Version 1.0.1 (#421)

* Update changelog.rst * Update changelog.rst * Update VERSION * Bug fix in setup.py * Updating patch from main (#420) * remove hard-wired RNG seeding (#417) * Fix Examples issue and update CI actions (#416) * Update ci_scheduled.yml - Removed MKL Linking tests - Removed complex cache@v2 that raises warnings and moved to setup-python@v4 * Update ci_PR.yml - Removed MKL linking - Updated setup-python version to v4 * Fix Example issues Fixed an issue with simulation examples * Removed cvxopt tests and replaced with quadprog * Updated selregparam tests - Moved tests to quadprog method - Introduced tighter bounds on the searchrange - Tested values are now mostly using grid method, except where this failed where a Brent method is taken. This is not idea but does at least freeze the situation. - change P in test_compensate_condition to match alpha tests * Hard code out 3.11 support * Rename file to American English --------- Co-authored-by: Stefan Stoll <stestoll@users.noreply.github.com> --------- Co-authored-by: Stefan Stoll <stestoll@users.noreply.github.com>
JeschkeLab · Mar 22, 2023 · 5496cff · 5496cff
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commit 5496cff
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diff --git a/.github/workflows/ci_PR.yml b/.github/workflows/ci_PR.yml
@@ -15,23 +15,18 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-      
+
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
+          cache: 'pip'
+          cache-dependency-path: setup.py
+      - run: |
           python -m pip install --upgrade pip
           pip install wheel
           pip install .
-      
-      - name: Windows MKL linking 
-        if: matrix.os == 'windows-latest'
-        run: |
-          python upgrade_mkl.py
-
+    
       - name: Test with pytest
         run: |
           pytest
diff --git a/.github/workflows/ci_scheduled.yml b/.github/workflows/ci_scheduled.yml
@@ -14,51 +14,57 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: [3.8, 3.9, "3.10", "3.11"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: setup.py
+      - run: |
+          python -m pip install --upgrade pip
+          pip install wheel
+          pip install .
 
-      - uses: actions/cache@v2
-        if: startsWith(runner.os, 'Windows')
-        with:
-          path: |
-            ~\AppData\Local\pip\Cache
-          key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
-          restore-keys: |
-            {{ runner.os }}-pip-
+#       - uses: actions/cache@v2
+#         if: startsWith(runner.os, 'Windows')
+#         with:
+#           path: |
+#             ~\AppData\Local\pip\Cache
+#           key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
+#           restore-keys: |
+#             {{ runner.os }}-pip-
 
-      - uses: actions/cache@v2
-        if: startsWith(runner.os, 'macOS')
-        with:
-          path: |
-            ~/Library/Caches/pip
-          key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
-          restore-keys: |
-            {{ runner.os }}-pip-
+#       - uses: actions/cache@v2
+#         if: startsWith(runner.os, 'macOS')
+#         with:
+#           path: |
+#             ~/Library/Caches/pip
+#           key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
+#           restore-keys: |
+#             {{ runner.os }}-pip-
 
-      - uses: actions/cache@v2
-        if: startsWith(runner.os, 'Linux')
-        with:
-          path: |
-            ~/.cache/pip
-          key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
-          restore-keys: |
-            {{ runner.os }}-pip-
+#       - uses: actions/cache@v2
+#         if: startsWith(runner.os, 'Linux')
+#         with:
+#           path: |
+#             ~/.cache/pip
+#           key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
+#           restore-keys: |
+#             {{ runner.os }}-pip-
 
-      - name: Install dependencies
-        if: steps.cache.outputs.cache-hit != 'false'
-        run: |
-          python -m pip install --upgrade pip
-          pip install wheel
-          pip install .
+#       - name: Install dependencies
+#         if: steps.cache.outputs.cache-hit != 'false'
+#         run: |
+#           python -m pip install --upgrade pip
+#           pip install wheel
+#           pip install .
 
