Merge pull request #7 from DeepanshS/v0.1.1merge_restructure

V0.1.1merge restructure: Using OpenBlas libraries

.flake8

@@ -0,0 +1,10 @@
+[flake8]
+ignore = E741, C901, W503, F401, F841, F811
+exclude = .eggs,*.egg,build
+filename = *.pyx,*.px*, *py
+max-line-length = 88
+max-complexity = 18
+select = B,C,E,F,W,T4,B9
+
+
+## E203, E266, E501, F403

.gitignore

@@ -22,7 +22,6 @@ wheels/
 .installed.cfg
 cython_debug/**
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -32,7 +31,6 @@ MANIFEST
 
 # Installer logs
 pip-log.txt
-pip-delete-this-directory.txt
 
 # Unit test / coverage reports
 htmlcov/
@@ -64,8 +62,10 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/_static/
-docs/_templates
+docs/api_c
+
+# Doxygen output
+doxyoutput/
 
 # PyBuilder
 target/
@@ -76,12 +76,6 @@ target/
 # pyenv
 .python-version
 
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
 # Environments
 .env
 .venv
@@ -95,9 +89,6 @@ venv.bak/
 .spyderproject
 .spyproject
 
-# Rope project settings
-.ropeproject
-
 # mkdocs documentation
 /site
 
@@ -110,14 +101,26 @@ venv.bak/
 # build
 *.DSYM/**
 
+# folders
+src/c_lib/test_c/**
+
 # files
 *.out
 *.prof
 *.ipynb
 *.mp4
 *.html
-*.png
 test_os.py
-
-# Cython build file
-src/c_lib/mrmethods/nmr_methods.c
+note.txt
+sideband2.c
+dmfit_comparision.py
+simulate_lineshape.py
+sideband.3
+sandbox.c
+nmr_methods.c
+main.c
+mrsimulator.code-workspace
+jquery.js
+setup.py.src
+setup.temp
+__config__.json

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3.7
 default_stages: [commit, push, manual]
 repos:
--   repo: https://github.com/ambv/black
+  - repo: https://github.com/ambv/black
     rev: stable
     hooks:
     - id: black
@@ -13,23 +13,23 @@ repos:
       types: [python]
       files: \.pyi?$
 
--   repo: https://github.com/asottile/blacken-docs
+  - repo: https://github.com/asottile/blacken-docs
     rev: v1.0.0
     hooks:
-    -   id: blacken-docs
-        additional_dependencies: [black==19.3b0]
-        language: python
-        language_version: python3.7
+    - id: blacken-docs
+      additional_dependencies: [black==19.3b0]
+      language: python
+      language_version: python3.7
 
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.2.3
     hooks:
     - id: check-yaml
       language: python
     - id: check-added-large-files
       language: python
-    # - id: fix-encoding-pragma
-    #   language: python
+    - id: fix-encoding-pragma
+      language: python
     - id: check-docstring-first
       language: python
     - id: flake8
@@ -46,7 +46,6 @@ repos:
       language: python
       types: [python]
 
-
 # -   repo: https://github.com/asottile/reorder_python_imports
 #     rev: v1.4.0
 #     hooks:

.readthedocs.yml

@@ -0,0 +1,20 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt

.travis.yml

@@ -1,9 +1,23 @@
-os: linux
+os:
+  - linux
+
 dist: xenial
 language: python
-cache: pip
+
 python:
-  - "3.6"
+  - '3.6'
+  - '3.7.3'
+
+env:
+  # - PKG1=mkl PKG2=mkl-include
+  - PKG1=nomkl PKG2=openblas
+
+cache:
+  pip: true
+  directories:
+    - $HOME/.ccache
+
+# safelist
 branches:
   only:
   - master
@@ -18,11 +32,12 @@ before_install:
   - conda info -a
   - conda create -q -n test-env python=$TRAVIS_PYTHON_VERSION pytest pytest-cov
   - source activate test-env
-  - conda install fftw mkl-service
-  - pip install -r requirements.txt
-  - pip install -r requirements-dev.txt  
+  - conda install -c anaconda $PKG1 $PKG2 --file requirements.txt
+  - pip install -r requirements-dev.txt
 
 install:
   - python setup.py develop
+
+# command to run tests
 script:
   - pytest

MANIFEST.in

@@ -1,5 +1,4 @@
 include README.md
-include src/c_lib/lib/*.c
-include src/c_lib/mrmethods/*.c
-include src/c_lib/include/*.*
-include src/c_lib/test/*.*
+
+recursive-include src/mrsimulator/examples *
+include src/mrsimulator/isotope_data.json

README.md

@@ -66,9 +66,9 @@ This will display the following message on the screen
 
     1H site 0 from isotopomer 0 @ 100.0% abundance
     ----------------------------------------------
-    isotropic chemical shift = 0.0 ppm
-    chemical shift anisotropy = 13.89 ppm
-    chemical shift asymmetry = 0.25
+    Isotropic chemical shift = 0.0 ppm
+    Shielding anisotropy = 13.89 ppm
+    Shielding asymmetry = 0.25
     Setting up the virtual NMR spectrometer
     ---------------------------------------
     Adjusting the magnetic flux density to 9.4 T.
@@ -79,9 +79,9 @@ This will display the following message on the screen
 
     1H site 0 from isotopomer 0 @ 100.0% abundance
     ----------------------------------------------
-    isotropic chemical shift = 0.0 ppm
-    chemical shift anisotropy = 13.89 ppm
-    chemical shift asymmetry = 0.25
+    Isotropic chemical shift = 0.0 ppm
+    Shielding anisotropy = 13.89 ppm
+    Shielding asymmetry = 0.25
 
 and the corresponding plot shown below.
 

dmfit_comparision.py.scr

@@ -0,0 +1,51 @@
+from mrsimulator.miscellaneous import read_dmfit_files
+import matplotlib.pyplot as plt
+from mrsimulator.python.simulator import simulator
+from mrsimulator import Simulator
+import numpy as np
+
+
+def _dmfit():
+    file_address = '/Users/deepansh/Documents/CSA_20kHz_0.1.txt'
+
+    freq, amp = read_dmfit_files(file_address)
+    max_amp = amp.max()
+    freq_at_max = freq[np.argmax(amp)]
+    print(freq_at_max, max_amp)
+
+    spectrum = {
+        "direct_dimension": {
+            "magnetic_flux_density": "9.4 T",
+            "rotor_frequency": "0 kHz",
+            "rotor_angle": "54.735 deg",
+            "number_of_points": 2048,
+            "spectral_width": "100 kHz",
+            "reference_offset": "0 kHz",
+            "isotope": "1H",
+        }
+    }
+    isotopomers = [
+        {
+            "sites": [
+                {
+                    "isotope": "1H",
+                    "isotropic_chemical_shift": "0 Hz",
+                    "shielding_symmetric": {"anisotropy": "20 kHz", "asymmetry": 0.1},
+                },
+            ]
+        }
+    ]
+    sp = Simulator()
+    sp.isotopomers = isotopomers
+    sp.spectrum = spectrum
+    f, a = simulator(isotopomers=sp._isotopomers_c, spectrum=sp._spectrum_c)
+    fig, ax = plt.subplots(2, 1)
+    ax[0].plot(freq, amp / amp.max(), 'r', label='dmfit')
+    ax[0].plot(f, a / a.max(), 'k', label='mrsimulator')
+    ax[0].legend()
+    ax[1].plot(f, (amp / amp.max())[::4] - a / a.max())
+    plt.show()
+
+
+if __name__ == '__main__':
+    _dmfit()

docs/Doxyfile

@@ -0,0 +1,59 @@
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL            = No
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE        = No
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC         = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS  = YES
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespace are hidden.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS  = NO

docs/Makefile

@@ -18,4 +18,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -E