diff --git a/_quarto.yml b/_quarto.yml deleted file mode 100644 index bae5ba17cf..0000000000 --- a/_quarto.yml +++ /dev/null @@ -1,22 +0,0 @@ - -project: - title: "Manopt.jl" - #execute-dir: project - -crossref: - fig-prefix: Figure - tbl-prefix: Table -fig-format: png - -execute: - freeze: auto - eval: true - echo: true - output: true - -format: - commonmark: - variant: -raw_html+tex_math_dollars - wrap: preserve - -jupyter: julia-1.9 diff --git a/docs/src/references.bib b/docs/src/references.bib index 671391787e..6ac72e27e5 100644 --- a/docs/src/references.bib +++ b/docs/src/references.bib @@ -113,7 +113,7 @@ @article{BergmannGousenbourger:2018 NOTE = {arXiv: [1807.10090](https://arxiv.org/abs/1807.10090)} } -@article{BergmannHerzog:2019:1, +@article{BergmannHerzog:2019, AUTHOR = {Bergmann, Ronny and Herzog, Roland}, DOI = {10.1137/18M1181602}, JOURNAL = {SIAM Journal on Optimization}, @@ -354,7 +354,7 @@ @article{HestenesStiefel:1952 VOLUME = {49}, YEAR = {1952} } -@thesis{Huang:2014, +@phdthesis{Huang:2014, AUTHOR = {Huang, W.}, SCHOOL = {Flordia State University}, TITLE = {Optimization algorithms on Riemannian manifolds with applications}, diff --git a/docs/src/tutorials/GeodesicRegression.md b/docs/src/tutorials/GeodesicRegression.md index 9bbdbe5657..c1fb3706eb 100644 --- a/docs/src/tutorials/GeodesicRegression.md +++ b/docs/src/tutorials/GeodesicRegression.md @@ -34,7 +34,7 @@ highlighted = 4; ## Time Labeled Data If for each data item $d_i$ we are also given a time point $t_i\in\mathbb R$, which are pairwise different, -then we can use the least squares error to state the objetive function as (Fletcher, 2013) +then we can use the least squares error to state the objetive function as [Fletcher, IJCV, 2013](@cite Fletcher:2013). ``` math F(p,X) = \frac{1}{2}\sum_{i=1}^n d_{\mathcal M}^2(γ_{p,X}(t_i), d_i), @@ -71,7 +71,7 @@ Due to linearity, the gradient of $F(p,X)$ is the sum of the single gradients of ``` which can be computed using a chain rule of the squared distance and the exponential map, -see for example (Bergmann and Gousenbourger, 2018) for details or Equations (7) and (8) of (Fletcher, 2013): +see for example [Bergmann, Gousenbourger, Front. Appl. Math. Stat., 2018](@cite BergmannGousenbourger:2018) for details or Equations (7) and (8) of [Fletcher, IJCV, 2013](@cite Fletcher:2013): ““” ``` julia @@ -514,6 +514,8 @@ Note that the geodesics from the data to the regression geodesic meet at a nearl ## Literature -Bergmann, R. and Gousenbourger, P.