Release v0.14.4

.github/actions/conda_build_publish_package/entrypoint.sh

@@ -26,7 +26,7 @@ build_package(){
     done
     for platform in "${PLATFORMS[@]}"; do 
         for filename in /$platform/*.tar.bz2; do
-            conda convert -p $platform linux-64/*.tar.bz2
+            conda convert /$platform/$filename -p $platform linux-64/*.tar.bz2 -o .
         done 
     done
 }
@@ -38,7 +38,7 @@ upload_package(){
     export ANACONDA_API_TOKEN=$INPUT_ANACONDATOKEN
 
     for platform in "${PLATFORMS[@]}"; do 
-        for filename in ./"$platform"/*.tar.bz2; do
+        for filename in ./$platform/*.tar.bz2; do
             anaconda upload $filename
         done
     done 

.github/workflows/deploy_ghpages.yml

@@ -12,10 +12,10 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v1
-    - name: Set up Python 3.7
+    - name: Set up Python 3.9
       uses: actions/setup-python@v1
       with:
-        python-version: 3.7
+        python-version: 3.9
     - uses: actions/cache@v2
       with:
         path: |
@@ -26,14 +26,14 @@ jobs:
     - name: Install dependencies
       run: |
            python -m pip install --upgrade pip
-           python -m pip install pydata-sphinx-theme
+           python -m pip install pydata-sphinx-theme==0.7.1
            python -m pip install numpydoc
            python -m pip install sphinx-gallery
            python -m pip install sphinxcontrib-httpdomain
            python -m pip install sphinxcontrib-ghcontributors
            python -m pip install sphinx-issues
            python -m pip install sphinx-copybutton  
-           python -m pip install sphinx
+           python -m pip install sphinx==4.2
            sudo apt install texlive-extra-utils
            sudo apt-get install texlive-latex-extra
            python -m pip install .

.github/workflows/docs_PR.yml

@@ -16,10 +16,10 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v1
-    - name: Set up Python 3.7
+    - name: Set up Python 3.9
       uses: actions/setup-python@v1
       with:
-        python-version: 3.7
+        python-version: 3.9
     - uses: actions/cache@v2
       with:
         path: |
@@ -30,14 +30,14 @@ jobs:
     - name: Install dependencies
       run: |
            python -m pip install --upgrade pip
-           python -m pip install pydata-sphinx-theme
+           python -m pip install pydata-sphinx-theme==0.7.1
            python -m pip install numpydoc
            python -m pip install sphinx-gallery
            python -m pip install sphinxcontrib-httpdomain
            python -m pip install sphinxcontrib-ghcontributors
            python -m pip install sphinx-copybutton  
            python -m pip install sphinx-issues
-           python -m pip install sphinx
+           python -m pip install sphinx==4.2
            sudo apt install texlive-extra-utils
            sudo apt-get install texlive-latex-extra
            python -m pip install .

.github/workflows/package_upload.yml

@@ -11,19 +11,16 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v1
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
-    - name: Install dependencies
-      run: |
-          python -m pip install setuptools --user
-          python -m pip install build --user
-          python -m pip install twine --user
-    - name: Build distribution
-      run: |
-          python setup.py sdist
-          ./setup.py bdist_wheel --user
+        python-version: "3.10"
+    - name: Install pypa/build
+      run: >-
+        python -m pip install build --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m build --sdist --wheel --outdir dist/
     - name: Publish distribution to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

VERSION

@@ -1 +1 @@
-v0.14.3
+v0.14.4

deerlab/classes.py

@@ -87,19 +87,34 @@ class UQResult:
     type : string
         Uncertainty quantification approach:
 
-            * 'covariance' - Covariance-based uncertainty analysis
-            * 'bootstrap' - Bootstrapped uncertainty analysis
+            * ``'covariance'`` - Covariance-based uncertainty analysis
+            * ``'bootstrap'`` - Bootstrapped uncertainty analysis
+            * ``'profile'`` - Likelihood profile uncertainty analysis
+            * ``'void'`` - Empty uncertainty analysis
 
     mean : ndarray
         Mean values of the uncertainty distribution of the parameters.
+
     median : ndarray
         Median values of the uncertainty distribution of the parameters.
+
     std : ndarray
         Standard deviations of the uncertainty distribution of the parameters.
+
     covmat : ndarray
         Covariance matrix
+
     nparam : int scalar
         Number of parameters in the analysis.
+
+    samples : ndarray 
+        Bootstrap samples of the parameters. Only available for ``type='bootstrap'``.
+
+    profile : ndarray 
+        Likelihood profile of the parameters. Only available for ``type='profile'``.
+
+    threshold : scalar
+        Treshold value used for the profile method. Only available for ``type='profile'``.  
 
