fontset: stix
		font.family: serif




		# -----------------------------------------------------------------------------

		.flush_kind:
		@@ -31,6 +34,9 @@ _default_style: &default_style
		.flush_helper:
		helpers: ~




		# -----------------------------------------------------------------------------
		# Demonstrates a line plot with errorbars
		### Start --- errorbars
		@@ -88,12 +94,14 @@ errorbars:
		### End --- errorbars
		<<: *default_style


		# Demonstrates a line plot with errorbands
		errorbands:
		based_on:
		- errorbars
		- .plot.facet_grid.errorbands


		# Demonstrates a stacked line plot
		stacked_transmission:
		based_on:
		@@ -121,6 +129,7 @@ stacked_transmission:
		set_title:
		title: Density of infected agents


		# Demonstrates a stacked averaged line plot
		stacked_transmission_averaged:
		based_on:
		@@ -152,6 +161,7 @@ stacked_transmission_averaged:
		set_title:
		title: Density of agent kinds


		# Demonstrates a stacked line plot with errorbands
		### Start --- stacked_errorbands
		stacked_errorbands:
		@@ -205,6 +215,7 @@ stacked_errorbands:
		axes.prop_cycle: cycler('color', ['#AFD8BC', '#FFCC66', '#006666' ])
		### End --- stacked_errorbands


		# Demonstrates a facet grid plot errorbands
		### Start --- facet_grid
		panel_errorbands:
		@@ -252,6 +263,7 @@ panel_errorbands:
		font.family: serif
		### End --- facet_grid


		# Demonstrates a facet grid of stacked line plots with errorbands
		panel_all:
		based_on:
		@@ -275,6 +287,7 @@ panel_all:
		set_limits:
		y: [ 0, 0.6 ]


		# Demonstrates subspace selection
		panel_subspace:
		based_on: panel_all
		@@ -292,6 +305,7 @@ panel_subspace:
		set_limits:
		y: [ 0, 0.6 ]


		# Demonstrates a histogram plot
		### Start --- histogram
		histogram:
		@@ -330,6 +344,7 @@ histogram:
		mathtext.fontset: stix
		font.family: serif


		### Start --- double_histogram
		double_histogram:
		based_on:
		@@ -385,6 +400,7 @@ double_histogram:
		sharex: true
		### End --- double_histogram


		# Demonstrates a facet grid 2d scatter plot
		### Start --- scatter_2d_facet
		scatter_2d_facet:
		@@ -436,6 +452,7 @@ scatter_2d_facet:
		### End --- scatter_2d_facet
		<<: *default_style


		# Demonstrates a facet grid 3d scatter plot
		scatter_3d:
		based_on:
		@@ -486,8 +503,8 @@ scatter_3d:
		y:
		major: [0, 0.05, 0.1]

		single_kdeplot:

		single_kdeplot:
		based_on:
		- .creator.multiverse
		- .plot.multiplot
		@@ -533,6 +550,7 @@ single_kdeplot:
		x: Infection peak
		y: ' '


		double_kdeplot:
		based_on: single_kdeplot
		to_plot:
		@@ -556,12 +574,14 @@ double_kdeplot:
		style:
		figure.figsize: [8, 4]

		# Demonstrates a scatterplot and an errorbar plot on a single axis using multiplot

		# Demonstrates a scatterplot and an errorbar plot on a single axis (multiplot)
		### Start --- multiplot
		multiplot:
		based_on:
		- .creator.multiverse
		- .plot.multiplot

		select_and_combine:
		fields:
		susceptible:
		@@ -590,16 +610,21 @@ multiplot:
		transform:
		- .coords: [!dag_tag infected, time]
		tag: time

		- .mean: [!dag_tag susceptible, seed]
		- .squeeze: [!dag_prev ]
		tag: mean_s

		- .std: [!dag_tag susceptible, seed]
		- .squeeze: [!dag_prev ]
		tag: std_s

		- .mean: [!dag_tag infected, seed]
		tag: mean_i

		- .mean: [!dag_tag recovered, seed]
		tag: mean_r

		- xr.Dataset:
		- infected: !dag_tag mean_i
		recovered: !dag_tag mean_r
		@@ -612,19 +637,21 @@ multiplot:
		yerr: !dag_result std_s
		label: Susceptible agents
		color: '#0099CC'
		- function: [xarray.plot, scatter]
		args:
		- !dag_result scatter_data
		x: time
		y: recovered
		hue: infected
		cmap:
		continuous: true
		from_values:
		0: '#006666'
		1: '#CC3333'
		label: Recovered agents
		zorder: 3

		# FIXME Not working with xarray 2022.10.0
		# - function: [xarray.plot, scatter]
		# args:
		# - !dag_result scatter_data
		# x: time
		# y: recovered
		# hue: infected
		# cmap:
		# continuous: true
		# from_values:
		# 0: '#006666'
		# 1: '#CC3333'
		# label: Recovered agents
		# zorder: 3

		helpers:
		set_labels: