Skip to content

Commit d0f65b4

Browse files
christopher-dGchristopher-dG
committed
Finish renaming DiffEqTutorials -> SciMLTutorials
1 parent a347890 commit d0f65b4

26 files changed

+61
-61
lines changed

Diff for: ‎LICENSE.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
The DiffEqTutorials.jl package is licensed under the MIT "Expat" License:
1+
The SciMLTutorials.jl package is licensed under the MIT "Expat" License:
22

33
> Copyright (c) 2016: ChrisRackauckas.
44
>

Diff for: ‎test/runtests.jl

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,2 @@
1-
using DiffEqTutorials
2-
DiffEqTutorials.weave_file(".","test.jmd")
1+
using SciMLTutorials
2+
SciMLTutorials.weave_file(".","test.jmd")

Diff for: ‎tutorials/advanced/01-beeler_reuter.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -656,6 +656,6 @@ heatmap(sol.u[end])
656656
We achieve around a 6x speedup with running the explicit portion of our IMEX solver on a GPU. The major bottleneck of this technique is the communication between CPU and GPU. In its current form, not all of the internals of the method utilize GPU acceleration. In particular, the implicit equations solved by GMRES are performed on the CPU. This partial CPU nature also increases the amount of data transfer that is required between the GPU and CPU (performed every f call). Compiling the full ODE solver to the GPU would solve both of these issues and potentially give a much larger speedup. [JuliaDiffEq developers are currently working on solutions to alleviate these issues](http://www.stochasticlifestyle.com/solving-systems-stochastic-pdes-using-gpus-julia/), but these will only be compatible with native Julia solvers (and not Sundials).
657657

658658
```{julia; echo=false; skip="notebook"}
659-
using DiffEqTutorials
660-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
659+
using SciMLTutorials
660+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
661661
```

Diff for: ‎tutorials/advanced/02-advanced_ODE_solving.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -506,6 +506,6 @@ need to make sure you choose
506506
[a solver that is compatible with DAEs](https://docs.juliadiffeq.org/latest/solvers/dae_solve/#dae_solve_full-1)
507507

508508
```{julia; echo=false; skip="notebook"}
509-
using DiffEqTutorials
510-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
509+
using SciMLTutorials
510+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
511511
```

Diff for: ‎tutorials/exercises/01-workshop_exercises.jmd

+3-3
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@ The exercises are described as follows:
4343
This exercise worksheet is meant to be a living document leading new users through
4444
a deep dive of the DifferentialEquations.jl feature set. If you further suggestions
4545
or want to contribute new problems, please open an issue or PR at the
46-
DiffEqTutorials.jl repository.
46+
SciMLTutorials.jl repository.
4747

4848
# Problem 1: Investigating Sources of Randomness and Uncertainty in a Stiff Biological System (B)
4949

@@ -438,15 +438,15 @@ at `x=y=0` and see a periodic orbit, e.g., `ts=0:0.05:22; plot(ts, sol1.(ts,
438438
idxs=1))`.
439439

440440
If you are not familiar with this process, see
441-
[the Gierer-Meinhardt example from the DiffEqTutorials.](http://juliadiffeq.org/DiffEqTutorials.jl/html/introduction/03-optimizing_diffeq_code.html)
441+
[the Gierer-Meinhardt example from the SciMLTutorials.](http://juliadiffeq.org/SciMLTutorials.jl/html/introduction/03-optimizing_diffeq_code.html)
442442

443443
Note: Start by doing the simplest implementation!
444444

445445
## Part 2: Optimizing the BRUSS Code
446446

447447
PDEs are expensive to solve, and so we will go nowhere without some code
448448
optimizing! Follow the steps described in the
449-
[the Gierer-Meinhardt example from the DiffEqTutorials](http://juliadiffeq.org/DiffEqTutorials.jl/html/introduction/03-optimizing_diffeq_code.html)
449+
[the Gierer-Meinhardt example from the SciMLTutorials](http://juliadiffeq.org/SciMLTutorials.jl/html/introduction/03-optimizing_diffeq_code.html)
450450
to optimize your Brusselator code. Try other formulations and see what ends
451451
up the fastest! Find a trade-off between performance and simplicity that suits
452452
your needs.

