From 452cec00113e6508973359d4b08c1f9c7d84227c Mon Sep 17 00:00:00 2001 From: George Simmons Date: Wed, 22 Jan 2025 14:43:54 +0000 Subject: [PATCH] docs update --- docs/examples/{tutorials.md => index.md} | 6 ++--- .../{mixing_problems.md => index.md} | 0 .../{population_modelling.md => index.md} | 0 .../{second_order_odes.md => index.md} | 0 .../getting_started.md => index.md} | 12 +++++----- docs/user_guide/simulation.md | 2 +- mkdocs.yml | 23 ++++++++++--------- 7 files changed, 22 insertions(+), 21 deletions(-) rename docs/examples/{tutorials.md => index.md} (90%) rename docs/examples/mixing_problems/{mixing_problems.md => index.md} (100%) rename docs/examples/population_dynamics/{population_modelling.md => index.md} (100%) rename docs/examples/second_order_odes/{second_order_odes.md => index.md} (100%) rename docs/{user_guide/getting_started.md => index.md} (81%) diff --git a/docs/examples/tutorials.md b/docs/examples/index.md similarity index 90% rename from docs/examples/tutorials.md rename to docs/examples/index.md index 362aa4b..35ea517 100644 --- a/docs/examples/tutorials.md +++ b/docs/examples/index.md @@ -14,7 +14,7 @@ These examples are arranged roughly in order of difficulty and complexity, with Population dynamics models, including exponential growth, the logistic equation, and predator-prey models. - [:octicons-arrow-right-24: Get started](./population_dynamics/population_modelling.md) + [:octicons-arrow-right-24: Get started](./population_dynamics/index.md) - :material-roman-numeral-2:{ .lg .middle } __Mixing problems__ @@ -22,7 +22,7 @@ These examples are arranged roughly in order of difficulty and complexity, with Mixing of solutions in a single tank or across any number of tanks. - [:octicons-arrow-right-24: Get started](./mixing_problems/mixing_problems.md) + [:octicons-arrow-right-24: Get started](./mixing_problems/index.md) - :material-roman-numeral-3:{ .lg .middle } __Second-order systems__ @@ -30,6 +30,6 @@ These examples are arranged roughly in order of difficulty and complexity, with How to simulate complex second-order or higher-order systems. - [:octicons-arrow-right-24: Get started](./second_order_odes/second_order_odes.md) + [:octicons-arrow-right-24: Get started](./second_order_odes/index.md) diff --git a/docs/examples/mixing_problems/mixing_problems.md b/docs/examples/mixing_problems/index.md similarity index 100% rename from docs/examples/mixing_problems/mixing_problems.md rename to docs/examples/mixing_problems/index.md diff --git a/docs/examples/population_dynamics/population_modelling.md b/docs/examples/population_dynamics/index.md similarity index 100% rename from docs/examples/population_dynamics/population_modelling.md rename to docs/examples/population_dynamics/index.md diff --git a/docs/examples/second_order_odes/second_order_odes.md b/docs/examples/second_order_odes/index.md similarity index 100% rename from docs/examples/second_order_odes/second_order_odes.md rename to docs/examples/second_order_odes/index.md diff --git a/docs/user_guide/getting_started.md b/docs/index.md similarity index 81% rename from docs/user_guide/getting_started.md rename to docs/index.md index 720cc19..22c9621 100644 --- a/docs/user_guide/getting_started.md +++ b/docs/index.md @@ -26,7 +26,7 @@ For most new users, going through the following resources in the suggested order Find out about the purpose and design principles of `psymple`. - [:octicons-arrow-right-24: Read more](../overview/introduction.md) + [:octicons-arrow-right-24: Read more](./overview/introduction.md) - :material-roman-numeral-2:{ .lg .middle } __Modelling in psymple__ @@ -34,7 +34,7 @@ For most new users, going through the following resources in the suggested order Learn how to capture functions and differential equations in `psymple`, and combine these into complex models. - [:octicons-arrow-right-24: Start modelling](../components/functional_ported_objects.md) + [:octicons-arrow-right-24: Start modelling](./components/functional_ported_objects.md) - :material-roman-numeral-3:{ .lg .middle } __Simulating models__ @@ -42,7 +42,7 @@ For most new users, going through the following resources in the suggested order Understand how to