update (#3)

* fix ishermitian for dense and sparse operator * Fix manybody deprecated syntax * Change steady state sorting (qojulia#231) * Sort by absolute value of real part * Move normalization and sort by absolute value * Update checking and error message * Fix steady eig docstring formatting * Bump REQUIRE to v0.7-beta2 (qojulia#230) * Bump REQUIRE to v0.7-beta2 * Fix deprecations * Fix deprecations * Remove Compat imports * Change WignerSymbols version * First successful build * Fock tests pass * Some more tests pass * All tests except printing pass * Replace Complex128 with ComplexF64 in tests * Rename Complex128 to ComplexF64 * Add FFTW requirement * Update printing * Add Arpack requirement * Add rounding to printing * Update tests to use 0.7 * Fix compilation deprecation warnings * Fix printing * Fix deprecations * Rename full to dense * Fix some more deprecations * More deprecations * Fix operator deprecations * Fix particle deprecations * Fix all deprecations occurring in tests * Update REQUIRE * Update appveyor * Fix a bug in subspace; export norm * Fix silly bug in subspace * v0.7 compatibility * Implement macros to skip checks commit f221430 Author: david-pl <[email protected]> Date: Fri Aug 17 11:16:22 2018 +0200 Update macro docstrings commit 62f10e8 Author: David Plankensteiner <[email protected]> Date: Tue Aug 14 21:17:58 2018 +0200 Fix stochastic checks commit 5c9eff5 Author: David Plankensteiner <[email protected]> Date: Tue Aug 14 20:45:51 2018 +0200 Rename macros commit f78cf33 Author: david-pl <[email protected]> Date: Tue Aug 14 16:01:36 2018 +0200 Start renaming stuff commit c5f8bd6 Author: David Plankensteiner <[email protected]> Date: Mon Aug 13 20:25:58 2018 +0200 Implement macros to skip checks * Define ' on Operator as dagger (qojulia#235) * fix typo * Enable v1.0 testing * Implement parametric types (qojulia#238) * Start parametric typing for Ket/Bra * Fix tensor vararg for StateVector * Fix subspacebasis field parameters * Fix semiclassical state for kets * Update testing scripts * Fix typo in appveyor * Fix semiclassical_stochastic ket typing * Fix travis 1.0 testing * Parametric typing for CompositeBasis * Rename Operator to AbstractOperator * Proper parametric type for CompositeBasis * Parametric typing for operators * Parametrize basis dimensions * Revert "Parametrize basis dimensions" This reverts commit b451987. * Update basis checks for states * Update basis checks for dense operators * Update basis checks for sparse operators * Update LazyProduct implementation * Update LazySum implementation * Update LazyTensor implementation * Add non-type parameters where needed to ensure correct basis dispatch * Update basis checks for schroedinger * Update basis checks for metrics * Update basis checks for phasespace * Update basis checks for master * Update basis checks for mcwf * Update basis checks for semiclassical * Update superoperators and steadystate * Update basis checks for stochastic solvers * Update timecorrelations basis checks * Added parameter to FFToperators so the gemv! is type stable * Add basis checks to FFT in-place multiplication * Implement transpose forsparse/dense operators * Proper recasting in mcwf * Add some missing basis checks * Fix silly copy-paste error * Less strict typing for liouvillian * Mention gitter in readme text * Some dots for states and operators Squashed commit of the following: commit abc523b Author: david-pl <[email protected]> Date: Fri Jan 11 10:28:33 2019 +0100 Broadcasting for states, operators and superoperators commit 838f717 Author: David Plankensteiner <[email protected]> Date: Sat Dec 8 12:59:47 2018 +0100 Use custom broadcasting styles commit bedef6e Author: David Plankensteiner <[email protected]> Date: Fri Dec 7 11:49:40 2018 +0100 Broadcasting for sparse and dense operators * Fix typo in macro export * Fix @warn and implement adjoint(StateVector) * Update tests to newer Julia versions * Fix documentation of gaussianstate * Patch failing tests * created coherentstate! for inplace operations * Fix bug in MCWF display_afterevent * before embedding check that the destination basis matches the operator basis (qojulia#246) * before embedding check that the destination basis matches the operator basis * Change embed to handle composite operators * perform embedding of an operator in a joint hilbert space * functional embedding with new syntax * more tests for composite bases * code review and a few more tests * Change Int64 to Int in type checks for x86 * remove intersect and union from sortedindices, as there are appropriate methods in Base * Fix default choice of noise for stochastics * Add Bloch-Redfield master equation (qojulia#250) * Added bloch_redfield_master submodule Added the option for a Bloch-Redfield master equation in the timeevolution module * Add files via upload * Delete bloch_redfield_master.jl * Delete QuantumOptics.jl * Update bloch_redfield_master.jl * Cleaned up and commented new bloch_redfield_master submodule * Delete bloch_redfield_master.jl * Moved bloch_redfield_master to correct location... * Re-added coherentstate! (inplace) * Add simple test * Include new test file * Replace vec2mat_index by CartesianIndices * Use timeevolution_base for BR master * Added docstrings and renamed c_ops kwarg to J Changed c_ops kwarg in bloch_redfield_tensor to J to be consistent with Linblad ME implementation * Fix a bug and better saving * Type-stable fout * Fixed docstring typos in bloch_redfield_master * Update README.md * Switch to Project.toml * Update Project.toml * Abstractions for quantum information on qubits (qojulia#251) * created abstractions for quantum information on qubits * changed how equality is handled and added tests * code review * cleanup on types and added tests * code review and composition for chi and ptm * better caching * code review for isapprox vs == * Move windows tests to travis * Improve in-place multiplication for lazy types * Patch bug in mcwf_dynamic * Make entropy_vn type-stable * Update Project.toml * Restrict broadcasting of functions on states and operators * Make bases immutable * use ARPACKException from Arpack.jl * Semiclassical MCWF (qojulia#255) * MCWF jump times and indices (qojulia#257) * semicl mcwf * semicl mcwf läuft * semiclassical mcfw * Change MCWF interface to display jumps * Semiclassical mcwf with display event * Add display_which and display_t to semiclassical mcwf * Clean up integrate_mcwf * Clean up semiclassical mcwf * Add docstrings * Add docstrings in semiclassical.mcwf * Fix tests * Update Project.toml * Remove QuantumOpticsBase functionality (qojulia#259) * Remove QuantumOpticsBase functionality * Re-add changes to mcwf interface lost during deletion * Update semiclassical mcwf docstrings * Fix precompilation * Add superoperator tests that cannot run in Base * Re-add spectralanalysis * Separate stochastic base functionality from timeevolution * Update Project.toml * Type-stable bloch_redfield_tensor (qojulia#262) * Made bloch_redfield_tensor function type-stable * Quick patch failing tests * Install TagBot as a GitHub Action * Update Project.toml Co-authored-by: goropikari <[email protected]> Co-authored-by: David Plankensteiner <[email protected]> Co-authored-by: David Nadlinger <[email protected]> Co-authored-by: Louis Ponet <[email protected]> Co-authored-by: wolfgang-n <[email protected]> Co-authored-by: alexander papageorge <[email protected]> Co-authored-by: sd109 <[email protected]> Co-authored-by: Kristoffer Carlsson <[email protected]> Co-authored-by: Julia TagBot <[email protected]>
karolpezet · Feb 12, 2020 · 6c37e18 · 6c37e18
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diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
@@ -0,0 +1,11 @@
+name: TagBot
+on:
+  schedule:
+    - cron: 0 * * * *
+jobs:
+  TagBot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.travis.yml b/.travis.yml
@@ -2,17 +2,15 @@ language: julia
 os:
     - osx
     - linux
+    - windows
 julia:
-    - 0.6
+    - 1
     - nightly
 matrix:
     allow_failures:
         - julia: nightly
 notifications:
     email: false
-script:
-    - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-    - julia -e 'Pkg.clone(pwd()); Pkg.build("QuantumOptics"); Pkg.test("QuantumOptics"; coverage=true)';
 after_success:
-    - julia -e 'cd(Pkg.dir("QuantumOptics")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
-    - julia -e 'cd(Pkg.dir("QuantumOptics")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())';
+    - julia -e 'import Pkg; cd(Pkg.dir("QuantumOptics")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
+    - julia -e 'import Pkg; cd(Pkg.dir("QuantumOptics")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())';
diff --git a/Project.toml b/Project.toml
@@ -0,0 +1,38 @@
+name = "QuantumOptics"
+uuid = "6e0679c1-51ea-5a7c-ac74-d61b76210b0c"
+version = "v0.7.1"
+
+[deps]
+QuantumOpticsBase = "4f57444f-1401-5e15-980d-4471b28d5678"
+Arpack = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97"
+DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
+FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
+WignerSymbols = "9f57e263-0b3d-5e2e-b1be-24f2bb48858b"
+
+[compat]
+QuantumOpticsBase = "0.1"
+Arpack = "0.4"
+DiffEqCallbacks = "2"
+FFTW = "1.2"
+OrdinaryDiffEq = "5"
+RecursiveArrayTools = "2"
+Reexport = "0.2"
+StochasticDiffEq = "6"
+WignerSymbols = "1"
+julia = "1"
+
+[extras]
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["LinearAlgebra", "SparseArrays", "Random", "Test"]
diff --git a/README.md b/README.md
@@ -9,18 +9,16 @@
 More information, documentation and examples can be found on our website http://qojulia.org.
 