     Methods
     -------

deerlab/dd_models.py

@@ -400,8 +400,8 @@ def _randcoil(r,Nres,scaling,length):
 dd_randcoil.description = 'Random-coil model for an unfolded peptide/protein'
 # Parameters
 dd_randcoil.Nres.set(description='Number of residues', lb=2.0, ub=1000, par0=50, unit='')
-dd_randcoil.scaling.set(description='Segment length', lb=0.1, ub=0.4, par0=0.2, unit='nm')
-dd_randcoil.length.set(description='Scaling exponent', lb=0.33, ub=1.00, par0=0.602, unit='')
+dd_randcoil.scaling.set(description='Scaling exponent', lb=0.1, ub=0.4, par0=0.2, unit='nm')
+dd_randcoil.length.set(description='Segment length', lb=0.33, ub=1.00, par0=0.602, unit='')
 # Add documentation
 dd_randcoil.__doc__ = _dd_docstring(dd_randcoil,notes) +  docstr_example('dd_randcoil')
 

deerlab/dipolarmodel.py

@@ -237,8 +237,8 @@ def Vnonlinear_fcn(*nonlin):
         for n in range(npathways):
             getattr(DipolarSignal,reftime_names[n]).set(
                 par0 = experiment.reftimes[n],
-                lb = experiment.reftimes[n] - 0.05,
-                ub = experiment.reftimes[n] + 0.05
+                lb = experiment.reftimes[n] - 3*experiment.pulselength,
+                ub = experiment.reftimes[n] + 3*experiment.pulselength
                 )
 
     # Set other dipolar model specific attributes
@@ -337,15 +337,16 @@ class ExperimentInfo():
     r"""
     Represents information about a dipolar EPR experiment"""
 
-    def __init__(self,name,reftimes,harmonics):
+    def __init__(self,name,reftimes,harmonics,pulselength):
         self.npathways = len(reftimes)
         self.reftimes = reftimes
         self.harmonics = harmonics
+        self.pulselength = pulselength
         self.name = name
 #===============================================================================
 
 #===============================================================================
-def ex_3pdeer(tau, pathways=None):
+def ex_3pdeer(tau, pathways=None, pulselength=0.016):
     r"""
     Generate a 3-pulse DEER dipolar experiment model. 
 
@@ -375,6 +376,10 @@ def ex_3pdeer(tau, pathways=None):
         Pathways to include in the model. The pathways are specified based to the pathways numbers. 
         By default, both pathways are included in the order given in the table above.
 
+    pulselength : float scalar, optional 
+        Length of the longest microwave pulse in the sequence in microseconds. Used to determine the uncertainty in the 
+        boundaries of the pathay refocusing times.
+
     Returns
     -------
     experiment : ``ExperimentInfo`` object
@@ -394,11 +399,11 @@ def ex_3pdeer(tau, pathways=None):
         reftimes = [reftimes[pathway-1] for pathway in pathways]
         harmonics = [harmonics[pathway-1] for pathway in pathways] 
 
-    return ExperimentInfo('3-pulse DEER',reftimes,harmonics)
+    return ExperimentInfo('3-pulse DEER',reftimes,harmonics,pulselength)
 #===============================================================================
 
 #===============================================================================
-def ex_4pdeer(tau1, tau2, pathways=None):
+def ex_4pdeer(tau1, tau2, pathways=None, pulselength=0.016):
     r"""
     Generate a 4-pulse DEER dipolar experiment model. 
 
@@ -432,6 +437,10 @@ def ex_4pdeer(tau1, tau2, pathways=None):
         Pathways to include in the model. The pathways are specified based to the pathways numbers. 
         By default, all 4 pathways are included in the order given in the table above.
 
+    pulselength : float scalar, optional 
+        Length of the longest microwave pulse in the sequence in microseconds. Used to determine the uncertainty in the 
+        boundaries of the pathay refocusing times.
+
     Returns
     -------
     experiment : ``ExperimentInfo`` object
@@ -450,11 +459,11 @@ def ex_4pdeer(tau1, tau2, pathways=None):
         reftimes = [reftimes[pathway-1] for pathway in pathways]
         harmonics = [harmonics[pathway-1] for pathway in pathways] 
 
-    return ExperimentInfo('4-pulse DEER', reftimes, harmonics)
+    return ExperimentInfo('4-pulse DEER', reftimes, harmonics, pulselength)
 #===============================================================================
 
 #===============================================================================
-def ex_rev5pdeer(tau1, tau2, tau3, pathways=None):
+def ex_rev5pdeer(tau1, tau2, tau3, pathways=None, pulselength=0.016):
     r"""
     Generate a reverse 5-pulse DEER dipolar experiment model. 
 