create and run simulations for `psymple` models. - [:octicons-arrow-right-24: Run simulations](./system.md) + [:octicons-arrow-right-24: Run simulations](system.md) - :material-roman-numeral-4:{ .lg .middle } __Tutorials__ @@ -50,7 +50,7 @@ For most new users, going through the following resources in the suggested order Work through full examples of implementing, parametrising and simulating models. - [:octicons-arrow-right-24: See more](../examples/tutorials.md) + [:octicons-arrow-right-24: See more](./examples/tutorials.md) - :material-roman-numeral-5:{ .lg .middle } __The mathematics__ @@ -58,7 +58,7 @@ For most new users, going through the following resources in the suggested order Learn more about the mathematical structures underneath psymple which tie everything together. - [:octicons-arrow-right-24: See the maths](../mathematics/ported_objects.md) + [:octicons-arrow-right-24: See the maths](./mathematics/ported_objects.md) - :material-roman-numeral-6:{ .lg .middle } __Get involved__ @@ -66,6 +66,6 @@ For most new users, going through the following resources in the suggested order Find out how you can get involved in the community by using or developing `psymple`. - [:octicons-arrow-right-24: Get involved](../development/development.md) + [:octicons-arrow-right-24: Get involved](./development/development.md) \ No newline at end of file diff --git a/docs/user_guide/simulation.md b/docs/user_guide/simulation.md index 404de68..84b7111 100644 --- a/docs/user_guide/simulation.md +++ b/docs/user_guide/simulation.md @@ -119,4 +119,4 @@ The time series used to plot each variable can also be accessed: ## Next steps -Many more examples of creating and simulating models in `psymple` can be found in the [Examples](../examples/tutorials.md) section. \ No newline at end of file +Many more examples of creating and simulating models in `psymple` can be found in the [Examples](../examples/index.md) section. \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 7327ab1..76baf04 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -15,6 +15,7 @@ theme: - content.code.annotate - navigation.tabs - navigation.tabs.sticky + - navigation.indexes - navigation.sections - navigation.footer - search.suggest @@ -69,8 +70,14 @@ extra: default: latest nav: + - Home: index.md + - Overview: + - Introduction: overview/introduction.md + - Statement of need: overview/statement_of_need.md + - Hybrid systems modelling: overview/modelling_systems.md + - Mechanistic and correlative models: overview/modelling_types.md + - System design: overview/system_design.md - User guide: - - user_guide/getting_started.md - Building a model: - Defining functions: components/functional_ported_objects.md - Defining ODEs: components/variable_ported_objects.md @@ -80,25 +87,19 @@ nav: - Building a system: user_guide/system.md - Running a simulation: - Simulations: user_guide/simulation.md - - Overview: - - Introduction: overview/introduction.md - - Statement of need: overview/statement_of_need.md - - Hybrid systems modelling: overview/modelling_systems.md - - Mechanistic and correlative models: overview/modelling_types.md - - System design: overview/system_design.md - Examples: - - examples/tutorials.md + - Examples: examples/index.md - Population dynamics: - - Population modelling: examples/population_dynamics/population_modelling.md + - Population modelling: examples/population_dynamics/index.md - Malthusian growth: examples/population_dynamics/malthusian_population.md - Logistic growth: examples/population_dynamics/logistic_growth.md - Predator-prey systems: examples/population_dynamics/predator_prey.md - Mixing problems: - - Mixing problems: examples/mixing_problems/mixing_problems.md + - Mixing problems: examples/mixing_problems/index.md - Single tank: examples/mixing_problems/single_tank.md - Multiple tanks: examples/mixing_problems/multiple_tanks.md - Second-order ODEs: - - Second-order ODEs: examples\second_order_odes\second_order_odes.md + - Second-order ODEs: examples\second_order_odes\index.md - Projectile motion: examples\second_order_odes\projectile_motion.md - Three body problem: examples\second_order_odes\three_body_problem.md - Mathematical components: