Merge branch 'v3' into hcga

sblunt · Jan 19, 2024 · d7f68d6 · d7f68d6
2 parents 1ea93f2 + 6bfa14b
commit d7f68d6
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diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml
@@ -32,5 +32,5 @@ jobs:
         python -m pip install . --no-build-isolation
     - name: Run tutorial notebooks
       run: |
-        py.test --nbmake docs/tutorials/*.ipynb
+        py.test --nbmake --nbmake-timeout=3000 docs/tutorials/*.ipynb
       
diff --git a/docs/index.rst b/docs/index.rst
@@ -54,6 +54,11 @@ User Guide:
 Changelog:
 ++++++++++
 
+**3.0.0 (TBD)**
+
+- discuss MCMC autocorrelation in MCMC tutorial (@michaelkmpoon)
+- add time warning if OFTI doesn't accept an orbit in first 60 s (@michaelkmpoon)
+
 **2.2.2 (2023-06-30)**
 
 - tests now overwrite any generated text files (@sblunt)

diff --git a/docs/tutorials/MCMC_tutorial.ipynb b/docs/tutorials/MCMC_tutorial.ipynb
diff --git a/docs/tutorials/MCMC_vs_OFTI.ipynb b/docs/tutorials/MCMC_vs_OFTI.ipynb
diff --git a/orbitize/nbody.py b/orbitize/nbody.py
@@ -83,7 +83,7 @@ def calc_orbit(
         for j,t in enumerate(te):
             sim.integrate(t/365.25)
             #for the star and each planet in each epoch denoted by j,t find the RA, Dec, and RV
-            com = sim.calculate_com()
+            com = sim.com()
             ra_reb[j,0] = -(ps[0].x-com.x)# ra is negative x
             dec_reb[j,0] = ps[0].y-com.y
             vz[j,0] = ps[0].vz

diff --git a/orbitize/sampler.py b/orbitize/sampler.py
diff --git a/tests/test_chi2_lnlike.py b/tests/test_chi2_lnlike.py
@@ -156,7 +156,7 @@ def test_log_vs_standard():
         56.95,
     )
     s_standard = myDriver_standard.sampler
-    _ = s_standard.run_sampler(500)
+    _ = s_standard.run_sampler(750)
 
     # initiate driver with log chi2
     myDriver_log = orbitize.driver.Driver(
@@ -168,7 +168,7 @@ def test_log_vs_standard():
         chi2_type="log",
     )
     s_log = myDriver_log.sampler
-    _ = s_log.run_sampler(500)
+    _ = s_log.run_sampler(750)
 
     # take mean of result objects
     myResults_standard = np.mean(s_standard.results.post, axis=0)
@@ -177,7 +177,7 @@ def test_log_vs_standard():
     print(myResults_log[1], myResults_standard[1])
 
     # check that the eccentricity means are about the same
-    assert myResults_log[1] == pytest.approx(myResults_standard[1], rel=0.1)
+    assert myResults_log[1] == pytest.approx(myResults_standard[1], rel=0.15)
 
 
 if __name__ == "__main__":

diff --git a/tests/test_hipparcos.py b/tests/test_hipparcos.py
@@ -156,7 +156,7 @@ def test_iad_refitting():
 
     # check that we get reasonable values for the posteriors of the refit IAD
     # (we're only running the MCMC for a few steps, so these are not strict)
-    assert np.isclose(0, np.median(post[:, -1]), atol=0.5)
+    assert np.isclose(0, np.median(post[:, -1]), atol=0.7)
     assert np.isclose(myHipLogProb.plx0, np.median(post[:, 0]), atol=0.5)