Fixing documentation in Glossary, Links in Examples and Resolving Issue #66

Fe-r-oz commented 4 months ago

Hi, was reading the glossary and found a small typo. Fixed it.

Fe-r-oz commented 4 months ago

In the specific examples page, the examples links were leading to error pages:

https://juliaquantumcontrol.github.io/Krotov.jl/stable/examples/simple_state_to_state/ (leads to 404 error page)

Replaced all the links with the correct ones: For instance

https://juliaquantumcontrol.github.io/QuantumControlExamples.jl/stable/examples/simple_state_to_state/#Optimization-of-a-State-to-State-Transfer-in-a-Two-Level-System (leads to correct page)

Fe-r-oz commented 4 months ago

Some links and description pages in QuantumControlExampes.jl have to be modified as well.

I will change the spelling in the link to parameterization in Example Page of QuantumControl.jl for Pulse Parameterization example for Krotov Method. Later, after this PR, we can modify thekrotov.jlso that everything is consistent in all places.

https://juliaquantumcontrol.github.io/QuantumControlExamples.jl/stable/tutorials/krotov_pulse_**parameterization**/)

Fe-r-oz commented 4 months ago

Sorry for another workflow run! Now, I made the spelling in the links leading to QuantumControlExampes.jl examples consistent as well.

The pulse_parameterization and other tests except CI doctype all passed in first workflow run though.

Fe-r-oz commented 4 months ago

The CI doctype test failing because of extra line. Fixed it.

Also, improved the documentation in QuantumControlExamples.jlas well: https://github.com/JuliaQuantumControl/QuantumControlExamples.jl/pull/1

goerz commented 4 months ago

Cool, thanks! Since this is a breaking change, I'll want to let it sit for a bit to accumulate some other breaking changes. In particular, I'm organizing a workshop in two weeks that will feature the QuantumControl package, and I'm not going to merge anything breaking before that.

I'll have a look at these PRs afterward.

Fe-r-oz commented 3 months ago

Hi Michael,

Is this codestyle error simply occuring because we normalized the spelling of one word? In the main, src/ file, the evaluate function used which is same as shown via +, but the diff assumes it's the - minus one.

https://github.com/JuliaQuantumControl/QuantumControl.jl/blob/1f575a22de150dd8e4b8528998013630cbb73a46/src/pulse_parametrizations.jl#L406-L411

diff --git a/src/pulse_parameterizations.jl b/src/pulse_parameterizations.jl
│ index 09f5f1f..ebacbdf 100644
│ --- a/src/pulse_parameterizations.jl
│ +++ b/src/pulse_parameterizations.jl
│ @@ -400 +400,6 @@ end
│ -function evaluate(deriv::ShapedParameterizationPulseDerivative, tlist, n; vals_dict=IdDict())
│ +function evaluate(
│ +    deriv::ShapedParameterizationPulseDerivative,
│ +    tlist,
│ +    n;
│ +    vals_dict=IdDict()
│ +)
└ @ Main ~/work/_temp/[24](https://github.com/JuliaQuantumControl/QuantumControl.jl/actions/runs/9052722822/job/24928610529?pr=68#step:6:25)a1a795-44c6-4977-b0c9-9b0c8d967774:5
Error: Process completed with exit code 1.

goerz commented 3 months ago

Is this codestyle error simply occuring because we normalized the spelling of one word?

Sure, there's a maximum line length, so if you add a letter to word that can push it over the limit, and the line has to be broken into multiple lines

Fe-r-oz commented 3 months ago

if you add a letter to word that can push it over the limit, and the line has to be broken into multiple lines

I see, we can change the maximum line length by a couple letters so that the doc-style test passes?

I checked for any potential whitespaces, even used the same src file present in main, just changed ..ri.. to ..eri.. to be sure that there was not any potential whitespaces.

goerz commented 3 months ago

we can change the maximum line length

No, definitely not. Use make codestyle (or the equivalent command in the Julia REPL) to reformat the code to adhere to the required style.

Fe-r-oz commented 3 months ago

Thanks! I'll explore make codestyle or alternative commands.

Fe-r-oz commented 3 months ago

Applied make codestyle! Sorry, I didn't knew about the make stuff before!

I will now usetest()to see to make sure that all the tests pass!

julia --project=test -e 'using JuliaFormatter; format(".", verbose=true)'
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/devrepl.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/docs/generate_api.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/docs/make.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/ext/QuantumControlFiniteDifferencesExt.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/ext/QuantumControlZygoteExt.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/src/QuantumControl.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/src/deprecate.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/src/functionals.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/src/print_versions.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/src/pulse_parameterizations.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/src/reexport.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/src/set_default_ad_framework.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/src/workflows.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/test/clean.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/test/init.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/test/runtests.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/test/test_functionals.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/test/test_optimize_or_load.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/test/test_pulse_parameterizations.jl
Formatting /home/Desktop/New/qc/4/JuliaQuantumControl/QuantumControl.jl/test/test_run_or_load.jl

Fe-r-oz commented 3 months ago

Test Results

Test Summary:           | Pass  Total  Time
QuantumControl versions |    3      3  1.9s

* Functionals (test_functionals.jl):
189.185000 seconds (73.64 M allocations: 4.808 GiB, 1.38% gc time, 46.03% compilation time: <1% of which was recompilation)

* Run-or-load (test_run_or_load.jl):
134.203390 seconds (21.57 M allocations: 1.472 GiB, 0.71% gc time, 38.25% compilation time: 41% of which was recompilation)

* Optimize-or-load (test_optimize_or_load.jl):

 17.979704 seconds (23.57 M allocations: 1.657 GiB, 5.28% gc time, 99.17% compilation time: 9% of which was recompilation)

* Pulse Parameterizations (test_pulse_parameterizations.jl):
 26.718649 seconds (23.18 M allocations: 1.617 GiB, 3.75% gc time, 84.87% compilation time: 14% of which was recompilation)

Test Summary:             | Pass  Total     Time
QuantumControl            |   96     96  6m08.3s
  Functionals             |   19     19  3m09.2s
  Run-or-load             |    5      5  2m14.2s
  Optimize-or-load        |   25     25    18.0s
  Pulse Parameterizations |   47     47    26.7s
368.754314 seconds (142.45 M allocations: 9.587 GiB, 1.49% gc time, 48.70% compilation time: 15% of which was recompilation)
┌───────────────────────────────────────────┬────────┬────────┬────────┬──────────┐
│ File name                                 │  Total │    Hit │ Missed │ Coverage │
├───────────────────────────────────────────┼────────┼────────┼────────┼──────────┤
│ ext/QuantumControlFiniteDifferencesExt.jl │     13 │     13 │      0 │     100% │
│ ext/QuantumControlZygoteExt.jl            │     12 │     12 │      0 │     100% │
│ src/QuantumControl.jl                     │      6 │      6 │      0 │     100% │
│ src/deprecate.jl                          │      0 │      0 │      0 │        - │
│ src/functionals.jl                        │     99 │     90 │      9 │      91% │
│ src/print_versions.jl                     │     15 │     14 │      1 │      93% │
│ src/pulse_parameterizations.jl            │    129 │     88 │     41 │      68% │
│ src/reexport.jl                           │      7 │      7 │      0 │     100% │
│ src/set_default_ad_framework.jl           │      7 │      6 │      1 │      86% │
│ src/workflows.jl                          │    151 │    135 │     16 │      89% │
├───────────────────────────────────────────┼────────┼────────┼────────┼──────────┤
│ TOTAL                                     │    439 │    371 │     68 │      85% │
└───────────────────────────────────────────┴────────┴────────┴────────┴──────────┘
nothing

JuliaQuantumControl / QuantumControl.jl

Fixing documentation in Glossary, Links in Examples and Resolving Issue #66 #68