Diff for: ‎tutorials/exercises/02-workshop_solutions.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -718,6 +718,6 @@ sim = solve(ensprob, Tsit5(), EnsembleGPUArray(), trajectories=length(z0))
718718
# Information on the Build
719719

720720
```{julia; echo=false; skip="notebook"}
721-
using DiffEqTutorials
722-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
721+
using SciMLTutorials
722+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
723723
```

Diff for: ‎tutorials/introduction/01-ode_introduction.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -341,6 +341,6 @@ sol[3]
341341
These are the basic controls in DifferentialEquations.jl. All equations are defined via a problem type, and the `solve` command is used with an algorithm choice (or the default) to get a solution. Every solution acts the same, like an array `sol[i]` with `sol.t[i]`, and also like a continuous function `sol(t)` with a nice plot command `plot(sol)`. The Common Solver Options can be used to control the solver for any equation type. Lastly, the types used in the numerical solving are determined by the input types, and this can be used to solve with arbitrary precision and add additional optimizations (this can be used to solve via GPUs for example!). While this was shown on ODEs, these techniques generalize to other types of equations as well.
342342

343343
```{julia; echo=false; skip="notebook"}
344-
using DiffEqTutorials
345-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
344+
using SciMLTutorials
345+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
346346
```

Diff for: ‎tutorials/introduction/02-choosing_algs.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -119,6 +119,6 @@ If you are familiar with MATLAB, SciPy, or R's DESolve, here's a quick translati
119119
significantly more efficient
120120

121121
```{julia; echo=false; skip="notebook"}
122-
using DiffEqTutorials
123-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
122+
using SciMLTutorials
123+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
124124
```

Diff for: ‎tutorials/introduction/03-optimizing_diffeq_code.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -487,6 +487,6 @@ Why is `CVODE_BDF` doing well? What's happening is that, because the problem is
487487
Julia gives you the tools to optimize the solver "all the way", but you need to make use of it. The main thing to avoid is temporary allocations. For small systems, this is effectively done via static arrays. For large systems, this is done via in-place operations and cache arrays. Either way, the resulting solution can be immensely sped up over vectorized formulations by using these principles.
488488

489489
```{julia; echo=false; skip="notebook"}
490-
using DiffEqTutorials
491-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
490+
using SciMLTutorials
491+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
492492
```

Diff for: ‎tutorials/introduction/04-callbacks_and_events.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -322,6 +322,6 @@ saved_values.saveval
322322
Go back to the Harmonic oscillator. Use the `SavingCallback` to save an array for the energy over time, and do this both with and without the `ManifoldProjection`. Plot the results to see the difference the projection makes.
323323

324324
```{julia; echo=false; skip="notebook"}
325-
using DiffEqTutorials
326-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
325+
using SciMLTutorials
326+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
327327
```

Diff for: ‎tutorials/introduction/05-formatting_plots.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -95,6 +95,6 @@ title!("I added a title")
9595
You can do all sorts of things. Have fun!
9696

9797
```{julia; echo=false; skip="notebook"}
98-
using DiffEqTutorials
99-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
98+
using SciMLTutorials
99+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
100100
```

Diff for: ‎tutorials/model_inference/02-monte_carlo_parameter_estim.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -120,6 +120,6 @@ result
120120
if you suspect error is the problem. However, if you're having problems it's most likely not the ODE solver tolerance and mostly because parameter inference is a very hard optimization problem.
121121

122122
```{julia; echo=false; skip="notebook"}
123-
using DiffEqTutorials
124-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
123+
using SciMLTutorials
124+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
125125
```

