Create emcee.py

.github/workflows/continuous-integration-pip.yml

@@ -72,7 +72,7 @@ jobs:
         run: pytest --cov=./ --cov-report=xml
 
       - name: Upload coverage
-        uses: codecov/codecov-action@v2.0.2
+        uses: codecov/codecov-action@v1
 
   # build_windows_test:
   #   needs: [code_lint]
@@ -112,7 +112,7 @@ jobs:
   #       run: pytest --cov=./ --cov-report=xml
 
   #     - name: Upload coverage
-  #       uses: codecov/codecov-action@v2.0.2
+  #       uses: codecov/codecov-action@v1
 
   testing_windows:
     needs: [code_lint]
@@ -148,4 +148,4 @@ jobs:
         shell: pwsh
         run: pytest --cov=./ --cov-report=xml
       - name: Upload coverage
-        uses: codecov/codecov-action@v2.0.2
+        uses: codecov/codecov-action@v1

.github/workflows/wheels.yml

@@ -33,7 +33,7 @@ jobs:
         run: pytest --cov=./ --cov-report=xml
 
       - name: Upload coverage
-        uses: codecov/codecov-action@v2.0.2
+        uses: codecov/codecov-action@v1
 
   source-distribution:
     needs: [build-test]

.gitignore

@@ -11,7 +11,6 @@ __pycache__/*
 .Python
 build/
 .vscode/*
-.idea/*
 develop-eggs/
 dist/
 downloads/
@@ -106,7 +105,6 @@ tests/simpson/quad/**
 version/
 docs/examples/
 docs/fitting/
-_temp/
 
 # files
 class-diagram*

.pre-commit-config.yaml

@@ -48,17 +48,6 @@ repos:
     hooks:
       - id: flake8
         language: python
-        args:
-          [
-            "--ignore=E402",
-            "--exclude=.eggs, *.egg,build, src/mrsimulator/__init__.py",
-            "--filename=*.pyx, *py",
-            "--max-line-length=88",
-            "--max-complexity=8",
-            "--select=B,C,E,F,W,T,N8",
-            "--count",
-            "--statistics",
-          ]
 
   - repo: https://github.com/asottile/reorder_python_imports
     rev: v2.4.0

.pylintrc

@@ -0,0 +1 @@
+issue code: redefined-builtin

CHANGELOG

@@ -1,23 +1,6 @@
 Upcoming Changes
 ----------------
 
-What's new
-''''''''''
-
-**Method**
-
-- New Event class---``SpectralEvent``, ``ConstantTimeEvent``, and ``MixingEvent``. The MixingEvent
-  controls the mixing of transitions in a multi-event method.
-- A ``TransitionPathway`` object now includes a weight attribute, which holds the probability of
-  the transition pathway based on the mixing events defined within the method.
-
-**SpinSystem**
-
-- Add a new function ``simplify()`` to the spin system object, which reduces a spin system to
-  a list of irreducible spin systems.
-- Add a new function ``site_generator()`` to the utility collection sub-module, which simplify
-  the process of creating Site objects in bulk.
-
 Changes
 '''''''
 

docs/api_py/method.rst

@@ -1,13 +1,10 @@
 Method
 ======
 
-Method is the root user-level object that may be used in creating custom NMR simulation
-methods.
-
 .. toctree::
 
     method/method
     method/spectral_dimension
     method/event
     method/freq_contrib
-    method/query
+    method/transition_query

docs/api_py/method/event.rst

@@ -15,7 +15,3 @@ Events
     :show-inheritance:
     :members:
     :inherited-members: BaseModel
-
-.. autoclass:: MixingEvent
-    :show-inheritance:
-    :members:

docs/api_py/method/query.rst → docs/api_py/method/transition_query.rst

@@ -1,3 +1,4 @@
+.. _transition_query_api:
 
 .. currentmodule:: mrsimulator.method.query
 

docs/api_py/methods-summary.rst

@@ -48,11 +48,6 @@ Summary
 
 .. ~Cosy
 
-UML Diagram
------------
-
-.. figure:: ../_static/classes_methods.*
-
 
 Table of contents
 -----------------

docs/api_py/utils.rst

@@ -7,7 +7,6 @@ Utility functions
 .. currentmodule:: mrsimulator.utils.collection
 