-Y. (2018) “A variational model for data fitting on manifolds by minimizing the acceleration of a Bézier curve,” *Frontiers in Applied Mathematics and Statistics*, 4. Available at: . +```@bibliography +Pages = ["tutorials/GeodesicRegression.md"] +Canonical=false +``` -Fletcher, P.T. (2013) “Geodesic regression and the theory of least squares on Riemannian manifolds,” *International Journal of Computer Vision*, 105(2), pp. 171–185. Available at: . diff --git a/docs/src/tutorials/InplaceGradient.md b/docs/src/tutorials/InplaceGradient.md index a66a011737..06b24bb1ab 100644 --- a/docs/src/tutorials/InplaceGradient.md +++ b/docs/src/tutorials/InplaceGradient.md @@ -57,14 +57,14 @@ We can also benchmark this as @benchmark gradient_descent($M, $f, $grad_f, $p0; stopping_criterion=$sc) ``` - BenchmarkTools.Trial: 102 samples with 1 evaluation. - Range (min … max): 47.810 ms … 53.557 ms ┊ GC (min … max): 5.09% … 6.53% - Time (median): 48.820 ms ┊ GC (median): 5.34% - Time (mean ± σ): 49.060 ms ± 818.642 μs ┊ GC (mean ± σ): 5.77% ± 0.64% + BenchmarkTools.Trial: 100 samples with 1 evaluation. + Range (min … max): 48.285 ms … 56.649 ms ┊ GC (min … max): 4.84% … 6.96% + Time (median): 49.552 ms ┊ GC (median): 5.41% + Time (mean ± σ): 50.151 ms ± 1.731 ms ┊ GC (mean ± σ): 5.56% ± 0.64% - ▅▅█ ▃▃ - ▄▃▁▅▄▁▅▃▃▄███▅▅▇▃▁▆███▁▃▅▁▃▁▁▁▁▁▁▁▁▁▁▁▃▃▃▁▁▁▃▁▁▁▁▁▁▁▁▁▁▁▁▁▁▃ ▃ - 47.8 ms Histogram: frequency by time 52.4 ms < + ▂▃ █▃▃▆ ▂ + ▅████████▅█▇█▄▅▇▁▅█▅▇▄▇▅▁▅▄▄▄▁▄▁▁▁▄▄▁▁▁▁▁▁▄▁▁▁▁▁▁▄▁▄▁▁▁▁▁▁▄ ▄ + 48.3 ms Histogram: frequency by time 56.6 ms < Memory estimate: 194.10 MiB, allocs estimate: 655347. @@ -115,14 +115,14 @@ We can again benchmark this ) setup = (m2 = deepcopy($p0)) ``` - BenchmarkTools.Trial: 179 samples with 1 evaluation. - Range (min … max): 27.027 ms … 31.367 ms ┊ GC (min … max): 0.00% … 11.00% - Time (median): 27.712 ms ┊ GC (median): 0.00% - Time (mean ± σ): 27.939 ms ± 779.920 μs ┊ GC (mean ± σ): 0.84% ± 2.56% + BenchmarkTools.Trial: 176 samples with 1 evaluation. + Range (min … max): 27.419 ms … 34.154 ms ┊ GC (min … max): 0.00% … 0.00% + Time (median): 28.001 ms ┊ GC (median): 0.00% + Time (mean ± σ): 28.412 ms ± 1.079 ms ┊ GC (mean ± σ): 0.73% ± 2.24% - ▄▃▆█▇▄▇ - ▅▁▁▅▅▅▇████████▅▇▆▁▅▁▁▅▁▁▁▅▁▁▁▁▁▁▁▁▁▁▁▁▅▁▁▁▅▁▁▁▁▁▅▆▁▅▅▁▁▁▇▁▇ ▅ - 27 ms Histogram: log(frequency) by time 30.7 ms < + ▁▅▇█▅▂▄ ▁ + ▄▁███████▆█▇█▄▆▃▃▃▃▁▁▃▁▁▃▁▃▃▁▄▁▁▃▃▁▁▄▁▁▃▅▃▃▃▁▃▃▁▁▁▁▁▁▁▁▃▁▁▃ ▃ + 27.4 ms Histogram: frequency by time 31.9 ms < Memory estimate: 3.76 MiB, allocs estimate: 5949. diff --git a/tutorials/ConstrainedOptimization.qmd b/tutorials/ConstrainedOptimization.qmd index 7cfd3826ac..22085957b2 100644 --- a/tutorials/ConstrainedOptimization.qmd +++ b/tutorials/ConstrainedOptimization.qmd @@ -252,5 +252,9 @@ maximum(g(M, w1)) ## Literature -::: {#refs} -::: \ No newline at end of file +````{=commonmark} +```@bibliography +Pages = ["tutorials/ConstrainedOptimization.md"] +Canonical=false +``` +```` diff --git a/tutorials/GeodesicRegression.qmd b/tutorials/GeodesicRegression.qmd index e9bae8aae3..f7d24aaff2 100644 --- a/tutorials/GeodesicRegression.qmd +++ b/tutorials/GeodesicRegression.qmd @@ -510,5 +510,9 @@ Note that the geodesics from the data to the regression geodesic meet at a nearl ## Literature -::: {#refs} -::: \ No newline at end of file +````{=commonmark} +```@bibliography +Pages = ["tutorials/GeodesicRegression.md"] +Canonical=false +``` +````