Diff for: ‎tutorials/models/01-classical_physics.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -406,6 +406,6 @@ plot(sol3.t, energy .- energy[1], title = "Change in Energy over Time", xaxis =
406406
Note that we are using the `DPRKN6` sovler at `reltol=1e-3` (the default), yet it has a smaller energy variation than `Vern9` at `abs_tol=1e-16, rel_tol=1e-16`. Therefore, using specialized solvers to solve its particular problem is very efficient.
407407

408408
```{julia; echo=false; skip="notebook"}
409-
using DiffEqTutorials
410-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
409+
using SciMLTutorials
410+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
411411
```

Diff for: ‎tutorials/models/02-conditional_dosing.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -74,6 +74,6 @@ plot(sol)
7474
```
7575

7676
```{julia; echo=false; skip="notebook"}
77-
using DiffEqTutorials
78-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
77+
using SciMLTutorials
78+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
7979
```

Diff for: ‎tutorials/models/03-diffeqbio_I_introduction.jmd

+5-5
Original file line numberDiff line numberDiff line change
@@ -256,12 +256,12 @@ If you think you've found a bug in DiffEqBiological, or would like to
256256
request/discuss new functionality, feel free to open an issue on
257257
[Github](https://github.com/JuliaDiffEq/DiffEqBiological.jl) (but please check
258258
there is no related issue already open). If you've found a bug in this tutorial,
259-
or have a suggestion, feel free to open an issue on the [DiffEqTutorials Github
260-
site](https://github.com/JuliaDiffEq/DiffEqTutorials.jl). Or, submit a pull
261-
request to DiffEqTutorials updating the tutorial!
259+
or have a suggestion, feel free to open an issue on the [SciMLTutorials Github
260+
site](https://github.com/JuliaDiffEq/SciMLTutorials.jl). Or, submit a pull
261+
request to SciMLTutorials updating the tutorial!
262262

263263
---
264264
```julia; echo=false; skip="notebook"
265-
using DiffEqTutorials
266-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file], remove_homedir=true)
265+
using SciMLTutorials
266+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file], remove_homedir=true)
267267
```

Diff for: ‎tutorials/models/04-diffeqbio_II_networkproperties.jmd

+5-5
Original file line numberDiff line numberDiff line change
@@ -477,12 +477,12 @@ If you think you've found a bug in DiffEqBiological, or would like to
477477
request/discuss new functionality, feel free to open an issue on
478478
[Github](https://github.com/JuliaDiffEq/DiffEqBiological.jl) (but please check
479479
there is no related issue already open). If you've found a bug in this tutorial,
480-
or have a suggestion, feel free to open an issue on the [DiffEqTutorials Github
481-
site](https://github.com/JuliaDiffEq/DiffEqTutorials.jl). Or, submit a pull
482-
request to DiffEqTutorials updating the tutorial!
480+
or have a suggestion, feel free to open an issue on the [SciMLTutorials Github
481+
site](https://github.com/JuliaDiffEq/SciMLTutorials.jl). Or, submit a pull
482+
request to SciMLTutorials updating the tutorial!
483483

484484
---
485485
```julia; echo=false; skip="notebook"
486-
using DiffEqTutorials
487-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file], remove_homedir=true)
486+
using SciMLTutorials
487+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file], remove_homedir=true)
488488
```

Diff for: ‎tutorials/models/04b-diffeqbio_III_steadystates.jmd

+5-5
Original file line numberDiff line numberDiff line change
@@ -180,12 +180,12 @@ If you think you've found a bug in DiffEqBiological, or would like to
180180
request/discuss new functionality, feel free to open an issue on
181181
[Github](https://github.com/JuliaDiffEq/DiffEqBiological.jl) (but please check
182182
there is no related issue already open). If you've found a bug in this tutorial,
183-
or have a suggestion, feel free to open an issue on the [DiffEqTutorials Github
184-
site](https://github.com/JuliaDiffEq/DiffEqTutorials.jl). Or, submit a pull
185-
request to DiffEqTutorials updating the tutorial!
183+
or have a suggestion, feel free to open an issue on the [SciMLTutorials Github
184+
site](https://github.com/JuliaDiffEq/SciMLTutorials.jl). Or, submit a pull
185+
request to SciMLTutorials updating the tutorial!
186186

187187
---
188188
```julia; echo=false; skip="notebook"
189-
using DiffEqTutorials
190-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file], remove_homedir=true)
189+
using SciMLTutorials
190+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file], remove_homedir=true)
191191
```

Diff for: ‎tutorials/models/05-kepler_problem.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -152,6 +152,6 @@ analysis_plot2(sol7, H, L)
152152
Again, we see what we expect.
153153

154154
```{julia; echo=false; skip="notebook"}
155-
using DiffEqTutorials
156-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
155+
using SciMLTutorials
156+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
157157
```

Diff for: ‎tutorials/models/07-outer_solar_system.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -72,6 +72,6 @@ orbitplot(sol,body_names=planets)
7272
```
7373