 .. autofunction:: single_site_system_generator
-.. autofunction:: site_generator
 
 
 .. currentmodule:: mrsimulator.utils

docs/getting_started-objects.rst

@@ -468,11 +468,7 @@ see the list of transition pathways, for example,
 
     >>> from pprint import pprint
     >>> pprint(sim.methods[0].get_transition_pathways(system_4)) # 17O
-    [|-2.5⟩⟨-1.5|, weight=(1+0j),
-     |-1.5⟩⟨-0.5|, weight=(1+0j),
-     |-0.5⟩⟨0.5|, weight=(1+0j),
-     |0.5⟩⟨1.5|, weight=(1+0j),
-     |1.5⟩⟨2.5|, weight=(1+0j)]
+    [|-2.5⟩⟨-1.5|, |-1.5⟩⟨-0.5|, |-0.5⟩⟨0.5|, |0.5⟩⟨1.5|, |1.5⟩⟨2.5|]
 
 Notice, there are five transition pathways for the :math:`^{17}\text{O}` site, one
 associated with the central-transition, two with the inner-satellites, and two with
@@ -497,7 +493,7 @@ the outer-satellites. For central transition selective simulation, use the
     ... )
     >>> # the transition pathways
     >>> print(sim.methods[0].get_transition_pathways(system_4)) # 17O
-    [|-0.5⟩⟨0.5|, weight=(1+0j)]
+    [|-0.5⟩⟨0.5|]
 
 Now, you may simulate the central transition selective spectrum.
 :numref:`fig8_using_obj` depicts a central transition selective spectrum.

docs/installation/requirements.rst

@@ -13,7 +13,7 @@ Package dependencies
 - typing-extensions>=3.7
 - `matplotlib>=3.3.3 <https://matplotlib.org>`_ for figures and visualization,
 - monty>=2.0.4
-- `csdmpy>=0.4.1 <https://csdmpy.readthedocs.io/en/stable/>`_
+- `csdmpy>=0.4 <https://csdmpy.readthedocs.io/en/stable/>`_
 - `pydantic>=1.0 <https://pydantic-docs.helpmanual.io>`_
 - monty>=2.0.4
 

docs/notebooks/examples/1D_simulation(crystalline)/plot_0_Wollastonite.ipynb

@@ -87,7 +87,7 @@
       },
       "outputs": [],
       "source": [
-        "method = BlochDecaySpectrum(\n    channels=[\"29Si\"],\n    magnetic_flux_density=14.1,  # in T\n    rotor_frequency=1500,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 2048,\n            \"spectral_width\": 25000,  # in Hz\n            \"reference_offset\": -10000,  # in Hz\n            \"label\": r\"$^{29}$Si resonances\",\n        }\n    ],\n)\n\n# A graphical representation of the method object.\nplt.figure(figsize=(4, 2))\nmethod.plot()\nplt.show()"
+        "method = BlochDecaySpectrum(\n    channels=[\"29Si\"],\n    magnetic_flux_density=14.1,  # in T\n    rotor_frequency=1500,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 2048,\n            \"spectral_width\": 25000,  # in Hz\n            \"reference_offset\": -10000,  # in Hz\n            \"label\": r\"$^{29}$Si resonances\",\n        }\n    ],\n)"
       ]
     },
     {
@@ -168,7 +168,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(crystalline)/plot_1_PotassiumSulfate.ipynb

@@ -69,7 +69,7 @@
       },
       "outputs": [],
       "source": [
-        "method = BlochDecayCTSpectrum(\n    channels=[\"33S\"],\n    magnetic_flux_density=21.14,  # in T\n    rotor_frequency=14000,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 2048,\n            \"spectral_width\": 5000,  # in Hz\n            \"reference_offset\": 22500,  # in Hz\n            \"label\": r\"$^{33}$S resonances\",\n        }\n    ],\n)\n\n# A graphical representation of the method object.\nplt.figure(figsize=(4, 3))\nmethod.plot()\nplt.show()"
+        "method = BlochDecayCTSpectrum(\n    channels=[\"33S\"],\n    magnetic_flux_density=21.14,  # in T\n    rotor_frequency=14000,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 2048,\n            \"spectral_width\": 5000,  # in Hz\n            \"reference_offset\": 22500,  # in Hz\n            \"label\": r\"$^{33}$S resonances\",\n        }\n    ],\n)"
       ]
     },
     {
@@ -150,7 +150,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(crystalline)/plot_2_Coesite.ipynb

@@ -175,7 +175,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(crystalline)/plot_3_quad_csa.ipynb