@@ -494,6 +503,10 @@ def ex_rev5pdeer(tau1, tau2, tau3, pathways=None):
         Pathways to include in the model. The pathways are specified based to the pathways numbers. 
         By default, all 8 pathways are included in the order given in the table above.
 
+    pulselength : float scalar, optional 
+        Length of the longest microwave pulse in the sequence in microseconds. Used to determine the uncertainty in the 
+        boundaries of the pathay refocusing times.
+
     Returns
     -------
     experiment : ``ExperimentInfo`` object
@@ -512,12 +525,12 @@ def ex_rev5pdeer(tau1, tau2, tau3, pathways=None):
         reftimes = [reftimes[pathway-1] for pathway in pathways]
         harmonics = [harmonics[pathway-1] for pathway in pathways]
 
-    return ExperimentInfo('Reverse 5-pulse DEER',reftimes,harmonics)
+    return ExperimentInfo('Reverse 5-pulse DEER',reftimes,harmonics,pulselength)
 #===============================================================================
 
 
 #===============================================================================
-def ex_fwd5pdeer(tau1, tau2, tau3, pathways=None):
+def ex_fwd5pdeer(tau1, tau2, tau3, pathways=None, pulselength=0.016):
     r"""
     Generate a forward 5-pulse DEER dipolar experiment model. 
 
@@ -557,6 +570,10 @@ def ex_fwd5pdeer(tau1, tau2, tau3, pathways=None):
         Pathways to include in the model. The pathways are specified based to the pathways numbers. 
         By default, all pathways are included in the order given in the table above.
 
+    pulselength : float scalar, optional 
+        Length of the longest microwave pulse in the sequence in microseconds. Used to determine the uncertainty in the 
+        boundaries of the pathay refocusing times.
+
     Returns
     -------
     experiment : ``ExperimentInfo`` object
@@ -575,11 +592,11 @@ def ex_fwd5pdeer(tau1, tau2, tau3, pathways=None):
         reftimes = [reftimes[pathway-1] for pathway in pathways]
         harmonics = [harmonics[pathway-1] for pathway in pathways] 
 
-    return ExperimentInfo('Forward 5-pulse DEER', reftimes, harmonics)
+    return ExperimentInfo('Forward 5-pulse DEER',reftimes,harmonics,pulselength)
 #===============================================================================
 
 #===============================================================================
-def ex_sifter(tau1, tau2, pathways=None):
+def ex_sifter(tau1, tau2, pathways=None, pulselength=0.016):
     r"""
     Generate a SIFTER dipolar experiment model. 
 
@@ -611,6 +628,10 @@ def ex_sifter(tau1, tau2, pathways=None):
         Pathways to include in the model. The pathways are specified based to the pathways numbers. 
         By default, all 3 pathways are included and ordered as given in the table above.
 
+    pulselength : float scalar, optional 
+        Length of the longest microwave pulse in the sequence in microseconds. Used to determine the uncertainty in the 
+        boundaries of the pathay refocusing times.
+
     Returns
     -------
     experiment : ``ExperimentInfo`` object
@@ -630,12 +651,12 @@ def ex_sifter(tau1, tau2, pathways=None):
         reftimes = [reftimes[pathway-1] for pathway in pathways]
         harmonics = [harmonics[pathway-1] for pathway in pathways]
 
-    return ExperimentInfo('SIFTER',reftimes,harmonics)
+    return ExperimentInfo('SIFTER',reftimes,harmonics,pulselength)
 #===============================================================================
 
 
 #===============================================================================
-def ex_ridme(tau1, tau2, pathways=None):
+def ex_ridme(tau1, tau2, pathways=None, pulselength=0.016):
     r"""
     Generate a RIDME dipolar experiment model. 
 
@@ -668,6 +689,10 @@ def ex_ridme(tau1, tau2, pathways=None):
         Pathways to include in the model. The pathways are specified based to the pathways numbers. 
         By default, all 4 pathways are included in the order given in the table above.
 
+    pulselength : float scalar, optional 
+        Length of the longest microwave pulse in the sequence in microseconds. Used to determine the uncertainty in the 
+        boundaries of the pathay refocusing times.
+
     Returns
     -------
     experiment : ``ExperimentInfo`` object
@@ -687,5 +712,5 @@ def ex_ridme(tau1, tau2, pathways=None):
         reftimes = [reftimes[pathway-1] for pathway in pathways]
         harmonics = [harmonics[pathway-1] for pathway in pathways] 
 
-    return ExperimentInfo('RIDME',reftimes,harmonics)
+    return ExperimentInfo('RIDME',reftimes,harmonics,pulselength)
 #===============================================================================