-      - name: Windows MKL linking 
-        if: matrix.os == 'windows-latest'
-        run: |
-          python upgrade_mkl.py
+#       - name: Windows MKL linking 
+#         if: matrix.os == 'windows-latest'
+#         run: |
+#           python upgrade_mkl.py
 
       - name: Test with pytest
         run: pytest
diff --git a/deerlab/classes.py b/deerlab/classes.py
@@ -650,7 +650,6 @@ def propagate(self,model,lb=None,ub=None,samples=None):
                 # Get the parameter uncertainty distribution
                 values,pdf = self.pardist(n)
                 # Random sampling form the uncertainty distribution
-                np.random.seed(0)
                 sampled_parameters[n] =  [np.random.choice(values, p=pdf/sum(pdf)) for _ in range(Nsamples)]
             # Convert to matrix
             sampled_parameters = np.atleast_2d(sampled_parameters)

diff --git a/deerlab/dipolarkernel.py b/deerlab/dipolarkernel.py
@@ -165,7 +165,7 @@ def dipolarkernel(t, r, *, pathways=None, mod=None, bg=None, method='fresnel', e
         The vector ``tinterp`` must cover all possible time shifts of the original ``t`` by the different refocusing times of the dipolar pathways.     
 
     Returns
-    --------
+    -------
     K : ndarray
         Dipolar kernel matrix.
 

diff --git a/deerlab/dipolarmodel.py b/deerlab/dipolarmodel.py
@@ -318,7 +318,6 @@ def dipolarpathways(*param):
     #-----------------------------------------------------------------------
     def _Pmultivar(param):
         rmeans,cholesky_factors = param[:Q], param[Q:]
-        np.random.seed(seed=1)
         Σ = choleskycovmat(Q,cholesky_factors)
         Pmultivar = multivariate_normal(rmeans, cov=Σ)
         return Pmultivar
@@ -470,7 +469,6 @@ def Vmultispin_nonlinear_fcn(*nonlin):
 
         # Sample from the multi-variate distance distribution
         Nsamples = 1000000
-        np.random.seed(seed=1)
         rsamples = Pmodel.nonlinmodel(nonlin[Psubset]).rvs(Nsamples)
         rsamples = np.maximum(rsamples,1e-16) # Avoid values exactly at zero 
 

diff --git a/docsrc/source/dipolar_guide_modelling.rst → docsrc/source/dipolar_guide_modeling.rst b/docsrc/source/dipolar_guide_modelling.rst → docsrc/source/dipolar_guide_modeling.rst
diff --git a/examples/basic_simulations/ex_simulate_4pdeer.py b/examples/basic_simulations/ex_simulate_4pdeer.py
@@ -37,9 +37,8 @@
 
 # Experiment model
 experiment = dl.ex_4pdeer(tau1,tau2, pathways=[1,2,3])
-reftime1 = experiment.reftimes[0]
-reftime2 = experiment.reftimes[1]
-reftime3 = experiment.reftimes[2]
+reftime1, reftime2, reftime3 = experiment.reftimes(tau1,tau2)
+
 
 # Construct the dipolar signal model
 Vmodel = dl.dipolarmodel(t,r,Pmodel=dl.dd_gauss, experiment=experiment) 

diff --git a/examples/basic_simulations/ex_simulate_5pdeer.py b/examples/basic_simulations/ex_simulate_5pdeer.py
@@ -37,8 +37,7 @@
 r = np.arange(rmin,rmax,Δr)
 
 experiment = dl.ex_rev5pdeer(tau1,tau2,tau3, pathways=[1,2])
-reftime1 = experiment.reftimes[0]
-reftime2 = experiment.reftimes[1]
+reftime1, reftime2 = experiment.reftimes(tau1,tau2,tau3)
 
 # Construct the dipolar signal model
 Vmodel = dl.dipolarmodel(t,r,Pmodel=dl.dd_gauss, experiment=experiment) 

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
         'Documentation': 'https://jeschkelab.github.io/DeerLab/',
         'Source': 'https://github.com/JeschkeLab/DeerLab',
     },
-    python_requires='>=3.8',
+    python_requires='>=3.8,<3.11',
     license='LICENSE.txt',
     include_package_data = True,
     keywords='data analysis modeling least-squares EPR spectroscopy DEER PELDOR'.split(),
@@ -22,7 +22,7 @@
                         'numpy>=1.22.4',
                         'cvxopt>=1.0.0',
                         'scipy>=1.6.3',
-                        'joblib>-1.0.0',
+                        'joblib>=1.0.0',
                         'dill>=0.3.0',
                         'tqdm>=4.51.0',
                         'matplotlib>=3.3.4',
@@ -44,4 +44,4 @@
         'Programming Language :: Python :: 3.10',
         'Topic :: Scientific/Engineering',
     ]
-)
+)