@@ -132,7 +132,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(crystalline)/plot_3_satellite_transition_sim.ipynb

@@ -69,7 +69,7 @@
       },
       "outputs": [],
       "source": [
-        "method = Method1D(\n    name=\"Inner Satellite Spectrum\",\n    channels=[\"27Al\"],\n    magnetic_flux_density=21.14,  # in T\n    rotor_frequency=1e9,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 1024,\n            \"spectral_width\": 1e4,  # in Hz\n            \"reference_offset\": 1e4,  # in Hz\n            \"events\": [\n                {\n                    \"transition_query\": [\n                        {\"P\": [-1], \"D\": [2]}  # <-- select inner satellite transitions\n                    ]\n                }\n            ],\n        }\n    ],\n)\n\n# A graphical representation of the method object.\nplt.figure(figsize=(5, 3))\nmethod.plot()\nplt.show()"
+        "method = Method1D(\n    channels=[\"27Al\"],\n    magnetic_flux_density=21.14,  # in T\n    rotor_frequency=1e9,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 1024,\n            \"spectral_width\": 1e4,  # in Hz\n            \"reference_offset\": 1e4,  # in Hz\n            \"events\": [\n                {\n                    \"transition_query\": [\n                        {\"P\": [-1], \"D\": [2]}  # <-- select inner satellite transitions\n                    ]\n                }\n            ],\n        }\n    ],\n)"
       ]
     },
     {
@@ -123,7 +123,7 @@
       },
       "outputs": [],
       "source": [
-        "method2 = Method1D(\n    name=\"Satellite Spectrum\",\n    channels=[\"27Al\"],\n    magnetic_flux_density=21.14,  # in T\n    rotor_frequency=1e9,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 1024,\n            \"spectral_width\": 1e4,  # in Hz\n            \"reference_offset\": 1e4,  # in Hz\n            \"events\": [\n                {\n                    \"transition_query\": [\n                        {\"P\": [-1], \"D\": [2]},  # <-- select inter satellite transitions\n                        {\"P\": [-1], \"D\": [4]},  # <-- select outer satellite transitions\n                    ]\n                }\n            ],\n        }\n    ],\n)\n\n# A graphical representation of the method object.\nplt.figure(figsize=(5, 3))\nmethod2.plot()\nplt.show()"
+        "method2 = Method1D(\n    channels=[\"27Al\"],\n    magnetic_flux_density=21.14,  # in T\n    rotor_frequency=1e9,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 1024,\n            \"spectral_width\": 1e4,  # in Hz\n            \"reference_offset\": 1e4,  # in Hz\n            \"events\": [\n                {\n                    \"transition_query\": [\n                        {\"P\": [-1], \"D\": [2]},  # <-- select inter satellite transitions\n                        {\"P\": [-1], \"D\": [4]},  # <-- select outer satellite transitions\n                    ]\n                }\n            ],\n        }\n    ],\n)"
       ]
     },
     {
@@ -179,7 +179,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(crystalline)/plot_4_multi-quantum_spectrum.ipynb

@@ -58,7 +58,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Selecting the triple-quantum transition\n\nFor single-site spin-5/2 spin system, there are three triple-quantum transition\n\n- $|1/2\\rangle\\rightarrow|-5/2\\rangle$ ($P=-3, D=6$)\n- $|3/2\\rangle\\rightarrow|-3/2\\rangle$ ($P=-3, D=0$)\n- $|5/2\\rangle\\rightarrow|-1/2\\rangle$ ($P=-3, D=-6$)\n\nTo select one or more triple-quantum transitions, assign the respective value of P and\nD to the `transition_query`. Here, we select the symmetric triple-quantum transition.\n\n"
+        "## Selecting the triple-quantum transition\n\nFor spin-site spin-5/2 spin system, there are three triple-quantum transition\n\n- $|1/2\\rangle\\rightarrow|-5/2\\rangle$ ($P=-3, D=6$)\n- $|3/2\\rangle\\rightarrow|-3/2\\rangle$ ($P=-3, D=0$)\n- $|5/2\\rangle\\rightarrow|-1/2\\rangle$ ($P=-3, D=-6$)\n\nTo select one or more triple-quantum transitions, assign the respective value of P and\nD to the `transition_query`.\n\n"
       ]
     },
     {
@@ -69,7 +69,7 @@
       },
       "outputs": [],
       "source": [
-        "method = Method1D(\n    name=\"Arbitrary Transition Method\",\n    channels=[\"27Al\"],\n    magnetic_flux_density=21.14,  # in T\n    rotor_frequency=1e9,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 1024,\n            \"spectral_width\": 5e3,  # in Hz\n            \"reference_offset\": 2.5e4,  # in Hz\n            \"events\": [\n                {  # symmetric triple quantum transitions\n                    \"transition_query\": [{\"P\": [-3], \"D\": [0]}]\n                }\n            ],\n        }\n    ],\n)\n\n# A graphical representation of the method object.\nplt.figure(figsize=(5, 3))\nmethod.plot()\nplt.show()"
+        "method = Method1D(\n    channels=[\"27Al\"],\n    magnetic_flux_density=21.14,  # in T\n    rotor_frequency=1e9,  # in Hz\n    spectral_dimensions=[\n        {\n            \"count\": 1024,\n            \"spectral_width\": 5e3,  # in Hz\n            \"reference_offset\": 2.5e4,  # in Hz\n            \"events\": [\n                {  # symmetric triple quantum transitions\n                    \"transition_query\": [{\"P\": [-3], \"D\": [0]}]\n                }\n            ],\n        }\n    ],\n)"
       ]
     },
     {
@@ -107,7 +107,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(crystalline)/plot_5_dipolar_coupled.ipynb

@@ -136,7 +136,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(crystalline)/plot_6_coupled_spin_system.ipynb

@@ -136,7 +136,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(crystalline)/plot_7_CAS_dipolar_J.ipynb

@@ -186,7 +186,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(crystalline)/plot_8_Ethanol.ipynb

@@ -222,7 +222,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(macro_amorphous)/plot_0_protein_GB1.ipynb

@@ -179,7 +179,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(macro_amorphous)/plot_3_amorphous_like.ipynb

@@ -87,7 +87,7 @@
       },
       "outputs": [],
       "source": [
-        "spin_systems = single_site_system_generator(\n    isotope=\"29Si\",\n    isotropic_chemical_shift=iso,\n    shielding_symmetric={\"zeta\": zeta, \"eta\": eta},\n    abundance=pdf,\n)"
+        "spin_systems = single_site_system_generator(\n    isotopes=\"29Si\",\n    isotropic_chemical_shifts=iso,\n    shielding_symmetric={\"zeta\": zeta, \"eta\": eta},\n    abundance=pdf,\n)"
       ]
     },
     {
@@ -258,7 +258,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(macro_amorphous)/plot_4_amorphous_like_quad.ipynb

@@ -80,7 +80,7 @@
       },
       "outputs": [],
       "source": [
-        "spin_systems = single_site_system_generator(\n    isotope=\"27Al\",\n    isotropic_chemical_shift=iso,\n    quadrupolar={\"Cq\": Cq * 1e6, \"eta\": eta},  # Cq in Hz\n    abundance=pdf,\n)"
+        "spin_systems = single_site_system_generator(\n    isotopes=\"27Al\",\n    isotropic_chemical_shifts=iso,\n    quadrupolar={\"Cq\": Cq * 1e6, \"eta\": eta},  # Cq in Hz\n    abundance=pdf,\n)"
       ]
     },
     {
@@ -208,7 +208,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,

docs/notebooks/examples/1D_simulation(macro_amorphous)/plot_5_czjzek_distribution.ipynb

@@ -87,7 +87,7 @@
       },
       "outputs": [],
       "source": [
-        "systems = single_site_system_generator(\n    isotope=\"13C\", shielding_symmetric={\"zeta\": z_dist, \"eta\": e_dist}, abundance=amp\n)"
+        "systems = single_site_system_generator(\n    isotopes=\"13C\", shielding_symmetric={\"zeta\": z_dist, \"eta\": e_dist}, abundance=amp\n)"
       ]
     },
     {
@@ -159,7 +159,7 @@
       },
       "outputs": [],
       "source": [
-        "systems = single_site_system_generator(\n    isotope=\"71Ga\", quadrupolar={\"Cq\": cq_dist * 1e6, \"eta\": e_dist}, abundance=amp\n)"
+        "systems = single_site_system_generator(\n    isotopes=\"71Ga\", quadrupolar={\"Cq\": cq_dist * 1e6, \"eta\": e_dist}, abundance=amp\n)"
       ]
     },
     {
@@ -215,7 +215,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.11"
+      "version": "3.8.10"
     }
   },
   "nbformat": 4,