musica 0.12.0__cp311-cp311-win_amd64.whl → 0.12.1__cp311-cp311-win_amd64.whl

{musica-0.12.0.dist-info → musica-0.12.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: musica
-Version: 0.12.0
+Version: 0.12.1
 Summary: MUSICA is a Python library for performing computational simulations in atmospheric chemistry.
 Author-Email: Matthew Dawsom <mattdawson@ucar.edu>, Jiwon Gim <jiwongim@ucar.edu>, David Fillmore <fillmore@ucar.edu>, Kyle Shores <kshores@ucar.edu>, Montek Thind <mthind@ucar.edu>
 Maintainer-Email: ACOM MUSICA Developers <musica-support@ucar.edu>
@@ -208,12 +208,23 @@ License:                                  Apache License
          
 Project-URL: homepage, https://wiki.ucar.edu/display/MUSICA/MUSICA+Home
 Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: xarray>=2022.3.0
+Requires-Dist: ussa1976>=v0.3.4
 Provides-Extra: test
 Requires-Dist: numpy; extra == "test"
 Requires-Dist: pytest; extra == "test"
+Requires-Dist: matplotlib; extra == "test"
 Provides-Extra: gpu
 Requires-Dist: nvidia-cublas-cu12; extra == "gpu"
 Requires-Dist: nvidia-cuda-runtime-cu12; extra == "gpu"
+Provides-Extra: tutorial
+Requires-Dist: pandas; extra == "tutorial"
+Requires-Dist: matplotlib; extra == "tutorial"
+Requires-Dist: numpy; extra == "tutorial"
+Requires-Dist: scipy; extra == "tutorial"
+Requires-Dist: seaborn; extra == "tutorial"
+Requires-Dist: dask[distributed]; extra == "tutorial"
+Requires-Dist: dask-jobqueue; extra == "tutorial"
 Description-Content-Type: text/markdown
 
 # MUSICA
@@ -228,6 +239,8 @@ Description-Content-Type: text/markdown
 [![PyPI version](https://badge.fury.io/py/musica.svg)](https://pypi.org/p/musica)
 [![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=22322&r=123)
 [![codecov](https://codecov.io/gh/NCAR/musica/branch/main/graph/badge.svg)](https://codecov.io/gh/NCAR/musica)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NCAR/musica/HEAD?filepath=tutorials)
+
 
 Multi-Scale Infrastructure for Chemistry and Aerosols
 
@@ -241,6 +254,9 @@ At present the project encompasses these core components
 - [MICM](https://github.com/NCAR/micm)
     - Model Independent Chemical Module
 
+- [CARMA](https://github.com/ESCOMP/CARMA)
+    - Community Aerosol and Radiation Model for Atmospheres (integration in development)
+
 - [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration)
     - The standardized format to describe atmospheric chemistry
 
@@ -257,6 +273,27 @@ MUSICA is installable via pip for Python or CMake for C++.
 pip install musica
 ```
 
+If you would like GPU support, you must first [add the NVIDIA pypi index](https://docs.nvidia.com/cuda/cuda-quick-start-guide/#pip-wheels-linux) and then you can specify the gpu install option for MUSICA. Note that GPU support has only been tested on linux.
+
+```
+pip install --upgrade setuptools pip wheel
+pip install nvidia-pyindex
+pip install musica[gpu]
+```
+
+To build the package locally,
+
+```
+pip install -e .
+```
+
+If you have an NVIDIA GPU and cuda installed, you can enable a build of musica with GPU support by setting the environment 
+variable `BUILD_GPU`.
+
+```
+BUILD_GPU=1 pip install -e .
+```
+
 ## CMake
 ```
 $ git clone https://github.com/NCAR/musica.git
@@ -270,7 +307,7 @@ $ make install
 
 # Using the MUSICA Python API
 MUSICA makes its chemical mechanism analysis and visualization available through a Python API. The following example works through solving a simple chemistry system. Please refer to the [official documentation](https://ncar.github.io/musica/index.html) for further tutorials and examples.
-```
+```python
 # --- Import Musica ---
 import musica
 import musica.mechanism_configuration as mc
@@ -305,7 +342,6 @@ pressure=101000.0
 state = solver.create_state()
 state.set_concentrations({"A": 1.0, "B": 3.0, "C": 5.0})
 state.set_conditions(temperature, pressure)
-initial_pressure = state.get_conditions()['air_density'][0] # store for visualization and output
 