 
-### Development status
-
 **Latest release:**
-  * [![Status of latest release on julia 0.6][pkg-0.6-img]][pkg-0.6-url]
+  * Version: [![Latest version tag][version-img]][version-url]
   * Test coverage:
         [![Test coverage status on coveralls][coveralls-img]][coveralls-url]
         [![Test coverage status on codecov][codecov-img]][codecov-url]
 
 
 ### Project structure
 
-The content associated with **QuantumOptics.jl** is distributed over several repositories under the [qojulia] organization on github:
+The source content associated with **QuantumOptics.jl** is distributed over several repositories under the [qojulia] organization on github:
 
 * The main code: https://github.com/qojulia/QuantumOptics.jl
 * Documentation: https://github.com/qojulia/QuantumOptics.jl-documentation
@@ -31,7 +29,7 @@ The content associated with **QuantumOptics.jl** is distributed over several rep
 
 ### Questions & Contributions
 
-Contributions of any kind are always welcome! Be it as questions, ideas for new features, bug reports or, our favorite case, sending pull requests.
+If you have any questions or need help, hop on our [gitter channel](https://gitter.im/QuantumOptics-jl/Lobby?source=orgpage) and ask away. Also, contributions of any kind are always welcome! Be it as ideas for new features, bug reports or, our favorite case, sending pull requests.
 
 ### Citing
 
@@ -62,3 +60,6 @@ If you like **QuantumOptics.jl**, we would appreciate it if you starred the repo
 
 [docs-url]: https://qojulia.org/documentation/
 [docs-img]: https://img.shields.io/badge/docs-stable-blue.svg
+
+[version-url]: https://github.com/qojulia/QuantumOptics.jl/releases
+[version-img]: https://img.shields.io/github/release/qojulia/QuantumOptics.jl.svg
diff --git a/REQUIRE b/REQUIRE
diff --git a/appveyor.yml b/appveyor.yml
diff --git a/src/QuantumOptics.jl b/src/QuantumOptics.jl
@@ -1,110 +1,40 @@
-__precompile__()
-
 module QuantumOptics
 
-export bases, Basis, GenericBasis, CompositeBasis, basis,
-        tensor, ⊗, permutesystems,
-        states, StateVector, Bra, Ket, basisstate,
-                dagger, normalize, normalize!,
-        operators, Operator, expect, variance, identityoperator, ptrace, embed,
-        operators_dense, DenseOperator, projector, dm,
-        operators_sparse, SparseOperator, diagonaloperator,
-        operators_lazysum, LazySum,
-        operators_lazyproduct, LazyProduct,
-        operators_lazytensor, LazyTensor,
-        superoperators, SuperOperator, DenseSuperOperator, SparseSuperOperator,
-                spre, spost, liouvillian,
-        fock, FockBasis, number, destroy, create,
-                fockstate, coherentstate, displace,
-        randstate, randoperator, thermalstate, coherentthermalstate, phase_average, passive_state,
-        spin, SpinBasis, sigmax, sigmay, sigmaz, sigmap, sigmam, spinup, spindown,
-        subspace, SubspaceBasis, projector,
-        particle, PositionBasis, MomentumBasis, samplepoints, gaussianstate,
-                position, momentum, potentialoperator, transform,
-        nlevel, NLevelBasis, transition, nlevelstate,
-        manybody, ManyBodyBasis, fermionstates, bosonstates,
-                manybodyoperator, onebodyexpect, occupation,
-        phasespace, qfunc, wigner, coherentspinstate, qfuncsu2, wignersu2, ylm,
-        metrics, tracenorm, tracenorm_h, tracenorm_nh,
-                tracedistance, tracedistance_h, tracedistance_nh,
-                entropy_vn, fidelity, ptranspose, PPT,
-                negativity, logarithmic_negativity,
-        spectralanalysis, eigenstates, eigenenergies, simdiag,
-        timeevolution, diagonaljumps,
+using Reexport
+@reexport using QuantumOpticsBase
+using SparseArrays, LinearAlgebra
+
+export qfunc, wigner, coherentspinstate, qfuncsu2, wignersu2, ylm,
+        eigenstates, eigenenergies, simdiag,
+        timeevolution, diagonaljumps, @skiptimechecks,
         steadystate,
         timecorrelations,
         semiclassical,
         stochastic
 
 
-include("sortedindices.jl")
-include("polynomials.jl")
-include("bases.jl")
-include("states.jl")
-include("operators.jl")
-include("operators_dense.jl")
-include("sparsematrix.jl")
-include("operators_sparse.jl")
-include("operators_lazysum.jl")
-include("operators_lazyproduct.jl")
-include("operators_lazytensor.jl")
-include("superoperators.jl")
-include("spin.jl")
-include("fock.jl")
-include("state_definitions.jl")
-include("subspace.jl")
-include("particle.jl")
-include("nlevel.jl")
-include("manybody.jl")
-include("transformations.jl")
 include("phasespace.jl")
-include("metrics.jl")
 module timeevolution
-    export diagonaljumps
+    export diagonaljumps, @skiptimechecks
+
     include("timeevolution_base.jl")
     include("master.jl")
     include("schroedinger.jl")
     include("mcwf.jl")
-    using .timeevolution_master
-    using .timeevolution_schroedinger
-    using .timeevolution_mcwf
+    include("bloch_redfield_master.jl")
 end
 include("steadystate.jl")
 include("timecorrelations.jl")
 include("spectralanalysis.jl")
 include("semiclassical.jl")
 module stochastic
+    include("stochastic_base.jl")
     include("stochastic_definitions.jl")
     include("stochastic_schroedinger.jl")
     include("stochastic_master.jl")
     include("stochastic_semiclassical.jl")
-    using .stochastic_schroedinger, .stochastic_master, .stochastic_semiclassical
-    using .stochastic_definitions
 end
-include("printing.jl")
 
-using .bases
-using .states
-using .operators
-using .operators_dense
-using .operators_sparse
-using .operators_lazysum
-using .operators_lazyproduct
-using .operators_lazytensor
-using .superoperators
-using .spin
-using .fock
-using .state_definitions
-using .subspace
-using .particle
-using .nlevel
-using .manybody
-using .phasespace
 using .timeevolution
-using .metrics
-using .spectralanalysis
-using .timecorrelations
-using .printing
-
 
 end # module