Merge branch 'v0.6.x' of https://github.com/DeepanshS/MRsimulator int…

…o v0.6.x

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

@@ -5,9 +5,13 @@ name: CI (pip)
 
 on:
   push:
-    branches: [master]
+    branches:
+      - master
+      - v?.?*
   pull_request:
-    branches: [master]
+    branches:
+      - master
+      - v?.?*
 
 jobs:
   code_lint:

docs/api_py/simulator.rst

@@ -18,6 +18,8 @@ Simulator
     .. automethod:: get_isotopes
     .. automethod:: load_spin_systems
     .. automethod:: export_spin_systems
+    .. automethod:: load_methods
+    .. automethod:: export_methods
     .. automethod:: run
     .. automethod:: save
     .. automethod:: load

docs/mrsim_IO.rst

@@ -28,7 +28,6 @@ as a string with a value and a unit.
 
 ..     >>> sim_coesite.save('sample_no_units.json', with_units=False)
 
-
 **Load simulator object from a JSON file**
 
 To load a JSON-compliant :ref:`simulator_api` serialized file, use the
@@ -54,10 +53,8 @@ parses the file for units.
     >>> import os
     >>> os.remove('sample.mrsim')
 
-
 ----
 
-
 Spin systems objects from Simulator class
 -----------------------------------------
 
@@ -103,6 +100,34 @@ class as
     >>> import os
     >>> os.remove('spin_systems.json')
 
+----
+
+Method objects from Simulator class
+-----------------------------------------
+
+**Export methods to a JSON file**
+
+Similarly, you may also serialize the method objects from the :ref:`simulator_api` object to
+a JSON-compliant file using :py:meth:`~mrsimulator.Simulator.export_methods` as
+
+.. doctest::
+
+    >>> sim_coesite.export_methods('coesite_method.mrmtd')
+
+
+**Import methods from a JSON file**
+
+Likewise, to import methods, use :py:meth:`~mrsimulator.Simulator.load_methods` as
+
+.. doctest::
+
+    >>> sim.load_methods('coesite_method.mrmtd')
+
+.. testsetup::
+    >>> import os
+    >>> os.remove('coesite_method.mrmtd')
+
+----
 
 Serialize simulation object from Method class as CSDM compliant file
 --------------------------------------------------------------------
@@ -116,6 +141,7 @@ save function as follows,
 
     >>> sim_coesite.method[0].simulation.save('coesite_simulation.csdf') # doctest:+SKIP
 
+----
 
 Serialize Simulator, SignalProcessor object to file
 ---------------------------------------------------

setup.py

@@ -204,7 +204,7 @@ def message(self, lib_centos, lib_ubuntu):
         print(f"For CentOS users\n\t{stat}")
         stat = f"sudo apt-get update\n\tsudo apt-get install {lib_ubuntu}"
         print(f"For Ubuntu users\n\t{stat}")
-        sys.exit(1)
+        # sys.exit(1)
 
 
 class MacOSSetup(Setup):

src/mrsimulator/__init__.py

@@ -22,7 +22,7 @@
 __license__ = "BSD License"
 __maintainer__ = "Deepansh J. Srivastava"
 __status__ = "Beta"
-__version__ = "0.6.0"
+__version__ = "0.6.1"
 
 import os
 

src/mrsimulator/methods/tests/test_method_updates.py

@@ -14,7 +14,7 @@
 sp = {"count": 1024, "spectral_width": 100}
 
 
-def test_read_write_methods():
+def test_read_write_obj_mrsim():
     for item in methods:
         kwargs = {"channels": ["93Nb"], "spectral_dimensions": [sp] * item.ndim}
 
@@ -27,6 +27,8 @@ def test_read_write_methods():
 
         sim = Simulator(spin_systems=[sys], methods=[fn1])
         sim.run()
+
+        # Test simulator object (.mrsim)
         sim.save("test.mrsim")
 
         sim2 = Simulator.load("test.mrsim")
@@ -36,4 +38,31 @@ def test_read_write_methods():
 
         assert sim == sim2, f"Error with {item} parse from Simulator.load()."
 
+        # Test spin system objects (.mrsys)
+        sim.export_spin_systems("test.mrsys")
+
+        sim2 = sim.copy()
+        sim2.load_spin_systems("test.mrsys")
+
+        assert (
+            sim.spin_systems == sim2.spin_systems
+        ), f"Error with {item} sim.load_spin_systems()."
+
+        # Test methods objects (.mrmth)
+        sim.export_methods("test.mrmth")
+
+        sim2 = sim.copy()
+        sim2.load_methods("test.mrmth")
+
+        # remove timestamps from csdm obj for testing
+        for mth in sim2.methods:
+            for item in [mth.simulation, mth.experiment]:
+                if item is not None:
+                    item._timestamp = ""
+            _ = [item.to("ppm", "nmr_frequency_ratio") for item in mth.simulation.x]
+
+        assert sim.methods == sim2.methods, f"Error with {item} sim.load_methods()."
+
     os.remove("test.mrsim")
+    os.remove("test.mrsys")
+    os.remove("test.mrmth")

src/mrsimulator/simulator/__init__.py

@@ -365,7 +365,6 @@ def load_spin_systems(self, filename: str):
         >>> sim.load_spin_systems(filename) # doctest:+SKIP
         """
         contents = import_json(filename)
-        # json_data = contents["spin_systems"]
         self.spin_systems = [SpinSystem.parse_dict_with_units(obj) for obj in contents]
 
     def export_spin_systems(self, filename: str):
@@ -384,12 +383,52 @@ def export_spin_systems(self, filename: str):
 
         >>> sim.export_spin_systems(filename) # doctest:+SKIP
         """
-        spin_sys = [SpinSystem.json(obj) for obj in self.spin_systems]
+        spin_sys = [obj.json() for obj in self.spin_systems]
         with open(filename, "w", encoding="utf8") as outfile:
             json.dump(
                 spin_sys, outfile, ensure_ascii=False, sort_keys=False, allow_nan=False
             )
 
+    def load_methods(self, filename: str):
+        """Load a list of methods from the given JSON serialized file.
+
+        Args:
+            str filename: A local or remote address to a JSON serialized file.
+
+        Example
+        -------
+
+        >>> sim.load_methods(filename) # doctest:+SKIP
+        """
+        contents = import_json(filename)
+        method_cls = [
+            Method
+            if obj["name"] not in __method_names__
+            else __sim_methods__[obj["name"]]
+            for obj in contents
+        ]
+
+        self.methods = [
+            fn.parse_dict_with_units(obj) for obj, fn in zip(contents, method_cls)
+        ]
+
+    def export_methods(self, filename: str):
+        """Export a list of methods to a JSON serialized file.
+
+        Args:
+            str filename: A filename of the serialized file.
+
+        Example
+        -------
+
+        >>> sim.export_methods(filename) # doctest:+SKIP
+        """
+        mth = [obj.json() for obj in self.methods]
+        with open(filename, "w", encoding="utf8") as outfile:
+            json.dump(
+                mth, outfile, ensure_ascii=False, sort_keys=False, allow_nan=False
+            )
+
     def run(
         self,
         method_index: list = None,