7474
```{julia; echo=false; skip="notebook"}
75-
using DiffEqTutorials
76-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
75+
using SciMLTutorials
76+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
7777
```

Diff for: ‎tutorials/ode_extras/01-ModelingToolkit.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -266,6 +266,6 @@ expand_derivatives(Dx(f(x)))
266266
```
267267

268268
```{julia; echo=false; skip="notebook"}
269-
using DiffEqTutorials
270-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
269+
using SciMLTutorials
270+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
271271
```

Diff for: ‎tutorials/ode_extras/02-feagin.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -62,6 +62,6 @@ This is a clear trend indicating that the convergence is truly Order 14, which
6262
is the estimated slope.
6363

6464
```{julia; echo=false; skip="notebook"}
65-
using DiffEqTutorials
66-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
65+
using SciMLTutorials
66+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
6767
```

Diff for: ‎tutorials/ode_extras/03-ode_minmax.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -126,6 +126,6 @@ scatter!([maxx],[maxf],label="Global Max")
126126
```
127127

128128
```{julia; echo=false; skip="notebook"}
129-
using DiffEqTutorials
130-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
129+
using SciMLTutorials
130+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
131131
```

Diff for: ‎tutorials/test.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,6 @@ author: Chris Rackauckas
66
This is a test of the builder system.
77

88
```{julia; echo=false; skip="notebook"}
9-
using DiffEqTutorials
10-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
9+
using SciMLTutorials
10+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
1111
```

Diff for: ‎tutorials/type_handling/01-number_types.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -104,6 +104,6 @@ At the time of writing this, Decimals are not compatible. This is not on Differe
104104
As you can see, DifferentialEquations.jl can use arbitrary Julia-defined number systems in its arithmetic. If you need 128-bit floats, i.e. a bit more precision but not arbitrary, DoubleFloats.jl is a very good choice! For arbitrary precision, ArbNumerics are the most feature-complete and give great performance compared to BigFloats, and thus I recommend their use when high-precision (less than 512-800 bits) is required. DecFP is a great library for high-performance decimal numbers and works well as well. Other number systems could use some modernization.
105105

106106
```{julia; echo=false; skip="notebook"}
107-
using DiffEqTutorials
108-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
107+
using SciMLTutorials
108+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
109109
```

Diff for: ‎tutorials/type_handling/02-uncertainties.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -170,6 +170,6 @@ plot(sol.t, getindex.(sol.u, 2), label = "Numerical")
170170
We note that in this case the period of the oscillations is not constant.
171171

172172
```{julia; echo=false; skip="notebook"}
173-
using DiffEqTutorials
174-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
173+
using SciMLTutorials
174+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
175175
```

Diff for: ‎tutorials/type_handling/03-unitful.jmd

+2-2
Original file line numberDiff line numberDiff line change
@@ -80,6 +80,6 @@ plot(ustrip(sol.t),ustrip(sol[:]),lw=3)
8080
```
8181

8282
```{julia; echo=false; skip="notebook"}
83-
using DiffEqTutorials
84-
DiffEqTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
83+
using SciMLTutorials
84+
SciMLTutorials.tutorial_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file])
8585
```

0 commit comments

Comments
 (0)