 # --- 6. Time parameters ---
 time_step = 4  # stepping
@@ -368,7 +404,7 @@ Introduced in [Pull Request #124](https://github.com/NCAR/musica/pull/124), it i
 | Musica Dependency                                      | Repository                | Branch, Tag or Hash|
 | ------------------------------------------------------ | --------------------------|--------------------|
 | [Google Test](https://github.com/google/googletest.git)| GOOGLETEST_GIT_REPOSITORY | GOOGLETEST_GIT_TAG |
-| [MICM](https://github.com/NCAR/mcim.git)               | MICM_GIT_REPOSITORY       | MICM_GIT_TAG       | 
+| [MICM](https://github.com/NCAR/micm.git)               | MICM_GIT_REPOSITORY       | MICM_GIT_TAG       | 
 | [TUV-X](https://github.com/NCAR/tuv-x.git)             | TUVX_GIT_REPOSITORY       | TUVX_GIT_TAG       |
 | [PyBind11](https://github.com/pybind/pybind11)         | PYBIND11_GIT_REPOSITORY   | PYBIND11_GIT_TAG   |
 | [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration.git) | MECH_CONFIG_GIT_REPOSITORY | MECH_CONFIG_GIT_TAG |
@@ -388,41 +424,6 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
     $ cmake .. \
         -DTUVX_GIT_TAG=a6b2c4d8745
 
-
-### Python build
-Musica has python bindings. If you want to install the python package, you may `pip install musica`.
-
-#### PyPi
-If you only want to use the CPU components, 
-
-```
-pip install musica
-```
-
-Note that GPU support has only been tested on linux. If you have an NVIDIA GPU and would like to take 
-advantage of our GPU solver, you must first [add the NVIDIA pypi index](https://docs.nvidia.com/cuda/cuda-quick-start-guide/#pip-wheels-linux) and then install musica with our gpu option.
-
-```
-pip install --upgrade setuptools pip wheel
-pip install nvidia-pyindex
-pip install musica[gpu]
-```
-
-#### Local build
-
-Musica has python bindings. To build the package locally,
-
-```
-pip install -e .
-```
-
-If you have an NVIDIA GPU and cuda installed, you can enable a build of musica with GPU support by setting the environment 
-variable `BUILD_GPU`.
-
-```
-BUILD_GPU=1 pip install -e .
-```
-
 # Contributing
 
 We welcome contributions from the community! Please see our [Contributing Guide](CONTRIBUTING.md) for information on how to get involved.

musica-0.12.1.dist-info/RECORD

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{musica-0.12.0.dist-info → musica-0.12.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.11.4
+Generator: scikit-build-core 0.11.5
 Root-Is-Purelib: false
 Tag: cp311-cp311-win_amd64
 

musica-0.12.1.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+musica-cli = musica.main:main
+

musica/test/examples/v0/config.json

@@ -1,7 +0,0 @@
-{
-    "camp-files": [
-      "species.json",
-      "reactions.json"
-    ]
-  }
-  

musica/test/examples/v0/config.yaml

@@ -1,3 +0,0 @@
-camp-files:
-- species.yaml
-- reactions.yaml

musica/test/examples/v0/reactions.json

@@ -1,193 +0,0 @@
-{
-  "camp-data": [
-    {
-      "type": "MECHANISM",
-      "name": "music box interactive configuration",
-      "reactions": [
-        {
-          "type": "PHOTOLYSIS",
-          "scaling factor": 1,
-          "MUSICA name": "foo",
-          "reactants": {
-            "foo": {}
-          },
-          "products": {
-            "buz": {
-              "yield": 1
-            },
-            "bar": {
-              "yield": 1
-            }
-          }
-        },
-        {
-          "type": "ARRHENIUS",
-          "A": 6e-34,
-          "Ea": 0,
-          "B": -2.4,
-          "D": 300,
-          "E": 0,
-          "reactants": {
-            "bar": {
-              "qty": 1
-            },
-            "quuz": {
-              "qty": 1
-            },
-            "M": {
-              "qty": 1
-            }
-          },
-          "products": {
-            "baz": {
-              "yield": 1
-            },
-            "M": {
-              "yield": 1
-            }
-          }
-        },
-        {
-          "type": "TROE",
-          "k0_A": 2.5e-31,
-          "k0_B": -1.8,
-          "k0_C": 0,
-          "kinf_A": 2.2e-11,
-          "kinf_B": -0.7,
-          "kinf_C": 0,
-          "Fc": 0.6,
-          "N": 1,
-          "reactants": {
-            "bar": {
-              "qty": 1
-            },
-            "foo": {
-              "qty": 1
-            }
-          },
-          "products": {
-            "baz": {
-              "yield": 1
-            }
-          }
-        },
-        {
-          "type": "EMISSION",
-          "scaling factor": 1,
-          "MUSICA name": "buz",
-          "species": "buz"
-        },
-        {
-          "type": "FIRST_ORDER_LOSS",
-          "species": "bar",
-          "MUSICA name": "bar",
-          "scaling factor": 2.5
-        },
-        {
-          "type": "TERNARY_CHEMICAL_ACTIVATION",
-          "reactants": {
-            "bar" : { },
-            "baz" : { }
-          },
-          "products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "k0_A": 32.1,
-          "k0_B": -2.3,
-          "k0_C": 102.3,
-          "kinf_A": 63.4,
-          "kinf_B": -1.3,
-          "kinf_C": 908.5,
-          "Fc": 1.3,
-          "N": 32.1
-        },
-        {
-          "type": "BRANCHED",
-          "reactants": {
-            "foo" : { },
-            "quz" : { "qty" :2 }
-          },
-          "alkoxy products": {
-            "bar": { "yield": 1.0 },
-            "baz": { "yield": 3.2 }
-          },
-          "nitrate products": {
-            "quz": { "yield": 1.0 }
-          },
-          "Y" : 42.3,
-          "X" : 12.3,
-          "a0" : 1.0e-5,
-          "n" : 3
-        },
-        {
-          "type": "WENNBERG_NO_RO2",
-          "reactants": {
-            "bar" : { },
-            "baz" : { }
-          },
-          "alkoxy products": {
-            "baz": { }
-          },
-          "nitrate products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "Y" : 2.3e8,
-          "X" : 0.32,
-          "a0" : 0.423,
-          "n" : 6
-        },
-        {
-          "type": "TUNNELING",
-          "reactants": {
-            "bar" : { },
-            "baz" : { }
-          },
-          "products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "A": 32.1,
-          "B": -2.3,
-          "C": 102.3
-        },
-        {
-          "type": "WENNBERG_TUNNELING",
-          "reactants": {
-            "bar2" : { },
-            "baz2" : { }
-          },
-          "products": {
-            "bar2": { "yield": 0.5 },
-            "foo2": { }
-          },
-          "A": 2.1,
-          "B": -1.3,
-          "C": 12.3
-        },
-        {
-          "type": "SURFACE",
-          "gas-phase reactant": "bar",
-          "gas-phase products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "reaction probability": 0.5,
-          "MUSICA name": "kbar"
-        },
-        {
-          "type": "USER_DEFINED",
-          "MUSICA name": "bar",
-          "reactants": { 
-            "foo" : { "qty": 2 }
-          },
-          "products": {
-            "bar" : { }
-          }, 
-          "scaling factor": 2.5
-        }
-      ]
-    }
-  ]
-}

musica/test/examples/v0/reactions.yaml

@@ -1,142 +0,0 @@
-camp-data:
-- name: music box interactive configuration
-  reactions:
-  - MUSICA name: foo
-    products:
-      bar:
-        yield: 1
-      buz:
-        yield: 1
-    reactants:
-      foo: {}
-    scaling factor: 1
-    type: PHOTOLYSIS
-  - A: 6.0e-34
-    B: -2.4
-    D: 300
-    E: 0
-    Ea: 0
-    products:
-      M:
-        yield: 1
-      baz:
-        yield: 1
-    reactants:
-      M:
-        qty: 1
-      bar:
-        qty: 1
-      quuz:
-        qty: 1
-    type: ARRHENIUS
-  - Fc: 0.6
-    N: 1
-    k0_A: 2.5e-31
-    k0_B: -1.8
-    k0_C: 0
-    kinf_A: 2.2e-11
-    kinf_B: -0.7
-    kinf_C: 0
-    products:
-      baz:
-        yield: 1
-    reactants:
-      bar:
-        qty: 1
-      foo:
-        qty: 1
-    type: TROE
-  - MUSICA name: buz
-    scaling factor: 1
-    species: buz
-    type: EMISSION
-  - MUSICA name: bar
-    scaling factor: 2.5
-    species: bar
-    type: FIRST_ORDER_LOSS
-  - Fc: 1.3
-    N: 32.1
-    k0_A: 32.1
-    k0_B: -2.3
-    k0_C: 102.3
-    kinf_A: 63.4
-    kinf_B: -1.3
-    kinf_C: 908.5
-    products:
-      bar:
-        yield: 0.5
-      foo: {}
-    reactants:
-      bar: {}
-      baz: {}
-    type: TERNARY_CHEMICAL_ACTIVATION
-  - X: 12.3
-    Y: 42.3
-    a0: 1.0e-05
-    alkoxy products:
-      bar:
-        yield: 1.0
-      baz:
-        yield: 3.2
-    n: 3
-    nitrate products:
-      quz:
-        yield: 1.0
-    reactants:
-      foo: {}
-      quz:
-        qty: 2
-    type: BRANCHED
-  - X: 0.32
-    Y: 230000000.0
-    a0: 0.423
-    alkoxy products:
-      baz: {}
-    n: 6
-    nitrate products:
-      bar:
-        yield: 0.5
-      foo: {}
-    reactants:
-      bar: {}
-      baz: {}
-    type: WENNBERG_NO_RO2
-  - A: 32.1
-    B: -2.3
-    C: 102.3
-    products:
-      bar:
-        yield: 0.5
-      foo: {}
-    reactants:
-      bar: {}
-      baz: {}
-    type: TUNNELING
-  - A: 2.1
-    B: -1.3
-    C: 12.3
-    products:
-      bar2:
-        yield: 0.5
-      foo2: {}
-    reactants:
-      bar2: {}
-      baz2: {}
-    type: WENNBERG_TUNNELING
-  - MUSICA name: kbar
-    gas-phase products:
-      bar:
-        yield: 0.5
-      foo: {}
-    gas-phase reactant: bar
-    reaction probability: 0.5
-    type: SURFACE
-  - MUSICA name: bar
-    products:
-      bar: {}
-    reactants:
-      foo:
-        qty: 2
-    scaling factor: 2.5
-    type: USER_DEFINED
-  type: MECHANISM

