Initial commit

.coveragerc

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+[run]
+branch = True
+
+omit =
+    */.local/*
+    /usr/*
+    tensiometer/test*
+
+[report]
+show_missing = True
+
+# Regexes for lines to exclude from consideration
+exclude_lines =
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+ignore_errors = True

.gitignore

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+*.DS_Store
+__pycache__/
+*.py[cod]
+*$py.class
+*.ipynb_checkpoints
+
+# Distribution / packaging
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/

.material.py

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+"""
+This is random material, do not read it :)
+"""
+
+def _temp_vec_kde_pdf(x, samples, weights):
+    """
+    Utility function to compute the KDE
+    """
+    X = np.subtract(x[np.newaxis, :, :], samples[:, np.newaxis, :])
+    _temp = np.dot(weights, np.exp(-0.5*(X*X).sum(axis=2)))
+    return np.log(_temp)
+
+
+
+C_p1, C_p12 = chain_2.cov(pars=param_names), chain_12.cov(pars=param_names)
+C_Pi = chain_prior.cov(pars=param_names)
+theta_1 = chain_2.getMeans(pars=[chain_1.index[name]
+                           for name in param_names])
+theta_12 = chain_12.getMeans(pars=[chain_12.index[name]
+                             for name in param_names])
+
+KL_eig, KL_eigv = utils.KL_decomposition(C_p1, C_p12)
+
+KL_eig
+
+prior_factor = 1000.0
+temp_C_p1 = utils.QR_inverse(utils.QR_inverse(C_p1) +prior_factor*utils.QR_inverse(C_Pi))
+temp_C_p12 = utils.QR_inverse(utils.QR_inverse(C_p12) +prior_factor*utils.QR_inverse(C_Pi))
+
+temp_theta_12 = np.dot(temp_C_p12,np.dot(theta_12,utils.QR_inverse(C_p12))+np.dot(theta_1,prior_factor*utils.QR_inverse(C_Pi)))
+
+
+KL_eig_2, KL_eigv_2 = utils.KL_decomposition(temp_C_p1, temp_C_p12)
+KL_eig_2
+
+plt.plot(KL_eig)
+plt.plot(KL_eig_2)
+
+helper_stat(theta_1-theta_12, KL_eig,KL_eigv, 1.05)
+helperplot(KL_eig,KL_eigv)
+
+helper_stat(theta_1-temp_theta_12, KL_eig_2,KL_eigv_2, 1.05)
+helperplot(KL_eig_2,KL_eigv_2)
+
+
+
+
+def helper_stat(shift, eig, eigv, lower_cutoff):
+    upper_cutoff = 100.
+    _filter = np.logical_and(eig > lower_cutoff, eig < upper_cutoff)
+    Q_UDM = np.sum(np.dot(eigv.T, shift)[_filter]**2./(eig[_filter]-1.))
+    dofs = np.sum(_filter)
+    P = scipy.stats.chi2.cdf(Q_UDM, dofs)
+    return utils.from_confidence_to_sigma(P)
+
+def helperplot(eig, eigv):
+    fish = np.sum(eigv*eigv/eig, axis=1)
+    fish = ((eigv*eigv/eig).T/fish).T
+    im1 = plt.imshow(fish, cmap='viridis')
+    num_params = len(fish)
+    for i in range(num_params):
+        for j in range(num_params):
+            if fish[j,i]>0.5:
+                col = 'k'
+            else:
+                col = 'w'
+            plt.text(i, j, np.round(fish[j,i],2), va='center', ha='center', color=col)
+    # label on the axis:
+    plt.xlabel('KL mode ($\\lambda^a-1$)');
+    plt.ylabel('Parameters');
+    # x axis:
+    ticks  = np.arange(num_params)
+    labels = [ str(t+1)+'\n ('+str(l)+')' for t,l in zip(ticks,np.round(eig-1.,2))]
+    plt.xticks(ticks, labels, horizontalalignment='center')
+    labels = [ '$'+chain_12.getParamNames().parWithName(name).label+'$' for name in param_names ]
+    plt.yticks(ticks, labels, horizontalalignment='right')
+    plt.show()

.travis.yml

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+os: linux
+language: python
+dist: bionic
+git:
+  depth: false
+
+
+jobs:
+  include:
+    - env:
+        - CHANNEL="defaults"
+        - PYDIST="ANACONDA"
+      python: "3.6"
+    - env:
+        - CHANNEL="conda-forge"
+        - PYDIST="ANACONDA"
+      python: "3.8"
+    - name: "3.7 with bionic"
+      python: "3.7"
+
+install:
+  # Setup anaconda following http://conda.pydata.org/docs/travis.html
+  - if [[ "$PYDIST" == "ANACONDA" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+      bash miniconda.sh -b -p $HOME/miniconda;
+      export PATH="$HOME/miniconda/bin:$PATH";
+      hash -r;
+      conda config --set always_yes yes --set changeps1 no;
+      conda info -a;
+      conda create -q -n test-environment -c $CHANNEL python=$TRAVIS_PYTHON_VERSION scipy matplotlib;
+      source activate test-environment;
+    fi
+  - python --version
+  - pip install .
+  - pip install PyYAML
+  - pip install coveralls
+
+script:
+  - make test_with_coverage
+
+after_success:
+  - coveralls