Fixed example bug and updated output. (#513)

* Fixed example bug and updated output. fixed a bug in the harmonic_oscillators.py example that wasn't actually retrieving the data from the results object for reverse exponential averaging. Added logging to the two harmonic oscillator files. Update the output of the example scripts since they were quite old. * format fixes for black * fix doc building * we need to add html_theme since that gets injected later by RTD --------- Co-authored-by: Mike Henry <[email protected]>
choderalab · Aug 24, 2023 · e5b7f12 · e5b7f12
1 parent 7b4f89f
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diff --git a/devtools/conda-envs/test_env_jax.yaml b/devtools/conda-envs/test_env_jax.yaml
@@ -22,5 +22,6 @@ dependencies:
   - xlrd
     # Docs
   - numpydoc
-  - sphinx <7
+  - sphinx
+  - sphinx-rtd-theme
   - sphinxcontrib-bibtex
diff --git a/docs/conf.py b/docs/conf.py
@@ -146,7 +146,7 @@
 # a list of builtin themes.
 # html_theme = "default"
 on_rtd = os.environ.get("READTHEDOCS", None) == "True"
-
+html_theme = "sphinx_rtd_theme"
 if not on_rtd:  # only import and set the theme if we're building docs locally
     import sphinx_rtd_theme
 

diff --git a/examples/harmonic-oscillators/QQMBARobserve.pdf b/examples/harmonic-oscillators/QQMBARobserve.pdf
diff --git a/examples/harmonic-oscillators/QQdf.pdf b/examples/harmonic-oscillators/QQdf.pdf
diff --git a/examples/harmonic-oscillators/QQstandardobserve.pdf b/examples/harmonic-oscillators/QQstandardobserve.pdf
diff --git a/examples/harmonic-oscillators/cumulative_probability_comparison_curves.pdf b/examples/harmonic-oscillators/cumulative_probability_comparison_curves.pdf
diff --git a/examples/harmonic-oscillators/harmonic-oscillators-distributions.py b/examples/harmonic-oscillators/harmonic-oscillators-distributions.py
@@ -34,6 +34,11 @@
 from pymbar import testsystems, MBAR, confidenceintervals
 from pymbar.utils import ParameterError, DataError
 
+import logging
+import sys
+
+logging.basicConfig(stream=sys.stdout, level=logging.INFO)
+
 # =============================================================================================
 # PARAMETERS
 # =============================================================================================

diff --git a/examples/harmonic-oscillators/harmonic-oscillators-distributions.py_output.txt b/examples/harmonic-oscillators/harmonic-oscillators-distributions.py_output.txt
diff --git a/examples/harmonic-oscillators/harmonic-oscillators.py b/examples/harmonic-oscillators/harmonic-oscillators.py
@@ -26,6 +26,11 @@
 from pymbar import testsystems, exp, exp_gauss, bar, MBAR, FES
 from pymbar.utils import ParameterError
 
+import logging
+import sys
+
+logging.basicConfig(stream=sys.stdout, level=logging.INFO)
+
 # =============================================================================================
 # HELPER FUNCTIONS
 # =============================================================================================
@@ -219,7 +224,7 @@ def get_analytical(beta, K, O, observables):
 for k in range(1, K):
     if N_k[k] != 0:
         w_R = u_kln[k, k - 1, 0 : N_k[k]] - u_kln[k, k, 0 : N_k[k]]  # reverse work
-        df_exp, ddf_exp = exp(w_R)
+        results = exp(w_R)
         df_exp = -results["Delta_f"]
         ddf_exp = results["dDelta_f"]
         exp_analytical = f_k_analytical[k] - f_k_analytical[k - 1]
@@ -805,7 +810,7 @@ def generate_fes_data(
 # Compute fre energy profile, first with histograms
 print("Solving for free energies of state to initialize free energy profile...")
 mbar_options = dict()
-mbar_options["verbose"] = True
+mbar_options["verbose"] = False
 fes = FES(u_kn, N_k, mbar_options=mbar_options)
 print("Computing free energy profile ...")
 histogram_parameters = dict()

diff --git a/examples/harmonic-oscillators/harmonic-oscillators.py_output.txt b/examples/harmonic-oscillators/harmonic-oscillators.py_output.txt