musica/test/examples/v0/species.json

@@ -1,40 +0,0 @@
-{
-  "camp-data": [
-    {
-      "name": "foo",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "bar",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "buz",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "quuz",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "foo2",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "bar2",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "baz",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "baz2",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "M",
-      "type": "CHEM_SPEC"
-    }
-  ]
-}

musica/test/examples/v0/species.yaml

@@ -1,19 +0,0 @@
-camp-data:
-- name: foo
-  type: CHEM_SPEC
-- name: bar
-  type: CHEM_SPEC
-- name: buz
-  type: CHEM_SPEC
-- name: quuz
-  type: CHEM_SPEC
-- name: foo2
-  type: CHEM_SPEC
-- name: bar2
-  type: CHEM_SPEC
-- name: baz
-  type: CHEM_SPEC
-- name: baz2
-  type: CHEM_SPEC
-- name: M
-  type: CHEM_SPEC

musica/test/test_parser.py

@@ -1,57 +0,0 @@
-import pytest
-from musica.mechanism_configuration import *
-from test_util_full_mechanism import get_fully_defined_mechanism, validate_full_v1_mechanism
-
-
-def test_parsed_full_v1_configuration():
-    parser = Parser()
-    extensions = [".yaml", ".json"]
-    for extension in extensions:
-        path = f"musica/test/examples/v1/full_configuration/full_configuration{extension}"
-        mechanism = parser.parse(path)
-        validate_full_v1_mechanism(mechanism)
-
-
-def test_parser_reports_bad_files():
-    parser = Parser()
-    extensions = [".yaml", ".json"]
-    for extension in extensions:
-        path = f"musica/test/examples/_missing_configuration{extension}"
-        with pytest.raises(Exception):
-            parser.parse(path)
-
-
-def test_hard_coded_full_v1_configuration():
-    MECHANISM_FULLY_DEFINED = get_fully_defined_mechanism()
-    validate_full_v1_mechanism(MECHANISM_FULLY_DEFINED)
-
-
-def test_hard_coded_default_constructed_types():
-    arrhenius = Arrhenius()
-    assert arrhenius.type == ReactionType.Arrhenius
-    condensed_phase_arrhenius = CondensedPhaseArrhenius()
-    assert condensed_phase_arrhenius.type == ReactionType.CondensedPhaseArrhenius
-    condensed_phase_photolysis = CondensedPhasePhotolysis()
-    assert condensed_phase_photolysis.type == ReactionType.CondensedPhasePhotolysis
-    emission = Emission()
-    assert emission.type == ReactionType.Emission
-    first_order_loss = FirstOrderLoss()
-    assert first_order_loss.type == ReactionType.FirstOrderLoss
-    henrys_law = HenrysLaw()
-    assert henrys_law.type == ReactionType.HenrysLaw
-    photolysis = Photolysis()
-    assert photolysis.type == ReactionType.Photolysis
-    simpol_phase_transfer = SimpolPhaseTransfer()
-    assert simpol_phase_transfer.type == ReactionType.SimpolPhaseTransfer
-    surface = Surface()
-    assert surface.type == ReactionType.Surface
-    troe = Troe()
-    assert troe.type == ReactionType.Troe
-    tunneling = Tunneling()
-    assert tunneling.type == ReactionType.Tunneling
-    wet_deposition = WetDeposition()
-    assert wet_deposition.type == ReactionType.WetDeposition
-    branched = Branched()
-    assert branched.type == ReactionType.Branched
-    user_defined = UserDefined()
-    assert user_defined.type == ReactionType.UserDefined