remove pybind submodule (#1556)

.gitmodules

@@ -1,6 +1,3 @@
-[submodule "pybind11"]
-	path = ext/pybind11
-	url = https://github.com/pybind/pybind11
 [submodule "doc/source/legacy-notebooks"]
 	path = doc/source/legacy-notebooks
 	url = https://github.com/markovmodel/PyEMMA_IPython.git

pyemma/msm/tests/test_its.py

@@ -263,8 +263,8 @@ def test_its_msm(self):
         assert np.allclose(estimator.timescales, ref, rtol=0.1, atol=10.0)
 
     def test_its_bmsm(self):
-        estimator = msm.its([self.double_well_data.dtraj_T100K_dt10_n6good], lags = [10, 50, 200],
-                            errors='bayes', nsamples=1000, n_jobs=2)
+        estimator = msm.timescales_msm([self.double_well_data.dtraj_T100K_dt10_n6good], lags = [10, 50, 200],
+                                       errors='bayes', nsamples=1000, n_jobs=1)
         ref = np.array([[ 284.87479737,    6.68390402,    3.0375248,     2.65314172,    1.93066562],
                         [ 320.08583492,   11.14612743,   10.3450663,     9.42799075,    8.2109752 ],
                         [ 351.41541961,   42.87427869,   41.17841657,   37.35485197,   23.24254608]])

pyproject.toml

@@ -6,8 +6,7 @@ requires = [
  "Cython>=0.22",
  "scipy",
  "mdtraj",
- # TODO: include again once https://github.com/pybind/pybind11/issues/1067 is fixed.
- #"pybind11",
+ "pybind11",
  "deeptime"
  ]
 

setup.py

@@ -31,6 +31,7 @@
 import versioneer
 import warnings
 from io import open
+import pybind11
 
 from setuptools import setup, Extension, find_packages
 
@@ -74,7 +75,7 @@
 def extensions():
     from Cython.Build import cythonize
     from numpy import get_include as np_get_include
-    pybind_inc = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'ext', 'pybind11', 'include')
+    pybind_inc = pybind11.get_include()
     assert os.path.exists(pybind_inc), 'pybind11 headers not found at %s' % pybind_inc
 
     from mdtraj import capi as mdtraj_capi
@@ -323,15 +324,6 @@ def build_extensions(self):
 
 if __name__ == '__main__':
     if parse_setuppy_commands():
-        # only require numpy and extensions in case of building/installing
-        # first initialize submodules
-        if os.path.exists('.git'):
-            import subprocess
-            modules = [os.path.join('ext', 'pybind11')]
-            cmd = "git submodule update --init {mod}"
-
-            for m in modules:
-                subprocess.check_call(cmd.format(mod=m).split(' '))
         # now build extension list.
         metadata['ext_modules'] = extensions()